The spatial structure of SEM1(68-107) peptide from molecular dynamics simulation

SEM1(68–107) is a 40-residue peptide corresponding to the semenogelin 1 68–107 residues. SEM1(68–107) is an abundant component of semen, it takes part in HIV infection enhancing by forming amyloid fibrils.
The combined approach based on the use of geometric restrictions of individual peptide fragments and molecular modeling was used for determination the spatial structure of SEM1(68-107). The N- (SEM1(68-85)) and C-terminuses (SEM1(86-107)) of SEM1(68-107) were chosen as two individual peptide fragments. Structure of SEM1(68-107) was calculated in the XPLOR-NIH program using the annealing technique, with geometrical restrains of SEM1(68-85) and SEM1(86-107). The SEM1(68-107) calculated spatial structure with the lowest energy was subjected to a 350-ns-long all-atom molecular dynamics by Gromacs software.
Here we present the ensemble data (pdb-format) obtained from the MD simulation: 1.35MD_SEM1(68-107): ensemble composed of 35 SEM1(68-107) structures (from 0 ns to 350 ns in 10 ns steps); 2. 50MD_SEM1(68-107): ensemble composed of 50 SEM1(68-107) structures (from 100 ns to 150 ns in 1 ns steps).

SEM1(68–107)是一段含40个残基的肽段，对应精液凝固蛋白1（semenogelin 1）的68~107位残基。该肽段是精液中的丰度较高的组分，可通过形成淀粉样纤维（amyloid fibrils）参与促进人类免疫缺陷病毒（HIV）感染的过程。
本研究采用基于单个肽段几何约束与分子建模的联合方法，解析SEM1(68-107)的空间结构。研究选取SEM1(68-107)的N端片段SEM1(68-85)与C端片段SEM1(86-107)作为两个独立肽段。借助XPLOR-NIH程序，以SEM1(68-85)与SEM1(86-107)的几何约束为基础，通过模拟退火技术计算得到SEM1(68-107)的空间结构。将能量最低的计算所得SEM1(68-107)空间结构，利用Gromacs软件开展时长为350 ns的全原子分子动力学（all-atom molecular dynamics）模拟。
本文提供了通过分子动力学（MD）模拟得到的PDB格式（pdb-format）集合数据：1. 35MD_SEM1(68-107)：该集合包含35个SEM1(68-107)结构，采样范围为0 ns至350 ns，步长为10 ns；2. 50MD_SEM1(68-107)：该集合包含50个SEM1(68-107)结构，采样范围为100 ns至150 ns，步长为1 ns。