MOLECULAR DYNAMICS STUDIES OF CRAMBIN AND BPTI IN TERMS OF ABEEM/MM METHOD

2008 ◽  
Vol 07 (04) ◽  
pp. 697-705 ◽  
Author(s):  
ZHONG-ZHI YANG ◽  
QING-MEI GUAN ◽  
DONG-XIA ZHAO
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Dynamics Simulation ◽  
Dihedral Angles ◽  
Mean Square ◽  
Simulation Studies ◽  
X Ray ◽  
Electronegativity Equalization Method ◽  
Atom Bond ◽  
Fluctuating Charge Force Field

Recently, the ABEEM/MM method (atom-bond electronegativity equalization method fused into molecular mechanics) has successfully been applied to study polypeptide conformations. In order to further test the reliability of this method as well as the transferability of the parameters (including ABEEM and force field parameters), molecular dynamics simulation studies on Crambin and BPTI (298 K, in vacuo) have been performed in terms of ABEEM/MM fluctuating charge force field. Some of their structural properties were obtained, and relative to the X-ray structures, the root-mean-square deviations (RMSD) of bond lengths, bond angles and key dihedral angles, and the coordinate RMSDs of atoms were calculated. The ABEEM/MM results are fairly consistent with those from X-ray experiment.

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

2019 ◽  
Vol 52 (6) ◽  
pp. 1253-1263 ◽  
Author(s):  
Angelo Gavezzotti ◽  
Leonardo Lo Presti
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Crystal Packing ◽  
Structural Information ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Intermolecular Potential ◽  
Organic Liquids ◽  
Organic Crystals ◽  
X Ray

The CLP-dyncry molecular dynamics (MD) program suite and force field environment is introduced and validated with its ad hoc features for the treatment of organic crystalline matter. The package, stemming from a preliminary implementation on organic liquids (Gavezzotti & Lo Presti, 2019), includes modules for the preliminary generation of molecular force field files from ab initio derived force constants, and for the preparation of crystalline simulation boxes from general crystallographic information, including Cambridge Structural Database CIFs. The intermolecular potential is the atom–atom Coulomb–London–Pauli force field, well tested as calibrated on sublimation enthalpies of organic crystals. These products are then submitted to a main MD module that drives the time integration and produces dynamic information in the form of coordinate and energy trajectories, which are in turn processed by several kinds of crystal-oriented analytic modules. The whole setup is tested on a variety of bulk crystals of rigid, non-rigid and hydrogen-bonded compounds for the reproduction of radial distribution functions and of crystal-specific collective orientational variables against X-ray data. In a series of parallel tests, some advantages of a dedicated program as opposed to software more oriented to biomolecular simulation (Gromacs) are highlighted. The different and improved view of crystal packing that results from joining static structural information from X-ray analysis with dynamic upgrades is also pointed out. The package is available for free distribution with I/O examples and Fortran source codes.

Ambient Pressure X-ray Photoelectron Spectroscopy and Molecular Dynamics Simulation Studies of Liquid/Vapor Interfaces of Aqueous NaCl, RbCl, and RbBr Solutions

2012 ◽  
Vol 116 (7) ◽  
pp. 4545-4555 ◽  
Author(s):  
Ming Hsin Cheng ◽  
Karen M. Callahan ◽  
Alexandria M. Margarella ◽  
Douglas J. Tobias ◽  
John C. Hemminger ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Photoelectron Spectroscopy ◽  
Ambient Pressure ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
X Ray ◽  
Liquid Vapor

scholarly journals Target SARS-CoV-2: Computation of Binding energies with drugs of Dexamethasone/Umifenovir by Molecular Dynamics using OPLS-AA force field

2020 ◽  
Author(s):  
Sk. Md Na ◽  
M. Srinivasa R
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Binding Energies ◽  
Drug Binding ◽  
Dynamics Simulation ◽  
Strong Interactions ◽  
Radius Of Gyration ◽  
Binding Affinities ◽  
Mean Square ◽  
Main Protease

Abstract Molecular Dynamics simulation using Gromacs with OPLS-AA force field is performed for 100ns between SARS-CoV-2 main protease and Dexamethasone / Umifenovir drugs at 300 K/1 atm pressure. The trajectory of Root Mean Square Deviation (RMSD) and Radius of Gyration(Rg) emphasized the achievement of equilibrium and compactness. The drug-binding affinities on SARS-CoV-2 main protease are estimated via MM/PBSA method. The sign with magnitude of computed Gibbs free energy indicated the presence of strong interactions between SARS-CoV-2 and drugs of Dexamethasone / Umifenovir. The study revealed that the drug Dexamethasone is more effective over Umifenovir in binding SARS-CoV-2 main protease.

scholarly journals Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 686 ◽  
Author(s):  
Alexander Neumann ◽  
Viktor Engel ◽  
Andhika B. Mahardhika ◽  
Clara T. Schoeder ◽  
Vigneshwaran Namasivayam ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
G Protein ◽  
Phenyl Ring ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Binding Modes ◽  
G Protein Coupled Receptor ◽  
G Protein Coupled

GPR18 is an orphan G protein-coupled receptor (GPCR) expressed in cells of the immune system. It is activated by the cannabinoid receptor (CB) agonist ∆9-tetrahydrocannabinol (THC). Several further lipids have been proposed to act as GPR18 agonists, but these results still require unambiguous confirmation. In the present study, we constructed a homology model of the human GPR18 based on an ensemble of three GPCR crystal structures to investigate the binding modes of the agonist THC and the recently reported antagonists which feature an imidazothiazinone core to which a (substituted) phenyl ring is connected via a lipophilic linker. Docking and molecular dynamics simulation studies were performed. As a result, a hydrophobic binding pocket is predicted to accommodate the imidazothiazinone core, while the terminal phenyl ring projects towards an aromatic pocket. Hydrophobic interaction of Cys251 with substituents on the phenyl ring could explain the high potency of the most potent derivatives. Molecular dynamics simulation studies suggest that the binding of imidazothiazinone antagonists stabilizes transmembrane regions TM1, TM6 and TM7 of the receptor through a salt bridge between Asp118 and Lys133. The agonist THC is presumed to bind differently to GPR18 than to the distantly related CB receptors. This study provides insights into the binding mode of GPR18 agonists and antagonists which will facilitate future drug design for this promising potential drug target.

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