A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling

2006 ◽  
Vol 2 (2) ◽  
pp. 217-228 ◽  
Author(s):  
Roman Affentranger ◽  
Ivano Tavernelli ◽  
Ernesto E. Di Iorio
Keyword(s):  
Conformational Space ◽  
Replica Exchange ◽  
Hamiltonian Replica Exchange ◽  
Conformational Space Sampling

scholarly journals Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins

2010 ◽  
Vol 132 (4) ◽  
pp. 1220-1221 ◽  
Author(s):  
Phineus R. L. Markwick ◽  
Carla F. Cervantes ◽  
Barrett L. Abel ◽  
Elizabeth A. Komives ◽  
Martin Blackledge ◽  
...  
Keyword(s):  
Chemical Shifts ◽  
Conformational Space ◽  
Conformational Space Sampling

Conformational Landscape of N-Glycosylated Peptides Detecting Autoantibodies in Multiple Sclerosis, Revealed by Hamiltonian Replica Exchange

2012 ◽  
Vol 116 (18) ◽  
pp. 5458-5467 ◽  
Author(s):  
Carlo Guardiani ◽  
Giorgio F. Signorini ◽  
Roberto Livi ◽  
Anna Maria Papini ◽  
Piero Procacci
Keyword(s):  
Multiple Sclerosis ◽  
Replica Exchange ◽  
Hamiltonian Replica Exchange ◽  
Conformational Landscape

scholarly journals The dissociation mechanism of processive cellulases

2019 ◽  
Vol 116 (46) ◽  
pp. 23061-23067 ◽  
Author(s):  
Josh V. Vermaas ◽  
Riin Kont ◽  
Gregg T. Beckham ◽  
Michael F. Crowley ◽  
Mikael Gudmundsson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Mechanisms ◽  
Soluble Sugars ◽  
Dissociation Rate ◽  
Replica Exchange ◽  
Wild Type ◽  
Replica Exchange Molecular Dynamics ◽  
Hamiltonian Replica Exchange ◽  
Biochemical Measurements ◽  
Rate Limiting

Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many sugar molecules in a processive manner without dissociating from the substrate. Within the complete processive cycle of CBHs, dissociation from the cellulose substrate is rate limiting, but the molecular mechanism of this step is unknown. Here, we present a direct comparison of potential molecular mechanisms for dissociation via Hamiltonian replica exchange molecular dynamics of the model fungal CBH, Trichoderma reesei Cel7A. Computational rate estimates indicate that stepwise cellulose dethreading from the binding tunnel is 4 orders of magnitude faster than a clamshell mechanism, in which the substrate-enclosing loops open and release the substrate without reversing. We also present the crystal structure of a disulfide variant that covalently links substrate-enclosing loops on either side of the substrate-binding tunnel, which constitutes a CBH that can only dissociate via stepwise dethreading. Biochemical measurements indicate that this variant has a dissociation rate constant essentially equivalent to the wild type, implying that dethreading is likely the predominant mechanism for dissociation.

UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations

2020 ◽  
Author(s):  
Paweł Krupa ◽  
Agnieszka S Karczyńska ◽  
Magdalena A Mozolewska ◽  
Adam Liwo ◽  
Cezary Czaplewski
Keyword(s):  
Protein Complexes ◽  
Md Simulations ◽  
Protein Docking ◽  
Conformational Space ◽  
Coarse Grained ◽  
Supplementary Information ◽  
Replica Exchange ◽  
Variable Degree ◽  
Single Chain ◽  
Simulation Speed

Abstract Motivation The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. Although there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide–protein and protein–protein docking is more challenging. In this work, we utilized multiplexed replica-exchange molecular dynamics (MREMD) simulations with the physics-based heavily coarse-grained UNRES model, which provides more than a 1000-fold simulation speed-up compared with all-atom approaches to predict structures of protein complexes. Results We present a new protein–protein and peptide–protein docking functionality of the UNRES package, which includes a variable degree of conformational flexibility. UNRES-Dock protocol was tested on a set of 55 complexes with size from 43 to 587 amino-acid residues, showing that structures of the complexes can be predicted with good quality, if the sampling of the conformational space is sufficient, especially for flexible peptide–protein systems. The developed automatized protocol has been implemented in the standalone UNRES package and in the UNRES server. Availability and implementation UNRES server: http://unres-server.chem.ug.edu.pl; UNRES package and data used in testing of UNRES-Dock: http://unres.pl. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Influence of Calcium Binding on Conformations and Motions of Anionic Polyamino Acids. Effect of Side Chain Length

Polymers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1279
Author(s):  
Dmitry Tolmachev ◽  
Natalia Lukasheva ◽  
George Mamistvalov ◽  
Mikko Karttunen
Keyword(s):  
Amino Acids ◽  
Chain Length ◽  
Calcium Binding ◽  
Md Simulations ◽  
Side Chain ◽  
Replica Exchange ◽  
Side Chain Length ◽  
Hamiltonian Replica Exchange ◽  
Cacl2 Concentration ◽  
Chain Lengths

Investigation of the effect of CaCl2 salt on conformations of two anionic poly(amino acids) with different side chain lengths, poly-(α-l glutamic acid) (PGA) and poly-(α-l aspartic acid) (PASA), was performed by atomistic molecular dynamics (MD) simulations. The simulations were performed using both unbiased MD and the Hamiltonian replica exchange (HRE) method. The results show that at low CaCl2 concentration adsorption of Ca2+ ions lead to a significant chain size reduction for both PGA and PASA. With the increase in concentration, the chains sizes partially recover due to electrostatic repulsion between the adsorbed Ca2+ ions. Here, the side chain length becomes important. Due to the longer side chain and its ability to distance the charged groups with adsorbed ions from both each other and the backbone, PGA remains longer in the collapsed state as the CaCl2 concentration is increased. The analysis of the distribution of the mineral ions suggests that both poly(amino acids) should induce the formation of mineral with the same structure of the crystal cell.

Sign in / Sign up

Export Citation Format

Share Document