The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding

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The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding.

Using an all-atom representation, we exhaustively enumerate all sterically allowed conformations for short polyalanyl chains. Only intrachain interactions are considered, including one adjustable parameter, a favorable backbone energy (e.g., a peptide hydrogen bond). The counting is used to reevaluate Flory's isolated-pair hypothesis, the simplifying assumption that each phi,psi pair is sterica...

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Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides.

The populations and transitions between Ramachandran basins are studied for combinations of the standard 20 amino acids in monomers, dimers and trimers using an implicit solvent Langevin dynamics algorithm and employing seven commonly used force-fields. Both the basin populations and inter-conversion rates are influenced by the nearest neighbor's conformation and identity, contrary to the Flory...

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Optimum folding pathways for growing protein chains.

The folding of a protein is studied as it grows residue by residue from the N-terminus and enters an environment that stabilizes the folded state. This mode of folding of a growing chain is different from refolding where the full chain folds from a disordered initial configuration to the native state. We propose a sequential dynamic optimization method that computes the evolution of optimum fol...

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C. Implications for Protein Folding

It has been evident for some time both that a random search through all conformations could not possibly explain protein folding (Levinthal, 1968) and also that the structures themselves show evidence of systematic local folding patterns. The consistent presence of domains in the larger proteins strongly suggests that they are folding units (Gratzer and Beaven, 1969; Wetlauter, 1973), and for s...

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ژورنال

عنوان ژورنال: Proceedings of the National Academy of Sciences

سال: 2000

ISSN: 0027-8424,1091-6490

DOI: 10.1073/pnas.97.23.12565