Karandur D, Pettitt B M
Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0304, USA.
Condens Matter Phys. 2016;19(2). doi: 10.5488/CMP.19.23802.
Protein solubility and conformational stability are a result of a balance of interactions both within a protein and between protein and solvent. The electrostatic solvation free energy of oligoglycines, models for the peptide backbone, becomes more favorable with an increasing length, yet longer peptides collapse due to the formation of favorable intrapeptide interactions between CO dipoles, in some cases without hydrogen bonds. The strongly repulsive solvent cavity formation is balanced by van der Waals attractions and electrostatic contributions. In order to investigate the competition between solvent exclusion and charge interactions we simulate the collapse of a long oligoglycine comprised of 15 residues while scaling the charges on the peptide from zero to fully charged. We examine the effect this has on the conformational properties of the peptide. We also describe the approximate thermodynamic changes that occur during the scaling both in terms of intrapeptide potentials and peptide-water potentials, and estimate the electrostatic solvation free energy of the system.
蛋白质的溶解度和构象稳定性是蛋白质内部以及蛋白质与溶剂之间相互作用平衡的结果。寡甘氨酸作为肽主链的模型,其静电溶剂化自由能随着长度增加而更有利,但较长的肽会由于CO偶极之间形成有利的肽内相互作用而折叠,在某些情况下没有氢键。强烈排斥的溶剂腔形成由范德华引力和静电作用平衡。为了研究溶剂排斥和电荷相互作用之间的竞争,我们模拟了由15个残基组成的长寡甘氨酸的折叠,同时将肽上的电荷从零缩放至完全带电。我们研究了这对肽的构象性质的影响。我们还从肽内势能和肽-水势能方面描述了缩放过程中发生的近似热力学变化,并估计了系统的静电溶剂化自由能。