Mechanism of Thermal Protein Aggregation: Experiments and Molecular Dynamics Simulations on the High-Temperature Behavior of Myoglobin

2021 ◽  
Author(s):  
Yuen Ki Ng ◽  
Nastaran N. Tajoddin ◽  
Pablo M. Scrosati ◽  
Lars Konermann
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Protein Aggregation ◽  
Molecular Dynamics Simulations ◽  
Temperature Behavior ◽  
High Temperature Behavior ◽  
Dynamics Simulations

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

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.

Phase transitions in tridymite studied using ‘Rigid Unit Mode’ theory, Reverse Monte Carlo methods and molecular dynamics simulations

2000 ◽  
Vol 64 (2) ◽  
pp. 267-283 ◽  
Author(s):  
M. T. Dove ◽  
A. K. A. Pryde ◽  
D. A. Keen
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Phase Transitions ◽  
High Temperature ◽  
Molecular Dynamics Simulations ◽  
High Temperature Phase ◽  
Temperature Phase ◽  
Reverse Monte Carlo ◽  
Mode Theory ◽  
Dynamics Simulations

AbstractThe phase transitions in tridymite and the nature of the high-temperature phase are investigated using a combination of Rigid Unit Mode theory, neutron total scattering measurements analysed using the Reverse Monte Carlo method, and molecular dynamics simulations. The unusually large number of phase transitions in tridymite can be explained within the Rigid Unit Mode theory. The Rigid Unit Mode theory also gives an interpretation of the disordered high-temperature phase as revealed by the neutron scattering data and the molecular dynamics simulations. There is a close correspondence between the structure of the disordered high-temperature phase of tridymite and that of β-cristobalite.

Direct Molecular Dynamics Simulations of Diffusion Mechanisms in NiAl

2000 ◽  
Vol 646 ◽  
Author(s):  
D. Farkas ◽  
B. Soulé de Bas
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulations ◽  
Sequential Analysis ◽  
Nearest Neighbor ◽  
Interatomic Potential ◽  
Embedded Atom ◽  
Diffusion Mechanisms ◽  
Dynamics Simulations ◽  
Potential Diffusion

ABSTRACTMolecular dynamics simulations of the diffusion process in ordered B2 NiAl at high temperature were performed using an embedded atom interatomic potential. Diffusion occurs through a variety of cyclic mechanisms that accomplish the motion of the vacancy through nearest neighbor jumps restoring order to the alloy at the end of the cycle. The traditionally postulated 6-jump cycle is only one of the various cycles observed and some of these are quite complex. A detailed sequential analysis of the observed 6-jump cycles was performed and the results are analyzed in terms of the activation energies for individual jumps calculated using molecular statics simulations.

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