In the centre of the famous Chinese painting, Qingrning Shanghe Tu, an arch-shaped timber bridge, Hongqiao, stands like a rainbow over the river Bianhe. Unfortunately, Hongqiao was damaged during floods from the Yello...In the centre of the famous Chinese painting, Qingrning Shanghe Tu, an arch-shaped timber bridge, Hongqiao, stands like a rainbow over the river Bianhe. Unfortunately, Hongqiao was damaged during floods from the Yellow River, and we can only see her beautiful form in Qingming Shanghe Tu. While, the geometrical dimensions, structural principle, as well as the construction methods of the bridge are still an interesting mystery. In the present paper, the author uncovers the structural principle and the geometric dimensions of the bridge as well as its history background. Furthermore, the author introduces two new structural systems, Lap-Beam and 1.5-Layer space frame, which are inspired by the structural principle of the Hongqiao.展开更多
In this study, we apply both palrwise AMBER03 force field and the recently developed polarized force field to study the folding process of EK peptide under various ion strength and pH conditions. The polarized force f...In this study, we apply both palrwise AMBER03 force field and the recently developed polarized force field to study the folding process of EK peptide under various ion strength and pH conditions. The polarized force field is based on our newly proposed adaptive hydrogen bond-specific charge （AHBC） scheme. These two force fields differ only by the atomic charges. Solvent effect is described with generalized Born models （IGB5 in AMBER 10 package）. The result shows that although when applying AMBER03 charge, the helical structure is preferred, its dependence on salt concentration and pH is qualitatively wrong. While using AHBC the peptide finds its native structure within 10 ns, and then fluctuates around this folded state. Under high salt concentration or extreme pH conditions the calculated helical structure probability drops, which is in qualitative agreement with the experiment. Analysis of the atomic charges and the interaction between the donor-acceptor pair in main hydrogen bonds shows that the helical structure is stabilized when polarization effect is counted. It again shows that polarization effect is a very important improvement over traditional force field and is essential for protein folding. We also prove that the salt bridge interaction between 4-residue apart GLU and LYS residues is not critical to the stability of helical structure of EK peptide, but is merely an auxiliary factor, also in agreement with the experiment.展开更多
文摘In the centre of the famous Chinese painting, Qingrning Shanghe Tu, an arch-shaped timber bridge, Hongqiao, stands like a rainbow over the river Bianhe. Unfortunately, Hongqiao was damaged during floods from the Yellow River, and we can only see her beautiful form in Qingming Shanghe Tu. While, the geometrical dimensions, structural principle, as well as the construction methods of the bridge are still an interesting mystery. In the present paper, the author uncovers the structural principle and the geometric dimensions of the bridge as well as its history background. Furthermore, the author introduces two new structural systems, Lap-Beam and 1.5-Layer space frame, which are inspired by the structural principle of the Hongqiao.
基金supported by the National Natural Science Foundation of China (20803034)the Shanghai Rising-Star Program+2 种基金supported by the Nanyang Technological University Start-up (M58110043)support from the National Natural Science Foundation of China (20933002)Shanghai Pujiang Program (09PJ1404000)
文摘In this study, we apply both palrwise AMBER03 force field and the recently developed polarized force field to study the folding process of EK peptide under various ion strength and pH conditions. The polarized force field is based on our newly proposed adaptive hydrogen bond-specific charge （AHBC） scheme. These two force fields differ only by the atomic charges. Solvent effect is described with generalized Born models （IGB5 in AMBER 10 package）. The result shows that although when applying AMBER03 charge, the helical structure is preferred, its dependence on salt concentration and pH is qualitatively wrong. While using AHBC the peptide finds its native structure within 10 ns, and then fluctuates around this folded state. Under high salt concentration or extreme pH conditions the calculated helical structure probability drops, which is in qualitative agreement with the experiment. Analysis of the atomic charges and the interaction between the donor-acceptor pair in main hydrogen bonds shows that the helical structure is stabilized when polarization effect is counted. It again shows that polarization effect is a very important improvement over traditional force field and is essential for protein folding. We also prove that the salt bridge interaction between 4-residue apart GLU and LYS residues is not critical to the stability of helical structure of EK peptide, but is merely an auxiliary factor, also in agreement with the experiment.
