Collective motions of myosin head derived from backbone molecular dynamics and combination with X-ray solution scattering data

2001 ◽  
Vol 22 (16) ◽  
pp. 1983-1994 ◽  
Author(s):  
Junichi Higo ◽  
Yasunobu Sugimoto ◽  
Katsuzo Wakabayashi ◽  
Haruki Nakamura
Keyword(s):  
Molecular Dynamics ◽  
Myosin Head ◽  
Scattering Data ◽  
X Ray ◽  
Collective Motions

scholarly journals Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

2020 ◽  
Vol 16 (4) ◽  
pp. e1007870 ◽  
Author(s):  
Andreas Haahr Larsen ◽  
Yong Wang ◽  
Sandro Bottaro ◽  
Sergei Grudinin ◽  
Lise Arleth ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Small Angle ◽  
Scattering Data ◽  
X Ray ◽  
Dynamics Simulations

scholarly journals Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

2019 ◽  
Author(s):  
David C. Wych ◽  
James S. Fraser ◽  
David L. Mobley ◽  
Michael E. Wall
Keyword(s):  
Molecular Dynamics ◽  
Rigid Body ◽  
Diffraction Data ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atom Pairs ◽  
Collective Motions ◽  
Rigid Body Motions ◽  
Insight Into

AbstractTo gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2×2×2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquid-like motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intra-protein) and between different protein molecules (inter-protein). The inter-protein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intra-protein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall our findings increase our understanding of the connection between molecular motions and diffraction data, and therefore advance efforts to extract information about functionally important motions from crystallography experiments.

scholarly journals Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data

2020 ◽  
Vol 152 (20) ◽  
pp. 204115 ◽  
Author(s):  
Darren J. Hsu ◽  
Denis Leshchev ◽  
Irina Kosheleva ◽  
Kevin L. Kohlstedt ◽  
Lin X. Chen
Keyword(s):  
Molecular Dynamics ◽  
Shell Structure ◽  
Solvation Shell ◽  
Scattering Data ◽  
X Ray

scholarly journals Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments

Membranes ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 507
Author(s):  
Nebojša Zec ◽  
Gaetano Mangiapia ◽  
Alex C. Hendry ◽  
Robert Barker ◽  
Alexandros Koutsioubas ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Scattering Length ◽  
Md Simulations ◽  
Real Space ◽  
Scattering Data ◽  
Phospholipid Membrane ◽  
Density Profiles ◽  
X Ray ◽  
Angle Scattering ◽  
Scattering Measurements

We showcase the combination of experimental neutron scattering data and molecular dynamics (MD) simulations for exemplary phospholipid membrane systems. Neutron and X-ray reflectometry and small-angle scattering measurements are determined by the scattering length density profile in real space, but it is not usually possible to retrieve this profile unambiguously from the data alone. MD simulations predict these density profiles, but they require experimental control. Both issues can be addressed simultaneously by cross-validating scattering data and MD results. The strengths and weaknesses of each technique are discussed in detail with the aim of optimizing the opportunities provided by this combination.

scholarly journals Interpretation of Solution X-Ray Scattering Data by Molecular Dynamics

2015 ◽  
Vol 108 (2) ◽  
pp. 191a
Author(s):  
Po-chia Chen ◽  
Levin Brinkmann ◽  
Jochen S. Hub
Keyword(s):  
Molecular Dynamics ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Molecular Dynamics Simulation of Atactic Polystyrene. 1. Comparison with X-ray Scattering Data

1994 ◽  
Vol 27 (13) ◽  
pp. 3566-3574 ◽  
Author(s):  
M. Mondello ◽  
Hyung-Jin Yang ◽  
Hidemine Furuya ◽  
Ryong-Joon Roe
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Atactic Polystyrene ◽  
Ray Scattering

scholarly journals Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

2019 ◽  
Author(s):  
Andreas Haahr Larsen ◽  
Yong Wang ◽  
Sandro Bottaro ◽  
Sergei Grudinin ◽  
Lise Arleth ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Small Angle ◽  
Coarse Grained ◽  
Scattering Data ◽  
General Strategy ◽  
X Ray ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations

AbstractMany proteins contain multiple folded domains separated by flexible linkers, and the ability to describe the structure and conformational heterogeneity of such flexible systems pushes the limits of structural biology. Using the three-domain protein TIA-1 as an example, we here combine coarse-grained molecular dynamics simulations with previously measured small-angle scattering data to study the conformation of TIA-1 in solution. We show that while the coarse-grained potential (Martini) in itself leads to too compact conformations, increasing the strength of protein-water interactions results in ensembles that are in very good agreement with experiments. We show how these ensembles can be refined further using a Bayesian/Maximum Entropy approach, and examine the robustness to errors in the energy function. In particular we find that as long as the initial simulation is relatively good, reweighting against experiments is very robust. We also study the relative information in X-ray and neutron scattering experiments and find that refining against the SAXS experiments leads to improvement in the SANS data. Our results suggest a general strategy for studying the conformation of multi-domain proteins in solution that combines coarse-grained simulations with small-angle X-ray scattering data that are generally most easy to obtain. These results may in turn be used to design further small-angle neutron scattering experiments that exploit contrast variation through 1H/2H isotope substitutions.

Sign in / Sign up

Export Citation Format

Share Document