scholarly journals Implicit solvent models fail to reproduce secondary structures of de novo designed peptides

2021 ◽  
Author(s):  
Eric Lang ◽  
Emily Baker ◽  
Derek Woolfson ◽  
Adrian Mulholland
Keyword(s):  
Molecular Dynamics ◽  
Secondary Structure ◽  
Molecular Dynamics Simulations ◽  
De Novo ◽  
Secondary Structures ◽  
Implicit Solvent ◽  
Helical Peptides ◽  
Solvent Models ◽  
Dynamics Simulations ◽  
Implicit Solvent Models

We test a range of standard implicit solvent models and protein forcefields for a set of 5 experimentally characterized, designed α-helical peptides. 65 combinations of forcefield and implicit solvent models are evaluated in >800 µs of molecular dynamics simulations. The data show that implicit solvent models generally fail to reproduce the experimentally observed secondary structure content, and none performs well for all 5 peptides. The results show that these models are not usefully predictive.

scholarly journals Understanding the R882H mutation effects of DNA methyltransferase DNMT3A: a combination of molecular dynamics simulations and QM/MM calculations

RSC Advances ◽  
2019 ◽  
Vol 9 (54) ◽  
pp. 31425-31434 ◽  
Author(s):  
Lanxuan Liu ◽  
Ting Shi ◽  
Kendall N. Houk ◽  
Yi-Lei Zhao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Human Beings ◽  
Epigenetic Methylation ◽  
Key Enzyme ◽  
Dynamics Simulations

The AML-related high-frequent R882H mutation of DNA (cytosine-5)-methyltransferase 3A (DNMT3A), a key enzyme for de novo epigenetic methylation in human beings, was characterized by a disturbing conformation of S-adenosylmethionine (SAM).

Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent

2009 ◽  
Vol 113 (1) ◽  
pp. 267-274 ◽  
Author(s):  
Yassmine Chebaro ◽  
Xiao Dong ◽  
Rozita Laghaei ◽  
Philippe Derreumaux ◽  
Normand Mousseau
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Replica Exchange ◽  
Implicit Solvent ◽  
Replica Exchange Molecular Dynamics ◽  
Dynamics Simulations

Characterization of de novo four-helix bundles by molecular dynamics simulations

2006 ◽  
Vol 64 (3) ◽  
pp. 719-729 ◽  
Author(s):  
Walter R. P. Scott ◽  
Emily Seo ◽  
Heidi Huttunen ◽  
Diana Wallhorn ◽  
John C. Sherman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
De Novo ◽  
Dynamics Simulations
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