cytochrome-c (cyt-c) is an electron transport protein, and it is present throughout the evolution. more than 280 sequences have been reported in the protein sequence database (www.uniprot.org). though sequentially diverse, cyt-c has essentially retained its tertiary structure or fold. thus a vast data set of varied sequences with retention of similar structure and function makes it a primary ca...

Bovine pancreatic trypsin inhibitor (BPTI) continues to be the only protein for which a detailed pathway of folding has been described. Previous studies led to the conclusion that nonnative states are well populated in the oxidative folding of BPTI. This conclusion has broadly influenced efforts to understand protein folding. The population of intermediates present during the folding of BPTI ha...

This review focuses on recent advances in understanding protein folding kinetics in the context of nucleation theory. We present basic concepts such as nucleation, folding nucleus, and transition state ensemble and then discuss recent advances and challenges in theoretical understanding of several key aspects of protein folding kinetics. We cover recent topology-based approaches as well as evol...

A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory is used to study the temperature dependences of folding rate of 15 proteins and their non-Arrhenius behavior can all be deduced in a natural way. A general ...

Protein molecules adopt a specific global 3D structure in order to carry out their biological function. To achieve this native state a newly formed protein molecule has to fold. The folding process and the final fold are both determined by the sequence of amino acids making up the protein chain. It is not currently possible to predict the conformation of the native state from the amino acid seq...

A hydrophobic folding unit cutting algorithm, originally developed for dissecting single-chain proteins, has been applied to a dataset of dissimilar two-chain protein-protein interfaces. Rather than consider each individual chain separately, the two-chain complex has been treated as a single chain. The two-chain parsing results presented in this work show hydrophobicity to be a critical attribu...

The amino acid sequence of a polypeptide defines both the folding pathway and the final three-dimensional structure of a protein. Eighteen amino acid substitutions have been identified in bacteriophage P22 coat protein that are defective in folding and cause their folding intermediates to be substrates for GroEL and GroES. These temperature-sensitive folding (tsf) substitutions identify amino a...

The classification of protein folds is necessarily based on the structural elements that distinguish domains. Classification of protein domains consists of two problems: the partition of structures into domains and the classification of domains into sets of similar structures (or folds). Although similar topologies may arise by convergent evolution, the similarity of their respective folding pa...

A protein molecule adopts a specific 3D structure, necessary for its function in the cell, through a process of folding. Modelling the folding process and predicting the final fold from the unique amino acid sequence remain challenging problems. We have previously described the application of L-systems, parallel rewriting rules, to modelling protein folding using two complementary approaches: a...

The Folding@home project harnesses a volunteer distributed computing network to perform ab initio molecular simulations of protein folding. Thanks to engineering innovations like a Graphical Processing Unit (GPU) client for running simulations, Folding@home is able to harness over 6.1 petaFLOPS of processing power, allowing it to simulate longer and more complex protein folding mechanisms than ...