摘要
从 6 0种球形蛋白质的结构出发 ,采用Miyazawa Jernigan相互作用矩阵 ,计算了蛋白质分子中氨基酸之间的相互作用能 .发现构成蛋白质分子的 2 0种氨基酸可分成疏水 (Hydrophobic ,H)、中性 (Neutral,N)、亲水(Hydrophilic ,P)基团 .在计算它们之间相互作用能的基础上 ,建立了蛋白质分子的HNP格点模型 .用这个模型计算了二维蛋白质分子在自然态 (Nativestate)时的构象性质 .同时研究了氨基酸序列为HHNHNPNHPP HPNPPHPHPPHHPHNH的折叠过程 ,得到其基态能量为 - 6 4 89RT .
Effective interresidue contact energies for proteins in solutions are estimated from the number of residue-residue contacts observed in crystal structures of globular proteins ( http://www.rcsb.org/) by means of the Miyazawa-Jerniganm (MJ) interaction matrix. It is found that residues can be classified into three groups according to the contact energies: hydrophobic residues (H), neutral residues (N), and hydrophilic residues (P). Here we develop a modified HP lattice model, i.e. a HNP lattice model. In this model, the contact Hamiltonian is simply written as H = Sigma(i<j)E(Si-Sj)delta(r(ij), l) (S-i = H, or N, or P) (4) Where EH-H = -5.59RT, EH-N = -3.68RT, EH-P = -3.07RT, EN-N = 2.23RT, EN-P = -1.78RT, EP-P = -1.37RT, and r(ij) is the distance between residues i and j. We first calculate the conformational properties of the native states of short protein chains using 2-dimensional HNP lattice model and enumeration calculation method. The distributions of various types of residue-residue contacts and three types of residues of the native states are discussed. We also investigate the folding of the protein with a sequence of HHNHNPNHPPHPNPPHPHPPHHPHNH using the modified HP lattice model. Here the sequence is selected at random. The folded conformation is obtained in square lattice, and the folding energy is - 64.89 RT. Our calculation shows that the HNP lattice model may be more reasonable for simulation of the folding behavior of real proteins.
出处
《高分子学报》
SCIE
CAS
CSCD
北大核心
2004年第2期273-276,共4页
Acta Polymerica Sinica
基金
国家自然科学基金 (基金号 2 98740 2 1
2 0 1740 3 6
2 0 2 740 40 )
浙江省自然科学基金 (基金号 10 10 0 2 )资助项目
