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Simulated folding in polypeptides of diversified molecular tacticity: Implications for protein folding and de novo design

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Title Simulated folding in polypeptides of diversified molecular tacticity: Implications for protein folding and de novo design
 
Creator RAMAKRISHNAN, V
RANBHOR, R
DURANI, S
 
Subject gramicidin
simulated annealing
molecular tacticity
de novo protein design
heterochiral peptides
protein folding
 
Description Stereochemistry could be a powerful variable for conformational tune up of polypeptides for de novo design. It may be also useful probe of possible role of interamide energetics in selection and stabilization of conformation. The homopolypeptides Ac-Xxx(30)-NHMe, with Xxx = Ala, Val, and Leu, of diversified stereochemical structure are generated by simulated racemization with a modified GROMOS-96 force field The polypeptides, and other systematic stereochemical variants, are folded by simulated annealing with another modified GROMOS-96 force field under the dielectric constant values 1, 4, and 10. The resultant 15,000 molecular folds of isotactic (poly-L-chiral), syndiotactic (alternating L,D-chiral), and heterotactic (random-L,D-chiral) stereochemical structure, belonging to three polypeptide series, achieved under three different folding conditions, are assessed statistically for structure-to-energy-to-conformation relationship. The results suggest that interamide electrostatics could be a major factor in secondgry-structure selection in polypeptides while main-chain stereochemistry could dictate molecular packing and therefore the relative magnitude of hydrogen-bond and Lennard-Jones (LJ) contributions in conformational energy. A method for computational design of heterotactic molecular folds in polypeptide structure has been developed, and the first road map for a chiral tune up of polypeptide structure based on stereochemical engineering has been laid down. Broad implications for protein structure, folding, and de novo design are briefly discussed © 2005 .
 
Publisher JOHN WILEY & SONS INC
 
Date 2011-08-16T14:07:07Z
2011-12-26T12:54:58Z
2011-12-27T05:43:27Z
2011-08-16T14:07:07Z
2011-12-26T12:54:58Z
2011-12-27T05:43:27Z
2005
 
Type Article
 
Identifier BIOPOLYMERS, 78(2), 96-105
0006-3525
http://dx.doi.org/10.1002/bip.20241
http://dspace.library.iitb.ac.in/xmlui/handle/10054/9521
http://hdl.handle.net/10054/9521
 
Language en