Chemmama Ilan E, Pelea Adam Colt, Bhandari Yuba R, Chapagain Prem P, Gerstman Bernard S
Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Sep;86(3 Pt 1):031915. doi: 10.1103/PhysRevE.86.031915. Epub 2012 Sep 17.
The helix-coil transition in peptides is a critical structural transition leading to functioning proteins. Peptide chains have a large number of possible configurations that must be accounted for in statistical mechanical investigations. Using hydrogen bond and local helix propensity interaction terms, we develop a method for obtaining and incorporating the degeneracy factor that allows the exact calculation of the partition function for a peptide as a function of chain length. The partition function is used in calculations for engineered peptide chains of various lengths that allow comparison with a variety of different types of experimentally measured quantities, such as fraction of helicity as a function of both temperature and chain length, heat capacity, and denaturation studies. When experimental sensitivity in helicity measurements is properly accounted for in the calculations, the calculated curves fit well with the experimental curves. We determine values of interaction energies for comparison with known biochemical interactions, as well as quantify the difference in the number of configurations available to an amino acid in a random coil configuration compared to a helical configuration.
肽中的螺旋-卷曲转变是导致功能性蛋白质形成的关键结构转变。肽链具有大量可能的构象，在统计力学研究中必须予以考虑。利用氢键和局部螺旋倾向相互作用项，我们开发了一种获取并纳入简并因子的方法，该方法能够精确计算肽的配分函数随链长的变化。配分函数用于计算各种长度的工程化肽链，从而可以与多种不同类型的实验测量量进行比较，例如螺旋度随温度和链长的变化、热容以及变性研究。当在计算中适当考虑螺旋度测量的实验灵敏度时，计算曲线与实验曲线拟合良好。我们确定相互作用能的值以与已知的生化相互作用进行比较，同时量化随机卷曲构象中的氨基酸与螺旋构象相比可利用的构象数量差异。
