Relationship Between The Folding Rate Constant And The Number Of Native Contacts Of The Proteins

In this paper,using the measured rate constant and native structure for a set of 22 small two-state proteins,discuss the rule of changing between the two parameters of the contacts and correlation of natural logarithm of the experimental folding rates and number of native contact.We find that,when the position of two amino acids is more than 12 amino acids and the straight-line distance between their Ca is less then 5.85(?),the linear correlation coefficient of the natural logarithm of the experimental folding rates and the number of residues in the protein is the max-value,R=0.861.The relation between folding rate and native stricture ensemble of small protein was studied with molecular dynamics simulations.A series of conformations ensembles of ten small proteins were obtained from molecular dynamics simulations depend-ing on the different definition of contact inside protein.The relation between topological parameters of ensembles and folding rate was studied,and the results were also compared with those from PDB single conformation.The pertinences with contact definition of main-chain atoms, better than others,and the relation between topological parameter obtained from native structure ensembles and folding rate can truly reflect the fact.Protein-folding rate prediction is one of the most important challenges in contemporary biophysics,and a great progress has been made in the past few years.Many empirical parameters have been proposed successively,such as contact order,long-range order,total contact distance,chain topology parameter,secondary structure content,effective length, helix parameter,n-order contact distance,etc.All of them have significant correlations with protein folding rates.The predicted results by the methods based on these parameters fit well with the experimental folding rates.