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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
 
Creator RAMAKRISHNAN, V
RANBHOR, R
KUMAR, A
DURANI, S
 
Subject random polypeptide chains
polyproline-ii structure
backbone conformation
secondary structure
unfolded proteins
alpha-helices
gramicidin-a
water
preferences
residues
 
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.
 
Publisher AMER CHEMICAL SOC
 
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
 
Type Article
 
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
 
Language en