Pitera J W, Kollman P A
Graduate Group in Biophysics, University of California-San Francisco, San Francisco, California 94143-0446, USA.
Proteins. 2000 Nov 15;41(3):385-97.
We have extended and applied a multicoordinate free energy method, chemical Monte Carlo/Molecular Dynamics (CMC/MD), to calculate the relative free energies of different amino acid side-chains. CMC/MD allows the calculation of the relative free energies for many chemical species from a single free energy calculation. We have previously shown its utility in host:guest chemistry (Pitera and Kollman, J Am Chem Soc 1998;120:7557-7567)1 and ligand design (Eriksson et al., J Med Chem 1999;42:868-881)2, and here demonstrate its utility in calculations of amino acid properties and protein stability. We first study the relative solvation free energies of N-methylated and acetylated alanine, valine, and serine amino acids. With careful inclusion of rotameric states, internal energies, and both the solution and vacuum states of the calculation, we calculate relative solvation free energies in good agreement with thermodynamic integration (TI) calculations. Interestingly, we find that a significant amount of the unfavorable solvation of valine seen in prior work (Sun et al., J Am Chem Soc 1992;114:6798-6801)3 is caused by restraining the backbone in an extended conformation. In contrast, the solvation free energy of serine is calculated to be less favorable than expected from experiment, due to the formation of a favorable intramolecular hydrogen bond in the vacuum state. These monomer calculations emphasize the need to accurately consider all significant conformations of flexible molecules in free energy calculations. This development of the CMC/MD method paves the way for computations of protein stability analogous to the biochemical technique of "exhaustive mutagenesis." We have carried out just such a calculation at position 133 of T4 lysozyme, where we use CMC/MD to calculate the relative stability of eight different side-chain mutants in a single free energy calculation. Our T4 calculations show good agreement with the prior free energy calculations of Veenstra et al. (Prot Eng 1997;10:789-807)4 and excellent agreement with the experiments of Mendel et al. (Science 1992;256:1798-1802).
我们扩展并应用了一种多坐标自由能方法——化学蒙特卡罗/分子动力学（CMC/MD），来计算不同氨基酸侧链的相对自由能。CMC/MD能够通过一次自由能计算得出多种化学物种的相对自由能。我们之前已证明其在主客体化学（皮特拉和科尔曼，《美国化学会志》1998年；120:7557 - 7567）[1]以及配体设计（埃里克森等人，《药物化学杂志》1999年；42:868 - 881）[2]中的实用性，在此展示其在氨基酸性质计算和蛋白质稳定性计算中的实用性。我们首先研究了N - 甲基化和乙酰化的丙氨酸、缬氨酸和丝氨酸氨基酸的相对溶剂化自由能。通过仔细考虑旋转异构体状态、内能以及计算中的溶液和真空状态，我们计算出的相对溶剂化自由能与热力学积分（TI）计算结果吻合良好。有趣的是，我们发现先前工作（孙等人，《美国化学会志》1992年；114:6798 - 6801）[3]中观察到的缬氨酸不利溶剂化的很大一部分是由于将主链限制在伸展构象中所致。相反，由于在真空状态下形成了有利的分子内氢键，丝氨酸的溶剂化自由能计算结果比实验预期的更不利。这些单体计算强调了在自由能计算中准确考虑柔性分子所有重要构象的必要性。CMC/MD方法的这一发展为类似于“彻底诱变”生化技术的蛋白质稳定性计算铺平了道路。我们在T4溶菌酶的第133位进行了这样的计算，其中我们使用CMC/MD在一次自由能计算中得出八个不同侧链突变体的相对稳定性。我们对T4的计算结果与维恩斯特拉等人（《蛋白质工程》1997年；10:789 - 807）[4]之前的自由能计算结果吻合良好，与门德尔等人（《科学》1992年；256:1798 - 1802）的实验结果高度一致。
