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  • 1
    Electronic Resource
    Electronic Resource
    A Model for the Helix-Coil Transition in Specific-Sequence Copolymers of Amino Acids (1971)
    s.l. : American Chemical Society
    Macromolecules 4 (1971), S. 692-709 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma60024a006
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  • 2
    Electronic Resource
    Electronic Resource
    Protein anatomy: Spontaneous formation of filamentous helical structures from the N-terminal module of barnase (1993)
    s.l. : American Chemical Society
    Biochemistry 32 (1993), S. 2162-2166 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00060a006
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Adaptive Amino Acid Replacements Accompanied by Domain Fusion in Reverse Transcriptase (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. S155 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Adaptive replacement — Ribonuclease H — Reverse transcriptase — Domain fusion — Molecular evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Two basic processes are involved in protein evolution: One is amino acid replacement and another is reorganization of structural or functional units of proteins. Multidomain or multifunctional proteins are thought to have evolved by fusion of smaller structural units such as modules or domains. Reverse transcriptase (RT) is one of such fused proteins. The N-terminal part forms of globular domain with polymerase activity and the C-terminal part forms another globular domain with ribonuclease H activity (RNase H domain). There are single-domain enzymes which are homologous with the RNase H domain. The group of enzymes is called type I ribonuclease H (RNase HI). It is most likely that the ancestors of RNase HI and the polymerase domain were fused and became contemporary RT. At fusion, amino acid replacements presumably occurred at the interface of the domains to reinforce the interdomain interactions. Such replaced amino acid residues are conserved during evolution of the fused enzyme. We analyzed the pattern of amino acid replacement at each residue site in the free form, RNase HI group, and the integrated form, RNase H domain group. Then we compared the patterns between the two forms. Drastic fitting replacements of amino acid residues occurred at four of 29 residue sites involved in interdomain contact. Hydrophilic amino acid residues of the free form were substituted with hydrophobic or ambivalent ones in the integrated form. These substitutions aid in stabilizing the fused conformation by hydrophobic interactions at the interface of the domains. These observations imply that domain fusion could have occurred with only a relatively small number of adaptive amino acid substitutions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00000068
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  • 4
    Electronic Resource
    Electronic Resource
    Domains and modules of proteins (1992)
    Springer
    The protein journal 11 (1992), S. 389-390 
    Details
    ISSN: 1573-4943
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01673747
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  • 5
    Electronic Resource
    Electronic Resource
    Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation (1993)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 16 (1993), S. 341-356 
    Details
    ISSN: 0887-3585
    Keywords: ribonuclease ; synthesized peptide ; protein folding ; protein conformation ; molecular evolution ; exon shuffling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Proteins consist of structural units such as globular domains, secondary structures, and modules. Modules were originally defined by partitioning a globular domain into compact regions, each of which is a contiguous polypeptide segment having a compact conformation. Since modules show close correlations with the intron positions of genes, they are regarded as primordial polypeptide pieces encoded by exons and shuffled, leading to yield new combination of them in early biological evolution. Do modules maintain their native conformations in solution when they are excised at their boundaries? In order to find answers to this question, we have synthesized modules of barnase, one of the bacterial RNases, and studied the solution structures of modules M2 (amino acid residues 24-52) and M3 (52-73) by 2D NMR studies. Some local secondary structures, α-helix, and β-turns in M2 and β-turns in M3, were observed in the modules at the similar positions to those in the intact barnase but the overall state seems to be in a mixture of random and native conformations. The present result shows that the excised modules have propensity to form similar secondary structures to those of the intact barnase. © 1993 Wiley-Liss, Inc.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340160404
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  • 6
    Electronic Resource
    Electronic Resource
    Localization of hydrogen-bonds within modules in barnase (1993)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 16 (1993), S. 357-363 
    Details
    ISSN: 0887-3585
    Keywords: hydrophobic core ; protein structure ; ribonuclease ; protein folding ; exon shuffling ; molecular evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Proteins in eukaryotes are composed of structural units, each encoded by discrete exons. The protein module is one such structural unit; it has been defined as the least extended or the most compact contiguous segment in a globular domain. To elucidate roles of modules in protein evolution and folding, we examined roles of hydrogen bonds and hydrophobic cores, as related to the stability of these modules. For this purpose we studied barnase, a bacterial Rnase from Bacillus amylolique-faciens. Barnase is decomposed into at least six modules, M1-M6; the module boundaries are identified at amino acid residues 24, 52, 73, 88, and 98. Hydrogen bonds are localized mainly within each of the modules, with only a few between them, thereby indicating that their locations are designed to primarily stabilize each individual module. To obtain support for this notion, an analysis was made of hypothetical modules defined as segments starting at a center of one module and ending at the center of the following one. We found that the hydrogen bonds did not localize in each hypothetical module and that many formed between the hypothetical modules. The native conformations of modules of barnase may be specified predominantly by interactions within the modules. © 1993 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340160405
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  • 7
    Electronic Resource
    Electronic Resource
    Molecular theory of the helix-coil transition in polyamino acids. V. Explanation of the different conformational behavior of valine, isoleucine, and leucine in aqueous solution (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1961-1977 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Even though poly(L-valine) and poly(L-isoleucine) both contain residues that are branched at their β-carbon atoms, they exhibit a different behavior of their Zimm-Bragg helix-growth parameter s in aqueous solution. This quantity increases with temperature for poly(L-valine) but decreases for poly(L-isoleucine). The origin of this behavioral difference was examined by computing theoretical values of s versus temperature from interatomic interaction energies, taking solvent (hydrophobic and hydrophilic) effects into account. The calculated s versus temperature curves for both homopolymers are consistent with the observed experimental behavior. The two homopolymers behave differently because of differences in the change in the number of hydration-shell water molecules accompanying their helix-coil transitions. The larger isoleucine side chains are more crowded together in both the α-helical and coil forms than are those of valine. Therefore, there is a smaller change in hydration of the isoleucine side chains compared to that of the valine side chains in the helix-coil transition. By analyzing the effects of hydration on the s versus temperature curves, it is possible to account also for the experimental curve for poly(L-leucine), which exhibits an intermediate behavior between those for poly(L-valine) and poly(L-isoleucine).
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360231012
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  • 8
    Electronic Resource
    Electronic Resource
    Fluctuations of an α-helix (1976)
    New York : Wiley-Blackwell
    Biopolymers 15 (1976), S. 1119-1127 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fluctuations in backbone dihedral angles in the α-helical conformation of homopolypeptides are studied based on an assumption that the conformational energy function of a polypeptide consisting of n amino-acid residues can be approximated by a 2n-dimensional parabola around the minimum point in the range of fluctuations. A formula is derived that relates 〈ΔθiΔθj〉, the mean value of the product of deviations of dihedral angles φi and ψi (collectively designated by θi) from their energy minimum values, with a matrix inverse to the second derivative matrix F,n of the conformational energy function at the minimum point. A method of calculating the inverse matrix Fn-1 explicitly is given. The method is applied to calculating 〈ΔθiΔθj〉 for the α-helices of poly(L-alanine) and polyglycine. The autocorrelations 〈(Δφi)2〉 and 〈(Δψi)2〉 at 300°K are found to be about 66 deg2 and 49 deg2, respectively, for poly(L-alanine), and 84 deg2 and 116 deg2, respectively, for polyglycine. The length of correlations of fluctuations along the chain is found for both polypeptides to be about eight residues long.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1976.360150608
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