ALBERT

Notes: A series of sequential oligopeptides having simple nonpolar side chains, Nps-(L-Ala-L-Leu-Gly)n- OEt has been prepared by a stepwise fragment-condensation method using Nps-L-alanyl-L-leucylglycine N-hydroxysuccinimide ester, which was prepared by the Nps-N-carboxy α-amino-acid-anhydride method. The success of the synthesis of the peptide having a high-molecular weight, such as octadecapeptide, results from the highest solubility of the tripeptide unit, L-alanyl-L-leucylglycine. The sequential polypeptide having the same tripeptide sequence was also prepared by polycondensation of the tripeptide N-hydroxy-succinimide ester.

Notes: The thermal transitions of single-stranded polynucleotides are noncooperative. In contrast, Cu(II) cooperatively disorders the single-stranded helical structures of poly(A) and poly(C), as demonstrated by ORD and UV spectral changes as a function of the Cu2+ activity, and by a dramatic chain-length dependence of the spectral changes. Equilibrium dialysis binding studies indicate that the cooperative disordering is paralleled by a somewhat less cooperative binding process.The difference between the thermal- and Cu(II)-induced transition is explained by the following mechanism. (1) Cu(II) initially binds in a noncooperative fashion to phosphate. (2) The Cu(II) so bound forms a second bond to a nonadjacent base site on the same polymer strand or another strand. These intramolecular and intermolecular crosslinks to the bases are responsible for the disordering. (3) The initial crosslinks formed provide nuclei for the cooperative formation of additional crosslinks, producing cooperative spectral changes paralleled by cooperative binding.A comparison of the spectral and binding transitions indicates that there is appreciable noncooperative binding of copper to phosphate, which produces no spectral changes in the presence of added electrolyte. This comparison also indicates that each copper crosslink disorders several bases. The formation of intermolecular crosslinks is demonstrated by a polymer concentration dependence of the disordering. The formation of intramolecular crosslinks can be deduced from the fact that the “cooperative unit” required to explain the differences between the hexamer, which does not readily form intramolecular crosslinks, and the polymer is considerably larger than the cooperative unit determined from the polymer results.The poly(A) disordering transition is less symmetrical than that of poly(C), particularly at low polymer concentrations. These results, together with other phenomena, are explained by a greater flexibility of poly(A), which favors the formation of small intramolecular loops.

Notes: Potential energy calculations were employed to examine the effect of ribose 2′-O-methylation on the conformation of GpC. Minimum energy conformations and allowed conformational regions were calculated for 2′MeGpC and Gp2′MeC. The two lowest energy conformations of 2′MeGpC and Gp2′MeC are similar to those of GpC itself. The helical RNA conformation (sugar pucker-C(3′)-endo, ω′ and ω,g-g-, bases-anti) is the global minimum, and a helix-reversing conformation with ω′, ω in the vicinity of 20°, 80° is next in energy. However, subtle differences between the three molecules are noted. When the substitution is on the 5′ ribose (Gp2′MeC), the energy of the helical conformation is less than that of GpC, due to favorable interactions of the added methyl group. When the substitution is at the 3′ ribose (2′MeGpC) these stabilizing interactions are outweighed by steric restrictions, and the helical conformation is of higher energy than for GpC. Furthermore, the statistical weight of the 2′MeGpC g- g- helical region is substantially less than the corresponding weight for Gp2′MeC. In addition, 2′MeGpC′s methoxy group is conformationally restricted to a narrow range centered at 76°. This group has a broadly allowed region between 50 and 175° in Gp2′MeC. These differences occur because the appended methyl group in 2′MeGpC is located in the interior of the helix cylinder, as it would be in polynucleotide, while it hangs unimpeded in Gp2′MeC. These findings suggest that 2′-O-methylation has both stabilizing and destabilizing influences on the helical conformation of RNA. For 2′MeGpC the destabilizing steric hindrance imposed by the nature of the guanine base dominates.

Notes: The molecular conformations of the linear oligopeptides H-(L-Ala)n-L-Pro-OH, with n = 1,2 and 3, have been investigated. 13C nmr observation of the equilibrium between the cis and trans forms of the Ala-Pro peptide bond indicated the occurrence of nonrandom conformations in solutions of these flexible peptides. The formation of the nonrandom species containing the cis form of the Ala-Pro bond was found to depend on the deprotonation of the carboxylic acid group of proline, the solvent, and the ionic strength in aqueous solution. The influence of intramolecular hydrogen bonding on the relative conformational energies of the species containing the cis and trans Ala-Pro peptide bond was studied by comparison of the peptides H-(Ala)n-Pro-OH with analogous molecules where hydrogen bond formation was excluded by the covalent structure. In earlier work a hydrogen bond between the protonated terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue had been suggested to stabilize conformations including trans proline. For the systems described here this hypothesis can be ruled out, since the cis:trans ratio is identical for molecules with methyl ester protected and free protonated terminal carboxylic acid groups of proline. Direct evidence for hydrogen bond formation between the deprotonated terminal carboxylic acid group and the amide proton of the penultimate amino acid residue in the molecular species containing cis proline was obtained from 1H nmr studies. However, the cis:trans ratio of the Ala-Pro bond was not affected by N-methylation of the penultimate amino acid residue, which prevents formation of this hydrogen bond. Overall the experimental observations lead to the conclusion that the relative energies of the peptide conformations including cis or trans proline are mainly determined by intramolecular electrostatic interactions, whereas in the molecules considered, intramolecular hydrogen bonding is a consequence of specific peptide backbone conformations rather than a cause for the occurrence of energetically favored species. Independent support for this conclusion was obtained from model consideration which indicated that electrostatic interactions between the terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue could indeed account for the observed relative conformational energies of the species containing cis and trans proline, respectively.

Notes: A method is described for predicting and solving crystal structures of linear homopolysaccharides. The method is based on the refinement of the structure with respect to either stereochemical constraints or x-ray diffraction intensities. In the refinement process, all conformational and packing features of the molecule, such as bond lengths, bond angles, conformational angles, nonbonded contacts, hydrogen bonds, etc., can be allowed to vary until the structure reaches both a conformation and crystalline packing that are in minimum disagreement with the stereochemical restraints and the diffraction data. In this fashion, both packing and conformational features of the structure can be simultaneously refined, and not separately as has been the custom in the past. The refinement procedure is based on a method of constrained optimization which possesses improved characteristics of reaching a solution and avoiding false minima, in comparison with least squares methods. The procedure is, in addition, capable of easily finding molecules of solvent of crystallization. The method was applied to further refining the previously solved crystal structure of V-amylose. The results indicated that contrary to the previously found six-fold molecular symmetry in the P212121 space group, the V-amylose molecule exhibits only two-fold symmetry with the asymmetric unit consisting of three glucose residues in one-half turn of the helix. The three residues are nonequivalent principally due to unequal rotational positions of the hydroxymethyl groups. The crystal structure of V-amylose predicted from stereochemical refinement was identical in all details with that obtained from refining against X-ray data. The excellent agreement with the diffraction data was indicated by the crystallographic disagreement index R = 0.25.

Notes: In order to obtain information about the conformational features of a 2′-O-methylated polyribonucleotide at the nearest neighbor level, a detailed nuclear magnetic resonance study of AmpA was undertaken. AmpA was isolated from alkali hydrolysates of yeast RNA, and proton spectra were recorded at 100 MHz in the Fourier transform mode in D2O solutions, 0.01 M, pH 5.4 and 1.5 at 25°C. 31P spectra were recorded at 40.48 MHz. Complete, accurate sets of nmr parameters derived for each nucleotidyl unit by simulation iteration methods.The nmr data were translated into conformational parameters for all the bonds using procedures developed in earlier studies from these laboratories. It is shown that AmpA exists in aqueous solution with a flexible molecular framework, which shows preferences for certain orientations. The ribose rings exist as a 2E ⇄ 3E equilibrium with the  - pA ribose showing a bias for the 3E pucker. The C(4′) - C(5′) bonds of both nucleotidyl units show significant preference (75-80%) to exist in gg conformation. The dominant conformer (80%) about C(5′) - O(5′) of the 5′-nucleotidyl unit is g′g′. Even though an unambiguous determination of the orientation of the 3′-phosphate group cannot be made, tentative evidence shows that it preferentially occupies g+ domains [O(3′) - P trans to C(3′) - C(2′)] in which the H(3′)  - C(3′) - O(3′) - P(3′) dihedral angle is about 31°. There is reasonable evidence that the 2′-O-methyl preferentially occupies the domain in which the O(2′) - CH3 bond is trans to C(2′) - C(1′).Lowering of pH to 1.5, which results in protonation of both the adenine moieties, causes destacking of AmpA. Such destacking is accompanied by small, but real, perturbations in the conformations about most of the bonds in the backbone.A detailed comparison of the solution conformations of ApA and AmpA clearly shows that 2′-O-methylation strongly influences the conformational preference about the C(3′) - O(3′) bond of the 3′-nucleotidyl unit, in addition to inducing small changes in the overall ribophosphate backbone conformational equilibria. The effect of 2′-O-methylation is such that the C(3′) - O(3′) is forced to occupy preferentially the g+ domain rather than the normally preferred g- domain [O(3′) - P trans to C(3′) - C(4′)] in ApA. The data on ApA and AmpA further reveal that the extent of stacking interaction is less in AmpA compared to ApA.It is suggested that stacked species of AmpA exist as right-handed stacks where the magnitude of ω and ω′ about O(5′) - P and P - O(3′) is about 290°. The reason for the lesser degree of stacking in AmpA compared to ApA is intramolecular interaction between 2′-O-methyl and the flexible O(3′) - P - O(5′) bridge, the interaction causing some perturbation in the magnitudes of ω/ω′, causing destacking. The destacking will lead to an increase in χCN by a few degrees, causing an increase in 2E populations; the latter in turn will shift the 3′ phosphate group from g- to g+ domains. In short, a coupled series of conformational events is envisioned at the onset of destacking, made feasible by the interaction between the 2′-O-methyl group and the swivel O(3′) - P - O(5′) bridge.

Notes: The binding isotherms of sodium decyl sulfate to poly(L-ornithine), poly(D,L-ornithine), and poly(L-lysine) at neutral pH were determined potentiometrically. The nature of a highly cooperative binding in all three cases suggests a micelle-like clustering of the surfactant ions onto the polypeptide side groups. The hydrophobic interaction between the nonpolar groups overshadows the coulombic interaction between the charged groups. The titration curves can be interpreted well by the Zimm-Bragg theory. The average cluster size of bound surfactant ions is sufficiently large to promote the β-structure of (L-Lys)n even at a very low binding ratio of surfactant to polypeptide residue, whereas the onset of the helical structure for (L-Orn)n begins after about 7 surfactant ions are bound to two turns of the helix. The CD results are consistent with this explanation.

Notes: The synthesis of a cross-linked polypentapeptide (an insoluble product) by means of a cross-linking reaction between a lysine-containing (1%) polypentapeptide and a glutamic acid-containing (2%) polypentapeptide is described, following description of the synthesis and polymerization of the corresponding pentapeptide p-nitrophenyl esters. The pentapeptide p-nitrophenylesters - H-Val1-Pro2-Gly3-Val4-Gly5-ONp, H-Val1-Pro2-Gly3-Lys4(ε-Z)-Gly5-ONp, and H-Val1-Pro2-Gly3-Glu4-Gly5-ONp - prior to polymerizing and the polypentapeptides prior to cross-linking were analyzed by proton and carbon-13 magnetic resonance. The cross-linking reaction was achieved in the coacervate state by intermolecular primary amide bond formation. The coupling reagent was a water-soluble carbodiimide (1-cyclohexyl-3-(2-N-methylmorpholinoethyl)-carbodiimide-p-toluenesulfonate).

Notes: It is concluded on the basis of comparison of polyelectrolyte theory with published data that the mean phosphate spacing b along the contour axis of an unfolded polynucleotide single strand is in the range 3-4 Å (polyelectrolyte parameter ξ ≈ 2), regardless of temperature, base composition, or extent of stacking. This result is consistent with the low-angle X-ray scattering measurements of Gulik, Inoue, and Luzzati on poly(C). No conclusion may be drawn from this value of b concerning the structure of the chain skeleton or the spatial arrangement of the bases other than that the chain is far from an all-trans local conformation (for which b would be about 6-7 Å, the length of a nucleotide unit). The structural implications, or lack thereof, are discussed in detail in the following paper.

Notes: The technique of intensity correlation light-scattering spectroscopy has been used to accurately determine the extent of physical swelling of lysozyme, ribonuclease, and chymotrypsinogen produced by thermal denaturation. The change in hydrodynamic radius is deduced from direct measurements of the diffusion coefficient, carried out in the temperature range 20° to 70°C at various values of pH in the range 1.0 to 3.0 at ionic strengths of from 0.01 M to 0.2 M. An average radius increase of 18% is observed for lysozyme and ribonuclease, with an estimate of 26% for chymotrypsinogen. Analysis of the pH dependence of the transition temperature leads to the conclusion that the lysozyme charge increases by approximately +2e during unfolding. We have applied this value of the charge increase along with the 18% average radius increase to estimate the electrostatic contribution to the free-energy change for denaturation of lysozyme. The results are consistent with the experimental observation that the transition temperature is nearly independent of ionic strength.

Notes: The normal vibration frequencies of poly(L-alanine) and poly(L-alanylglycine) in the antiparallel chain-pleated sheet structure have been calculated, using the force field for polyglycine I from the previous paper (Biopolymers 15, 2439-2464) plus additional force constants for the methyl group. The agreement with observed ir and Raman bands is very good. This substantiates the excellent transferability of the force field, since polyglycine I was shown to have a rippled-sheet structure. The amide I and amide II mode splittings are very well accounted for by transition dipole coupling, showing that subtle structural differences are sensitively manifested through this mechanism.

Notes: Conformational energy calculations were performed on monosaccharide and oligosaccharide inhibitors and substrates of lysozyme to examine the preferred conformations of these molecules. A grid-search method was used to locate all of the low-energy conformational regions for N-acetyl-β-D-glycosamine (NAG), and energy minimization was then carried out in each of these regions. Three stable positions for the N-acetyl group have ben located, in two of which the plane of the amide unit is normal to the mean plane of the pyranosyl ring. Nine local energy minima were located for the  - CH2OH group. The positions of the two vicinal cis  - OH groups are determined predominantly by interactions with either the  - CH2OH or the N-acetyl group. The most stable conformations of β-N-acetylmuramic acid (NAM) were determined from the study of the low-energy conformations of NAG. In the two stable orientations for the D-lactic acid side chain, the O - C - C′ plane (C′ being the carbon atom of the terminal carboxyl group) was found to be normal to the mean plane of the pyranosyl ring. The low-energy positions for the COOH group of NAM are determined mainly by interactions with neighboring groups.The conformational preferences of the α-anomers of NAG and NAM were also explored. The calculated conformation of the N-acetyl group for α-NAG was quite close to that determined by X-ray analysis. Two of the three lowest energy conformations of α-NAM are similar to the corresponding conformations of the β-anomer. A third low-energy structure, which has a hydrogen bond from the NH of the N-acetyl group to the C=O of the lactic acid group, corresponds very closely to the X-ray structure of this molecule.The preferred conformations of the disaccharides NAG-NAG, NAM-NAG and NAG-NAM were also investigated. Two preferred orientations of the reducing pyranosyl ring relative to the nonreducing ring were found for all of these disaccharides, both of which are close to the extended conformation. In one of these conformations, a hydrogen bond can form between the OH group attached to C3 of the reducing sugar and the ring oxygen of the preceding residue. Each conformation can be stabilized further by a hydrogen bond between the CH2OH (donor) of residue i + 1 and the C=O of residue i (acceptor). The interactions that determine conformations for all oligosaccharides containing both NAG and NAM are shown to be exclusively intraresidue and nearest neighbor interactions, so that it is possible to predict all stable conformations of oligosaccharides containing NAG and NAM in any sequence.

Notes: The influence on the excess scattering function P(μ) of flutuations in the electron density ρ within a macromolecule is treated, to the approximation that the solvent is a structureless medium of constant electron density ρ0. The results for P(μ) and the apparent value of the mean square radius Rapp2, can be expressed as functions of the excess electron density Δρ: P(μ) = X(μ) + (Δρ)-1Y(μ) + (Δρ)-2Z(μ) and Rapp2 = Rx2 + (Δρ)-1Ry2 + (Δρ)-2Rz2, where X(μ) and Rx2 depend only on the shape of the macromolecule, while Y(μ) and Ry2 as well as Z(μ) and Rz2 depend on the shape and the fluctuations in ρ. By varying the electron density of the solvent, the contributions of the shape and the internal structure of the macromolecule can be resolved. The quantities Rx2, Ry2, and Rz2 are evaluated for seven models to illustrate the relative importance of these contributions for representative structures.

Notes: The chiroptical properties of the cyclic dipeptides cyclo (L-alanyl-L-tyrosine) and cyclo(L-tyrosyl-L-tyrosine) have been investigated as a function of molecular conformation. Theoretical optical calculations and conformational energy calculations have been carried out as a function of the side-chain dihedral angles χ1 and χ2, and as a function of the angle of fold of the cyclic dipeptide backbone. The results of these theoretical calculations have been compared with experimental circular dichroism (CD) data. Theoretical predictions are in very good agreement with experiment for c(L-Tyr-L-Tyr). Agreement was not quite as good for c(L-Ala-L-Tyr), although the signs of all of the Cotton effects were apparently predicted correctly except for that associated with the lowest energy tyrosine absorption band.

Notes: The slow kinetics of annealing processes in multistranded nucleic acids is spectrophotometrically investigated using poly(A)·2poly(U) as a model system. The absorbance changes at specific wavelengths show that double-helical (A·U) base pairs appear as transient intermediates. The annealing process is identified by the enlargement of triple-helical sequences at the cost of (A·U) base pairs and unpaired (U) residues. A large time range in the reorganization of mismatched chain configurations is characterized by a logarithmic dependence on time. This observation is quantitatively described by a kinetic model developed by Jackson. In Jackson's model the rate-limiting process in the slow annealing phase of maximizing triple-helical sequences, is the removal of strand entanglements, knots, and hairpin loops by complete unwinding of those helical stretches which stabilize the mismatched configurations. The results of the present study are briefly discussed in terms of optimum conditions for hybridization experiments and for the preparation of polynucleotide complexes commonly used to produce interferons.

Notes: The effects of anions of neutral salts on the fluorescence emission of six proteins as well as on tryptophan and tyrosine were studied in relation to the structure of proteins. Most anions are good quenchers of tryptophyl and tyrosyl fluorescence, free or in proteins. The results with tryptophan and tyrosine indicate involvement of a collisional quenching mechanism due to agreement with Stern-Volmer law. The deactivation of fluorescence probably occurs because of the transition from singlet state to triplet state. Lehrer's modification of Stern-Volmer law was applied to proteins. The effective quenching constants ([KQ]eff) and the fraction of fluorescence available ([fa]eff) to the quencher are also calculated.In contrast to its effect on tryptophan, CH3COO- quenches tyrosyl fluorescence and ClO4- does not. The effects on fluorescence of ribonuclease and free tyrosine are similar and without any changes in emission maximum. The anions are divided into three groups based on the effect they have on tryptophan-containing proteins. (1) NO3-, NO2-, Br-, and I- have high [KQ]eff values and readily quench tryptophyl fluorescence of proteins causing a shift of emission maximum to a shorter wavelength. This change is due to the specific quenching of “exposed” tryptophan residues which are accessible to quenchers and the observed residual fluorescence is from the “buried” tryptophyls. (2) ClO4- and SCN- also quench fluorescence of tryptophan in proteins and have lower ([KQ]eff) values. In their presence the fluorescence maximum is shifted to a longer wavelength, which indicates the unfolding of a protein with [(fa)eff] = 1. (3) Cl-, CH3COO-, and SO4— do not have a direct effect on the fluorescence of tryptophan. Besides the “direct” effects, “indirect” effects on fluorophors in protein are also seen, pointing out that the neutral salts can interact in more than one manner with proteins. The effectiveness of anions in quenching fluorescence of proteins follows similar sequences which almost resemble the Hofmeister series, viz., SO4=, CH3COO- ≃ Cl- 〈 ClO4- 〈 SCN- 〈 Br- 〈 I- 〈 NO3- 〈 NO2-.

Notes: The influence of pH upon CD spectra of H-Trp-Trp-OH, H-Trp-Trp-Gly-OH, and H-Gly-Trp-Trp-OH is investigated and data are compared with those obtained for peptides containing only one tryptophyl residue. A negative Cotton effect at around 225 nm, which in previous work has been related to an increase of the conformational rigidity in compounds having the sequence -CO-Trp-Trp, is also observed in the case of H-Trp-Trp-OH and H-Trp-Trp-Gly-OH upon deprotonation of the terminal α-amino group. These data, together with observations arising from solvent and temperature effects, give evidence that H-Trp-Trp-OH undergoes a conformational change upon going from acid to alkaline conditions, where the two aromatic side chains become conformationally more rigid relative to each other. This rigidity generates an exciton coupling between the Bb transitions of the two indoles. Hydrophobic forces, including stacking interactions, do not appear important in stabilizing this conformationally rigid structure. Rather, intramolecular electrostatic interactions (e.g., hydrogen bondings or polar interactions between the aromatic side chain and the peptide backbone) as well as interactions with the OH group(s) of the solvent, are suggested to be the salient forces. Possible structures which obey these requisites are discussed.

Notes: The fine structure of the thermal denaturation of viral DNA's was analyzed with the spectral method established by Felsenfeld and Hirschman, and Fresco et al. A fully automated system measuring melting curves at four wavelengths at the same time was developed for this purpose. With this device, (G + C)-contents of melting components of λ DNA's were determined. The correlation between the (G + C)-content and the melting temperature of each melting component is found to be well described by the linear relationship given by Marmur and Doty. The denaturation of each component is regarded as cooperative. The Marmur-Doty relation also stands for the local denaturation of T2 DNA, which has a narrow melting range.

Notes: Manning's and Scatchard's models for the description of ion-polyelectrolyte interactions are compared in the case of linear polyelectrolytes and bivalent counterions, where “condensation” of the counterions is known to occur for certain concentration ratios of the two species in solution. This comparison leads to the definition of certain conditions on Scatchard's parameters for a precise structural interpretation of Scatchard's plots to be valid. Experimental data obtained with both models are compared and found in good agreement under such conditions.

Notes: Semi-empirical energy calculations for an internal Pro-Pro dimer are presented that take into account the nature of the flexibility of the proline ring due to its puckering. Calculations show that three stable conformations are available for the dimer: the cis (ω = 0°, ψ = 160°); the trans (ω = 180°, ψ = 160°, also referred to as trans′); and the cis′ (ω = 180°, ψ = -40°) conformations. The best conformational pathways between these stable conformations are determined. Calculations also show that the barrier for cis′-trans′ conversion is of the same order of magnitude as that for cis-trans conversion.

Notes: We have constructed an apparatus for the simultaneous measurement of electrophoretic mobility, μ, and diffusion coefficient, D, of macromolecules and cells. It combines band electrophoresis in a vertical, sucrose-gradient stabilized column, with quasielastic laser light-scattering determination of the diffusion coefficient of the species within the band. The entire electrophoresis cell is scanned through the laser beam of the quasielastic laser light-scattering apparatus by a vertical translation stage. Total intensity light-scattering measurement at each point in the cell gives the macromolecular concentration at that point. Solvent viscosity and electrical potential are measured at each point in the cell. Application of this apparatus to resealed red blood cell ghosts and to bovine hemoglobin indicates that measurements of field, viscosity, and migration distance are reliable, and that electroosmosis is insignificant. Application to T4D bacteriophage gives μ20,w = (-1.05 ± 0.05) × 10-4 cm2/V sec and D20,w = (3.35 ± 0.10) × 10-8 cm2/sec for fiberless particles, and μ20,w = -(0.59 ± 0.03) × 10-4 cm2/V sec and D20,w = (2.86 ± 0.09) × 10-8 cm2/sec for whole phage with 6 fibers. Approximate analysis of these results with the Henry electrophoresis theory for spheres in dicates that each fiber contributes about 193 positive charges to the phage particle, compared with 327 from amino-acid analysis. The advantages and disadvantages of this apparatus, relative to conventional electrophoresis and to electrophoretic light scattering, are discussed.

Notes: Poly(His-Ala-Glu) and poly(Lys-Ala-Glu) were examined by viscosity and potentiometric titration. These measurements were interpreted in terms of the hydrodynamic size of the above sequential polypeptides. Effects of polymer, size and concentration, and solution-salt concentration were demonstrated. Although the sequential polypeptides generally behave like polyampholytes, they do demonstrate some differences. These differences my be attributed to the ability of ionized side chains three residues apart to repel themselves, in the order His 〈 Glu 〈 Lys.

Notes: Proton magnetic resonance spectra of model dipeptide molecules R1-C′1O1-N2H2-C2αH2αR2-C′2O2-N3H3-R3 in CCl4 solutions exhibit splited signals when investigating on mixtures of L and D enantiomers differing from the racemic composition. The major effect is observed on amide proton signals which are the ones most sensitive to the ratio of aggregation. The stereoselective dimerization of enantiomeric molecules in the so-called C5 conformational state is shown to be responsible for such a phenomenon, the intensity of which depends on the bulkiness of the side chain R2. A theoretical approach is proposed which gives predictions in close agreement with our own experimental findings.

Notes: The depolarization thermal current method is applied to the study of the polarization phenomena in the keratin-water system. Three depolarization thermal current peaks have been evidenced in hair keratin. This paper deals with the detailed study of peak II. For the first time, the mechanism responsible for this peak is ascribed to molecular reorientation. The effect of water upon the characteristics of peak II is also described, and an activation energy of 8.4 kcal/mol is computed. These results, in connection with other studies, lead us to interpret peak II as due to the reorientation in the bound or intermediate water molecules. The effect of copper confirms that the carboxyl groups are hydration sites.

Notes: Infrared spectroscopy was used for the determination of the base-pairing content of four specific tRNAs in deuterium oxide solution. Infrared spectra were obtained in the 1750-1550 cm-1 region at various temperatures ranging from about 15 to 90°C. Melting curves were constructed by plotting the molar extinction coefficient at ν = 1657 cm-1 versus temperature. These transition curves enabled us to determine the ranges of temperature which correspond to the ordered (partially double-stranded) or randomly coiled structure of the tRNA. For a set of wavenumbers the extinction coefficients at these temperatures were used for the calculation of the base-pairing content. The procedure employed here is based on a method described earlier by Thomas [(1969) Biopolymers 7, 325-334]. For the conditions selected for this investigation (Mg2+-free D2O-buffer; 0.01M tris-DCl, 0.015M NaCl, pD 7.5) the results of this determination agree within the limits of errors with the number of base pairs predicted by the cloverleaf model.

Notes: We have calculated the translational and rotational frictional coefficients of structures related to T2 and T4 bacteriophage, using the theoretical framework developed in the preceding two papers. The structures considered were models for tail-fiberless phage, and for whole phage with fibers in the extended and retracted portions. We also computed and compared with the experiment the changes in translational frictional coefficient produced by successive addition of 1-6 fibers to the fiberless particle. Agreement with experimental results is markedly improved over previous theoretical efforts, especially with respect to the effect of tail-fiber extension. Some significant discrepancies remain, however, in the comparison of fiber-retracted and fiberless phage.

Notes: We have used the modified Oseen hydrodynamic interaction tensor along with iterative numerical solution of the coupled hydrodynamic interaction equations to calculate the rotational diffusion coefficients of macromolecular complexes composed of nonidentical spherical subunits. For the one structure, a prolate ellipsoid of revolution, for which exact solutions are available, a subunit model with the same length and volume gives asymptotic agreement with the Perrin equations. Other structures considered include plane polygonal rings, lollipops, and dumbbells.

Notes: We have studied the effects of temperature, EDTA, and ionic strength on C-polysaccharides in solution by examining the details of the time-correlation function using a 96-channel single-clipped photon correlation spectrometer. Our linewidth results have shown that the C-polysaccharides in buffer solution form aggregates of very broad distributions. Thus, fractionation by gel-filtration chromatography is only mildly effective. Although the aggregate sizes seem to remain relatively constant from 4 to 25°C, a fraction of those aggregates break up to form smaller fragments or monomers at higher temperatures. However, the dissolution-association process is quite slow and takes days even at room temperatures before the equilibrium is reached. We have also shown that by adding an excess amoutn of EDTA, the aggregates can be broken up. Again the dramatic changes occur only at short delay times suggesting that a protion of the larger aggregates remains. Finally, the amount and size of aggregates depend upon the ionic strength which exhibit a maximum ΓT/sin2 (θ/2) around 0.1-0.2 M KCl.If the activities of polysaccharides in solution depend upon molecular size, the standard techniques such as gel-permeation chromatography and ultracentrifugation cannot properly characterize the detailed size distribution. Quasielastic laser light scattering can provide us with a qualitative model. The quantitative details must necessarily await more extensive investigations using a combination of the techniques and better fractionation procedures in an appropriate buffer solution.

Notes: The coupling of N-acyl-α-amino-acids with α-hydroxyacid-methyl amides results in depsipeptide molecules containing two chiral centers and one ester function inserted between two amide functions. Their conformational features have been investigated by IR spectroscopy, proton magnetic resonance, X-ray diffraction, and theoretical P.C.I.L.O. calculations.It is shown that most of these molecules are folded by an intramolecular 4 → 1 hydrogen bonding. Two folded conformations, similar to the well known β turn in peptides, are described, the stability of which depends on the configurational sequence in the investigated molecule.LL and LD species are folded in two different ways whereas LG sequences containing an achiral hydroxy-acid residue accommodate both of them. The presence of a N-terminal achiral amino acid noticeably decreases the folding ratio.The above conclusions are then compared with the conformational features of homologous tripeptide molecules.

Notes: The kinetics of complex formation between fluorescein mercuric acetate and heat-denatured DNA were studied by measuring the fluorescence quenching of this reagent. This quenching process involved no immeasurably rapid phase and it was shown that this reaction follows simple second-order kinetics. The rate constant at 25°C was estimated to be 2.9 × 104M-1 sec-1 for calf-thymus DNA (42% G + C) and 1.1 × 104M-1 sec-1 for Micrococcus lysodeikticus DNA (72% G + C). Activation parameters for this reaction were calculated from the temperature dependence of the reaction rate, and the activation entropy was found to be highly negative (-27.5 cal/mol deg for calf-thymus DNA and -25.5 cal/mol deg for M. lysodeikticus DNA). The binding of fluorescein mercuric acetate to native DNA, which requires the opening of the double-helical structure, was also followed by measuring the absorbance change of this reagent. There was a lag phase in this binding process, and the enthalpy change for the opening step corresponded roughly to that for the opening of one base pair. These findings are discussed in relation to the results of a similar study with formaldehyde.

Notes: The formation of collagen fibrils from soluble monomers and aggregates by thermal gelation at neutral pH can be divided into two distinct stages: a nucleation phase and a growth phase. Turbidity studies of the kinetics of the precipitation reaction show that the lag-phase time or nucleation reaction time, t′l, is markedly temperature dependent while the growth reaction time is temperature independent. The activation energy of the nucleation reaction is essentially constant over the temperature range studied. In monitoring the nucleation-phase reaction by various physicochemical techniques, including viscosity, sedimentation equilibrium, and light scattering, no evidence for the formation of aggregates was observed. Enrichment of the initial collagen solution with aggregates accelerates nucleation, but de novo nuclei formation is still required even in highly aggregated collagen preparations. Removal of pepsin and pronase susceptible peptides lengthens the nucleation reaction time and increases the sensitivity of the rate of nuclei formation to changes in ionic strength. Electron microscope studies show the fibrils formed from the protease-treated collagen to be less well organized. With pepsin-treated collagen, subfibrils and obliquely striated fibrils are seen, showing that while microfibrils are formed interactions between them are modulated by the enzyme susceptible peptides in the same way that these regions modulate nuclei assembly. It appears that pepsin and pronase susceptible peptide regions of collagen play a more prominent role in the in vitro assembly of collagen molecules to form D-stagger nuclei and fibrils than do ionic interactions between helical molecular regions. A mechanism of nucleation of collagen fibrillogenesis is discussed.

Notes: Circular dichroism spectra of the nucleic acid monomers have been measured in aqueous solution and extended into the vacuum ultraviolet region to about 166 nm. Measurements were made on ribo and deoxyribo derivatives of adenine, guanine, hypoxanthine, cytosine, thymine, and uracil derivatives both with and without the 5′-phosphate (with the exception of ribosyl thymine 5′-phosphate). Absorption spectra of the deoxyribonucleotides measured to about 175 nm are also presented. The results demonstrate that both the circular dichroism and absorption spectra observed below 200 nm are no more complicated than the spectra normally recorded above 200 nm. In most cases, the circular dichroism spectra of the various derivatives of a given base are similar, indicating that the conformations are similar. On the other hand, the differences among the circular dichroism spectra of the various derivatives of a given base are sufficient to identify a particular derivative. The average circular dichroism for the deoxyribonucleotides is compared with the circular dichroism of native E. coli DNA. The comparison reveals that the circular dichroism of DNA below 200 nm is due principally to the interaction between the bases rather than the intrinsic circular dichroism of the monomers. The monomer transitions are discussed in relationship to the absorption and circular dichroism spectra presented.

Notes: A theory for the determination of DNA arrangements in DNA-containing specimens, using planar aromatic dye molecules as probes for plane polarization of fluorescence, has been described. At low dye-to-DNA concentrations, the dye molecules are sandwiched between the stacked bases of DNA; hence, the fluorescence from the dye bound to a local region of DNA helix is plane-polarized with the polarization direction perpendicular to the local axis of DNA. The degree of such polarization from an aligned DNA-specimen complexed with dye is determined both by the DNA orientation and the conformational state (e.g., base tilt) of DNA into that specimen. Analysis has been made of the relationship between the degree of polarization and the orientation of the emitting dipoles of dye. The dye complexes may be aligned in a mechanical shear or electric field. However, any change in the orientation distribution of the emitting dipoles due to force fields should be taken into account. With some assumptions and approximations, the magnitude and the direction of maximum polarization can be related to different orders of DNA coiling and to their various combinations. Since the measured polarization is averaged over all DNA regions of the specimen, if the magnitude of polarization is appreciable and the polarization occurs in the specific direction of the specimen, the theory helps to eliminate several probable arrangements of DNA. The predominant molecular features of the actual DNA arrangement can be determined through this process of elimination, as explained in two subsequent papers with T-even bacteriophage and chromosome systems.

Notes: Fluorescence of 2-p-toluidinylnaphthalene-6-sulfonate (TNS) was enhanced in the presence of maltooligosaccharides, amylose, and other α-glucans. The dependence of relative TNS fluorescence intensity per glucose unit on chain length of oligosaccharides was examined. The values of binding constant and thermodynamic parameters, assuming the 1:1 complex for TNS-amylose (number-average degree of polymerization, DPN = 17), were determined by the fluorescence titration. The values of thermodynamic parameters for 1:1 complex formation of TNS-α- and β-cyclodextrins were also determined and compared with those of TNS-amylose (DPN = 17). The fluorescence intensity of TNS in the presence of amylose (DPN = 600) decreased by the action of glucoamylase and taka-amylase A. The fluorescence of TNS-amylose (DPN = 17) system increased with the increased ionic strength. In the presence of pullulan, TNS fluorescence was also enhanced and decreased by the action of pullulanase. Amylopectin enhanced TNS fluorescence rather more strongly than amylose (DPN = 17) at the same concentration. In the presence of dextran, the fluorescence of TNS was scarcely enhanced. The degree of fluorescence enhancement of TNS in the presence of α-glucans seems to reflect the structures of α-glucans in solution, since TNS fluorescence is enhanced in the hydrophobic environment or by the disturbance of free intramolecular rotation.

Notes: Water-soluble, random copolymers containing L-methionine and N5-(3-hydroxypropyl)-L-glutamine have been prepared, fractionated, and characterized. The thermally induced helix-coil transitions of these copolymers in water have been investigated, and it has been found that incorporation of L-methionine increases the helix content of the polymers at all temperatures in the range of 0-60°C. The Zimm-Bragg parameters σ and s for the helix-coil transition in poly(L-methionine) in water were deduced from an analysis of the melting curves of the copolymers using the methods described in earlier papers.

Notes: Normal vibrational analysis was carried out for DNA molecules in both A and B conformations as well as for A-RNA. A simplified backbone model was examined and expanded to include the backbone phosphate-group and the ribose ring. We applied the new force-constant refinement procedure discussed in the preceeding paper [Van Zandt, L. L., Lu, K.-C. & Prohofsky, E. W. (1977) Biopolymers, 16, 2481-90] to fit some observed frequencies in the Raman spectra for all three nucleic acids with the same set of force constants. The results indicate that the observed frequency shift can be attributed to the conformational change solely. We ignored the second-order differences in force constants for the different geometries. The agreement between the observed and calculated frequencies derived from the final refined set of force constants is good and apparently justifies this assumption. Two modes previously assigned to the symmetric diester O-P-O stretch and the symmetric dioxy O‥P‥O stretch are actually fitted. They are mainly backbone phosphate-group modes. The refined ribose-ring force-constants were transferred to the calculation of the vibrational spectrum of tetrahydrofuran. The overall agreement is again good. We discuss these calculations and the resulting normal modes. We also discuss the application of the Green-function refinement scheme and several strategies adopted to bias the convergence of the procedure.

Notes: Using the free energy difference between double-helix and random-coil forms of DNA as a measure of the stability of the double helix, we calculate the dependence of the stability on excess univalent cation concentration and on polynucleotide phosphate concentration, both as functions of the equivalent ratio r of divalent cation-to-phosphate concentrations. The theoretical tool is merely to compare the free energy of one polyelectrolyte solution, characterized by the polyelectrolyte linear charge density, with the free energy of another, characterized by a different value of the charge density. It is assumed only that the charge density of the double helix is greater than that of the coil form. The calculation represents the only molecular theory given to date (for r ≠ O) for these aspects of helix stability.We find that, as excess univalent cation concentration increases, the helix stability increases if r is small but decreases if r is large (i.e., of the order of unity). Moreover, as the concentration of nucleotide phosphate increases, the helix stability does not change for small values of r but increases for large values. For both effects, a continuous transition as a function of r bridges the low-r and high-r behaviour.

Notes: The association of chloroform-soluble derivatives of uracil and adenine has been examined in chloroform solution in the presence of dissolved water. Analysis by infrared spectroscopy shows that complex formation still occurs in these conditions, and that the extent of association is substantially unchanged by the presence of water. Evidence is presented for the coexistence of two kinds of base pair (involving, respectively, the C2 and C4 carbonyl groups of the pyrimidine) in the solutions, and for some displacement in their relative balance by the added water. The binding of water to the C2 and C4 carbonyl groups can be separately observed in both the free uracil derivative and its 1:1 complex with 9-ethyladenine. Little or no competition has been found to occur between the formation of base pairs and binding of water to the bases, as judged by measurements of water solubility in chloroform solutions of the bases individually and in 1:1 mixtures. The evidence suggests that this phenomenon can be largely explained by the formation of double hydrogen bonds by the uracil carbonyl groups. Taken together with recent published observations, the results indicate that hydrogen bonding may make a much greater energetic contribution to conformational stability of biopolymers in aqueous solution that has been supposed.

Notes: By use of a polycondensation procedure free of racemization, stereoregular polymethionines have been synthesized from C-activated D-methionyl-L-methionine and L-methionyl-D-methionyl-L-methionine.The poly(D-methionyl-L-methionine) and poly(L-methionyl-D-methionyl-L-methionine) so prepared are soluble in chloroform and can be purified through dissolution in this solvent and precipitation by ligroin.Poly(D-Met-L-Met)which is obtained in a 25% yield, is about 5000 in average molecular weight. It has no discernible optical activity when examined between 400 and 600 nm in a trifluoroacetic acid solution.Poly(L-Met-D-Met-L-Met) (40% yield, M. W. = 10,000) is an optically active polymer. [α]43624 ≈ + 170° for a chloroformic solution (c = 0.2 CHCl3).

Notes: A study of the conformational states of the dinucleotide coenzyme NAD+ has been made using semiempirical energy calculations. Taking low-energy mononucleotide structures as starting conformations, energy minimizations have been performed. The lowest energy states are stacked structures, with interactions between the adenine and nicotinamide rings. Some structures show stabilization gained from electrostatic attractions between the positively charged nicotinamide and negatively charged phosphate oxygens. These predictions correlate well with the available experimental data.

Notes: Water-soluble block copolymers of the type (A)m-(B)n-(A)p, where (A)m,p was either poly(D,L-lysine-α,β,β,γ,γ,δ,δ-d7) or poly(D,L-lysine) and (B)n was either poly(L-alanine) or poly(L-phenylalanine), were synthesized for conformational studies by proton magnetic resonance spectroscopy. Analytical determination of the amount of the initiator fragment (n-hexylamine) at the C-terminus of the copolymers was used to obtain the number-average degrees of polymerization, DPn, and thereby, together with the amino acid composition, to establish the covalent structures of the polymers. The values of DPn were found to be much lower than those deduced from sedimentation equilibrium or form viscosity measurements. These deviations, which also are thought to have arisen in similar studies reported in the literature, are attributable to intermolecular aggregation; the relation of such aggregation to covalent structure (and its effect on the polymerization reaction) is discussed in terms of the conditions and mechanism of synthesis of block copolymers of amino acids.

Notes: We have tested 21 different basis sets of synthetic DNA circular dichroism spectra and have slected one for use in spectral analyses of natural DNAs. This “standard” set consists of spectra of eight polymers: poly[d(A-A-T)·d(A-T-T)], poly[d(A-G-G)·d(C-C-T)], poly[d(A-T)·d(A-T)], poly[d(G-C)·d(G-C)], poly[d(A-G)·d(C-T)], poly[d(A-C)·d(G-T)], poly[d(A-T-C)·d(G-A-T)], and poly[d(A-G-C)·d(G-C-T)]. This basis set, applied according to the first-neighbor polymer procedure of Gray and Tinoco, allows a more uniformly accurate spectral analysis of six natural complex DNAs and eight (A+T)-rich satellite DNAs for base composition and first-neighbor frequencies than was previously possible. We find that spectra of poly[d(A)·d(T)] and/or poly[d(A-C-T-)·d(A-G-T)] are not generally required for good analysis results but we show in this and the following paper that these spectra are needed for the most accurate analyses of some satellite DNAs.

Notes: Poly(Lys48, His52), a random copolypeptide of L-lysine (48%) and L-histidine (52%), was used as a model protein for investigating the effects of protonation on the imidazole group of histidines on protein binding to DNA. The complexes formed between poly(Lys48, His52) and DNA were examined using absorbance, circular dichroism (CD), and thermal denaturation. Although increasing pH reduces the charges on histidine side chains in the model protein, the protein still binds the DNA with approximately one positive charge per negative charge in protein-bound regions. Nevertheless, CD and melting properties of poly(Lys48, His52)-DNA complexes still depend upon the solution pH which determines the protonation state of imidazole group of histidine side chains. At pH 7.0, the complexes show two characteristic melting bands with a tm (46-51°C) for free base pairs and a t′m (94°C) for protein-bound base pairs. The t′m of the complexes is reduced to 90°C at pH 9.2, although at this pH there is still one lysine per phosphate in protein-bound regions. Presumably, the presence of deprotonated histidine residues destabilizes the native structure of protein-bound DNA. The binding of this model protein to DNA causes a red shift of the crossover point and both a red shift and a reduction of the positive CD band of DNA near 275 nm. This phenomenon is similar to that caused by polylysine binding. These effects, however, are greatly diminished when histidine side chains in the model protein are deprotonated. The structure of already formed poly(Lys48, His52)·DNA complexes can be perturbed by changing the solution pH. However, the results suggest a readjustment of the complex to accommodate charge interactions rather than a full dissociation of the complex followed by reassociation between the model protein and DNA.

Notes: A theoretical analysis of the conformation of the octapeptide hormone Asn1, Val5 angiotensin II has been carried out by semiempirical potential energy calculations. A preliminary study of the Ala6-Pro-Ala molecule, which mimics the angiotensin backbone, provided us with likely backbone structures on which the effect of the full side chains of the hormone could be assessed. For angiotensin II, the calculations show that only a small number of folded, compact conformations have a high probability of existence. This is the consequence of favorable packing and of the presence of proline in position 7. These results are consistent with various experimental data, both structural and biological. This method is readily applicable to the study of analogs of the hormone or to other peptides of comparable size.

Notes: The interaction between DNA and ionen polymers, -[N+(CH3)2(CH2)mN+(CH3)2(CH2)n]l-, with m-n of 3-3, 6-6, and 6-10 were examined in order to know how the binding behavior of cationic polymers with DNA depends on the charge density of polycation. The ionen polymer has no bulky side chain and the binding forces with DNA would be attributed mainly to electrostatic interaction. When 3-3 ionen polymers were added to DNA solution, precipitable complexes with the ratio of cationic residue to DNA phosphate (+/-) of 1/1 and the free DNA molecules were segregated, while 6-6 and 6-10 ionen polymers formed soluble complexes with DNA molecules up to (+/-) = 0.5. This suggests that 3-3 ionen polymers bind cooperatively with DNA while 6-6 and 6-10 ionen polymers bind noncooperatively. The cooperative binding of 3-3 ionen polymer and the noncooperative binding of 6-6 ionen polymer were also supported by the thermal melting and recooling profiles from the midpoint between first and second meltings. It was concluded that the charge density of DNA phosphate is a critical value determining whether the ionen polymers bind to DNA by a cooperative or by a noncooperative binding, since the distance between successive cationic charges of 3-3 ionen polymer is shorter than that between successive phosphate charges on DNA double helix and those of 6-6 and 6-10 ionen polymers are longer.

Notes: Quasielastic light scattering is used to study the effect of ionic strength on the dynamic behaviour of DNA. In a first approach the spectrum of scattered light is analyzed in terms of a single relaxation process. The large difference between the observed behaviour and that expected according to a pure diffusional process reflects the contribution associated with internal modes, which increases with decreasing ionic strength. Such behaviour is better analyzed in terms of a double relaxation process by using two relaxation times, the reciprocals of which are equal to DK2 and DK2 + τi-1 (K), respectively, where τi (K) is an average value describing the set of modes observed at a given K value. Relative intensity and relaxation times, which are the more accurate parameters, were used to interpret the results. The observed increase of the relative contribution of internal modes with decreasing ionic strength is actually a relative decrease of the diffusional contribution induced by a corresponding increase of the radius of gyration RG. On the other hand, the reciprocal τi-1 (K) of the relaxation time is a linear function of K2 in the analyzed KRG range and is insensitive to ionic strength between 10-2M and 1M. These results, when discussed according to Rouse's model, lead to define for each value of τi-1 (K) a corresponding mean-squared equilibrium length 〈μi2〉 which is found to be a linear function of K-2.

Notes: The structure of β-chitin has been refined by rigid-body least-squares methods, based on the intensity data for highly crystalline specimens from the pogonophore Oligobrachia ivanovi. The structure consists of an array of poly-N-acetyl-D-glucosamine chains all having the same sense, which are linked together in sheets by N—H … O=C hydrogen bonding of the amide groups. In addition to the O-3′—H … O-5 intramolecular hydrogen bond, analogous to that in cellulose, the CH2OH side chain forms an intrasheet hydrogen bond to the carbonyl oxygen on the next chain. This structure shows considerably better agreement between observed and calculated intensities than that possessing an intersheet hydrogen bond, as had been proposed previously. The structure is consistent with the swelling properties of β-chitin and can also be seen to be analogous to that of native cellulose.

Notes: Conformational analysis of N-methylamide of pyroglutamic acid has been performed by theoretical energy calculations and experimental physical techniques, namely, laser Raman spectroscopy and depolarized Rayleigh scattering. The two theoretically predicted conformations are evidenced in crystalline state (ψ1 = +169°) and in aqueous solution (ψ1 ≃ -20°). This study confirms the interest of a careful vibrational analysis of peptides and N-deuterated derivatives for providing an estimate of the dihedral angle ψ. The relationship between amide III frequency and ψ values is emphasized.

Notes: The adsorption of globular proteins at solid/liquid or liquid/liquid interfaces provides evidence of unfolded molecular conformation. Proteins with high apolar character are strongly unfolded, while those with high polar character are generally incompletely unfolded. Structural changes of globular proteins at adsorption on mercury electrodes were studied by ac polarography and capacity-time curves. The surface area per molecule of nine globular proteins was determined from the adsorption kinetics at the dropping mercury electrode. For all the proteins investigated, this value was greater than the maximal molecular cross section of the native proteins. The surface area was about 19 Å2 per amino acid residue, which coincides with the value for unfolded proteins at the water/air interface. Differences between dropping mercury electrode and hanging drop mercury electrode occurred only with lysozyme and phosphorylase; for the other proteins, the structure of the adsorption layer was independent of the time of interaction at the electrode. Since not all of the reducible groups of the adsorbed proteins come into contact with the electrode, the flattening should be incomplete.

Notes: Classical potential energy calculations have been made for the ribodinucleoside monophosphates ApA, CpC, GpG, and UpU. Van der Waal's, electrostatic, and torsional contributions to the energy were calculated, and the energy was minimized with the seven backbone conformational angles as simultaneously variable parameters. At the global minimum, ApA and CpC have conformations like double helical RNA: the angles ω′ and ω are g-g-, the sugar pucker is C3′-endo, and the bases are anti. GpG and UpU, on the other hand, have the ω′,ω angle pair g-t at the global minimum, and for GpG the bases are syn. Energy contour maps for ω′ and ω show two broad, low energy regions for ApA, CpC, and UpU: one is g-g-, and the second encompasses g-t and g+g+ within a single lowenergy contour. The two regions are connected by a path at 10-13 kcal./mole. For GpG, with bases syn, however, only a small low-energy region at g-t is found. The helical ‘A’ RNA conformation is 8.5 kcal/mole higher for this molecule. Thus, the base composition is shown to influence the conformations adopted by dinucleoside phosphates. Comparison of calculations with experimetal data, where available, show good agreement.

Notes: The far infrared spectra of poly(L-proline) I (190-35 cm-1) and II (400-35 cm-1) were obtained in the solid state at both 300° and 110°K. A significant difference in the region below 100 cm-1 was observed. A very intense band located at 60 cm-1 in the infrared spectrum of form II has no counterpart in form I. This indicates the sensitivity of low-frequency vibrations to the difference in conformation assumed by both forms in the solid state.Additional bands observed in this study are correlated with ir and Raman data previously reported and tentative assignments are made using the results of normal mode calculations (in the single-chain approximation) which have been reported.

Notes: Potentiometric titrations of poly(S-carboxymethyl-L-cysteine) and poly(S-carboxy-ethyl-L-cysteine) were carried out in aqueous sodium chloride solutions and in water. For samples of both polymers of high molecular weight, a new pattern was observed concerning the change of titration curve with time; the β-coil transition became sharper and the transition free energy increased by about 100 cal mole-1 as the equilibrium was approached. This suggests that equilibrium data were not obtained in most previous studies on the titration involving the β-coil transition. It also shows that the reversbility is not necessarily sufficient to confirm the equilibrium. Another pattern, which was previously observed, was also confirmed with a low molecular weight sample of poly(S-carboxymethytl-L-cysteine). The titration curves were shown to be insensitive to polymer concentration, even when aggregation or phase separation was present. The validity of the Gouy model to describe the titration curve of the β-structure was found to depend on molecular weight as well as on the nature of the side chain.

Notes: Three kinds of fluorescence enhancement result from the interaction of 2-p-toluidinylnaphthalene-6-sulfonate and calf-skin collagen. They are negatively cooperative, independent, and highly cooperative fluorescence enhancement. In the independent region at pH 3.7, the binding number is about 36 moles of 2-p-toluidinylnaphthalene-6-sulfonate per mole of tropocollagen with a binding constant of 2.0 × 104 M-1; with ΔG = -5.7 kcal/mole, ΔH = -4.0 kcal/mole, and ΔS = 6 e.u. The pH dependence of fluorescence of native collagen shows that the deprotonated forms of the β and γ carboxyl groups of aspartic and glutamic acid decrease the intensity, possibly by charge repulsion of the negatively charged sulfonate group of 2-p-toluidinylnaphthalene-6-sulfonate. The positive charge of lysine is found to be unimportant in the interaction of 2-p-toluidinylnaphthalene-6-sulfonate with collagen. Fluorescence enhancement is caused mainly by the hydrophobic interactions of 2-p-toluidinylnaphthalene-6-sulfonate and collagen. Salt bridge formation between basic and acidic side chains in very low salt concentration may be detectable by 2-p-toluidinylnaphthalene-6-sulfonate fluorescence.

Notes: A series of copolymers of L-lysine and L-valine [poly(L-lysinef L-valine100-f)] containing 0-13% L-valine have been studied, in 0.10M KF solution, using potentiometric titration and circular dichroism spectroscopy. Incorporation of increasing amounts of valine into the copolymers favors β-sheet formation over α-helix formation at high pH and room temperature. The titrations were analyzed using the method of Zimm and Rice and the partial free energy (ΔG0cβ) for the coil-to-β-sheet transition for valine is estimated at 900 cal/mole at 25°C. From the temperature dependence of the free energy, the partial enthalpy, ΔH0cβ, and entropy, ΔS0cβ, of the transition for valine is estimated to be 854 cal/mole and 6.0 e.u., respectively. The corresponding partial thermodynamic parameters for L-lysine are in agreement with published results. The fraction of β-sheet versus pH has been calculated for poly(L-lysine86.8 L-valine13.2) at 25.0°C using the titration data; data obtained from circular dichroism spectroscopy for the same copolymer are in good accord. It is concluded from these results that L-valine is a very strong β-sheet forming amino acid. Furthermore, these results indicate that the Zimm-Rice method is applicable to transitions between the coil and β-sheet states for a polypeptide containing two different residues.

Notes: Conformational analysis of double-stranded helical polynucleotides was carried out in terms of internal and external parameters, using semiempirical energy potential functions. The results obtained show that the structures proposed on the basis of the X-ray analysis for A-DNA and RNA's are almost identical to those corresponding to the conformational energy minima, whereas that proposed for B-DNA still appears to suffer from conformational strains. On the other hand, the B-DNA structure theoretically predicted is stabilized by both van der Waals energy and possible specific interactions with water molecules and counterions. This may explain the stability of the B form with respect to the A form at high relative humidity and ion strength. A possible role of the A + T fraction in stabilizing the B-type DNA emerges in connection with its preferential ability to bind ions. This agrees with the results on the crystalline structures of GpC and ApU. For RNA's, the occurrence of only A-type structures is explained as being due to the C(3′)-endo puckering of ribose in a double helix.

Notes: A very general approach to the chemical equilibria between many interacting molecules during sedimentation (boundary, band, or active enzyme) taking into account boundary conditions, cell geometry, equilibrium constants, diffusion, enzyme kinetics, etc., is presented. Through a Fortran program, the method has been applied to two very simple but typical cases. With only minor adjustments, the method presented here for sedimentation studies can be extended to all sorts of problems in which “pools” of various species are interacting with each other.

Notes: Derivatives and peptides of β-nitrobenzyl-L-aspartates were studied with high-field nmr. Differences were observed between the chemical shifts of protons located near the extremity of the principal chain as a function of the terminal group. These differences are explained by conformational calculations which exclude the existence of an hydrogen bond and demonstrate the influence of the aromatic ring position on the protons of the main chain. Both nmr experiments and conformational analysis indicate that conformations are nearly the same for ortho, meta, and para nitro substitution. These conclusions are in good agreement with Karplus relationship applied to the α and β protons.

Notes: The theoretical study of the cooperative binding of a small ligand to a linear homopolymer is extended to systems in which two different complexes can form. The binding isotherms are derived under the assumption that the cooperative interactions exist only between molecules belonging to the same type of binding mode and are limited to nearest neighbors (Ising model). The binding to a single-stranded chain is first considered and two extreme cases are studied: (1) the two complexes can form independently from each other (model of independent classes of binding sites); (2) only one class of binding site exists, each possessing two different states of complexation (three-state model).Binding to a double-helical chain is also considered. Three simple types of competition between the different modes of binding are distinguished. The corresponding models are defined as: (1) the model of independent classes of binding sites; (2) the model of monoexclusive interactions between the different kinds of complexes (the symmetric and asymmetric cases are both considered); (3) the model of biexclusive interactions. The comparative study of the different cases shows that the binding isotherms are very similar at large polymer-to-ligand concentration ratios, while they can be very different at low polymer-to-ligand ratios. This can be used to obtain information on the mechanism of dye binding to nucleic acids by equilibrium studies as shown in a subsequent paper.

Notes: The infrared spectra of poly(L-valine)'s with varying degrees of polymerization have been investigated, as well as copolymers of L-alanine and L-valine. The spectra of nujol mulls of various molecular-weight poly(L-valine)'s, isolated directly from the polymerization media, as well as spectra of these same samples after treatment with strong acid, are recorded. In the 700-250-cm-1 region, bands at 543 and 414 cm-1 are found to increase with increasing degree of polymerization in the nujol mulls, but are missing in the acid-treated samples. These bands are assigned to the L-valine residues with an β-helixlike local conformation. It is inferred that the polymerization proceeds initially in the β form, and after a critical degree of polymerization the chains adopt an appreciable amount of an α-helixlike local conformation.

Notes: The interaction of counterions with a suitably long, charged oligomer appears susceptible to treatment in the context of polyelectrolyte theory by the introduction of an end-effect parameter that reflects the reduced association of counterions with the terminal regions of the oligo-ion. Use of a physically reasonable value for the end-effect parameter provides excellent agreement between theory and the experimental data of Elson, Scheffler, and Baldwin [J. Mol. Biol. 54, 401-415 (1970)] on the dependences of melting temperature on salt concentration and chain length for a series of hairpin helices formed by d(TA) oligomers. The differences in behavior expected for hairpin, dimer, and oligomer-polymer helices are discussed. The salt dependence of the end-joining equilibrium investigated for λ DNA by Wang and Davidson [Cold Spring Harbor Symp. Quant. Biol. 33, 409-415 (1968)] is treated as an oligomer-polymer interconversion. The dependence of equilibrium constant for this reaction on counterion concentration is in good agreement with that predicted by theory for an end-region totalling 24 nucleotides, the known length of the λ ends.

Notes: Solvent denaturation is developed along thermodynamic lines rather than from multiple-binding theory. Almost all the relations derivable from site-binding theory have their counterparts in the thermodynamic formulation showing that the details of binding models may be sufficient but are not necessary for the general description of solvent denaturation. Equations are derived for the effect of denaturant concentration on stability at constant temperature and on tm. It is recommended that the thermodynamic treatment be used instead of binding models unless stoichiometric interactions are demonstrable experimentally.

Notes: The optical properties of the 1,N6 - etheno derivative of ApA (εApεA) have been studied. Absorbance and CD measurements suggest that (1) neutral salts tend to unstack this molecule and (2) the stacking interaction is weaker than in ApA. εApεA is found to be quenched strongly with respect to the monomer. (εAMP); this quenching is solvent dependent (1M NaCl 〉 5M NaClo4〉40%glycerol) and increases with the ratio of temperature to viscosity (T/η) in each case. Fluorescence lifetime measurements also reveal a temperature- and solvent-dependent decay which is nonlinear on a semilog plot. In the presence of 95% glycerol, this decay return to linearity. These data have been considered from two points of view: (1) two-state pictures which are based on thermodynamic least-squares fit to quatum yield and CD curves, together with two exponential fits to the decay curves and (2) a dynamical model in which relatives fluorophore motion leads to deexcitation via intramolecular collision. A simple model of type (2) gives qualitative agreement with the observed behavior.

Notes: Fluorescent probe analysis of purified elastin using 1-anilinonaphthalene-8-sulfonate has been used to investigate reversible structural changes that accompany stretching of this rubberlike protein. There is a specific binding of 1-anilinonaphthalene-8-sulfonate to elastin with a single dye molecule attached per 74,000 molecular-weight protein subunit. When labeled elastin is stretched, the intensity of the 1-anilinonaphthalene-8-sulfonate fluorescence decreases reversibly, and this decrease appears to be linked to an increase in the environmental polarity in the immediate vicinity of the bound dye molecule. The results of experiments carried out in H2O and D2O indicate that this polarity change is due to an increase in the exposure of the 1-anilinonaphthalene-8-sulfonate to water as the hydrophobic interior of the protein subunit is unfolded during stretching. The data are consistent with the proposal that the elastin network is a two-phase system of hydrophobic protein globules surrounded by free solvent spaces.

Notes: The native antibiotic polymyxin B, carrying five positive charges, displaces the monoacetylated on from its adsorbed state at the interface between negatively charged lipid layers ans water. A simulation model for asdorption, governed by electrostatic forces, is presented. The model adequently representes the competitive adsorption kinetics and equilibria.

Notes: In order to study the role of D-amino acid residues in keeping the stable β-sheet conformation and in the antimicrobial activity of gramicidin S (GS), the four analogs of GS containing D-Ala, L-Ala, Gly, and Aib (α-aminoisobutyric acid) in place of D-Phe were synthesized. D-Ala-and Gly-containing analogs showed antimicrobial activity, while those containing L-Ala and Aib showed no activity. Conformation of these analogs and their derivatives were studied by comparison of ORD and CD spectra and by slective methylation method. It is concluded that the biologically active analogs have β-sheet conformation while inactive analogs have a much different conformation from that of GS. This indicates that D-Ala-Pro and Gly-Pro sequences favor taking a β-bend form but L-Ala-Pro and Aib-Pro sequences do not because the presence of L-side methyl group on the α-carbon atom of LAla and Aib residues destabilizes the β-bend form. This would explain why the inactive analogs which take a different conformation from that of the active ones result in the loss of activity.

Notes: Earlier studies by the authors showed that the collagen fibrils in rat-tail tendon have a bi-modal distribution of fibril diameters from a time shortly after birth through to the onset of maturity at about 3-4 months. Present work has extended those observations for rats up to the age of 2 years. Histograms of the fibril diameter distributions for mature tail tendon and direct electron microscope observations show that the fibrils break down as the tendon ages. Further work on the constant diameter subfibrils of diameter 140 Å described previously, has confirmed that these are part of the elastic fibers present in tendon at all ages. It has been shown that there is relatively little variation in the collagen fibril diameter distribution as a function of the position of the specimen in the tail, and as the measured percentage of the area taken by the collagen fibrils present at any particular point. Estimation of the fibrillar collagen content of rat-tail tendon as a function of age indicates that it increases steadily from birth and reaches a maximum at the onset of maturity, beyond which the fibrillar collagen content appears to remain constant.

Notes: We have made quantitative estimates of some of the energetic factors to be considered in packaging of double-stranded DNA in virus particles. Numerical calculations were made using parameters appropriate for T4 bacteriophage. The unfavorable factors, and the Gibbs free energies per mole virus at 20°C associated with them, are bending, 1.5 × 103 kcal/mol; conformational restriction upon condensation, 5.1 × 102 kcal/mol; polyelectrolyte repulsion, 2.1 × 105kcal/mol; and melting or kinking, 6.9 × 103 kcal/mol. These must be counterbalanced in the assembled phage by noncovalent bonding interactions between protein subunits in the phage-head shell; by interactions between the DNA and polyvalent cations, especially putrescine and spermidine; nad perhaps by repulsive excluded volume and electrostatic interaction between the DNA and acidic polypeptides. Indeed, a rough estimate of the standard free energey of interaction between T4 DNA and the putrescine and spermidine contained in the head is --2.1 × 105 kcal/mol. In the absence of the other two sources of stabilization, each head protein subunit must contribute about 210 kcal/mol of binding energy.

Notes: A theoretical basis for thin-film dialysis involving binding between a ligand and nondialyzing species is presented. A general differential equation that applies to the case of equivalent, noninteracting sites is derived relating [A]F, [A]T, [P]T, and K. Numerical solutions to this equation are used to develop a series of escape curves corresponding to specific values of the parameters [P]T, [A]i, K, and k0. A general method for determining an equilibrium binding constant from thin-film dialysis data is given. A comparison of thin-film dialysis results predicted by this theory with literature data shows essential agreement.

Notes: The normal and vacuum uv spectra of cytosine, 5-azacytosine, and 6-azacytosine thin layers were determined. The spectra were resolved into a series of Gaussian bands and the experimental band positions and oscillator strengths were compared with the calculated values. The calculations were carried out with the PPP-SCF-CI method. The agreement of the calculations with those of others and with the experiment is discussed.

Notes: A model for the electrostatic properties of hydrated collagen fibrils, based on the concept of a “penetrable” protein, has been evaluated through studies of collagen fibrils that had been chemically modified to change their electrostatic properties,. A value of 0.28 ± 0.07 ml/g was found for the intrafibrillar space sterically inaccessible to a molecule that had an equivalent spherical radius of 4.5 Å.The net intrinsic charge on reconstituted collagen is +14 mol/mol under physiological conditions, but decreases, at constant pH, with ionic strength. A value of 7.1 for the pK of the histidine and α-amino groups in reconstituted collagen was obtained through the application of the electrostatic model to this effect.The values obtained for calcium binding parameters for collagen fibrils, under solution conditions in which the nonspecific electrostatic properties of collagen fibrils were eliminated (3-5 M tetramethyl ammonium chloride), were in agreement with values obtained in 0.16 M NaCl solutions calculated through the use of the electrostatic theory. These are 0.73 ± 0.23 and 56.2 ± 12.3 sites per molecule with intrinsic association constants of 1101 ± 386 and 21.4 ± 5.2 M-1, respectively.The model also predicts that an average 4-mV potential difference exists between the reconstituted collagen fibrils and physiological solutions, and that collagen fibrils under such conditions have piezoelectriclike properties.The pattern of interaction of ions with collagen fibrils is such that an allosteric mechanism for the catalytic step in the mineralization of collagen is a possibility.

Notes: Raman spectra of native and solubilized feather keratin have been obtained, and the amide I and amide III regions have been analyzed by band resolution techniques. The amide I region of the native form indicates that at least 64% of the protein has an antiparallel chain pleated sheet structure, the remainder being unordered. For the solubilized keratin all of the protein is in an unordered state. The amide III region is not as easily analyzed into component contributions. Normal vibration analyses on N-acetyl-L-alanine-N-methylamide support the conclusion that the amide III region is not as satisfactory as the amide I region in characterizing unordered structures. Even in the latter case caution must be used, since the observed amide I band is an average over the conformational distribution in the particular unordered system.

Notes: The optical birefringence induced in DNA solutions by both oscillating hydrodynamic fields (flow birefringence) and oscillating electric fields (Kerr effect) is measured over a wide frequency range. The observed frequency response of the birefrigence is compared with theories for rigid ellipsoidal particles and for Gaussian chains. DNA at 6 × 105 molecular weight is found to exhibit rigid particle hydrodynamic behavior, while DNA at 5 × 106 molecular weight behaves like a flexible chain. Characterization of the hydrodynamic relaxation spectra for the DNA's by oscillatory flow birefringence allows precise comparison between theory and the experimental Kerr effect response. The dielectric model for DNA contains both permanent and dispersionless induced dipole moments. The dielectric behavior of DNA has the character of a permanent dipole but with anomalous low-frequency dispersion in the Kerr effect. The existing theories do not adequately describe this dispersion. A fluctuation dipole mechanism with relaxation times comparable to those associated with the hydrodynamic motion could possibly demonstrate the observed polar behavior.

Notes: Conformational energies have been estimated for the tripeptide fragments L-Ala-N-methyl-L-Ala-L-Ala, L-Ala-L-Ala-N-methyl-L-Ala, L-Ala-Sar-L-Ala, and L-Ala-Gly-N-methyl-L-Ala. The peptide bonds connecting L-Ala and Gly with N-methyl-L-Ala and L-Ala with Sar were permitted to adopt the planar cis as well as the usual trans conformation. Contour maps of the conformational energies of the central residue in these tripeptide fragments are presented and compared to the conformational energy maps previously calculated for unmethylated L-Ala and Gly surrounded by residues which are also unmethylated. In generl it is observed that L-Ala and Gly residues that are either N-methylated in their conformational freedom relative to the same residues in an unmethylated polypeptide chain.

Notes: Circular dichroism and absorption spectra have been measured on solutions of acridine orange and poly(L-glutamic acid) mixed at two molar ratios of carboxyl group-to-dye, P/D 25 and 0.8, and at different pH's. Characteristic circular dichroism is induced at the absorption bands of acridine orange when the P/D is 25 and the solution is acidic. Another type of circular dichroism is manifest at neutral and alkaline pH when P/D is 0.8. For the induction of the former type of circular dichroism, a helical array of acridine-orange dimers bound to the α-helix is postulated, in which the dye molecular planes are almost perpendicular to the helical axis. Assuming the helical geometry and optical parameters, combined with the observed magnitude of transition electric moment, the rotatory strength of the complex is calculated to the zeroth order approximation, and the observed circular dichroism spectra have been reproduced.

Notes: Sequential determination of glycyl residues (and in several cases different amino-acid residues) in tetra and branched peptides using the nmr technique is reported. The method is based on changes in the nmr spectra of (1) the peptide hydrogens of the different residues and (2) the methylene groups of the glycyl residues, as a result of increasing the rate of the base-catalyzed exchange reaction of the peptide hydrogens. Hence, the spectral changes are pH dependent. However, the exact pH dependence is a function of the location of the residue in the peptide molecule. Thus, it is possible to determine the sequence of the amino-acid residues by studying the changes in the spectra with pH.For peptide molecules of known sequences, the above method can be used for unequivocal assignment of the peptide hydrogen signals.

Notes: The induced circular dichroism (CD) in the visible region of acridine orange bound to the double-stranded RNA from cytoplasmic polyhedrosis virus and to yeast tRNA has been measured as a function of RNA phosphate-to-dye ratio (P/D), under the conditions of 0.01 M Na+ at pH 7.0. The shape of the CD spectrum of acridine orange bound to the double-stranded RNA was quite different from the spectrum of the dye bound to DNA. The CD spectral features of acridine orange bound to the double-stranded regions in tRNA closely resembled those of the double-stranded RNA-dye complex, suggesting that the dyes bind similarly to the two RNA's. It was further found that the CD spectrum of the tRNA-dye complex at sufficiently high P/D ratios, which is assignable to monomeric, intercalated dye to the base-paired parts in tRNA, is also distinct from the corresponding spectrum of the DNA-dye complex.

Notes: A least squares analysis of the titration properties of several dinucleoside monophosphates enables calculation of the pK's for protonation. These pK's are used to resolve the spectral properties of dinucleoside monophosphates with one base charged from the apparent spectral properties of a dinucleoside monophosphate in aqueous solution. This method is applied to dinucleoside monophosphates containing adenosine and/or cytidine. Results of CD, nmr, and CD-temperature dependence measurements are presented. The results indicate that singly protonated dimers of these nucleosides stack as do their unprotonated analogs. It is suggested that this is true for all dimers with one base charged.

Notes: Connectors for CPK space-filling molecular models have been supplemented with pointed steel wires (φ = 1.59 mm) of appropriate lengths and positions to represent atomic bonds. For illustration purposes, the polypeptide backbone of glucagon was equipped with such wire-core connectors and given a possible conformation. The molecular model was packed into a cubic box and, using a clinical instrument, X-ray films were taken from three orthogonal directions. Atomic coordinates on the films were then corrected to real-space coordinates.This method for retrieving atomic coordinates from space-filling models of modium-sized polypeptides is easy and can be done wih equipement available everywhere. Coordinates obtained in this way should be useful as starting points for energy minimization, for the calculation of frictional coefficients, and in attempts to solve crystal structures by X-ray diffraction, using molecular replacement methodology.