Three-Dimensional Structure and Dynamics of a de Novo Designed, Amphiphilic, Metallo-Porphyrin-Binding Protein Maquette at Soft Interfaces by Molecular Dynamics Simulations

2007 ◽  
Vol 111 (7) ◽  
pp. 1823-1833 ◽  
Author(s):  
Hongling Zou ◽  
Joseph Strzalka ◽  
Ting Xu ◽  
Andrey Tronin ◽  
J. Kent Blasie
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
De Novo ◽  
Binding Protein ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Soft Interfaces ◽  
Structure And Dynamics ◽  
Dynamics Simulations

scholarly journals Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Sandro Bottaro ◽  
Giovanni Bussi ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Genomic Region ◽  
Dimensional Structure ◽  
Structure Based Drug Design ◽  
Stem Loop ◽  
Rna Molecules ◽  
Conformational Ensembles ◽  
Dynamics Simulations

The 5' untranslated region (UTR) of SARS-CoV-2 genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structure is not known yet. Here, we predict structure and dynamics of five RNA stem-loops in the 5'-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrengements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterisation of these systems, and provide putative three-dimensional models for structure-based drug design studies.

scholarly journals Molecular dynamics simulations of potassium channels

2007 ◽  
Vol 5 (3) ◽  
pp. 635-671 ◽  
Author(s):  
Carmen Domene
Keyword(s):  
Molecular Dynamics ◽  
Potassium Channels ◽  
Molecular Dynamics Simulations ◽  
Experimental Work ◽  
Three Dimensional ◽  
Md Simulations ◽  
Structure And Dynamics ◽  
Dynamics Simulations ◽  
New Algorithms

AbstractDespite the complexity of ion-channels, MD simulations based on realistic all-atom models have become a powerful technique for providing accurate descriptions of the structure and dynamics of these systems, complementing and reinforcing experimental work. Successful multidisciplinary collaborations, progress in the experimental determination of three-dimensional structures of membrane proteins together with new algorithms for molecular simulations and the increasing speed and availability of supercomputers, have made possible a considerable progress in this area of biophysics. This review aims at highlighting some of the work in the area of potassium channels and molecular dynamics simulations where numerous fundamental questions about the structure, function, folding and dynamics of these systems remain as yet unresolved challenges.

Molecular modelling studies of sirtuin 2 inhibitors using three-dimensional structure–activity relationship analysis and molecular dynamics simulations

2015 ◽  
Vol 11 (3) ◽  
pp. 723-733 ◽  
Author(s):  
Yu-Chung Chuang ◽  
Ching-Hsun Chang ◽  
Jen-Tai Lin ◽  
Chia-Ning Yang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Comfa Model ◽  
Relationship Analysis ◽  
Structure Activity ◽  
Molecular Modelling Studies ◽  
Modelling Studies ◽  
Dynamics Simulations

In this work, a CoMFA model and molecular dynamics simulations provide guidelines for drug development of SIRT2 inhibitors.

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