title: Prediction of protein folding rates from simplified secondary structure alphabet.
abstract: Protein folding is a very complicated and highly cooperative dynamic process. However, the folding kinetics is likely to depend more on a few key structural features. Here we find that secondary structures can determine folding rates of only large, multi-state folding proteins and fails to predict those for small, two-state proteins. The importance of secondary structures for protein folding is ordered as: extended β strand > α helix > bend > turn > undefined secondary structure>310 helix > isolated β strand > π helix. Only the first three secondary structures, extended β strand, α helix and bend, can achieve a good correlation with folding rates. This suggests that the rate-limiting step of protein folding would depend upon the formation of regular secondary structures and the buckling of chain. The reduced secondary structure alphabet provides a simplified description for the machine learning applications in protein design.
authors.affiliation: Department of Chemistry and National Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China. Electronic address: jthuang@nankai.edu.cn.
authors.forename: Jitao T
authors.initials: JT
authors.lastname: Huang
authors.affiliation: Department of Chemistry and National Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China.
authors.forename: Titi
authors.initials: T
authors.lastname: Wang
authors.affiliation: Department of Chemistry and National Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China.
authors.forename: Shanran R
authors.initials: SR
authors.lastname: Huang
authors.affiliation: Department of Chemistry and National Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
keywords: Key secondary structures; Kinetic prediction; Protein folding mechanism; Reduced alphabet of secondary structures