Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics

2015 ◽  
Vol 83 (9) ◽  
pp. 1665-1676 ◽  
Author(s):  
George A. Pantelopulos ◽  
Sudipto Mukherjee ◽  
Vincent A. Voelz
Keyword(s):  
Force Field ◽  
Conformational Dynamics ◽  
Insight Into

Structural insight into conformational dynamics of non-active site mutations in KasA: A Mycobacterium tuberculosis target protein

Gene ◽  
2019 ◽  
Vol 720 ◽  
pp. 144082 ◽  
Author(s):  
Manikandan Jayaraman ◽  
Savita Kumari Rajendra ◽  
Krishna Ramadas
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Active Site ◽  
Conformational Dynamics ◽  
Target Protein ◽  
Structural Insight ◽  
Insight Into ◽  
Active Site Mutations

Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics

1996 ◽  
Vol 17 (13) ◽  
pp. 1541-1548 ◽  
Author(s):  
Wendy D. Cornell ◽  
Maria P. Ha ◽  
Yax Sun ◽  
Peter A. Kollman
Keyword(s):  
Force Field ◽  
Conformational Dynamics

ChemInform Abstract: Simulation of Conformational Dynamics with the MM3 Force Field: The Pseudorotation of Cyclopentane.

ChemInform ◽  
2010 ◽  
Vol 24 (35) ◽  
pp. no-no
Author(s):  
W. CUI ◽  
F. LI ◽  
N. L. ALLINGER
Keyword(s):  
Force Field ◽  
Conformational Dynamics ◽  
Mm3 Force Field

An insight into antagonist binding and induced conformational dynamics of class B GPCR corticotropin-releasing factor receptor 1

2015 ◽  
Vol 11 (7) ◽  
pp. 2042-2050 ◽  
Author(s):  
Junli Xu ◽  
Zhonghua Wang ◽  
Pi Liu ◽  
Dongmei Li ◽  
Jianping Lin
Keyword(s):  
Small Molecule ◽  
Conformational Dynamics ◽  
Corticotropin Releasing Factor ◽  
Class B ◽  
Antagonist Binding ◽  
Insight Into ◽  
Class B Gpcr

The binding of small-molecule antagonists, CP-376395 and MTIP, would induce conformational dynamics behaviors of CRF1R.

scholarly journals Analysis of the motion and stability of the holonomic mechanical system in the arbitrary force field

2021 ◽  
Vol 49 (1) ◽  
pp. 195-205
Author(s):  
Mitra Vesović ◽  
Goran Petrović ◽  
Radoslav Radulović
Keyword(s):  
Force Field ◽  
Mechanical System ◽  
Friction Force ◽  
Mechanical Engineering ◽  
Specific Problem ◽  
Analytical Mechanics ◽  
Stability Of Motion ◽  
Generalized Coordinates ◽  
Theoretical Foundations ◽  
Insight Into

In order to give an insight into the work of the machine before the production and assembly and to obtain good analysis, this paper presents detailed solutions to the specific problem occured in the field of analytical mechanics. In addition to numerical procedures in the paper, a review of the theoretical foundations was made.Various types of analysis are very common in mechanical engineering, due to the possibility of an approximation of complex machines. For the proposed system, Lagrange's equations of the first kind, covariant and contravariant equations, Hamiltons equations and the generalized coordinates, as well as insight in Coulumb friction force are provided.Also, the conditions of static equilibrium are solved numerically and using intersection of the two curves. Finally, stability of motion for the disturbed and undisturbed system was investigated.

scholarly journals Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

2018 ◽  
Author(s):  
Elena Papaleo ◽  
Carlo Camilloni ◽  
Kaare Teilum ◽  
Michele Vendruscolo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Force Field ◽  
Chemical Shifts ◽  
Molten Globule ◽  
Conformational Dynamics ◽  
Nmr Relaxation ◽  
Structural Heterogeneity ◽  
Order Parameters ◽  
Protein Domain ◽  
Conformational Ensemble ◽  
Native State

ABSTRACTMany proteins display complex dynamical properties that are often intimately linked to their biological functions. As the native state of a protein is best described as an ensemble of confor-mations, it is important to be able to generate models of native state ensembles with high accuracy. Due to limitations in sampling efficiency and force field accuracy it is, however, challenging to obtain accurate ensembles of protein conformations by the use of molecular simulations alone. Here we show that dynamic ensemble refinement, which combines an accurate atomistic force field with commonly available nuclear magnetic resonance (NMR) chemical shifts and NOEs, can provide a detailed and accurate description of the conformational ensemble of the native state of a highly dynamic protein. As both NOEs and chemical shifts are averaged on timescales up to milliseconds, the resulting ensembles reflect the structural heterogeneity that goes beyond that probed e.g. by NMR relaxation order parameters. We selected the small protein domain NCBD as object of our study since this protein, which has been characterized experimentally in substantial detail, displays a rich and complex dynamical behaviour. In particular, the protein has been described as having a molten-globule like structure, but with a relatively rigid core. Our approach allowed us to describe the conformational dynamics of NCBD in solution, and to probe the structural heterogeneity resulting from both short- and long-time-scale dynamics by the calculation of order parameters on different time scales. These results illustrate the usefulness of our approach since they show that NCBD is rather rigid on the nanosecond timescale, but interconverts within a broader ensemble on longer timescales, thus enabling the derivation of a coherent set of conclusions from various NMR experiments on this protein, which could otherwise appear in contradiction with each other.

Human EGF-derived direct and reverse short linear motifs: conformational dynamics insight into the receptor-binding residues

2017 ◽  
Vol 36 (5) ◽  
pp. 1286-1305
Author(s):  
Nurbubu T. Moldogazieva ◽  
Konstantin V. Shaitan ◽  
Mikhail Yu. Antonov ◽  
Innokenty M. Mokhosoev ◽  
Olga V. Levtsova ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Conformational Dynamics ◽  
Short Linear Motifs ◽  
Binding Residues ◽  
Linear Motifs ◽  
Insight Into

Atomic insight into iron corrosion exposed to supercritical water environment with an improved Fe-H2O reactive force field

2021 ◽  
pp. 152300
Author(s):  
Yun Huang ◽  
Chaowei Hu ◽  
Zigen Xiao ◽  
Ning Gao ◽  
Qingtian Wang ◽  
...  
Keyword(s):  
Force Field ◽  
Supercritical Water ◽  
Water Environment ◽  
Reactive Force ◽  
Iron Corrosion ◽  
Reactive Force Field ◽  
Insight Into

scholarly journals Investigation of a new chiral auxiliary derived chemoenzymatically from toluene: experimental and computational study

2016 ◽  
Vol 94 (10) ◽  
pp. 848-856 ◽  
Author(s):  
Ivan Šnajdr ◽  
Jordan Froese ◽  
Travis Dudding ◽  
Pavlína Horáková ◽  
Tomáš Hudlický
Keyword(s):  
Monte Carlo ◽  
Force Field ◽  
Spectral Data ◽  
Computational Study ◽  
Enantiomeric Excess ◽  
Diels Alder ◽  
Chiral Auxiliary ◽  
Asymmetric Induction ◽  
Low Levels ◽  
Insight Into

A tricyclic chiral auxiliary, prepared from the enzymatically derived cis-arene dihydrodiol metabolite of toluene, was investigated as a means of asymmetric induction in several different reactions. The auxiliary was converted to an oxaziridine, and its utility in hydroxylation, providing low levels of enantiomeric excess, was compared with that of Davis’s oxaziridine. Insight into the origin of stereoinduction in this reaction is provided and is based on computational Monte Carlo Multiple Minimum (MCMM) searches using the OPLS3 force field. The use of the auxiliary group in the alkylation of appended esters proved disappointing. Diels-Alder cycloaddition of an acrylate, derived from the auxiliary group, with cyclohexadiene furnished a mixture of diastereomeric adducts in essentially equal amounts. The adducts were separated and the corresponding enantiomeric residues were isolated with good enantiomeric excess. Evidence of reasonable levels of asymmetric induction in the above processes was lacking. Experimental and spectral data are provided for all key compounds.

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