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Diffuse X-ray scattering from correlated motions in a protein crystal.

Meisburger SP, Case DA, Ando N
Nat Commun 11 1271 (2020)
Cited: 21 times
EuropePMC logo PMID: 32152274

Abstract

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 finely sampled diffuse scattering map from triclinic lysozyme with unprecedented accuracy and detail, clearly resolving both the 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.

Reviews - 6o2h mentioned but not cited (1)

  1. Correlated Motions in Structural Biology. Xu D, Meisburger SP, Ando N. Biochemistry 60 2331-2340 (2021)

Articles - 6o2h mentioned but not cited (1)

  1. Diffuse X-ray scattering from correlated motions in a protein crystal. Meisburger SP, Case DA, Ando N. Nat Commun 11 1271 (2020)


Reviews citing this publication (6)

  1. Advances in methods for atomic resolution macromolecular structure determination. Thompson MC, Yeates TO, Rodriguez JA. F1000Res 9 F1000 Faculty Rev-667 (2020)
  2. Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light. Wilson MA. Annu Rev Biophys 51 79-98 (2022)
  3. Computational anti-COVID-19 drug design: progress and challenges. Wang J, Zhang Y, Nie W, Luo Y, Deng L. Brief Bioinform 23 bbab484 (2022)
  4. Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources. Aller P, Orville AM. Methods Mol Biol 2305 203-228 (2021)
  5. Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics. Hekstra DR. Annu Rev Biophys 52 255-274 (2023)
  6. Transactions from the 69th Annual Meeting of the American Crystallographic Association: Data best practices-current state and future needs. Sauter NK, Rose JP, Bhat TN. Struct Dyn 7 021301 (2020)

Articles citing this publication (13)

  1. A method for intuitively extracting macromolecular dynamics from structural disorder. Pearce NM, Gros P. Nat Commun 12 5493 (2021)
  2. Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure-function studies. Helliwell JR. Acta Crystallogr A Found Adv 77 173-185 (2021)
  3. Molecular-dynamics simulation methods for macromolecular crystallography. Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME. Acta Crystallogr D Struct Biol 79 50-65 (2023)
  4. Room-temperature serial synchrotron crystallography of the human phosphatase PTP1B. Sharma S, Ebrahim A, Keedy DA. Acta Crystallogr F Struct Biol Commun 79 23-30 (2023)
  5. Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters. Su Z, Dasgupta M, Poitevin F, Mathews II, van den Bedem H, Wall ME, Yoon CH, Wilson MA. Struct Dyn 8 044701 (2021)
  6. Robust total X-ray scattering workflow to study correlated motion of proteins in crystals. Meisburger SP, Case DA, Ando N. Nat Commun 14 1228 (2023)
  7. Torsion angles to map and visualize the conformational space of a protein. Ginn HM. Protein Sci 32 e4608 (2023)
  8. Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography. Helliwell JR. Methods Mol Biol 2449 235-261 (2022)
  9. Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography. Liu N, Mikhailovskii O, Skrynnikov NR, Xue Y. IUCrJ 10 16-26 (2023)
  10. Validation of X-ray Crystal Structure Ensemble Representations of SARS-CoV-2 Main Protease by Solution NMR Residual Dipolar Couplings. Shen Y, Robertson AJ, Bax A. J Mol Biol 168067 (2023)
  11. Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase. Plapp BV, Gakhar L, Subramanian R. Acta Crystallogr D Struct Biol 78 1221-1234 (2022)
  12. High-Resolution Electron Diffraction of Hydrated Protein Crystals at Room Temperature. Plana-Ruiz S, Gómez-Pérez A, Budayova-Spano M, Foley DL, Portillo-Serra J, Rauch E, Grivas E, Housset D, Das PP, Taheri ML, Nicolopoulos S, Ling WL. ACS Nano 17 24802-24813 (2023)
  13. Quantifying Molecular Disorder in Tri-Isopropyl Silane (TIPS) Pentacene Using Variable Coherence Transmission Electron Microscopy. Alanazi F, Eggeman AS, Stavrou K, Danos A, Monkman AP, Mendis BG. J Phys Chem Lett 14 8183-8190 (2023)


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