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Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded proteins fold reproducibly following explicit physical folding codes in aqueous environments due to electrostatic attractions. Superfast folding of protein is found to be powered by the contribution of the formation of hydrogen bonds. Temperature-induced torsional waves propagating along unfolded proteins break the parallel distributed state of specific amino acids, inferred as the beginning of folding. Electric charge and rotational resistance differences among neighboring side-chains are used to decipher the physical folding codes by means of which precise secondary structures develop. We present a powerful method of decoding amino acid sequences to predict native structures of proteins. The method is verified by comparing the results available from experiments in the literature.
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very low thermody
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts MP contacts
Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a natively-knotted N-ace
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that
Energy landscape theory describes how a full-length protein can attain its native fold after sampling only a tiny fraction of all possible structures. Although protein folding is now understood to be concomitant with synthesis on the ribosome there h