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亮氨酸和异亮氨酸肽在水中的热力学性质

Thermodynamics Properties of Leucine and Isoleucine Peptides in Water.

作者信息

Chapagain Samundra, Ojha Shishir, Khanal Shyam Prakash, Adhikari Narayan Prasad

机构信息

Central Department of Physics, Tribhuvan University, Kathmandu, Nepal.

出版信息

ChemistryOpen. 2025 Apr;14(4):e202400209. doi: 10.1002/open.202400209. Epub 2025 Jan 28.

DOI:10.1002/open.202400209
PMID:39871704
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11973509/
Abstract

Thermodynamic properties of amino acids explore the ideas about the energetic contribution in biomolecular interfaces. In our work, we have estimated the solvation free energy of leucine and isoleucine peptides with the variation of chain length or residues of different monomer units (n=1, 2, 4, 8 & 16) using molecular dynamic simulation. We modeled our system using OPLS-AA force field and TIP3P water model at 310 K temperature. Solvation free energy of both leucine and isoleucine peptides increases with increase in chain length, which have been reported by using TI, TI-CUBIC and BAR methods. The increase in solvation free energy with increase in chain length of both peptides is also supported by the increase in hydrogen bond and solvent accessible surface area (SASA) with the number of residues.

摘要

氨基酸的热力学性质探讨了生物分子界面中能量贡献的相关概念。在我们的工作中，我们使用分子动力学模拟，估计了亮氨酸和异亮氨酸肽在链长或不同单体单元残基（n = 1、2、4、8和16）变化时的溶剂化自由能。我们在310 K温度下，使用OPLS-AA力场和TIP3P水模型对系统进行建模。亮氨酸和异亮氨酸肽的溶剂化自由能均随链长增加而增加，这已通过热力学积分（TI）、TI-立方（TI-CUBIC）和 Bennett接受比（BAR）方法得到报道。两种肽的溶剂化自由能随链长增加而增加，这也得到了氢键数量和溶剂可及表面积（SASA）随残基数增加的支持。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/804c56422c3f/OPEN-14-e202400209-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/abbd69460225/OPEN-14-e202400209-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/dbe39634799b/OPEN-14-e202400209-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/55080f594478/OPEN-14-e202400209-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/c492ed57243c/OPEN-14-e202400209-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/369fbb37dbd8/OPEN-14-e202400209-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/9e567d4f8f93/OPEN-14-e202400209-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/804c56422c3f/OPEN-14-e202400209-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/abbd69460225/OPEN-14-e202400209-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/dbe39634799b/OPEN-14-e202400209-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/55080f594478/OPEN-14-e202400209-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/c492ed57243c/OPEN-14-e202400209-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/369fbb37dbd8/OPEN-14-e202400209-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/9e567d4f8f93/OPEN-14-e202400209-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9db/11973509/804c56422c3f/OPEN-14-e202400209-g005.jpg

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本文引用的文献

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Protective Mechanism of Leucine and Isoleucine against HO-Induced Oxidative Damage in Bovine Mammary Epithelial Cells.亮氨酸和异亮氨酸对 HO 诱导的奶牛乳腺上皮细胞氧化损伤的保护机制。
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Solvation free energies of alanine peptides: the effect of flexibility.丙氨酸肽的溶剂化自由能：柔性的影响。
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Are solvation free energies of homogeneous helical peptides additive?均匀螺旋肽的溶剂化自由能是否具有加和性？
J Phys Chem B. 2005 Oct 13;109(40):19000-7. doi: 10.1021/jp052403x.
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Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides.一类主客体五肽中氨基酸侧链和主链的溶剂化能
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