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Exploring the protein-folding problem has been a long-standing challenge in molecular biology. Protein folding is highly dependent on folding of secondary structures as the way to pave a native folding pathway. Here, we demonstrate that a feature of a large hydrophobic surface area covering most side-chains on one side or the other side of adjacent $beta$-strands of a $beta$-sheet is prevail in almost all experimentally determined $beta$-sheets, indicating that folding of $beta$-sheets is most likely triggered by multistage hydrophobic interactions among neighbored side-chains of unfolded polypeptides, enable $beta$-sheets fold reproducibly following explicit physical folding codes in aqueous environments. $beta$-turns often contain five types of residues characterized with relatively small exposed hydrophobic proportions of their side-chains, that is explained as these residues can block hydrophobic effect among neighbored side-chains in sequence. Temperature dependence of the folding of $beta$-sheet is thus attributed to temperature dependence of the strength of the hydrophobicity. The hydrophobic-effect-based mechanism responsible for $beta$-sheets folding is verified by bioinformatics analyses of thousands of results available from experiments. The folding codes in amino acid sequence that dictate formation of a $beta$-hairpin can be deciphered through evaluating hydrophobic interaction among side-chains of an unfolded polypeptide from a $beta$-strand-like thermodynamic metastable state.
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
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a crucial as
Pathological folding and oligomer formation of the amyloid beta-protein (Abeta) are widely perceived as central to Alzheimers disease (AD). Experimental approaches to study Abeta self-assembly are problematic, because most relevant aggregates are qua
By means of computer simulations of a coarse-grained DNA model we show that the DNA hairpin zippering dynamics is anomalous, i.e. the characteristic time T scales non-linearly with N, the hairpin length: T ~ N^a with a>1. This is in sharp contrast wi
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino acids, the bioc