scholarly journals Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study

2012 ◽  
Vol 8 (9) ◽  
pp. e1002682 ◽  
Author(s):  
Iskra Staneva ◽  
Yongqi Huang ◽  
Zhirong Liu ◽  
Stefan Wallin
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Protein A ◽  
Specific Protein ◽  
Intrinsically Disordered ◽  
Disordered Peptides

scholarly journals Molecular Dynamics Ensemble Refinement of Intrinsically Disordered Peptides According to Deconvoluted Spectra from Circular Dichroism

2020 ◽  
Vol 118 (7) ◽  
pp. 1665-1678 ◽  
Author(s):  
Jacob C. Ezerski ◽  
Pengzhi Zhang ◽  
Nathaniel C. Jennings ◽  
M. Neal Waxham ◽  
Margaret S. Cheung
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Intrinsically Disordered ◽  
Disordered Peptides ◽  
Circular Dichroïsm

Numerical Methods for the Kinetic Theory of Fluids

2018 ◽  
Author(s):  
Sauro Succi
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Numerical Methods ◽  
Kinetic Theory ◽  
Computational Efficiency ◽  
Lattice Boltzmann ◽  
Direct Simulation Monte Carlo ◽  
Particle Methods ◽  
Direct Simulation ◽  
Simulation Monte Carlo

This chapter provides a bird’s eye view of the main numerical particle methods used in the kinetic theory of fluids, the main purpose being of locating Lattice Boltzmann in the broader context of computational kinetic theory. The leading numerical methods for dense and rarified fluids are Molecular Dynamics (MD) and Direct Simulation Monte Carlo (DSMC), respectively. These methods date of the mid 50s and 60s, respectively, and, ever since, they have undergone a series of impressive developments and refinements which have turned them in major tools of investigation, discovery and design. However, they are both very demanding on computational grounds, which motivates a ceaseless demand for new and improved variants aimed at enhancing their computational efficiency without losing physical fidelity and vice versa, enhance their physical fidelity without compromising computational viability.

scholarly journals Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

2019 ◽  
Vol 116 (41) ◽  
pp. 20446-20452 ◽  
Author(s):  
Utsab R. Shrestha ◽  
Puneet Juneja ◽  
Qiu Zhang ◽  
Viswanathan Gurumoorthy ◽  
Jose M. Borreguero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Intrinsically Disordered Protein ◽  
Physical Models ◽  
Dynamics Simulation ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Eukaryotic Proteomes ◽  
Heterogeneous Ensemble

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.

Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble

1996 ◽  
Vol 259 (3-4) ◽  
pp. 321-330 ◽  
Author(s):  
Ulrich H.E. Hansmann ◽  
Yuko Okamoto ◽  
Frank Eisenmenger
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Monte Carlo Simulations

scholarly journals Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

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