Acidic‐basic properties of three alanine‐based peptides containing acidic and basic side chains: Comparison between theory and experiment
Acidic‐basic properties of three alanine‐based peptides containing acidic and basic side chains: Comparison between theory and experiment
复制标题
三种含有酸性和碱性侧链的丙氨酸肽的酸碱特性：理论与实验的比较
作者：
J. Makowska;K. Bagińska;A. Liwo;L. Chmurzyński;H. Scheraga
本研究的目的是评估丙氨酸肽中可电离端基的性质和溶剂对其酸碱性质的影响。因此，三种基于丙氨酸的肽的酸碱性质：Ac‐KK‐(A)7‐KK‐NH2 (KAK), Ac‐OO‐(A)7‐DD‐NH2 (OAD), Ac‐KK‐(A)7‐EE‐NH2 (KAE)，其中A、D、E、K和O分别表示丙氨酸、天冬氨酸、谷氨酸、赖氨酸和鸟氨酸，通过电位测定法在水和甲醇中测定。利用这些数据，评估了两种理论方法模拟这些肽的pH -计量滴定的能力：(i)使用ECEPP/3力场和泊松-玻尔兹曼方法计算溶剂化能（EDMC/PB/pH）的静电驱动蒙特卡罗方法，以及（ii）使用AMBER力场和广义Born模型（MD/GB/pH）的分子动力学方法。对于OAD和KAE， pKa1和pKa2对应于酸性侧链。对于两种溶剂中的所有三种化合物，pKa1值明显低于模拟各自孤立侧链的化合物的pKa，这可以解释为来自带正电的鸟氨酸或赖氨酸侧链的静电场的影响。MD/GB/pH方法可以很好地再现实验滴定曲线，如果在构象搜索中加入核磁共振测量得到的约束，一致性更好。EDMC/PB/pH法的一致性较差。©2008 Wiley期刊公司高分子材料工程学报（自然科学版），2009,31(2):444 - 444。
The purpose of this work was to evaluate the effect of the nature of the ionizable end groups, and the solvent, on their acid‐base properties in alanine‐based peptides. Hence, the acid‐base properties of three alanine‐based peptides: Ac‐KK‐(A)7‐KK‐NH2 (KAK), Ac‐OO‐(A)7‐DD‐NH2 (OAD), Ac‐KK‐(A)7‐EE‐NH2 (KAE), where A, D, E, K, and O denote alanine, aspartic acid, glutamic acid, lysine, and ornithine, respectively, were determined in water and in methanol by potentiometry. With the availability of these data, the ability of two theoretical methods to simulate pH‐metric titration of those peptides was assessed: (i) the electrostatically driven Monte Carlo method with the ECEPP/3 force field and the Poisson‐Boltzmann approach to compute solvation energy (EDMC/PB/pH), and (ii) the molecular dynamics method with the AMBER force field and the Generalized Born model (MD/GB/pH). For OAD and KAE, pKa1 and pKa2 correspond to the acidic side chains. For all three compounds in both solvents, the pKa1 value is remarkably lower than the pKa of a compound modeling the respective isolated side chain, which can be explained by the influence of the electrostatic field from positively charged ornithine or lysine side chains. The experimental titration curves are reproduced well by the MD/GB/pH approach, the agreement being better if restraints derived from NMR measurements are incorporated in the conformational search. Poorer agreement is achieved by the EDMC/PB/pH method. © 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 724–732, 2008.
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DOI：
10.1073/pnas.0510549103
发表时间：
2006-02-07
影响因子：
11.1
作者：
Makowska, J;Rodziewicz-Motowidlo, S;Scheraga, HA
通讯作者：
Scheraga, HA
通过外推至零变性剂对蛋白质未折叠状态下的 pKa 值进行 NMR 分析。
影响因子：
3.8
作者：
Quijada,Jeniffer;Lopez,Gary;Versace,Rodney;Ramirez,Luis;Tasayco,MariaLuisa
通讯作者：
Tasayco,MariaLuisa
XAO 肽中不存在聚脯氨酸 II 延伸的进一步证据。
影响因子：
3.4
作者：
Makowska,Joanna;Rodziewicz-Motowidlo,Sylwia;Baginska,Katarzyna;Makowski,Mariusz;Vila,JorgeA;Liwo,Adam;Chmurzynski,Lech;Scheraga,HaroldA
通讯作者：
Scheraga,HaroldA
影响因子：
5.6
作者：
Ripoll, DR;Vorobjev, YN;Scheraga, HA
通讯作者：
Scheraga, HA