Jitao T Huang

Nankai University, T’ien-ching-shih, Tianjin Shi, China

Are you Jitao T Huang?

Claim your profile

Publications (4)12.94 Total impact

  • Jitao T. Huang, Wei Huang, Shanran R. Huang, Xin Li
    [Show abstract] [Hide abstract]
    ABSTRACT: Proteins fold by either two-state or multi-state kinetic mechanism. We observe that amino acids play different roles in different mechanism. Many residues that are easy to form regular secondary structures (α helices, β sheets and turns) can promote the two-state folding reactions of small proteins. Most of hydrophilic residues can speed up the multi-state folding reactions of large proteins. Folding rates of large proteins are equally responsive to the flexibility of partial amino acids. Other properties of amino acids (including volume, polarity, accessible surface, exposure degree, isoelectric point, and phase transfer energy) have contributed little to folding kinetics of the proteins. Cysteine is a special residue, it triggers two-state folding reaction and but inhibits multi-state folding reaction. These findings not only provide a new insight into protein structure prediction, but also could be used to direct the point mutations that can change folding rate. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.
    Proteins Structure Function and Bioinformatics 05/2014; · 3.34 Impact Factor
  • Shanran Huang, Jitao T Huang
    [Show abstract] [Hide abstract]
    ABSTRACT: In recent years, there have been many breakthroughs in the prediction of protein folding kinetics using empirical and theoretical methods. These predictions focus primarily on the structural parameters in concert with contacting residues. The non-covalent contacts are a simplified model of the interactions found in proteins. Here we investigate the physico-chemical origin and derive the approximate formula lnk(f)=a+b×Σ1/d(6), where d is the distance between different residues of the protein structure. It achieves -0.83 correlation with experimental over 57 two- and multi-state folding proteins, indicating that protein folding kinetics is determined by the interactions between all pairs of residues. The interaction is a short-range coupling that is effective only when two residues are in close proximity, consistent with the dominant role of the contacts in determining folding rates.
    Journal of Theoretical Biology 10/2012; · 2.35 Impact Factor
  • Jitao T Huang, Dajie J Xing, Wei Huang
    [Show abstract] [Hide abstract]
    ABSTRACT: Bioinformatical studies suggest that additional information provided by nucleic acids is necessary to construct protein three-dimensional structures. We find underlying correlations between the contents of bases. All correlations occur at the third codon position of a gene sequence. Four inverse relationships are observed between u(3) and c(3), between a(3) and g(3), between u(3) and g(3), and between c(3) and a(3); and two positive relationships are apparent between u(3) and a(3), and between c(3) and g(3). Their correlation coefficients reach -0.92, -0.89, -0.83, -0.85, 0.83, and 0.66, respectively, for large proteins with multistate folding kinetics. The interconnection of bases can be ascribed to choice of synonymous codons associated with protein folding in vivo. In this study, the refolding rate constants of large proteins correlate with the contents of the third base, suggesting that there is underlying biochemical rationale of guiding protein folding in choosing synonymous codons.
    Proteins Structure Function and Bioinformatics 04/2012; 80(8):2056-62. · 3.34 Impact Factor
  • Jitao T Huang, Dajie J Xing, Wei Huang
    [Show abstract] [Hide abstract]
    ABSTRACT: The successful prediction of protein-folding rates based on the sequence-predicted secondary structure suggests that the folding rates might be predicted from sequence alone. To pursue this question, we directly predict the folding rates from amino acid sequences, which do not require any information on secondary or tertiary structure. Our work achieves 88% correlation with folding rates determined experimentally for proteins of all folding types and peptide, suggesting that almost all of the information needed to specify a protein's folding kinetics and mechanism is comprised within its amino acid sequence. The influence of residue on folding rate is related to amino acid properties. Hydrophobic character of amino acids may be an important determinant of folding kinetics, whereas other properties, size, flexibility, polarity and isoelectric point, of amino acids have contributed little to the folding rate constant.
    Amino Acids 12/2011; 43(2):567-72. · 3.91 Impact Factor