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of outstanding interest. The structural basis for determining the order of folding transition is studied. For proteins with a large number of nonlocal contacts, the folding transition is first-order, whereas for ones with local contacts it is not. This difference in cooperativity is shown to have dramatic implications for folding kinetics and stability.
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Abkevich AI, Gutin AM, Shakhnovich EI. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. of outstanding interest J Mol Biol. 252:1995;460-471 The structural basis for determining the order of folding transition is studied. For proteins with a large number of nonlocal contacts, the folding transition is first-order, whereas for ones with local contacts it is not. This difference in cooperativity is shown to have dramatic implications for folding kinetics and stability.
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of special interest. Different structures are analyzed in two papers [4,6] from the standpoint of their 'designability', and the ones that are more designable are attributed to commonly observed structures.
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of special interest. The folding of cubic lattice 125-mers is studied using interaction potentials that assign stronger attraction to native contacts than to non-native ones (the 'Go' model). It is shown that the internal stable core forms first, and that the remaining part of the structure fluctuates around this, sometimes approaching but not completely reaching, the native structure.
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Hao M-H, Scheraga H. How optimization of potential function affects protein folding. of special interest Proc Natl Acad Sci USA. 93:1996;4984-4989 A thorough study of the lattice model in which potentials are optimized to make a 'native' conformation for a given sequence a pronounced energy minimum.
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of special interest A method to derive the protein-folding potential from a PDB file is suggested to be the optimization of the space parameters to make all proteins stable. The method is tested on lattice models with 20 types of amino acids in which it is shown to recover the 'true' potential with 91% accuracy. Other popular methods are also tested and evaluated
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Mirny L, Shakhnovich EI. How to determine protein folding potential? A new approach to the old problem. of special interest J Mol Biol. 1997; A method to derive the protein-folding potential from a PDB file is suggested to be the optimization of the space parameters to make all proteins stable. The method is tested on lattice models with 20 types of amino acids in which it is shown to recover the 'true' potential with 91% accuracy. Other popular methods are also tested and evaluated.
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