2019/01/04 by Xiaoliang Ma, Ma, Xiaoliang, Chengyu Hou +13
Biochemistry, Genetics and Molecular Biology · #Biochemical and Structural Characterization #Biomolecules (q-bio.BM) #FOS: Biological sciences #Protein Structure and Dynamics #RNA and protein synthesis mechanisms #q-bio.BM
paper · pdf · doi:10.48550/arxiv.1901.00991
19 pages, 7 figures, 8 tables
arxiv created 2019/01/04 · openalex publication_date 2019/01/04 · arxiv updated 2019/01/11 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.