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Wych DC, Wall ME. Molecular-dynamics simulations of macromolecular diffraction, part I: Preparation of protein crystal simulations. Methods Enzymol 2023; 688:87-114. [PMID: 37748833 DOI: 10.1016/bs.mie.2023.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Molecular-dynamics (MD) simulations of protein crystals enable the prediction of structural and dynamical features of both the protein and the solvent components of macromolecular crystals, which can be validated against diffraction data from X-ray crystallographic experiments. The simulations have been useful for studying and predicting both Bragg and diffuse scattering in protein crystallography; however, the preparation is not yet automated and includes choices and tradeoffs that can impact the results. Here we examine some of the intricacies and consequences of the choices involved in setting up MD simulations of protein crystals for the study of diffraction data, and provide a recipe for preparing the simulations, packaged in an accompanying Jupyter notebook. This article and the accompanying notebook are intended to serve as practical resources for researchers wishing to put these models to work.
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Affiliation(s)
- David C Wych
- Computer, Computational and Statistical Sciences Division, Los Alamos, NM, United States; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Michael E Wall
- Computer, Computational and Statistical Sciences Division, Los Alamos, NM, United States.
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Goudiaby I, Malliavin TE, Mocchetti E, Mathiot S, Acherar S, Frochot C, Barberi-Heyob M, Guillot B, Favier F, Didierjean C, Jelsch C. New Crystal Form of Human Neuropilin-1 b1 Fragment with Six Electrostatic Mutations Complexed with KDKPPR Peptide Ligand. Molecules 2023; 28:5603. [PMID: 37513474 PMCID: PMC10385628 DOI: 10.3390/molecules28145603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Neuropilin 1 (NRP1), a cell-surface co-receptor of a number of growth factors and other signaling molecules, has long been the focus of attention due to its association with the development and the progression of several types of cancer. For example, the KDKPPR peptide has recently been combined with a photosensitizer and a contrast agent to bind NRP1 for the detection and treatment by photodynamic therapy of glioblastoma, an aggressive brain cancer. The main therapeutic target is a pocket of the fragment b1 of NRP1 (NRP1-b1), in which vascular endothelial growth factors (VEGFs) bind. In the crystal packing of native human NRP1-b1, the VEGF-binding site is obstructed by a crystallographic symmetry neighbor protein, which prevents the binding of ligands. Six charged amino acids located at the protein surface were mutated to allow the protein to form a new crystal packing. The structure of the mutated fragment b1 complexed with the KDKPPR peptide was determined by X-ray crystallography. The variant crystallized in a new crystal form with the VEGF-binding cleft exposed to the solvent and, as expected, filled by the C-terminal moiety of the peptide. The atomic interactions were analyzed using new approaches based on a multipolar electron density model. Among other things, these methods indicated the role played by Asp320 and Glu348 in the electrostatic steering of the ligand in its binding site. Molecular dynamics simulations were carried out to further analyze the peptide binding and motion of the wild-type and mutant proteins. The simulations revealed that specific loops interacting with the peptide exhibited mobility in both the unbound and bound forms.
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Affiliation(s)
- Ibrahima Goudiaby
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
- Université Assane Seck de Ziguinchor, Laboratoire de Chimie et de Physique des Matériaux (LCPM), 523 Ziguinchor, Senegal
| | | | - Eva Mocchetti
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Sandrine Mathiot
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Samir Acherar
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France
| | - Céline Frochot
- Université de Lorraine, CNRS, LRGP, F-54000 Nancy, France
| | | | - Benoît Guillot
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Frédérique Favier
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Claude Didierjean
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Christian Jelsch
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
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Nestor G, Ruda A, Anderson T, Oscarson S, Widmalm G, Gronenborn AM. A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations. Glycobiology 2020; 31:508-518. [PMID: 32902635 PMCID: PMC8091458 DOI: 10.1093/glycob/cwaa081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 11/12/2022] Open
Abstract
Cyanovirin-N (CV-N) is a cyanobacterial lectin with antiviral activity towards HIV and several other viruses. Here, we identify mannoside hydroxyl protons that are hydrogen bonded to the protein backbone of the CV-N domain B binding site, using NMR spectroscopy. For the two carbohydrate ligands Manα(1→2)ManαOMe and Manα(1→2) Manα(1→6)ManαOMe five hydroxyl protons are involved in hydrogen-bonding networks. Comparison with previous crystallographic results revealed that four of these hydroxyl protons donate hydrogen bonds to protein backbone carbonyl oxygens in solution and in the crystal. Hydrogen bonds were not detected between the side chains of Glu41 and Arg76 with sugar hydroxyls, as previously proposed for CV-N binding of mannosides. Molecular dynamics simulations of the CV-N/Manα(1→2)Manα(1→6)ManαOMe complex confirmed the NMR-determined hydrogen-bonding network. Detailed characterization of CV-N/mannoside complexes provides a better understanding of lectin-carbohydrate interactions and opens up to the use of CV-N and similar lectins as antiviral agents.
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Affiliation(s)
- Gustav Nestor
- Department of Structural Biology, University of Pittsburgh School of Medicine,1051 BST3, 3501 Fifth Ave, Pittsburgh, PA 15261, USA.,Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden
| | - Alessandro Ruda
- Department of Organic Chemistry, Stockholm University, Svante Arrhenius väg 16C, Stockholm, Sweden
| | - Taigh Anderson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Göran Widmalm
- Department of Organic Chemistry, Stockholm University, Svante Arrhenius väg 16C, Stockholm, Sweden
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine,1051 BST3, 3501 Fifth Ave, Pittsburgh, PA 15261, USA
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Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
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Cerutti DS, Case DA. Molecular Dynamics Simulations of Macromolecular Crystals. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018; 9. [PMID: 31662799 DOI: 10.1002/wcms.1402] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structures of biological macromolecules would not be known to their present extent without X-ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of water molecules, but the standard simulation employing periodic boundary conditions is already close to a crystal lattice environment. With simple protocols, the same software and molecular models can perform simulations of the crystal lattice, including all asymmetric units and solvent to fill the box. Throughout the history of molecular dynamics, studies of crystal lattices have served to investigate the quality of the underlying force fields, correlate the simulated ensembles to experimental structure factors, and extrapolate the behavior in lattices to behavior in solution. Powerful new computers are enabling molecular simulations with greater realism and statistical convergence. Meanwhile, the advent of exciting new methods in crystallography, including femtosecond free-electron lasers and image reconstruction for time-resolved crystallography on slurries of small crystals, is expanding the range of structures accessible to X-ray diffraction. We review past fusions of simulations and crystallography, then look ahead to the ways that simulations of crystal structures will enhance structural biology in the future.
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Affiliation(s)
- David S Cerutti
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8066
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8066
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Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F. Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. Int J Mol Sci 2018; 19:E3401. [PMID: 30380757 PMCID: PMC6274748 DOI: 10.3390/ijms19113401] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/20/2018] [Accepted: 10/27/2018] [Indexed: 12/13/2022] Open
Abstract
Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.
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Affiliation(s)
- Ashutosh Srivastava
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Tetsuro Nagai
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Arpita Srivastava
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Osamu Miyashita
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
| | - Florence Tama
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
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Li J, Hu Z, Beuerman R, Verma C. Molecular Environment Modulates Conformational Differences between Crystal and Solution States of Human β-Defensin 2. J Phys Chem B 2017; 121:2739-2747. [DOI: 10.1021/acs.jpcb.7b00083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jianguo Li
- Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore 168751
- Bioinformatics Institute (A*-STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Zhongqiao Hu
- Bioinformatics Institute (A*-STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Roger Beuerman
- Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore 168751
- Department
of Ophthalmology, National University of Singapore, Singapore 119074
- School of
Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459
| | - Chandra Verma
- Singapore Eye Research Institute, 11 Third Hospital Avenue, #06-00, Singapore 168751
- Bioinformatics Institute (A*-STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
- Department
of Biological Sciences, National University of Singapore, Singapore 117543
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