A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physic...A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physical algorithm for protein structure prediction problem is put forward. First, by elaborately simulating the movement of the smooth elastic balls in the physical world, the algorithm finds low energy configurations for a given monomer chain. An ＂off-trap＂ strategy is then proposed to get out of local minima. Experimental results show promising performance. For all chains with lengths 13≤n ≤55, the proposed algorithm finds states with lower energy than the putative ground states reported in literatures. Furthermore, for chain lengths n = 21, 34, and 55, the algorithm finds new low energy configurations different from those given in literatures.展开更多
The folding dynamics and structural characteristics of peptides RTKAWNRQLYPEW （P1） and RTKQLYPEW （P2） are investigated by using all-atomic simulation procedure CHARMM in this work. The results show that P1, a segm...The folding dynamics and structural characteristics of peptides RTKAWNRQLYPEW （P1） and RTKQLYPEW （P2） are investigated by using all-atomic simulation procedure CHARMM in this work. The results show that P1, a segment of an antigen, has a folding motif of α-helix, whereas P2, which is derived by deleting four residues AWNR from peptide P1, prevents the formation of helix and presents a β-strand. And peptlde P1 experiences a more rugged energy landscape than peptide P2. From our results, it is inferred that the antibody CD8 cytolytic T lymphocyte prefers an antigen with a β-folding structure to that with an α-helical one.展开更多
基金The National Natural Science Founda-tion of China (No.10471051) and the National Basic Research Program (973) of China (No.2004CB318000)
文摘A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physical algorithm for protein structure prediction problem is put forward. First, by elaborately simulating the movement of the smooth elastic balls in the physical world, the algorithm finds low energy configurations for a given monomer chain. An ＂off-trap＂ strategy is then proposed to get out of local minima. Experimental results show promising performance. For all chains with lengths 13≤n ≤55, the proposed algorithm finds states with lower energy than the putative ground states reported in literatures. Furthermore, for chain lengths n = 21, 34, and 55, the algorithm finds new low energy configurations different from those given in literatures.
基金Project supported by the National Natural Science Foundation of China （Grant Nos 90103031, 10474041, 90403120 and 10021001）, and the Nonlinear Project （973） of the NSM.
文摘The folding dynamics and structural characteristics of peptides RTKAWNRQLYPEW （P1） and RTKQLYPEW （P2） are investigated by using all-atomic simulation procedure CHARMM in this work. The results show that P1, a segment of an antigen, has a folding motif of α-helix, whereas P2, which is derived by deleting four residues AWNR from peptide P1, prevents the formation of helix and presents a β-strand. And peptlde P1 experiences a more rugged energy landscape than peptide P2. From our results, it is inferred that the antibody CD8 cytolytic T lymphocyte prefers an antigen with a β-folding structure to that with an α-helical one.
