ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    facet.materialart.
    Unknown
    A model for the binding of lac repressor to the lac operator (1976)
    Springer
    Details
    Publication Date: 1976-04-01
    Print ISSN: 0301-4851
    Electronic ISSN: 1573-4978
    Topics: Biology
    Published by Springer
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    A code controlling specific binding of regulatory proteins to DNA (1976)
    Springer
    Details
    Publication Date: 1976-04-01
    Print ISSN: 0301-4851
    Electronic ISSN: 1573-4978
    Topics: Biology
    Published by Springer
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software (2001)
    Oxford University Press
    Details
    Publication Date: 2001-11-01
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 4
    Electronic Resource
    Electronic Resource
    A code controlling specific binding of regulatory proteins to DNA (1976)
    Springer
    Molecular biology reports 2 (1976), S. 413-425 
    Details
    ISSN: 1573-4978
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A possible code is suggested that describes a correspondence between amino acid sequences in stereospecific sites of regulatory proteins and nucleotide sequences at the control sites on DNA. Stereospecific sites of regulatory proteins are assumed to contain pairs of antiparallel polypeptide chain segments which form a right-hand twisted antiparallel β-sheet with single-stranded regions at the ends of the β-structure. The binding reaction between regulatory protein and double-helical DNA is accompanied by significant structural alterations at stereospecific sites of the protein and DNA. Half of the hydrogen bonds normally existing in β-structure are broken upon complex formation with DNA and a new set of hydrogen bonds is formed between polypeptide amide groups and DNA base pairs. The code states a correspondence between four amino acid residues at a stereospecific site of the regulatory protein and an AT (GC) base pair at the control site. It predicts that there are six fundamental amino acid residues (serine, threonine, histidine, asparagine, glutamine and cysteine) whose arrangement in the stereospecific site determines the base pair sequence to which a given regulatory protein would bind preferentially.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00366264
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 5
    Electronic Resource
    Electronic Resource
    A model for the binding of lac repressor to the lac operator (1976)
    Springer
    Molecular biology reports 2 (1976), S. 427-434 
    Details
    ISSN: 1573-4978
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A model is suggested for the lac repressor binding to the lac operator in which the repressor polypeptide chain sequences from Gly 14 to Ala 32 and from Ala 53 to Leu 71 are involved in specific interaction with operator DNA. A correspondence between the protein and DNA sequences is found which explains specificity of the repressor binding to the lac operator. The model can be extended to describe specific binding of other regulatory proteins to DNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00366265
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 6
    Electronic Resource
    Electronic Resource
    Conformational studies of double-helical polynucleotides by the method of pair-wise potential functionsPrepented at the International Conference on Quantum Chemistry, Biology, and Pharmacology held at Keiv, U.S.S.R., September 1978. (1980)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 17 (1980), S. 321-326 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Double-helical polynucleotide conformations, poly(dA)·poly(dT), poly(d(A-T))·poly(d(T-A))·poly(dG)·poly(dC), and poly(d(G-C))·poly(d(C-G)) are analyzed by the atom-atom potential method. The energy optimization is carried out in the space of eight independent geometric parameters using analytical procedures for the constraints, taking into account the flexibility of the β-D-deoxyribose rings. At the first stage, the full screening of atomic partial charges was assumed. The structures of the calculated B and the A forms of DNA are characterized by low energy and absence of short contacts; the dihedral angles are near the average values in the monomers. With the typical energy difference of 3-5 kcal/mol nucleotide pairs in all cases, the B form is more preferable as compared to the A form. At the final step the effect of the Coulomb term is evaluated for poly(dA)·poly(dT) using various values of the effective dielectric constant (ε = 28, 24, 20, 18, 14, 12, 10, 8, 6, 4, and 1). If ε ≤24, the energy optimization leads A to B. We discuss the stereochemical details of the intermediate conformations on the A-B path and hypothesize the nature of stability of the A and the B forms and the mechanism of the A-B transition.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560170215
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 7
    Electronic Resource
    Electronic Resource
    Conformational analysis of polytripeptides (Gly-Pro-Ala)n, (Gly-Ala-Hyp)n, and (Gly-Ala-Ala)n in connection with the problem of collagen structure (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1499-1512 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational analysis of triple helics of a type of collagen was performed with typical collagen tripeptide sequences based on Gly-Pro-Ala, Gly-Ala-Hyp, and Gly-Ala-Ala. During energy minimization, the possibility of continual deformation of the pyrrolidine cycle was taken into account in order to achieve better accuracy in the resulting structure. The (Gly-Pro-Ala)n structure is almost isomorphic to the (Gly-Pro-Hyp)n structure obtained in the previous work [Tumanyan, V. G. & Esipova, N.G. (1982) Biopolymers 21, 475-497]. For a collagen-type structure, the optimal conformation of (Gly-Ala-Hyp)n tends to have a decreased unit twist (t = 15°), although the energy advantage with respect to the conformation with t = 45° is not so significant. A similar situation is observed for (Gly-Ala-Ala)n. In this case, the energy decrease during unwinding to t = 15° from t = 45° is quite small. The conformations of (Gly-Ala-Hyp)n and (Gly-Ala-Ala)n with t = 15° exhibit a similarity with a triple complex of polyproline II helices - a noncoiled coil such as (Gly-Pro-Hyp)n and (Gly-Pro-Ala)n. A similar structure may be postulated for subcomponent cq1 of the first component of a human complement containing substantial Gly-X-Pro and Gly-X-Y tripeptide derivatives in the primary structure (X, Y = any amino acid). The results suggest that the observed helical symmetry of collagen (t = 36°) is a consequence of superposition of diffraction patterns (for sufficiently long segments) from various helices (t varies from ∼15° for Gly-X-Hyp and Gly-X-Y to ∼56° for Gly-Pro-Ala). For short alternating segments, some unification of different helical structures is possible.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360230806
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 8
    Electronic Resource
    Electronic Resource
    Structural principles of B-DNA grooves hydration in fibers as revealed by Monte Carlo simulations and x-ray diffraction (1990)
    New York : Wiley-Blackwell
    Biopolymers 29 (1990), S. 1453-1464 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Being interested in possible effects of sequence-dependent hydration of B-DNA with mixed sequence in fibers, we performed a series of Monte Carlo calculations of hydration of polydeoxyribonucleotides in B form, considering all sequences with dinucleotide repeat. The computational results allow the ten base-stacking types to be classified in accordance with their primary hydration in the minor groove. As a rule, the minor groove is occupied by two water molecules per base pair in the depth of the groove, which are located nearly midway between the planes of successive base pairs and symmetrically according to the dyad there. The primary hydration of the major groove depends on the type of the given base pair. The coordinates of 3 water molecules per base pair in the depth of the major groove are determined by the type of this pair together with its position and orientation in the helix, and are practically independent on the adjacent base pairs. A/T-homopolymer tracts do not fit into this hydration pattern; the base pair edges are hydrated autonomously in both grooves.Analysis of the Li-B-DNA x-ray diffraction intensities reveals those two water positions in the minor groove. In the major groove, no electronic density peaks in suffiecient distance from the base edges were found, thus confirming the absence of any helical invariance of primary hydration in this region.With the help of the rules proposed in this paper it is possible to position the water molecules of the first hydration shell in the grooves of canonical B-DNA for any given sequence.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360291012
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 9
    Electronic Resource
    Electronic Resource
    Structure of the hydration shells of oligo(dA-dT)·oligo(dA-dT) and oligo(dA)·oligo(dT) tracts in B-type conformation on the basis of Monte Carlo calculations (1990)
    New York : Wiley-Blackwell
    Biopolymers 30 (1990), S. 563-581 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Monte Carlo simulations [(N, V, T)-ensemble] were performed for the hydration shell of poly(dA-dT)·poly(dA-dT) in canonical B form and for the hydration shell of poly(dA) ·poly(dT) in canonical B conformation and in a conformation with narrow minor groove, highly inclined bases, but with a nearly zero-inclined base pair plane (B′ conformation). We introduced helical periodic boundary conditions with a rather small unit cell and a limited number of water molecules to reduce the dimensionality of the configuration space. The coordinates of local maxima of water density and the properties of one- and two-membered water bridges between polar groups of the DNA were obtained.The AT-alternating duplex hydration mirrors the dyad symmetry of polar group distribution. At the dApdT step, a water bridge between the two carbonyl oxygens O2 of thymines is formed as in the central base-pair step of Dickerson's dodecamer. In the major groove, 5-membered water chains along the tetranucleotide pattern d (TATA) · d (TATA) are observed.The hydration geometry of poly (dA) · poly(dT) in canonical B conformation is distinguished by autonomous primary hydration of the base-pair edges in both grooves. When this polymer adopts a conformation with highly inclined bases and narrow minor groove, the water density distribution in the minor groove is in excellent agreement with Dickerson's spine model. One local maximum per base pair of the first layer is located near the dyad axis between adjacent base pairs, and one local maximum per base pair in the second shell lies near the dyad axis of the base pair itself. The water bridge between the two strands formed within the first layer was observed with high probability. But the water molecules of the second layer do not have a statistically favored orientation necessary for bridging first layer waters. In the major groove, the hydration geometry of the (A · T) base-pair edge resembles the main features of the AT-pair hydration derived from other sequences for the canonical B form. The preference of the B′ conformation for oligo(dA) · oligo(dT) tracts may express the tendency to common hydration of base-pair edges of successive base pairs in the grooves of B-type DNA.The mean potential energy of hydration of canonical B-DNA was estimated to be -60 to -80 kJ/mole nucleotides in dependence on the (G · C) contents. Because of the small system size, this estimation is preliminary.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360300509
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 10
    Electronic Resource
    Electronic Resource
    Hydration of B-DNA: Comparison between the water network around poly(dG) · poly(dC) and poly(dG-dC) · poly(dG-dC) on the basis of Monte Carlo computations (1989)
    New York : Wiley-Blackwell
    Biopolymers 28 (1989), S. 741-761 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A computational method is elaborated for studying the water environment around regular polynucleotide duplexes; it allows rigorous structural information on the hydration shell of DNA to be obtained. The crucial aspect of this Monte Carlo simulation is the use of periodical boundary conditions. The output data consists of local maxima of water density in the space near the DNA molecule and the properties of one- and two-membered water bridges as function of pairs of polar groups of DNA.In the present paper the results for poly(dG) · poly(dC) and poly(dG-dC) · poly(dG-dC) are presented. The differences in their hydration shells are of a purely structural nature and are caused by the symmetry of the polar groups of the polymers under study, the symmetry being reflected by the hydration shell.The homopolymer duplex hydration shell mirrors the mononucleotide repeat. The water molecules contacting the polynucleotide in the minor groove are located nearly in the plane midway between the planes of successive base pairs. One water molecule per base pair forms a water bridge facing two polar groups of bases from adjacent base pairs and on different strands making a “spine”-like structure. In contrast, the major groove hydration is stabilized exclusively by two-membered water bridges; the water molecules deepest in the groove are concentrated near the plane of the corresponding base pair.The alternating polymer is characterized by a marked dyad symmetry of the hydration shell corresponding to the axis between two successive base pairs. The minor groove hydration of the dCpdG step resembles the characteristic features of the homopolymer, but the bridge between the O2 oxygens of the other base-stacking type is formed by two water molecules. The major groove hydration is characterized by high probability of one-membered water bridges and by localization of a water molecule on the dyad axis of the dGpdC step.The found structural elements are discussed as reasonable invariants of a dynamic hydration shell.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360280305
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...