Calibrated Langevin-dynamics simulations of intrinsically disordered proteins.

  title={Calibrated Langevin-dynamics simulations of intrinsically disordered proteins.},
  author={W. Wendell Smith and Po-yi Ho and Corey S. O’Hern},
  journal={Physical review. E, Statistical, nonlinear, and soft matter physics},
  volume={90 4},
We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the interresidue separations for 36 pairs… 
Concentrated Solutions of Single-Chain Nanoparticles: A Simple Model for Intrinsically Disordered Proteins under Crowding Conditions.
The results for SCNPs--a model system free of specific interactions--propose a general scenario for the effect of steric crowding on IDPs: collapse from sparse conformations at high dilution to crumpled globular conformations in cell environments.
Unraveling molecular interactions in a phase-separating protein by atomistic simulations
This work exploited explicit-solvent atomistic simulations to disentangle the molecular interactions governing the phase behaviour of the N-terminal disordered region of DEAD-box helicase 4 (NDDX4), which is a well-established model for phase separation in vitro and in vivo.
Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment
Experimental studies of binding mechanisms of IDPs using NMR spectroscopy and transient kinetic techniques are reviewed, as well as the underlying theoretical concepts and numerical methods that can be applied to describe these interactions at the atomic level.
Understanding the physical basis for the side‐chain conformational preferences of methionine
This work identifies minimal additions to the hard‐sphere dipeptide model necessary to quantitatively predict P(χ3) of Met, and its near isosteres norleucine (Nle) and selenomethionine (Mse), and finds that adding weak attractive interactions between hydrogen atoms to the model is sufficient to achieve predictions that closely match the observed P(⩽3) distributions.
Effect of chain stiffness on the structure of single-chain polymer nanoparticles.
The conformational properties of SCNPs as a function of the bending stiffness of their linear polymer precursors are investigated by means of computer simulations and a new strategy to tune the global structure ofSCNPs is proposed.
Using physical features of protein core packing to distinguish real proteins from decoys
A feed‐forward neural network is developed, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence.
Understanding the dynamics of monomeric, dimeric, and tetrameric α‐synuclein structures in water
A comparative analysis of monomeric, dimeric, and tetrameric αS models reveals pronounced differences in their structure and stability, emphasizing the importance of small oligomers, particularly dimers, in the process of misfolding.
A novel fluorescent multi-domain protein construct reveals the individual steps of the unfoldase action of Hsp70
A reporter chaperone substrate, MLucV, composed of a stress-labile luciferase core, flanked by stress-resistant fluorescent mTFP and Venus domains, which upon denaturation formed a discrete stable population of small aggregates, unambiguously excluded binding and preventing aggregation from the non-equilibirum mechanism by which Hsp70 converts stable aggregates into metastable native proteins.
Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones
These results are in quantitative agreement with recent single-molecule FRET experiments and highlight the stark non-equilibrium nature of the process, showing that Hsp70s are optimized to effectively convert chemical energy into mechanical work close to physiological conditions.
Biomolecular response to hour-long ultralow field microwave radiation: An effective coarse-grained model simulation.
The model is applied to describe a biomolecule, hen egg white lysozyme, and simulate its structural evolution under ultralow strength electromagnetic radiation and believes that it harnesses the potential in studying the structural dynamics of any biopolymer under external perturbation over an extended time scale.


Computer Simulation of Liquids
Introduction Statistical mechanics Molecular dynamics Monte Carlo methods Some tricks of the trade How to analyse the results Advanced simulation techniques Non-equilibrium molecular dynamics
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In supernova (SN) spectroscopy relatively little attention has been given to the properties of optically thick spectral lines in epochs following the photosphere’s recession. Most treatments and
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The data matrix was taken from Clark (2011) analyses of Fruitachampsa. Clark (2011) developed upon character’s taken mostly from Pol and Gasparini (2009) work. Pol and Gasparini (2009) matrix was
The Biophysical Journal
Other Professional Positions and Major Visiting Appointments: 1983–1984 Laboratory Instructor in Electrical Engineering, Yale University, New Haven, CT 1984–1986 Electrical Engineer, Hewlett-Packard
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