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 Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

scholarly journals From deep TLS validation to ensembles of atomic models built from elemental motions

2015 ◽  
Author(s):  
Alexandre Urzhumtsev ◽  
Pavel Afonine ◽  
Andrew H Van Benschoten ◽  
James Fraser ◽  
Paul D Adams
Keyword(s):  
Rigid Body ◽  
Diffraction Data ◽  
Harmonic Vibration ◽  
Mathematical Framework ◽  
Matrix Elements ◽  
Computational Tools ◽  
X Ray ◽  
Structural Ensembles ◽  
The Matrix ◽  
Rigid Body Motions

The widely used Translation Libration Screw (TLS) approximation describes concerted motions of atomic groups in X-ray refinement. TLS refinement often provides a better interpretation of diffraction data and the resulting rigid body motions may subsequently be assigned biochemical significance. In TLS refinement, three matrices (T, L and S) describe harmonic vibration, libration and their correlation. Because these matrices describe specific motions, they impose a number of conditions on their elements. Ignoring these conditions while refining the matrix elements may result in matrices that cannot be interpreted in terms of physically realistic motions. We describe a mathematical framework and the computational tools to analyze refined TLS matrices through their decomposition into descriptors of underlying motions. This allows for straightforward validation and identification of implausible TLS parameters. An algorithm for the generation of structural ensembles that are consistent with given TLS parameters, implemented as a part of the Phenix project, is also described.

Kinematics Meets Crystallography: The Concept of a Motion Space

2014 ◽  
Author(s):  
Gregory S. Chirikjian
Keyword(s):  
Rigid Body ◽  
Molecular Structures ◽  
New Drugs ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Rigid Body Motions ◽  
Diffraction Patterns

In this paper, it is shown how rigid-body kinematics can be used to assist in determining the atomic structure of proteins and nucleic acids when using x-ray crystallography, which is a powerful method for structure determination. The importance of determining molecular structures for understanding biological processes and for the design of new drugs is well known. Phasing is a necessary step in determining the three-dimensional structure of molecules from x-ray diffraction patterns. A computational approach called molecular replacement (MR) is a well-established method for phasing of x-ray diffraction patterns for crystals composed of biological macromolecules. In MR, a search is performed over positions and orientations of a known biomolecular structure within a model of the crystallographic asymmetric unit, or, equivalently, multiple symmetry-related molecules in the crystallographic unit cell. Unlike the discrete space groups known to crystallographers and the continuous rigid-body motions known to kinematicians, the set of motions over which molecular replacement searches are performed does not form a group. Rather, it is a coset space of the group of continuous rigid-body motions, SE(3), with respect to the crystallographic space group of the crystal, which is a discrete sub-group of SE(3). Properties of these ‘motion spaces’ (which are compact manifolds) are investigated here.

scholarly journals Spontaneous self-assembly and structure of perfluoroalkylalkane surfactant hemimicelles by molecular dynamics simulations

2019 ◽  
Vol 116 (30) ◽  
pp. 14868-14873 ◽  
Author(s):  
Gonçalo M. C. Silva ◽  
Pedro Morgado ◽  
Pedro Lourenço ◽  
Michel Goldmann ◽  
Eduardo J. M. Filipe
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Md Simulation ◽  
Grazing Incidence ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Spontaneous Formation ◽  
Rational Explanation ◽  
Dynamics Simulations

Fully atomistic molecular-dynamics (MD) simulations of perfluoroalkylalkane molecules at the surface of water show the spontaneous formation of aggregates whose size and topography closely resemble the experimentally observed hemimicelles for this system. Furthermore, the grazing incidence X-ray diffraction (GIXD) pattern calculated from the simulation trajectories reproduces the experimental GIXD spectra previously obtained, fully validating the MD simulation results. The detailed analysis of the internal structure of the aggregates obtained by the MD simulations supports a definite rational explanation for the spontaneous formation, stability, size, and shape of perfluoroalkylalkane hemimicelles at the surface of water.

Kinematics Meets Crystallography: The Concept of a Motion Space1

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Gregory S. Chirikjian
Keyword(s):  
Rigid Body ◽  
Discrete Subgroup ◽  
Molecular Structures ◽  
New Drugs ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
Rigid Body Motions ◽  
Diffraction Patterns

In this paper, it is shown how rigid-body kinematics can be used to assist in determining the atomic structure of proteins and nucleic acids when using x-ray crystallography, which is a powerful method for structure determination. The importance of determining molecular structures for understanding biological processes and for the design of new drugs is well known. Phasing is a necessary step in determining the three-dimensional structure of molecules from x-ray diffraction patterns. A computational approach called molecular replacement (MR) is a well-established method for phasing of x-ray diffraction patterns for crystals composed of biological macromolecules. In MR, a search is performed over positions and orientations of a known biomolecular structure within a model of the crystallographic asymmetric unit, or, equivalently, multiple symmetry-related molecules in the crystallographic unit cell. Unlike the discrete space groups known to crystallographers and the continuous rigid-body motions known to kinematicians, the set of motions over which MR searches are performed does not form a group. Rather, it is a coset space of the group of continuous rigid-body motions, SE(3), with respect to the crystallographic space group of the crystal, which is a discrete subgroup of SE(3). Properties of these “motion spaces” (which are compact manifolds) are investigated here.

Effect of water on the structure of a prototype ionic liquid

2016 ◽  
Vol 18 (34) ◽  
pp. 23474-23481 ◽  
Author(s):  
Oleg Borodin ◽  
David L. Price ◽  
Bachir Aoun ◽  
Miguel A. González ◽  
Justin B. Hooper ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Md Simulations ◽  
High Energy ◽  
X Ray Diffraction ◽  
X Ray ◽  
Effect Of Water ◽  
Influence Of Water

The influence of water on the structure of a prototype ionic liquid (IL) 1-octyl-3-methylimidazolium tetrafluoroborate (C8mimBF4) is examined in the IL-rich regime using high-energy X-ray diffraction (HEXRD) and molecular dynamics (MD) simulations.

scholarly journals Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

2017 ◽  
Vol 13 ◽  
pp. 714-719 ◽  
Author(s):  
Franca Castiglione ◽  
Fabio Ganazzoli ◽  
Luciana Malpezzi ◽  
Andrea Mele ◽  
Walter Panzeri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Inclusion Complexes ◽  
Water Solution ◽  
Md Simulations ◽  
Conformational Transitions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Fused Ring ◽  
Explicit Water

Tricyclic fused-ring cyclobenzaprine (1) and amitriptyline (2) form 1:1 inclusion complexes with β-cyclodextrin (β-CD) in the solid state and in water solution. Rotating frame NOE experiments (ROESY) showed the same geometry of inclusion for both 1/β-CD and 2/β-CD complexes, with the aromatic ring system entering the cavity from the large rim of the cyclodextrin and the alkylammonium chain protruding out of the cavity and facing the secondary OH rim. These features matched those found in the molecular dynamics (MD) simulations in solution and in the solid state from single-crystal X-ray diffraction of 1/β-CD and 2/β-CD complexes. The latter complex was found in a single conformation in the solid state, whilst the MD simulations in explicit water reproduced the conformational transitions observed experimentally for the free molecule.

An MD Simulation of Concentrated Aqueous Solutions of Caesium Iodide

1991 ◽  
Vol 46 (12) ◽  
pp. 1083-1094 ◽  
Author(s):  
Y. Tamura ◽  
H. Ohtaki ◽  
I. Okada
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solutions ◽  
Diffraction Data ◽  
Md Simulation ◽  
Ion Pairs ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrated Ions ◽  
Effects Of Temperature ◽  
Dynamics Simulations

Abstract Molecular dynamics simulations of concentrated aqueous Csl solutions have been performed for Csl: H2O = 1:20 (2.78 molal) at 298 K and 341 K and 1:10 (5.56 molal) at 349 K. Effects of temperature and concentration on the structures of the hydrated ions, the ion pairs, and ionic aggregates are discussed by comparing the results with X-ray diffraction data obtained under similar conditions [1]

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