摘要
It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimensional compact polymer chains by calculating the probability distribution p（r） of end-to-end distance r using the enumeration calculation method and HP model on two-dimensional square lattice. The probability distribution of end-to-end distance p（r） of short two-dimensional compact polymers chains may consist of two parts, i.e. p（r） = p1（r） ＋ p2（r）, where p1（r） and p2（r） are different for small r. The rate of contact formation decreases monotonically with the number of bonds N, and the rate approximately conforms to the scaling relation of k（N）∝ N^-α. Here the value of α increases with the contact radius a and it also depends on the percentage of H （hydrophobic） residues in the sequences of compact chains and the energy parameters of ^εНН、 ^εНН and ^εpp. Some comparisons of theoretical predictions with experimental results are also made. This investigation may help us to understand the protein folding.
It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimensional compact polymer chains by calculating the probability distribution p（r） of end-to-end distance r using the enumeration calculation method and HP model on two-dimensional square lattice. The probability distribution of end-to-end distance p（r） of short two-dimensional compact polymers chains may consist of two parts, i.e. p（r） = p1（r） ＋ p2（r）, where p1（r） and p2（r） are different for small r. The rate of contact formation decreases monotonically with the number of bonds N, and the rate approximately conforms to the scaling relation of k（N）∝ N^-α. Here the value of α increases with the contact radius a and it also depends on the percentage of H （hydrophobic） residues in the sequences of compact chains and the energy parameters of ^εНН、 ^εНН and ^εpp. Some comparisons of theoretical predictions with experimental results are also made. This investigation may help us to understand the protein folding.
基金
This research was financially supported by the National Natural Science Foundation of China(Nos.20174036,20274074,20574052)the Natural Science Foundation of Zhejiang Province(No.R404047).
