MOLSIM: A modular molecular simulation software

Reščič, Jurij; Linse, Per

doi:10.1002/jcc.23919

Cited by 58 publications

(24 citation statements)

References 49 publications

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“…It is estimated from the deviation among the means of the subdivisions of the total number of MC passes according to:σ2(〈x〉)=1ns(ns−1)·∑s=1ns〈x〉s−〈x〉2, where 〈x〉s is the average of quantity x from one subdivision, 〈x〉 the average of x from the total simulation, and ns the number of subdivisions used which here is 10. The simulations were performed by using the integrated Monte Carlo/molecular dynamics/Brownian dynamics simulation package Molsim [37].…”

Section: Materials and Methodsmentioning

confidence: 99%

Dynamical Oligomerisation of Histidine Rich Intrinsically Disordered Proteins Is Regulated through Zinc-Histidine Interactions

et al. 2019

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Intrinsically disordered proteins (IDPs) can form functional oligomers and in some cases, insoluble disease related aggregates. It is therefore vital to understand processes and mechanisms that control pathway distribution. Divalent cations including Zn2+ can initiate IDP oligomerisation through the interaction with histidine residues but the mechanisms of doing so are far from understood. Here we apply a multi-disciplinary approach using small angle X-ray scattering, nuclear magnetic resonance spectroscopy, calorimetry and computations to show that that saliva protein Histatin 5 forms highly dynamic oligomers in the presence of Zn2+. The process is critically dependent upon interaction between Zn2+ ions and distinct histidine rich binding motifs which allows for thermodynamic switching between states. We propose a molecular mechanism of oligomerisation, which may be generally applicable to other histidine rich IDPs. Finally, as Histatin 5 is an important saliva component, we suggest that Zn2+ induced oligomerisation may be crucial for maintaining saliva homeostasis.

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Section: Materials and Methodsmentioning

confidence: 99%

Dynamical Oligomerisation of Histidine Rich Intrinsically Disordered Proteins Is Regulated through Zinc-Histidine Interactions

et al. 2019

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“…The equilibrium properties of the coarse-grained Monte Carlo simulations were evaluated using the Metropolis algorithm. For this purpose, the integrated Monte Carlo/molecular dynamics/Brownian dynamics simulation package Molsim [52] was used. The simulations were performed in the canonical ensemble.…”

Section: Monte Carlo Parametersmentioning

confidence: 99%

Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo Simulations

et al. 2020

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Gluten protein crosslinking is a predetermined process where specific intra- and intermolecular disulfide bonds differ depending on the protein and cysteine motif. In this article, all-atom Monte Carlo simulations were used to understand the formation of disulfide bonds in gliadins and low molecular weight glutenin subunits (LMW-GS). The two intrinsically disordered proteins appeared to contain mostly turns and loops and showed “self-avoiding walk” behavior in water. Cysteine residues involved in intramolecular disulfide bonds were located next to hydrophobic peptide sections in the primary sequence. Hydrophobicity of neighboring peptide sections, synthesis chronology, and amino acid chain flexibility were identified as important factors in securing the specificity of intramolecular disulfide bonds formed directly after synthesis. The two LMW-GS cysteine residues that form intermolecular disulfide bonds were positioned next to peptide sections of lower hydrophobicity, and these cysteine residues are more exposed to the cytosolic conditions, which influence the crosslinking behavior. In addition, coarse-grained Monte Carlo simulations revealed that the protein folding is independent of ionic strength. The potential molecular behavior associated with disulfide bonds, as reported here, increases the biological understanding of seed storage protein function and provides opportunities to tailor their functional properties for different applications.

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“…The simulations are performed using the integrated Monte Carlo/molecular dynamics/Brownian dynamics simulation package Molsim. 39 Owing to (i) the long-range electrostatic attraction between the polyion and the arm section of the capsomers and (ii) the short-range attractive interaction among the lateral sides of the capsomers, complexes consisting of capsomers and polyions are formed. Their time-evolution was followed using the reduced time t* = t(ε rep,cb /m cb σ cb 2 ) 1/2 where t is the simulation time and m cb mass of the repulsive beads belonging to the capsomer truncated part.…”

Section: B Simulation Detailsmentioning

confidence: 99%

Assembled viral-like nanoparticles from elastic capsomers and polyion

Angelescu

2017

The Journal of Chemical Physics

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Molecular dynamics simulations are carried out on a coarse-grained model to describe the polyion driven co-assembly of elastic capsomers as viral-like aggregates. The kinetics and structural properties of the complexes are examined using cationic capsomers, an anionic polyion, both modelled using beads connected by springs, and counterions neutralizing separately the two charged species. Polyion overcharging the capsid is encapsulated owing to combined effects of the capsomer-capsomer short-range interactions, the polyion ability to follow a Hamiltonian path, and Donnan equilibrium. Conditions leading to a high yield of viral-like nanoparticles are found, and the simulations demonstrate that the capsomer elasticity provides mechanisms that improve the reliability toward correctly formed capsids. These mechanisms are related to a highly irregular capsomer cluster growth followed by the appearance of two stable capsomer clusters with the polyion acting as a tether between them. Elevated capsomeric flexibility provides an additional pathway to anneal the kinetically trapped structures by the ejection of a capsomeric monomer from a malformed complex followed by a rebinding step to form a correct capsid.

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MOLSIM: A modular molecular simulation software

Cited by 58 publications

References 49 publications

Dynamical Oligomerisation of Histidine Rich Intrinsically Disordered Proteins Is Regulated through Zinc-Histidine Interactions

Dynamical Oligomerisation of Histidine Rich Intrinsically Disordered Proteins Is Regulated through Zinc-Histidine Interactions

Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo Simulations

Assembled viral-like nanoparticles from elastic capsomers and polyion

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