Bringing diffuse X-ray scattering into focus

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

doi:10.1016/j.sbi.2018.01.009

Cited by 35 publications

(25 citation statements)

References 64 publications

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“…However, this treatment suppresses features that are derived from long-ranged correlations extending beyond the unit cell and may also alter the information contained in the remaining signal. The emerging view is that long-ranged correlations must be considered (2,19,21), but despite the advent of pixel array detectors that are newly enabling (22,23), diffuse scattering data capable of testing such models have not been reported.…”

Section: Introductionmentioning

confidence: 99%

Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

Meisburger

Case

Ando

2019

Preprint

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Protein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic information contained in the diffuse scattering background. However, the origin of macromolecular diffuse scattering has been poorly understood, limiting its applicability. We present a detailed diffuse scattering map from triclinic lysozyme that resolves both inter-and intramolecular correlations. These correlations are studied theoretically using both all-atom molecular dynamics and simple vibrational models. Although lattice dynamics reproduce most of the diffuse pattern, protein internal dynamics, which include hinge-bending motions, are needed to explain the short-ranged correlations revealed by Patterson analysis. These insights lay the groundwork for animating crystal structures with biochemically relevant motions.

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Section: Introductionmentioning

confidence: 99%

Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

Meisburger

Case

Ando

2019

Preprint

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“…In parallel, advances in computer modeling of multiple conformational substates now enable visualizing minor populations of crystalline protein structural ensembles. These approaches have permitted identification of networks of sidechain disorder (20), allowed refinement of whole-protein ensemble models (21), aided identification of minor binding modes of therapeutic ligands (22), and characterized spatial correlations in protein mobility (23).…”

Section: Introductionmentioning

confidence: 99%

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

Dasgupta

Budday

Oliveira

et al. 2019

Preprint

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Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site electrostatic environment. Although a vast number of enzymes rely on cysteine modification for function, precisely how altered structural and electrostatic states of cysteine affect protein dynamics remains poorly understood.Here we use X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent modification of the active site cysteine residue in isocyanide hydratase (ICH) affects the protein conformational ensemble. ICH exhibits a concerted helical displacement upon cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained residue Ile152. The mobile helix samples alternative conformations in crystals exposed to synchrotron X-ray radiation due to the X-rayinduced formation of a cysteine-sulfenic acid at the catalytic nucleophile (Cys101-SOH). This oxidized cysteine residue resembles the proposed thioimidate intermediate in ICH catalysis. Neither cysteine modification nor helical disorder were observed in X-ray free electron laser (XFEL) diffraction data. Computer simulations confirm cysteine modification-gated helical motion and show how structural changes allosterically propagate through the ICH dimer. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce the ICH catalytic rate and alter its presteady state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. Our results suggest that cysteine modification may be a common and likely underreported means for regulating protein conformational dynamics. Figure 2: Cys101 oxidation leads to a weakening of the Ile152-Cys101 H-bond. Electrostatic Poisson-Boltzmann surfaces (red negative, blue positive charge) calculated from the Cys101-Ile152 (A) and Cys-SOH-Ile152 (B) environments. Cysteine photooxidation neutralizes the negative charge of the sulfur atom, weakening the N-H … S hydrogen bond. (C-E) Schematic showing covalent modification of Cys101 weakens the hydrogen bond (red dotted/dashed line) to Ile152 and allows relaxation of backbone strain (curved arrow). (F) The catalytic thioimidate covalent intermediate resembles photooxidized Cys101-SOH. Both modifications neutralize negative charge on Cys Sγ.

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“…Crystals are often illustrated using identical repeating units; however, in real crystals, each copy of a molecule can adopt a somewhat different structure as long as the overall order is maintained. Although structural variations occur in small-molecule crystals, 1 the problem of conformational heterogeneity is especially important for macromolecular crystals, which have many more degrees of freedom and a high solvent content 2,3 . Understanding the structural variations in crystals can potentially be used for increasing the accuracy of crystal structure models 4 and for developing crystallography as a tool for characterizing conformational heterogeneity and dynamics in structural biology 5 …”

Section: Introductionmentioning

confidence: 99%

“…Models with different correlations lead to distinct patterns of diffuse scattering that appear as intensity beneath and between the Bragg peaks in diffraction images. Recent years have seen a renaissance in methods for processing and modeling diffuse scattering 2,3,13 . However, studies of diffuse scattering have differed in their conclusions, both about the degree to which the signal can be explained by various models of correlated motion and about the importance of different types of motion in determining the conformational variations in protein crystals 2,14–17 .…”

Section: Introductionmentioning

confidence: 99%

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

Wych

Fraser

Mobley

et al. 2019

Structural Dynamics

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To 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 liquidlike 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 (intraprotein) and between different protein molecules (interprotein). The interprotein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intraprotein 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.

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Bringing diffuse X-ray scattering into focus

Cited by 35 publications

References 64 publications

Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

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

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