The link between sequence and conformation in protein structures appears to be stereochemically established
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Title |
The link between sequence and conformation in protein structures appears to be stereochemically established
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Creator |
RAMAKRISHNAN, V
RANBHOR, R KUMAR, A DURANI, S |
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Subject |
random polypeptide chains
polyproline-ii structure backbone conformation secondary structure unfolded proteins alpha-helices gramicidin-a water preferences residues |
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Description |
In search of the link between sequence and conformation in protein structures, we perform molecular dynamics analysis of the effect of stereochemical mutation in end-protected octa-alanine Ac-Ala(8)-NHMe from poly-L to an alternating-L, D structure. The mutation has a dramatic effect, transforming the peptide from a condition of extreme sensitivity to one of extreme insensitivity to solvent. Examining the molecular folds of poly-L and alternating- L, D structure in atomistic detail, we find them to differ in the relationship between peptide dipolar interactions at the local and nonlocal levels, either conflicting or harmonious depending upon the chain stereochemistry. The stereochemical transformation of interpeptide electrostatics from a condition of conflict to one of harmony explains the long-standing puzzle of why poly-L and alternating- L, D peptides strongly differ in properties such as "stiffness" and solvent sensitivity. Furthermore, it is possible that poly-L stereochemistry is also the fulcrum of protein sensitivity to the effects of amino acid side-chain structures via dielectric arbitrations in interpeptide electrostatics. Indeed the evidence is accumulating that the amino acid side chains differing in alpha-helix and beta-sheet propensities also differ in their desolvating effects in the adjacent and nearest-neighbor peptides and thus possibly in the solvent screening of peptide dipolar interactions.
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Publisher |
AMER CHEMICAL SOC
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Date |
2011-07-15T02:01:45Z
2011-12-26T12:49:10Z 2011-12-27T05:34:57Z 2011-07-15T02:01:45Z 2011-12-26T12:49:10Z 2011-12-27T05:34:57Z 2006 |
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Type |
Article
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Identifier |
JOURNAL OF PHYSICAL CHEMISTRY B, 110(18), 9314-9323
1520-6106 http://dx.doi.org/10.1021/jp056417e http://dspace.library.iitb.ac.in/xmlui/handle/10054/4121 http://hdl.handle.net/10054/4121 |
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Language |
en
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