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  • 1
    Electronic Resource
    Electronic Resource
    Proton NMR assignments of systemin (1992)
    Springer
    The protein journal 11 (1992), S. 265-274 
    Details
    ISSN: 1573-4943
    Keywords: NMR ; peptide ; hormone ; systemin ; proton assignments
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Complete proton NMR assignments have been made for a synthetic 18-amino acid peptide named systemin, which functions as a wound-induced polypeptide hormone in tomato plants, and three of its derivatives. The wild-type peptide and this synthetic homolog have equivalent activities in their functional roles as systemic inducing signals in tomato plants. Proton NMR studies were carried out to characterize the solution properties of systemin. A variety of homonuclear proton NMR experiments at both 500 and 600 MHz were utilized in making these assignments, which have resulted in additional structural information. Whereas these results provide no evidence for persistence of common secondary (helix, sheet) or tertiary structural elements in the systemin polypeptide, there is evidence for two distinct molecular conformations at the carboxy terminus.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01024865
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  • 2
    Electronic Resource
    Electronic Resource
    Structural Features of Glycera dibranchiata Monomer Hemoglobins. Primary Sequences of Monomer Hemoglobin Components II and III (1997)
    Springer
    The protein journal 16 (1997), S. 139-150 
    Details
    ISSN: 1573-4943
    Keywords: Glycera dibranchiata ; monomer hemoglobin ; primary sequence ; mass spectrometry ; HPLC ; alignments
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Primary sequences for the remaining two members (GMH2, GMH3) of the group of three major monomeric hemoglobins from the marine annelid Glycera dibranchiata have been obtained. Full sequences of each 147-amino acid globin were achieved with a high degree of confidence using standard Edman technology in combination with molecular mass determinations of the intact globins and of the cyanogen bromide cleavage fragments using electrospray ionization mass spectrometry. When minor assumptions concerning Q/E identities are made these new results indicate the likely correspondence of GMG2 with the protein represented by the first Glycera dibranchiata monomer hemoglobin complete sequence [Imamura et al., (1972), J. Biol. Chem. 247, 2785–2797]. When these new sequences are combined with the previously determined primary sequence for the third major monomer hemoglobin, GMH4 [Alam et al., J. Protein Chem. (1994), 13, 151–164], it becomes clear that these three (GMG2–4) are truly distinct proteins, contrary to previous suggestions. Surprisingly, our results show that none of these three primary sequences is identical to the published sequence of the refined monomer hemoglobin crystal structure protein; however, there is a strong correspondence to the GMG2 sequence. The present sequencing results, in combination with the published GMH4 sequence, confirm the presence of a distal Leu in place of the more commonly encountered distal His in all three of the major monomer hemoglobins isolated in this laboratory and indicate that the unusual B10 Phe occurs only in GMH4. Analysis of the sequences presented here, along with comparison of amino acid content for Glycera dibranchiata monomer hemoglobins isolated from three different laboratories, and comparison of NMR results from two laboratories suggest further correspondences which unify disparate published isolations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1026346202134
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  • 3
    Electronic Resource
    Electronic Resource
    Electrospray Ionization Mass Spectrometric Study of the Multiple Intracellular Monomeric and Polymeric Hemoglobins of Glycera dibranchiata (1998)
    Springer
    The protein journal 17 (1998), S. 85-97 
    Details
    ISSN: 1573-4943
    Keywords: Intracellular hemoglobin ; Glycera dibranchiata ; electrospray ionization mass spectrometry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The intracellular hemoglobin (Hb) of the marine polychaete Glycera dibranchiata is comprised of two groups of globins differing in their primary structures and state of aggregation. About six electrophoretically and chromatographically distinct monomeric Hbs which have Leu as the distal residue, and an equal number of polymeric Hbs which have the usual distal His, have been identified to date. Deconvolution of the electrospray ionization mass spectra (ESI-MS) of the Hbs and of their carbamidomethylated, reduced, and reduced/carbamidomethylated forms, using a maximum entropy-based approach (MaxEnt), showed the presence of at least 18 peaks attributable to monomer Hbs (14,500–15,200 Da) and an approximately equal number of polymer Hb peaks (15,500–16,400 Da). Although the ratio of the monomer to polymer components in pooled Hb preparations remained constant at 60:40, Hb from individuals had generally less than 6 monomer and 6 polymer components; 2 of the 19 individuals appeared to be deficient in polymer Hbs. Taking into account possible fragmentations of the known monomeric and polymeric globin sequences, we estimate conservatively that there are 10 monomeric and an equal number of polymeric Hbs, the majority comprising a single free Cys. Surprisingly, the calculated mass of the sequence deduced from the high-resolution monomer Hb crystal structures does not correspond to any of the observed masses. ESI-MS of the monomer Hb crystal revealed 11 components, of which 5, accounting for 67% of total, were related to the three major sequences GMG2–4. These findings underline the need for routine mass spectrometric characterization of all protein preparations. The complete resolution of the Glycera Hb ESI-MS using MaxEnt processing illustrates the power of this method to resolve complex protein mixtures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1022519230412
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  • 4
    Electronic Resource
    Electronic Resource
    A comparison of spectral and physicochemical properties of yeast iso-1 cytochrome c and Cys 102-modified derivatives of the protein (1995)
    Springer
    The protein journal 14 (1995), S. 567-582 
    Details
    ISSN: 1573-4943
    Keywords: Yeast iso-1 cytochrome c ; chemical modification ; cysteine 102
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Derivatives of yeast iso-1 cytochrome c, chemically modified at Cys-102 (Cys-102 acetamide-derivatized monomer, Cys-102 thionitrobenzoate-derivatized monomer, Cys-102 S-methylated monomer, and the disulfide dimer), exhibit different spectral and physicochemical properties relative to the native, unmodified protein, depending on the nature of the modifying group. The results of proton NMR studies on the Cys-102 acetamidederivatized monomer of iso-1 ferricytochrome c indicate that the conformational characteristics of the heme environment in this protein derivative are intermediate between those of the unmodified monomer and disulfide dimer forms of the protein. Measurements of the pKa of the alkaline transitions of the five forms of iso-1 ferricytochrome c provided values of 8.89, 8.82, 8.67, 8.47, and 8.50 for the unmodified monomer, S-methylated monomer, acetamide-derivatized monomer, thionitrobenzoate-derivatized monomer, and disulfide dimer, respectively. The results of proton NMR studies of the reduced form of these proteins suggest that the heme environments of the unmodified monomer and disulfide dimer derivatives of iso-1 ferrocytochrome c are similar and indicate that treatment of the thionitrobenzoate-derivatized and disulfide dimer forms of the protein with sodium dithionite results in cleavage of the disulfide bonds at position 102. Circular dichroism studies reveal that only the disulfide dimer form of iso-1 ferricytochrome c exhibits a Soret CD spectrum which differs from the native, unmodified monomer in that the intensity of the negative band at approximately 420 nm is diminished in the spectrum of the dimer relative to the spectrum of the monomer. Soret CD spectra of the ascorbate-reduced form of all protein derivatives are similar. The process of “autoreduction” of yeast iso-1 ferricytochrome c is shown to occur in the absence of a free sulfhydryl group at position 102 and is exacerbated under moderately high pH conditions. These results are suggestive of the presence of a redox-active amino acid, perhaps a tyrosine, in yeast iso-1 cytochrome c.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01886883
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  • 5
    Electronic Resource
    Electronic Resource
    Temperature, pH, and Solvent Isotope Effects on Cytochrome c Peroxidase Mutant N82A Studied by Proton NMR (2000)
    Springer
    The protein journal 19 (2000), S. 535-542 
    Details
    ISSN: 1573-4943
    Keywords: Cytochrome c peroxidase ; CcP ; NMR ; A82CcP mutant ; solvent isotope effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The mutant of baker's yeast cytochrome c peroxidase-CN with Ala82 in place of Asn82, [N82A]CcPCN, exhibits a complex solution behavior featuring dynamic interconversion among three enzyme forms that so far have only been detected by NMR spectroscopy. Proton NMR studies of [N82A]CcPCN reveal resonances from each of the three enzyme forms and show that the interconversion among forms is controlled by the pH, temperature, and isotope composition (H2O vs. D2O) of the buffer solution. No evidence for a key hydrogen bond between His52 and heme-coordinated cyanide is found in any of the enzyme forms, indicating that disruption of the extensive distal hydrogen bonding network is the source of this phenomenon.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1026513818176
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  • 6
    Electronic Resource
    Electronic Resource
    Complete amino acid sequence of theGlycera dibranchiata monomer hemoglobin Component IV: Structural implications (1994)
    Springer
    The protein journal 13 (1994), S. 151-164 
    Details
    ISSN: 1573-4943
    Keywords: Hemoglobin ; amino acid sequence ; mass spectrometry ; molecular modeling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The globin derived from the monomer Component IV hemoglobin of the marine annelid,Glycera dibranchiata, has been completely sequenced, and the resulting information has been used to create a structural model of the protein. The most important result is that the consensus sequence of Component IV differs by 3 amino acids from a cDNA-predicted amino acid sequence thought earlier to encode the Component IV hemoglobin. This work reveals that the histidine (E7), typical of most heme-containing globins, is replaced by leucine in Component IV. Also significant is that this sequence is not identical to any of the previously reportedGlycera dibranchiata monomer hemoglobin sequences, including the sequence from a previously reported crystal structure, but has high identity to all. A three-dimensional structual model for monomer Component IV hemoglobin was constructed using the published 1.5 å crystal structure of a monomer hemoglobin fromGlycera dibranchiata as a template. The model shows several interesting features: (1) a Phe31 (B10) that is positioned in the active site; (2) a His39 occurs in an interhelical region occupied by Pro in 98.2% of reported globin sequences; and (3) a Met41 is found at a position that emerges from this work as a previously unrecognized heme contact.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01891974
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  • 7
    Electronic Resource
    Electronic Resource
    Detailed NMR Analysis of the Heme-Protein Interactions in Component IV Glycera dibranchiata Monomeric Hemoglobin-CO (1998)
    Springer
    Journal of biomolecular NMR 11 (1998), S. 119-133 
    Details
    ISSN: 1573-5001
    Keywords: complete assignments ; heme ; heme protein ; secondary structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Complete 13C, 15N, and 1H resonance assignments have been obtained for the recombinant, ferrous CO-ligated form of component IV monomeric hemoglobin from Glycera dibranchiata. This 15642 Da myoglobin-like protein contains a large number of glycine and alanine residues (47) and a heme prosthetic group. Coupling constant information has allowed the determination of χ1 and χ2 torsion angles, backbone φ angles, as well as 43 of 81 possible assignments to Hβ2/β3 pairs. The 13Cα, 13Cβ, 13C′, and 1Hα assignments yield a consensus chemical shift index (CSI) that, in combination with NOE information and backbone torsion angles, defines seven distinct helical regions for the protein's global architecture. Discrepancies between the CSI and NOE/3JHNHα-based secondary structure definitions have been attributed to heme ring current shifts on the basis of calculations from a model structure [Alam et al. (1994) J. Protein Chem., 13, 151-164]. The agreement can be improved by correcting the 1Hα chemical shifts for the ring current contributions. Because the holoprotein was assembled from isotopically enriched globin and natural isotope-abundance heme, data from 13C-filtered/13C-edited and 13C-filtered/13C-filtered 2D NOESY experiments could be used to determine complete heme proton assignments and to position the heme within the protein. The results confirm the unusual presence of Phe31(B10) and Leu58(E7) side chains near the heme ligand binding site which may alter the polarity and steric environment and thus the functional properties of this protein.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008202621725
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  • 8
    Electronic Resource
    Electronic Resource
    Sequential Main-Chain Proton and Carbon Resonance Assignments for Wild-Type Yeast Iso-1 Ferrocytochrome c and Identification of Secondary Structural Elements (1997)
    Springer
    The protein journal 16 (1997), S. 775-786 
    Details
    ISSN: 1573-4943
    Keywords: Cytochrome c ; assignments ; ferrocytochrome c ; NMR ; 1H NMR ; 13C NMR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Yeast iso-1 cytochrome c is a naturally occurring protein that possesses an unusually reactive Cysl02 that imbues iso-1 with a complicated solution chemistry which includes spontaneous dimerization and poorly characterized redox reactions. For this reason previous studies of this typical member of the c-type cytochromes have been relegated to variant proteins in which the 102 position has been mutated, with most common changes involving serine and threonine. However, we have determined sequential 1H resonance assignments for the wild-type native protein because it is the actual participant in yeast mitochondrial electron transfer processes and because the wild-type native protein should be the fundamental assignment basis. In addition to 1H resonance assignments for 97 of 106 amino acids, we have also provided an extensive database of long-range NOEs. Comparison of these NOEs and a chemical shift index based upon α-H resonances has lead to identification of solution secondary structural elements that are consistent with the solid-state crystal structure. Although there is currently no efficient expression system that would facilitate isotope labeling of iso-1 cytochrome c, we tried to assess the usefulness of future heteronuclear experiments by using natural-abundance 1H/13C HMQC experiments to unambiguously assign 35 α-C resonances.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1026315900800
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