Electric charge and salting in/out effects on glucagon's dipole moments and polarizabilities using the GruPol database.

IF 1.3 3区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY
Raphael F Ligorio, Rasmus H M Gehle, Leonardo H R Dos Santos, Anna Krawczuk
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引用次数: 0

Abstract

This work demonstrates the use of the GruPol database to predict the functional group dipole moments and polarizabilities of glucagon in the presence of NaCl, simulating an electric charge distribution on the protein's backbone. A new feature of the database allows for the inclusion of ions on the protein backbone, effectively simulating a protein salt and predicting the impact on electrical properties. Glucagon was selected as a proof-of-concept molecule due to its relatively small chain, which enabled benchmarking against quantum mechanical calculations. Firstly, we simulated 70 different ionic configurations, varying the number of Na+ and Cl- ions from zero to four NaCl moieties. Additionally, we investigated the effects of solvation under two distinct conditions: one involving just the peptide and water, and the other also including NaCl at a concentration of approximately 4.2 mol L-1. Regarding the ab initio results, GruPol showed good accuracy, with an angular direction error of around 10° and a 15% difference in the magnitude of the dipole moments. However, the error in polarizability values was higher, most likely due to the lack of an augmented basis set in the ab initio quantum calculations (M06-HF/cc-pVDZ). The database entries were generated using the same functional along with the aug-cc-pVDZ basis set. In solution, a high ionic concentration lowered the overall dipole moment, while the main components of polarizability increased.

利用GruPol数据库研究电荷和盐入/盐出对胰高血糖素偶极矩和极化率的影响。
这项工作演示了使用GruPol数据库来预测在NaCl存在下胰高血糖素的官能团偶极矩和极化率,模拟了蛋白质主链上的电荷分布。该数据库的一个新功能允许在蛋白质主链上包含离子,有效地模拟蛋白质盐并预测对电性能的影响。胰高血糖素被选为概念验证分子,因为它的链相对较小,可以对量子力学计算进行基准测试。首先,我们模拟了70种不同的离子构型,改变了Na+和Cl-离子的数量,从0到4个NaCl基团。此外,我们研究了两种不同条件下的溶剂化效应:一种只涉及肽和水,另一种还包括浓度约为4.2 mol L-1的NaCl。对于从头算结果,GruPol显示出良好的精度,角方向误差约为10°,偶极矩大小相差15%。然而,极化率值的误差较大,很可能是由于从头算量子计算中缺乏增广基集(M06-HF/cc-pVDZ)。使用相同的函数以及aug-cc-pVDZ基集生成数据库条目。在溶液中,高离子浓度降低了总偶极矩,而极化率的主要成分增加。
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来源期刊
Acta crystallographica Section B, Structural science, crystal engineering and materials
Acta crystallographica Section B, Structural science, crystal engineering and materials CHEMISTRY, MULTIDISCIPLINARYCRYSTALLOGRAPH-CRYSTALLOGRAPHY
CiteScore
3.60
自引率
5.30%
发文量
0
期刊介绍: Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials publishes scientific articles related to the structural science of compounds and materials in the widest sense. Knowledge of the arrangements of atoms, including their temporal variations and dependencies on temperature and pressure, is often the key to understanding physical and chemical phenomena and is crucial for the design of new materials and supramolecular devices. Acta Crystallographica B is the forum for the publication of such contributions. Scientific developments based on experimental studies as well as those based on theoretical approaches, including crystal-structure prediction, structure-property relations and the use of databases of crystal structures, are published.
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