Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi, USA.
PLoS One. 2013 Aug 13;8(8):e70847. doi: 10.1371/journal.pone.0070847. eCollection 2013.
A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 ((1)H (2)S (3)S (4)Y (5)W (6)Y (7)A (8)F (9)N (10)N (11)K (12)T) is considered as an example to illustrate the utility. We find that peptides assemble rather fast into globular aggregates at low temperatures and disperse as random-coil at high temperatures. The specificity of the mass distribution of the self-assembly depends on the temperature and spatial lengths which are identified from the scaling of the structure factor. Analysis of energy and mobility profiles, gyration radius of peptide, and radial distribution function of the assembly provide insight into the multi-scale (intra- and inter-chain) characteristics. Thermal response of the global assembly with the simulated residue-residue interaction is consistent with that of the knowledge-based analysis despite expected quantitative differences.
我们提出了一种分层计算方法（从原子到所有残基的肽），以研究肽作为温度函数的自组织结构。使用涉及全原子描述的模拟残基-残基相互作用作为输入，类似于基于知识的分析（具有不同的输入），用于大规模计算机模拟的唯象粗粒度相互作用。我们考虑了一组短肽 P1((1)H(2)S(3)S(4)Y(5)W(6)Y(7)A(8)F(9)N(10)N(11)K(12)T)作为示例来说明其实用性。我们发现，肽在低温下相当快地组装成球状聚集体，而在高温下则分散成无规卷曲。自组装的质量分布特异性取决于温度和空间长度，这些可以从结构因子的标度中识别出来。对能量和迁移率分布、肽的回转半径和组装的径向分布函数的分析提供了对多尺度（链内和链间）特性的深入了解。尽管预期存在定量差异，但与基于知识的分析相比，模拟残基-残基相互作用的全局组装的热响应是一致的。
