scholarly journals How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations

2021 ◽  
Vol 19 ◽  
pp. 2097-2105
Author(s):  
Fanny Kozak ◽  
Dennis Kurzbach
Keyword(s):  
Molecular Dynamics ◽  
Transcription Factors ◽  
Molecular Dynamics Simulations ◽  
Structural Dynamics ◽  
Dynamics Simulations

Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations

2005 ◽  
Vol 351 (4) ◽  
pp. 731-748 ◽  
Author(s):  
Maryna V. Krasovska ◽  
Jana Sefcikova ◽  
Nad'a Špačková ◽  
Jiří Šponer ◽  
Nils G. Walter
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Dynamics ◽  
Hepatitis Delta Virus ◽  
Hepatitis Delta ◽  
Dynamics Simulations ◽  
Delta Virus

scholarly journals Molecular Dynamics Simulations of resistin and RELMβ proteins: Insight into structural dynamics

2021 ◽  
Author(s):  
L. América Chi Uluac ◽  
M. Cristina Vargas González
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulations ◽  
Structural Dynamics ◽  
Protein Structures ◽  
Globular Domain ◽  
The Family ◽  
Network Of Hydrogen Bonds ◽  
Dynamics Simulations ◽  
Metabolic Dysfunctions

Diabetes mellitus and high levels of resistin are risk factors for COVID-19, suggest- ing a shared mechanism for their contribution to the increased severity of COVID-19. Resistin belongs to the family of resistin-like molecules (RELMs) whose implications for inflammatory and metabolic dysfunctions warrant its study in order to shed light on the etiology of these concerning pathologies. In this work, our objective is to char- acterize the structural dynamics of the reported crystallized resistin-like molecules. We performed molecular dynamics simulations of all-atom solvated protein at physiological and high temperatures for the three mouse structures reported so far. We found that in all the structures studied, there is a loss of helicity as a first step of protein denat- uration. There is a high stability of the globular β-sheet domain in resistin protein structures that is not conserved for RELMβ. At high temperature, we found a partial interconversion of α-helices into β-sheets in all proteins, indicating that this propensity is not only found during aggregation but also heating. We had been able to identify a largely persistent hydrogen-bond network shared by all the proteins in the interchain globular domain at room temperature. This network of hydrogen bonds is conserved considerably at high temperature in resistin structures, but not in RELMβ. These findings may guide future studies to increase our understanding of the different and shared mechanisms of action of RELMs.

scholarly journals Structural dynamics of an excited donor–acceptor complex from ultrafast polarized infrared spectroscopy, molecular dynamics simulations, and quantum chemical calculations

2019 ◽  
Vol 21 (22) ◽  
pp. 11797-11809 ◽  
Author(s):  
Christopher A. Rumble ◽  
Eric Vauthey
Keyword(s):  
Molecular Dynamics ◽  
Infrared Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Structural Dynamics ◽  
Quantum Chemical ◽  
Large Scale ◽  
Acceptor Complex ◽  
Polarized Infrared Spectroscopy ◽  
Donor Acceptor ◽  
Dynamics Simulations

Infrared anisotropy experiments and mixed quantum/classical computations demonstrate large scale reorientation following excitation of a donor/acceptor complex.

The folding mechanism and key metastable state identification of the PrP127–147 monomer studied by molecular dynamics simulations and Markov state model analysis

2017 ◽  
Vol 19 (18) ◽  
pp. 11249-11259 ◽  
Author(s):  
Shuangyan Zhou ◽  
Qianqian Wang ◽  
Yuwei Wang ◽  
Xiaojun Yao ◽  
Wei Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Structural Dynamics ◽  
Md Simulation ◽  
Markov State Model ◽  
Markov State ◽  
Folding Mechanism ◽  
State Identification ◽  
Dynamics Simulations

MD simulation combined with MSM analysis was employed to investigate the structural dynamics and the folding mechanism of the key fragment 127–147 monomer of prion protein.

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