scholarly journals Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a β-sheet miniprotein

2007 ◽  
Vol 70 (4) ◽  
pp. 1185-1195 ◽  
Author(s):  
Stefanie Muff ◽  
Amedeo Caflisch
Keyword(s):  
Molecular Dynamics ◽  
Kinetic Analysis ◽  
Molecular Dynamics Simulations ◽  
Point Mutation ◽  
Single Point ◽  
Single Point Mutation ◽  
Denatured State ◽  
Folding Pathways ◽  
Dynamics Simulations ◽  
Β Sheet

scholarly journals Assessing the capability ofin silicomutation protocols for predicting the finite temperature conformation of amino acids

2018 ◽  
Vol 20 (40) ◽  
pp. 25901-25909 ◽  
Author(s):  
Rodrigo Ochoa ◽  
Miguel A. Soler ◽  
Alessandro Laio ◽  
Pilar Cossio
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulations ◽  
Point Mutation ◽  
Finite Temperature ◽  
Single Point ◽  
Single Point Mutation ◽  
Equilibrium Configurations ◽  
Dynamics Simulations

Single-point mutation protocols based on backbone-dependent rotamer libraries show the best performance in predicting equilibrium configurations from molecular dynamics simulations.

scholarly journals Insight into a Novel p53 Single Point Mutation (G389E) by Molecular Dynamics Simulations

2010 ◽  
Vol 12 (1) ◽  
pp. 128-140 ◽  
Author(s):  
Davide Pirolli ◽  
Cristiana Carelli Alinovi ◽  
Ettore Capoluongo ◽  
Maria Antonia Satta ◽  
Paola Concolino ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Point Mutation ◽  
Single Point ◽  
Single Point Mutation ◽  
Dynamics Simulations ◽  
Insight Into

scholarly journals Mutation-Induced Conformational Changes and Energetics for Binding of FMN Ligand in Flavin Mononucleotide Riboswitch by Molecular Dynamics Simulations

2019 ◽  
Vol 92 (2) ◽  
pp. 241-247
Author(s):  
Padmaja D. Wakchaure ◽  
Bishwajit Ganguly
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Single Point ◽  
Regulatory Elements ◽  
Flavin Mononucleotide ◽  
Single Point Mutation ◽  
Valuable Insight ◽  
Natural Ligand ◽  
Dynamics Simulations

Riboswitches are the type of regulatory elements present in the untranslated region of mRNA and specifically bind to the natural ligand to regulate gene expression. This binding specificity can be affected by even single point mutation incorporated in the core of the riboswitch. In this work, we have examined the mutations at the binding site residue in Flavin Mononucleotide (FMN) riboswitch structure with 30ns molecular dynamics simulations. The interaction of ligand (FMN) with riboswitch has been characterized using root mean square deviation, hydrogen bonding analysis, and the calculated binding affinities. Mutation at A48G and G62U show the enhanced binding energy however, the mutation at A85G, are energetically unfavorable compared to the wild type. This work gives valuable insight into the structures and energetics of the mutated FMN riboswitch to design new hits for biological applications.

scholarly journals Structural Influence and Interactive Binding Behavior of Dopamine and Norepinephrine on the Greek-Key-Like Core of α-Synuclein Protofibril Revealed by Molecular Dynamics Simulations

Processes ◽  
2019 ◽  
Vol 7 (11) ◽  
pp. 850
Author(s):  
Yu Zou ◽  
Zhiwei Liu ◽  
Zhiqiang Zhu ◽  
Zhenyu Qian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Therapeutic Strategy ◽  
Binding Capacity ◽  
Salt Bridges ◽  
Drug Candidates ◽  
Binding Behavior ◽  
Dynamics Simulations ◽  
Structural Influence ◽  
Β Sheet

The pathogenesis of Parkinson’s disease (PD) is closely associated with the aggregation of α-synuclein (αS) protein. Finding the effective inhibitors of αS aggregation has been considered as the primary therapeutic strategy for PD. Recent studies reported that two neurotransmitters, dopamine (DA) and norepinephrine (NE), can effectively inhibit αS aggregation and disrupt the preformed αS fibrils. However, the atomistic details of αS-DA/NE interaction remain unclear. Here, using molecular dynamics simulations, we investigated the binding behavior of DA/NE molecules and their structural influence on αS44–96 (Greek-key-like core of full length αS) protofibrillar tetramer. Our results showed that DA/NE molecules destabilize αS protofibrillar tetramer by disrupting the β-sheet structure and destroying the intra- and inter-peptide E46–K80 salt bridges, and they can also destroy the inter-chain backbone hydrogen bonds. Three binding sites were identified for both DA and NE molecules interacting with αS tetramer: T54–T72, Q79–A85, and F94–K96, and NE molecules had a stronger binding capacity to these sites than DA. The binding of DA/NE molecules to αS tetramer is dominantly driven by electrostatic and hydrogen bonding interactions. Through aromatic π-stacking, DA and NE molecules can bind to αS protofibril interactively. Our work reveals the detailed disruptive mechanism of protofibrillar αS oligomer by DA/NE molecules, which is helpful for the development of drug candidates against PD. Given that exercise as a stressor can stimulate DA/NE secretion and elevated levels of DA/NE could delay the progress of PD, this work also enhances our understanding of the biological mechanism by which exercise prevents and alleviates PD.

Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides

Peptides ◽  
2010 ◽  
Vol 31 (11) ◽  
pp. 2100-2108 ◽  
Author(s):  
Neil J. Bruce ◽  
Deliang Chen ◽  
Shubhra G. Dastidar ◽  
Gabriel E. Marks ◽  
Catherine H. Schein ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Β Sheet

Kinetic analysis of homogeneous droplet nucleation using large-scale molecular dynamics simulations

2018 ◽  
Vol 149 (4) ◽  
pp. 044504 ◽  
Author(s):  
Sho Ayuba ◽  
Donguk Suh ◽  
Kentaro Nomura ◽  
Toshikazu Ebisuzaki ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Kinetic Analysis ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Droplet Nucleation ◽  
Dynamics Simulations
Sign in / Sign up

Export Citation Format

Share Document