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).