Protein folding for finding active sites by the VMD tool and force field simulation

2009 ◽  
Vol 19 (4) ◽  
pp. 717-723
Author(s):  
Wen-Tsai Sung
Keyword(s):  
Protein Folding ◽  
Force Field ◽  
Active Sites ◽  
Field Simulation

scholarly journals Conjugate of Thiol and Guanidyl Units with Oligoethylene Glycol Linkage for Manipulation of Oxidative Protein Folding

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 879
Author(s):  
Shunsuke Okada ◽  
Motonori Matsusaki ◽  
Masaki Okumura ◽  
Takahiro Muraoka
Keyword(s):  
Protein Folding ◽  
Active Sites ◽  
Biological Process ◽  
Thiol Group ◽  
Native Conformation ◽  
Thiol Compounds ◽  
Oxidative Protein Folding ◽  
Redox Active ◽  
A Cell ◽  
Protein Disulfide

Oxidative protein folding is a biological process to obtain a native conformation of a protein through disulfide-bond formation between cysteine residues. In a cell, disulfide-catalysts such as protein disulfide isomerase promote the oxidative protein folding. Inspired by the active sites of the disulfide-catalysts, synthetic redox-active thiol compounds have been developed, which have shown significant promotion of the folding processes. In our previous study, coupling effects of a thiol group and guanidyl unit on the folding promotion were reported. Herein, we investigated the influences of a spacer between the thiol group and guanidyl unit. A conjugate between thiol and guanidyl units with a diethylene glycol spacer (GdnDEG-SH) showed lower folding promotion effect compared to the thiol–guanidyl conjugate without the spacer (GdnSH). Lower acidity and a more reductive property of the thiol group of GdnDEG-SH compared to those of GdnSH likely resulted in the reduced efficiency of the folding promotion. Thus, the spacer between the thiol and guanidyl groups is critical for the promotion of oxidative protein folding.

scholarly journals Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

2020 ◽  
Vol 76 (1) ◽  
pp. 51-62 ◽  
Author(s):  
Nigel W. Moriarty ◽  
Pawel A. Janowski ◽  
Jason M. Swails ◽  
Hai Nguyen ◽  
Jane S. Richardson ◽  
...  
Keyword(s):  
Force Field ◽  
Active Sites ◽  
Protein Structures ◽  
Target Function ◽  
Real Space ◽  
Model Quality ◽  
Nonbonded Interactions ◽  
Amber Force Field ◽  
Quantum Mechanical Representation ◽  
Improved Model

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard–Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing.

scholarly journals How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

2011 ◽  
Vol 100 (9) ◽  
pp. L47-L49 ◽  
Author(s):  
Stefano Piana ◽  
Kresten Lindorff-Larsen ◽  
David E. Shaw
Keyword(s):  
Protein Folding ◽  
Force Field ◽  
Force Field Parameterization ◽  
Folding Simulations

Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight

2020 ◽  
Vol 31 (12) ◽  
pp. 2954-2967
Author(s):  
Ping Gao ◽  
Xiaohui Duan ◽  
Tingjian Zhang ◽  
Meng Zhang ◽  
Bertil Schmidt ◽  
...  
Keyword(s):  
Force Field ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Field Simulation ◽  
Sunway Taihulight

Twin Induced Sensitivity Enhancement of HMX versus Shock: A Molecular Reactive Force Field Simulation

2013 ◽  
Vol 117 (46) ◽  
pp. 24368-24374 ◽  
Author(s):  
Yushi Wen ◽  
Xianggui Xue ◽  
Xiaoqing Zhou ◽  
Feng Guo ◽  
Xinping Long ◽  
...  
Keyword(s):  
Force Field ◽  
Sensitivity Enhancement ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Field Simulation
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