Erratum: “Equilibrium simulation of trp-cage in the presence of protein crowders” [J. Chem. Phys. 143, 175102 (2015)]

Bille, Anna; Linse, Björn; Mohanty, Sandipan; Irbäck, Anders

doi:10.1063/1.4943574

Cited by 3 publications

(4 citation statements)

References 1 publication

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“…[29][30][31][32][33][34] Recently, it was used by us to simulate the peptides trp-cage and GB1m3 in the presence of protein crowders. 8,26 Our simulations use the same fully atomistic representation of both the GB1m3 peptide and the crowder proteins. However, because of their high thermal stability, 24,25 the crowder proteins are modeled with a fixed backbone, and thus with side-chain rotations as their only internal degrees of freedom.…”

Section: B Biophysical Modelmentioning

confidence: 99%

“…A growing body of evidence indicates, however, that the effects of macromolecular crowding on properties such as protein stability cannot be explained in terms of steric repulsion alone. [1][2][3] To understand the role of other interactions, in recent years, there have been increasing efforts to perform computer simulations with realistic crowder molecules, [4][5][6][7][8][9][10][11] rather than hard-sphere crowders. When analyzing these large systems, a major challenge lies in identifying the main states and dynamical modes, which may not be easily anticipated.…”

Section: Introductionmentioning

confidence: 99%

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Markov modeling of peptide folding in the presence of protein crowders

Nilsson

Mohanty

Irbäck

2018

The Journal of Chemical Physics

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We use Markov state models (MSMs) to analyze the dynamics of a β-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin inhibitor (BPTI) and GB1]. In these systems, at the temperature used, the peptide can be folded or unfolded and bound or unbound to crowder molecules. Four or five major freeenergy minima can be identified. To estimate the dominant MC relaxation times of the peptide, we build MSMs using a range of different time resolutions or lag times. We show that stable relaxation-time estimates can be obtained from the MSM eigenfunctions through fits to autocorrelation data. The eigenfunctions remain sufficiently accurate to permit stable relaxation-time estimation down to small lag times, at which point simple estimates based on the corresponding eigenvalues have large systematic uncertainties. The presence of the crowders have a stabilizing effect on the peptide, especially with BPTI crowders, which can be attributed to a reduced unfolding rate k u , while the folding rate k f is left largely unchanged.

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Section: B Biophysical Modelmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Markov modeling of peptide folding in the presence of protein crowders

Nilsson

Mohanty

Irbäck

2018

The Journal of Chemical Physics

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“…Several experimental 107‐109,129‐144 and computational studies 68,92,118,145‐169 have investigated the folding of Trp‐cage. The presence of intermediate metastable states has been observed computationally 151,170 and experimentally 131 .…”

Section: Resultsmentioning

confidence: 99%

An interoperable implementation of collective‐variable based enhanced sampling methods in extended phase space within the OpenMM package

et al. 2023

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Collective variable (CV)‐based enhanced sampling techniques are widely used today for accelerating barrier‐crossing events in molecular simulations. A class of these methods, which includes temperature accelerated molecular dynamics (TAMD)/driven‐adiabatic free energy dynamics (d‐AFED), unified free energy dynamics (UFED), and temperature accelerated sliced sampling (TASS), uses an extended variable formalism to achieve quick exploration of conformational space. These techniques are powerful, as they enhance the sampling of a large number of CVs simultaneously compared to other techniques. Extended variables are kept at a much higher temperature than the physical temperature by ensuring adiabatic separation between the extended and physical subsystems and employing rigorous thermostatting. In this work, we present a computational platform to perform extended phase space enhanced sampling simulations using the open‐source molecular dynamics engine OpenMM. The implementation allows users to have interoperability of sampling techniques, as well as employ state‐of‐the‐art thermostats and multiple time‐stepping. This work also presents protocols for determining the critical parameters and procedures for reconstructing high‐dimensional free energy surfaces. As a demonstration, we present simulation results on the high dimensional conformational landscapes of the alanine tripeptide in vacuo, tetra‐N‐methylglycine (tetra‐sarcosine) peptoid in implicit solvent, and the Trp‐cage mini protein in explicit water.

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“…Coarse-graining is a widely employed modelling strategy to reduce the degrees of freedom of many-body macromolecular systems as heteropolymers [9,17]. Moreover, the study of protein folding and aggregation, specially in crowded media [18], has also largely benefited from such approach [17]. In this vein, PHAST incorporates a configurable force field able to describe semi-flexible linear heteropolymers 1 [8,19,20,21] and general properties of protein-like structural phase transitions [10,11,12,13].…”

Section: Modelling Proteins and Polymersmentioning

confidence: 99%

PHAST: Protein-like heteropolymer analysis by statistical thermodynamics

Frigori

2017

Computer Physics Communications

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PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for proteins. The outcome data can be straightforwardly analyzed within its microcanonical Statistical Thermodynamics module, which allows for computing the entropy, caloric curve, specific heat and free energies. As a case study, we investigate the aggregation of heteropolymers bioinspired on Aβ 25−33 fragments and their cross-seeding with IAP P 20−29 isoforms. Excellent parallel scaling is observed, even under numerically difficult first-order like phase transitions, which are properly described by the built-in fully reconfigurable force fields. Still, the package is free and open source, this shall motivate users to readily adapt it to specific purposes. Nature of the problem: Nowadays powerful multicore processors (CPUs) and Graphical Processing Units (GPUs) became much popular and cost-effective, so enabling thermostatistical studies of complex molecular systems to be performed even in personal computers. PHAST provides not only an easily-reconfigurable parallel program for Monte Carlo simulations of linear heteropolymers, as coarse-grained models of proteins, but also permits the automatized microcanonical thermodynamic analysis of those systems. PROGRAM SUMMARYSolution method: PHAST has three main modules for complementary tasks as: to map any .pdb filesequence to its inner lexicon by using a configurable hydrophobic scale, while the main simulational module performs parallel Monte Carlo simulations in the multicanonical (MUCA) ensemble and, the analysis module which extracts microcanonical observables from MUCA weights.

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Erratum: “Equilibrium simulation of trp-cage in the presence of protein crowders” [J. Chem. Phys. 143, 175102 (2015)]

Cited by 3 publications

References 1 publication

Markov modeling of peptide folding in the presence of protein crowders

Markov modeling of peptide folding in the presence of protein crowders

An interoperable implementation of collective‐variable based enhanced sampling methods in extended phase space within the OpenMM package

PHAST: Protein-like heteropolymer analysis by statistical thermodynamics

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