Lattice Dynamics of a Protein Crystal

Meinhold, Lars; Merzel, Franci; Smith, Jeremy C.

doi:10.1103/physrevlett.99.138101

Cited by 50 publications

(49 citation statements)

References 31 publications

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“…Recently reported all-atom lattice-dynamical calculations for a crystalline protein, ribonuclease A, showed that the sound velocities, density of states, heat capacity (C V ) and thermal diffuse scattering are all consistent with available experimental data (55). C V was found to be proportional to T -1.68 for T < 35 K, significantly deviating from a Debye solid.…”

Section: Figure 4: Mean-square Fluctuations Of the Protein Side-chainsupporting

confidence: 65%

Structure and Dynamics of Biological Systems: Integration of Neutron Scattering with Computer Simulation

Smith

Krishnan

Petridis

et al. 2011

Dynamics of Soft Matter

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The combination of molecular dynamics simulation and neutron scattering techniques has emerged as a highly synergistic approach to elucidate the atomistic details of the structure, dynamics and functions of biological systems. Simulation models can be tested by calculating neutron scattering structure factors and comparing the results directly with experiments. If the scattering profiles agree the simulations can be used to provide a detailed decomposition and interpretation of the experiments, and if not, the models can be rationally adjusted. Comparison with neutron experiment can be made at the level of the scattering functions or, less directly, of structural and dynamical quantities derived from them. Here, we examine the combination of simulation and experiment in the interpretation of SANS and inelastic scattering experiments on the structure and dynamics of proteins and other biopolymers.2

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Section: Figure 4: Mean-square Fluctuations Of the Protein Side-chainsupporting

confidence: 65%

Structure and Dynamics of Biological Systems: Integration of Neutron Scattering with Computer Simulation

Smith

Krishnan

Petridis

et al. 2011

Dynamics of Soft Matter

Self Cite

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“…Those calculations included all proteins and waters in the unit cell, and were the first attempts to include crystal contact forces. However, there is some evidence that crystal contact forces are weak 32,46 and as we are interested in the intramolecular motions rather than the lattice phonons, we assume zero-crystal contact forces and calculate the net crystal response by summing the single-molecule response over the unit cell, accounting for the molecular rotations for the crystal symmetry group:…”

Section: Methodsmentioning

confidence: 99%

Optical measurements of long-range protein vibrations

et al. 2014

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Protein biological function depends on structural flexibility and change. From cellular communication through membrane ion channels to oxygen uptake and delivery by haemoglobin, structural changes are critical. It has been suggested that vibrations that extend through the protein play a crucial role in controlling these structural changes. While nature may utilize such long-range vibrations for optimization of biological processes, bench-top characterization of these extended structural motions for engineered biochemistry has been elusive. Here we show the first optical observation of long-range protein vibrational modes. This is achieved by orientation-sensitive terahertz near-field microscopy measurements of chicken egg white lysozyme single crystals. Underdamped modes are found to exist for frequencies 410 cm À 1 . The existence of these persisting motions indicates that damping and intermode coupling are weaker than previously assumed. The methodology developed permits protein engineering based on dynamical network optimization.

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“…There is also a long-standing interest both in using diffuse scattering to validate improvements in MD simulations and in using MD to derive a structural basis for the protein motions that give rise to diffuse scattering (13,31,(34)(35)(36)(37)(38)(39). Recent advances in computing now enable microsecond duration simulations (13) that can overcome past barriers to accurate calculations seen using 10-ns or shorter MD trajectories (35,38).…”

Section: Significancementioning

confidence: 99%

Measuring and modeling diffuse scattering in protein X-ray crystallography

Benschoten

Liu

González

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation-libration-screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.protein dynamics | normal modes | structural biology | diffuse scattering | liquid-like motions X -ray crystallography can be a key tool for elucidating the structural basis of protein motions that play critical roles in enzymatic reactions, protein-protein interactions, and signaling cascades (1). X-ray diffraction yields an ensemble-averaged picture of the protein structure: each photon simultaneously probes multiple unit cells that can vary because of internal rearrangements or changes to the crystal lattice. Bragg analysis of X-ray diffraction only yields the mean charge density of the unit cell, however, which fundamentally limits the information that can be obtained about protein dynamics (2, 3).An inherent limitation in Bragg analysis is that models with different concerted motions can yield the same mean charge density (4). The traditional approach assumes a single structural model with individual atomic displacement parameters (B factors). Given enough data, anisotropic displacement parameters can be modeled. When the data are more limited, translation-libration-screw (TLS) refinement, which models rigid-body motions of subdomains (5), is often used [22% of Protein Data Bank (PDB) depositions (6, 7)]. Variations in the TLS domains can predict very different motions that agree equally well with the Bragg data (8, 9).Bragg analysis can be combined ...

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Lattice Dynamics of a Protein Crystal

Cited by 50 publications

References 31 publications

Structure and Dynamics of Biological Systems: Integration of Neutron Scattering with Computer Simulation

Structure and Dynamics of Biological Systems: Integration of Neutron Scattering with Computer Simulation

Optical measurements of long-range protein vibrations

Measuring and modeling diffuse scattering in protein X-ray crystallography

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