Direct folding simulation of helical proteins using an effective polarizable bond force field

2017 ◽  
Vol 19 (23) ◽  
pp. 15273-15284 ◽  
Author(s):  
Lili Duan ◽  
Tong Zhu ◽  
Changge Ji ◽  
Qinggang Zhang ◽  
John Z. H. Zhang
Keyword(s):  
Force Field ◽  
Bond Force ◽  
Folding Simulation ◽  
Helical Proteins

Snapshots of the intermediate conformation of Trp-cage at various simulation times using AMBER03, EPB03, AMBER12SB, and EPB12SB. Here, the N terminal is always on the top.

An empirical force field for ethylenes

1970 ◽  
Vol 23 (5) ◽  
pp. 873
Author(s):  
K Ramaswamy ◽  
V Devarajan
Keyword(s):  
Force Field ◽  
Bond Length ◽  
Ethylene Molecule ◽  
Bond Force ◽  
Empirical Force Field ◽  
New Type

A new type of force field on the lines of the hybrid bond force field has been suggested, and it has been successfully applied to the case of the ethylene molecule. The value (∂r/∂λ)CH and (∂R/∂X)cc (variation of bond length with respect to variation in hybridization) has been found to be approximately equal to + 0.ll �.

Folding simulation of Trp-cage utilizing a new AMBER compatible force field with coupled main chain torsions

2014 ◽  
Vol 13 (04) ◽  
pp. 1450026 ◽  
Author(s):  
Lirong Mou ◽  
Xiangyu Jia ◽  
Ya Gao ◽  
Yongxiu Li ◽  
John Z. H. Zhang ◽  
...  
Keyword(s):  
Force Field ◽  
Main Chain ◽  
Md Simulations ◽  
Replica Exchange ◽  
Hydrophobic Core ◽  
Native Structure ◽  
Folding Simulation ◽  
Torsion Potential ◽  
Folding Simulations ◽  
Α Helix

A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER032D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity Cvis only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER032Dis an accurate force field that can be used for protein folding simulations.

scholarly journals Molecular Dynamics Folding Simulation of β-hairpin Protein (1E0Q)

2014 ◽  
Vol 7 (2) ◽  
Author(s):  
Nur Shima Fadhilah Mazlan ◽  
Nurul Bahiyah Ahmad Khairudin
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Secondary Structure ◽  
Force Field ◽  
Structure Analysis ◽  
Md Simulation ◽  
Folding Pathway ◽  
Mutant Peptide ◽  
Secondary Structure Analysis ◽  
Folding Simulation

The structure and trajectories of the mutant peptide of ubiquitin (PDB ID: 1E0Q) has been studied using Molecular Dynamics (MD) simulation. The simulation was performed using AMBER 11 utilizing force field 99 for 50 ns at constant temperature 325 K. The purpose of this study is to investigate the protein folding pathway of protein 1E0Q. In this simulation, the protein 1E0Q has folded into its near native β-hairpin structure within 5 ns. The RMSD value as compared to the NMR structure from the first residue to 17 residues is 2.17 Å. It has been observed that Gly 10 had been responsible to promote β-turn which caused the structure to turn into β-hairpin. In secondary structure analysis, it is shown that the residue from Thr 6 to Lys 11 has formed a bend in the structure. Two beta strands has also been found comprising residues Glu 2 to Lys 5 and Ile 13 to Glu 16.

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