Representing environment-induced helix-coil transitions in a coarse grained peptide model
Representing environment-induced helix-coil transitions in a coarse grained peptide model
复制标题
代表粗粒肽模型中环境诱导的螺旋-螺旋转变
DOI：
10.1140/epjst/e2016-60147-8
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
C. Peter
中科院分区：
文献类型：
--
作者：
C. Dalgicdir;C. Globisch;M. Sayar;C. Peter
粗粒（CG）模型被广泛用于研究多肽自组装和纳米结构的形成。CG建模中经常遇到的挑战之一是有限的可转移性问题，例如不同的热力学状态点和系统组成。了解可移植性通常是了解模型可以可靠地用于哪些问题和预测的先决条件。对于肽，一个关键的可转移性问题是模型是否再现了分子对其分子环境变化的构象响应。这是特别重要的，因为CG肽模型往往不得不求助于辅助的相互作用，帮助二级结构的形成。这种相互作用照顾在粗粒化过程中本身丢失的真实的系统的性质，例如沿着主链或主链氢键的二面角相关性。这些辅助相互作用可能容易使某些构象倾向过度稳定，从而破坏模型对刺激和环境变化的反应能力，即它们阻碍了可转移性。在本论文中，我们已经研究了一个短肽与两亲性EALA重复，经历了一个无序和螺旋状态之间的构象转变时，pH值的变化，或由于存在一个软的非极性/极性界面。我们设计了一个基础CG肽模型，它不携带对二级结构的特定（骨架）偏好。该基础模型与两种典型的确保二级结构形成的方法相结合，即aCα-C α-C α-Cα假二面角势或模拟氢键的虚拟位点相互作用。我们已经调查了两个CG模型的能力，代表环境引起的构象变化的螺旋线圈平衡的EALA。我们表明，这两种方法可以获得CG肽模型，是环境可转移的，并正确地表示肽的构象响应不同的刺激相比，原子参考模拟。这两种类型的辅助相互作用导致不同的动力学行为，以及完全形成的螺旋和折叠中间体的不同的结构特性，我们讨论了这些方法的优点和缺点。
Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely aCα-Cα-Cα-Cαpseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that correctly represents the peptide's conformational response to different stimuli compared to atomistic reference simulations. The two types of auxiliary interactions lead to different kinetic behavior as well as to different structural properties for fully formed helices and folding intermediates, and we discuss the advantages and disadvantages of these approaches.
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两亲肽在空气/水界面的吸附、折叠和堆积。
影响因子：
3.3
作者：
O. Engin;M. Sayar
通讯作者：
M. Sayar
影响因子：
6.8
作者：
Chun Wu;J. Shea
通讯作者：
Chun Wu;J. Shea
高 pH 条件下牛肝过氧化氢酶的碱性解折叠和盐诱导折叠。
DOI：
10.1046/j.1432-1327.1998.2550178.x
发表时间：
1998
期刊：
European journal of biochemistry
影响因子：
--
作者：
Shashi Prajapati;V. Bhakuni;K. R. Babu;S. K. Jain
通讯作者：
S. K. Jain
将量表从疾病到α-螺旋中倾斜：在存在宏观和分子界面的情况下两亲性肽的折叠。
影响因子：
4.3
作者：
Dalgicdir C;Globisch C;Peter C;Sayar M
通讯作者：
Sayar M
影响因子：
6.1
作者：
V. Tozzini
通讯作者：
V. Tozzini