scholarly journals Internal Protein Motions in Molecular Dynamics Simulations of Bragg and Diffuse X-ray Scattering

2017 ◽  
Author(s):  
Michael E. Wall
Keyword(s):  
Molecular Dynamics ◽  
Cell Model ◽  
Md Simulations ◽  
Unit Cell ◽  
X Ray ◽  
Protein Motions ◽  
X Ray Scattering ◽  
Unit Cells ◽  
Packing Interactions ◽  
Ray Scattering

SynopsisA molecular dynamics simulation of diffuse X-ray scattering from staphylococcal nuclease crystals is greatly improved when the unit cell model is expanded to a 2×2×2 layout of eight unit cells. The dynamics are dominated by internal protein motions rather than rigid packing interactions.AbstractMolecular dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that, compared to a single periodic unit cell model, the accuracy in simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell, consisting of a 2×2×2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a longer duration simulation might be required to achieve convergence of the diffuse scattering calculation using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a small fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics can be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

scholarly journals Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

IUCrJ ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. 172-181 ◽  
Author(s):  
Michael E. Wall
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Diffuse Scattering ◽  
Md Simulations ◽  
Unit Cell ◽  
Protein Crystal ◽  
X Ray ◽  
Protein Motions ◽  
X Ray Scattering ◽  
Ray Scattering

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

The Effect of Thermal Vibrations on the Intensities of the Diffracted Beams

1997 ◽  
Author(s):  
Philip Coppens
Keyword(s):  
Electron Density ◽  
Normal Modes ◽  
Unit Cell ◽  
Thermal Motion ◽  
X Ray ◽  
X Ray Scattering ◽  
Point Motion ◽  
Unit Cells ◽  
Thermal Vibrations ◽  
Ray Scattering

The atoms in a crystal are vibrating with amplitudes determined by the force constants of the crystal’s normal modes. This motion can never be frozen out because of the persistence of zero-point motion, and it has important consequences for the scattering intensities. Since X-ray scattering (and, to a lesser extent, neutron scattering) is a very fast process, taking place on a time scale of 10−18 s, the photon-matter interaction time is much shorter than the period of a lattice vibration, which is of the order Thus, the recorded X-ray scattering pattern is the sum over the scattering of a large number of 1/v, or ≈10−13s. instantaneous states of the crystal. To an extremely good approximation, the scattering averaged over the instantaneous distributions is equivalent to the scattering of the time-averaged distribution of the scattering matter (Stewart and Feil 1980). The structure factor expression for coherent elastic Bragg scattering of X-rays may therefore be written in terms 〈ρ(r)〉, of the thermally averaged electron density: . . . F(H)=∫unit cell〈ρ(r)〉 exp (2πi H ·r) dr (2.1) . . . The smearing of the electron density due to thermal vibrations reduces the intensity of the diffracted beams, except in the forward |S| = 0 direction, for which all electrons scatter in phase, independent of their distribution. The reduction of the intensity of the Bragg peaks can be understood in terms of the diffraction pattern of a more diffuse electron distribution being more compact, due to the inverse relation between crystal and scattering space, discussed in chapter 1. The reduction in intensity due to thermal motion is accompanied by an increase in the incoherent elastic scattering, ensuring conservation of energy. In this respect, thermal motion is much like disorder, with the Bragg intensities representing the average distribution, and the deviations from the average appearing as a continuous, though not uniform, background, generally referred to as thermal diffuse scattering or TDS. A crystal with n atoms per unit cell has 3nN degrees of freedom, N being the number of unit cells in the crystal.

X-ray and molecular dynamics studies of butylammonium butanoate–water binary mixtures

2017 ◽  
Vol 19 (3) ◽  
pp. 1975-1981 ◽  
Author(s):  
Umme Salma ◽  
Marianna Usula ◽  
Ruggero Caminiti ◽  
Lorenzo Gontrani ◽  
Natalia V. Plechkova ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Binary Mixtures ◽  
Md Simulations ◽  
Wide Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

The nanostructural organisation of mixtures of the ionic liquid (butylammonium butanoate) and water at several mole fractions of water has been investigated using small and wide angle X-ray scattering (S-WAXS) and molecular dynamics (MD) simulations.

Liquid Structure of 1-Ethyl-3-methylimidazolium Alkyl Sulfates by X-ray Scattering and Molecular Dynamics

2012 ◽  
Vol 116 (45) ◽  
pp. 13448-13458 ◽  
Author(s):  
Marina Macchiagodena ◽  
Fabio Ramondo ◽  
Alessandro Triolo ◽  
Lorenzo Gontrani ◽  
Ruggero Caminiti
Keyword(s):  
Molecular Dynamics ◽  
Liquid Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Alkyl Sulfates ◽  
Ray Scattering

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

Liquid Structure of 1-Propanol by Molecular Dynamics Simulations and X-Ray Scattering

2004 ◽  
Vol 33 (6/7) ◽  
pp. 797-809 ◽  
Author(s):  
Isao Akiyama ◽  
Masaya Ogawa ◽  
Keiichi Takase ◽  
Toshiyuki Takamuku ◽  
Toshio Yamaguchi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Liquid Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Dynamics Simulations ◽  
Ray Scattering

scholarly journals Combining solution wide-angle X-ray scattering and crystallography: determination of molecular envelope and heavy-atom sites

2009 ◽  
Vol 42 (2) ◽  
pp. 259-264 ◽  
Author(s):  
Xinguo Hong ◽  
Quan Hao
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Unit Cell ◽  
Wide Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Molecular Envelope ◽  
Waxs Data ◽  
Ray Scattering

Solving the phase problem remains central to crystallographic structure determination. A six-dimensional search method of molecular replacement (FSEARCH) can be used to locate a low-resolution molecular envelope determined from small-angle X-ray scattering (SAXS) within the crystallographic unit cell. This method has now been applied using the higher-resolution envelope provided by combining SAXS and WAXS (wide-angle X-ray scattering) data. The method was tested on horse hemoglobin, using the most probable model selected from a set of a dozen bead models constructed from SAXS/WAXS data using the programGASBORat 5 Å resolution (qmax= 1.25 Å−1) to phase a set of single-crystal diffraction data. It was found that inclusion of WAXS data is essential for correctly locating the molecular envelope in the crystal unit cell, as well as for locating heavy-atom sites. An anomalous difference map was calculated using phases out to 8 Å resolution from the correctly positioned envelope; four distinct peaks at the 3.2σ level were identified, which agree well with the four iron sites of the known structure (Protein Data Bank code 1ns9). In contrast, no peaks could be found close to the iron sites if the molecular envelope was constructed using the data from SAXS alone (qmax= 0.25 Å−1). The initial phases can be used as a starting point for a variety of phase-extension techniques, successful application of which will result in complete phasing of a crystallographic data set and determination of the internal structure of a macromolecule to atomic resolution. It is anticipated that the combination ofFSEARCHand WAXS techniques will facilitate the initial structure determination of proteins and provide a good foundation for further structure refinement.

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