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Srinivasan B. Words of advice: teaching macromolecular crystallography. FEBS J 2023; 290:5441-5455. [PMID: 37014311 DOI: 10.1111/febs.16790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023]
Abstract
The ability to view structures of proteins at atomic resolution, facilitated by the rise of macromolecular crystallography, has had a tremendous impact in many areas of sciences, including molecular pharmacology, drug discovery and biotechnology. However, the teaching of macromolecular crystallography in universities across the globe has been less than optimal. This could be attributed to the interdisciplinary nature of this subject, making it appear esoteric and incomprehensible, at least at first glance, for students who have exclusive training in only one specific discipline. For the instructor, this problem is compounded further by the plethora of complex concepts and specialized terminologies that the science of macromolecular crystallography has accumulated over the course of its evolution. Moreover, the advent of robotics and several sophisticated software algorithms have reduced the incentive to understand the beautiful conceptual bedrock on which this subject is based. As a way of addressing some of the challenges delineated above, this Words of Advice article attempts to formulate the broad framework within which the teaching and learning of macromolecular crystallography should be approached. It advocates the acknowledgement that this is an interdisciplinary field, with substantial contributions from chemical, physical, biological and mathematical sciences, requiring the evolution of teaching approaches that acknowledge this reality. Moreover, it suggests the use of visual tools, use of computational resources and history to make the subject more relatable to students.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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Neijenhuis T, van Keulen SC, Bonvin AMJJ. Interface refinement of low- to medium-resolution Cryo-EM complexes using HADDOCK2.4. Structure 2022; 30:476-484.e3. [PMID: 35216656 DOI: 10.1016/j.str.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/25/2021] [Accepted: 01/28/2022] [Indexed: 10/19/2022]
Abstract
A wide range of cellular processes requires the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The density maps produced can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low- to medium-resolution maps. Unfortunately, the models produced frequently contain atomic clashes at the protein-protein interfaces (PPIs), as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best-performing protocol, consisting of a semi-flexible simulated annealing refinement with centroid restraints on the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.
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Affiliation(s)
- Tim Neijenhuis
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Siri C van Keulen
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
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Chakraborti S, Hatti K, Srinivasan N. ' All That Glitters Is Not Gold': High-Resolution Crystal Structures of Ligand-Protein Complexes Need Not Always Represent Confident Binding Poses. Int J Mol Sci 2021; 22:6830. [PMID: 34202053 DOI: 10.3390/ijms22136830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 01/09/2023] Open
Abstract
Our understanding of the structure–function relationships of biomolecules and thereby applying it to drug discovery programs are substantially dependent on the availability of the structural information of ligand–protein complexes. However, the correct interpretation of the electron density of a small molecule bound to a crystal structure of a macromolecule is not trivial. Our analysis involving quality assessment of ~0.28 million small molecule–protein binding site pairs derived from crystal structures corresponding to ~66,000 PDB entries indicates that the majority (65%) of the pairs might need little (54%) or no (11%) attention. Out of the remaining 35% of pairs that need attention, 11% of the pairs (including structures with high/moderate resolution) pose serious concerns. Unfortunately, most users of crystal structures lack the training to evaluate the quality of a crystal structure against its experimental data and, in general, rely on the resolution as a ‘gold standard’ quality metric. Our work aims to sensitize the non-crystallographers that resolution, which is a global quality metric, need not be an accurate indicator of local structural quality. In this article, we demonstrate the use of several freely available tools that quantify local structural quality and are easy to use from a non-crystallographer’s perspective. We further propose a few solutions for consideration by the scientific community to promote quality research in structural biology and applied areas.
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Cereto-Massagué A, Ojeda MJ, Joosten RP, Valls C, Mulero M, Salvado MJ, Arola-Arnal A, Arola L, Garcia-Vallvé S, Pujadas G. The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. J Cheminform 2013; 5:36. [PMID: 23895374 PMCID: PMC3733808 DOI: 10.1186/1758-2946-5-36] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/18/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Many Protein Data Bank (PDB) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom coordinates is not homogeneous between models or throughout the same model. To avoid basing a research project on a flawed model, we present a tool for assessing the quality of ligands and binding sites in crystallographic models from the PDB. RESULTS The Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e., users with little or no crystallography knowledge). Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed. CONCLUSIONS VHELIBS allows inexperienced users to examine the binding site and the ligand coordinates in relation to the experimental data. This is an important step to evaluate models for their fitness for drug discovery purposes such as structure-based pharmacophore development and protein-ligand docking experiments.
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Affiliation(s)
- Adrià Cereto-Massagué
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marceŀlí Domingo s/n, Tarragona, Catalonia 43007, Spain
| | - María José Ojeda
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marceŀlí Domingo s/n, Tarragona, Catalonia 43007, Spain
| | - Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Cristina Valls
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marceŀlí Domingo s/n, Tarragona, Catalonia 43007, Spain
| | - Miquel Mulero
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marceŀlí Domingo s/n, Tarragona, Catalonia 43007, Spain
| | - M Josepa Salvado
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marceŀlí Domingo s/n, Tarragona, Catalonia 43007, Spain
| | - Anna Arola-Arnal
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marceŀlí Domingo s/n, Tarragona, Catalonia 43007, Spain
| | - Lluís Arola
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marceŀlí Domingo s/n, Tarragona, Catalonia 43007, Spain
- Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat 1, Reus, Catalonia 43204, Spain
| | - Santiago Garcia-Vallvé
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marceŀlí Domingo s/n, Tarragona, Catalonia 43007, Spain
- Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat 1, Reus, Catalonia 43204, Spain
| | - Gerard Pujadas
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/ Marceŀlí Domingo s/n, Tarragona, Catalonia 43007, Spain
- Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat 1, Reus, Catalonia 43204, Spain
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Abstract
An electron density map produced by x-ray diffraction analysis of concanavalin A has been calculated to 4.25 A from data of three isomorphous heavy atom derivatives. The crystals are orthorhombic, with unit-cell dimensions of 63.1, 87.0, and 89.2 A for a, b, and c, respectively. The space group is I222, with eight asymmetric units per unit cell. The crystal asymmetric unit contains 27,000 daltons of protein and reflects the chemically unique component (protomer) within the oligomer. Separate chemical studies indicate that the protomer consists of two different polypeptide chains. Four protomers cluster around the intersection of three mutually perpendicular two-fold rotation axes to form a molecule of 108,000 daltons. The molecule can also be subdivided into two-protomer units of 54,000 daltons. Within the two-protomer unit, there are significantly more contacts joining the protomers than there are between adjacent two-protomer units that form the total molecule. These results provide a possible explanation for disagreement in molecular weights obtained in previous ultracentrifugal studies.
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