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Tuvi-Arad I, Shalit Y. The SARS-CoV-2 spike protein structure: a symmetry tale on distortion trail. Phys Chem Chem Phys 2023; 25:14430-14439. [PMID: 37184521 DOI: 10.1039/d3cp00163f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A preliminary step in the SARS-CoV-2 human infection process is a conformational change of the receptor binding domain (RBD) of its spike protein, characterized by a significant loss of symmetry. During this process, the residues which later on bind to the human angiotensin converting enzyme 2 (ACE2) receptor, become exposed at the surface of the protein. Symmetry analysis of a data set of 33 protein structures from experimental measurements and 32 structures from molecular dynamics simulation, show that the initial state carries clear indications on the structure of the final state, with respect to the local distortion along the sequence. This surprising finding implies that this type of analysis predicts the mechanism of change. We further show that the level of local distortion at the initial state increases with variant's transmissibility, for the wild type (WT) along with past and present variants of concern (WT ∼ alpha < beta < delta < Omicron BA.1), in accordance with the trend of their evolutionary path. In other words, the initial structure of the variant which is most infectious is also the most distorted, making its path to the final state shorter. It has been claimed that the RBD migration of the spike protein is allosterically controlled. Our analysis provides a quantitative support to a major theorem in this respect - that information about an allosteric process is encoded in the structure itself, suggesting that the path of local distortion is related to an allosteric information network.
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Affiliation(s)
- Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel.
| | - Yaffa Shalit
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel.
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2
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Reply to Ocklenburg and Mundorf: The interplay of developmental bias and natural selection. Proc Natl Acad Sci U S A 2022; 119:e2205299119. [PMID: 35787035 PMCID: PMC9282226 DOI: 10.1073/pnas.2205299119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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3
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Youkharibache P. Topological and Structural Plasticity of the Single Ig Fold and the Double Ig Fold Present in CD19. Biomolecules 2021; 11:biom11091290. [PMID: 34572502 PMCID: PMC8470474 DOI: 10.3390/biom11091290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 12/12/2022] Open
Abstract
The Ig fold has had a remarkable success in vertebrate evolution, with a presence in over 2% of human genes. The Ig fold is not just the elementary structural domain of antibodies and TCRs, it is also at the heart of a staggering 30% of immunologic cell surface receptors, making it a major orchestrator of cell–cell interactions. While BCRs, TCRs, and numerous Ig-based cell surface receptors form homo- or heterodimers on the same cell surface (in cis), many of them interface as ligand-receptors (checkpoints) on interacting cells (in trans) through their Ig domains. New Ig-Ig interfaces are still being discovered between Ig-based cell surface receptors, even in well-known families such as B7. What is largely ignored, however, is that the Ig fold itself is pseudosymmetric, a property that makes the Ig domain a versatile self-associative 3D structure and may, in part, explain its success in evolution, especially through its ability to bind in cis or in trans in the context of cell surface receptor–ligand interactions. In this paper, we review the Ig domains’ tertiary and quaternary pseudosymmetries, with particular attention to the newly identified double Ig fold in the solved CD19 molecular structure to highlight the underlying fundamental folding elements of Ig domains, i.e., Ig protodomains. This pseudosymmetric property of Ig domains gives us a decoding frame of reference to understand the fold, relate all Ig domain forms, single or double, and suggest new protein engineering avenues.
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4
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Gaber A, Pavšič M. Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches. Int J Mol Sci 2021; 22:9081. [PMID: 34445785 PMCID: PMC8396596 DOI: 10.3390/ijms22169081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.
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5
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Tetter S, Terasaka N, Steinauer A, Bingham RJ, Clark S, Scott AJP, Patel N, Leibundgut M, Wroblewski E, Ban N, Stockley PG, Twarock R, Hilvert D. Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein. Science 2021; 372:1220-1224. [PMID: 34112695 DOI: 10.1126/science.abg2822] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/29/2021] [Indexed: 12/14/2022]
Abstract
Viruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution to convert a bacterial enzyme that lacks affinity for nucleic acids into an artificial nucleocapsid that efficiently packages and protects multiple copies of its own encoding messenger RNA. Revealing remarkable convergence on the molecular hallmarks of natural viruses, the accompanying changes reorganized the protein building blocks into an interlaced 240-subunit icosahedral capsid that is impermeable to nucleases, and emergence of a robust RNA stem-loop packaging cassette ensured high encapsidation yields and specificity. In addition to evincing a plausible evolutionary pathway for primordial viruses, these findings highlight practical strategies for developing nonviral carriers for diverse vaccine and delivery applications.
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Affiliation(s)
- Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Naohiro Terasaka
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Richard J Bingham
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
| | - Sam Clark
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
| | - Andrew J P Scott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Marc Leibundgut
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Reidun Twarock
- Departments of Mathematics and Biology, University of York, York YO10 5DD, UK
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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6
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Targeting protein self-association in drug design. Drug Discov Today 2021; 26:1148-1163. [PMID: 33548462 DOI: 10.1016/j.drudis.2021.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Protein self-association is a universal phenomenon essential for stability and molecular recognition. Disrupting constitutive homomers constitutes an original and emerging strategy in drug design. Inhibition of homomeric proteins can be achieved through direct complex disruption, subunit intercalation, or by promoting inactive oligomeric states. Targeting self-interaction grants several advantages over active site inhibition because of the stimulation of protein degradation, the enhancement of selectivity, substoichiometric inhibition, and by-pass of compensatory mechanisms. This new landscape in protein inhibition is driven by the development of biophysical and biochemical tools suited for the study of homomeric proteins, such as differential scanning fluorimetry (DSF), native mass spectrometry (MS), Förster resonance energy transfer (FRET) spectroscopy, 2D nuclear magnetic resonance (NMR), and X-ray crystallography. In this review, we discuss the different aspects of this new paradigm in drug design.
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Fossépré M, Tuvi-Arad I, Beljonne D, Richeter S, Clément S, Surin M. Binding Mode Multiplicity and Multiscale Chirality in the Supramolecular Assembly of DNA and a π-Conjugated Polymer. Chemphyschem 2020; 21:2543-2552. [PMID: 32910539 DOI: 10.1002/cphc.202000630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/04/2020] [Indexed: 02/04/2023]
Abstract
Water-soluble π-conjugated polymers are increasingly considered for DNA biosensing. However, the conformational rearrangement, supramolecular organization and dynamics upon interaction with DNA have been overlooked, which prevents the rational design of such detection tools. To elucidate the binding of a cationic polythiophene (CPT) to DNA with atomistic resolution, we performed molecular simulations of their supramolecular assembly. Comparison of replicated simulations show a multiplicity of CPT binding geometries that contribute to the wrapping of CPT around DNA. The different binding geometries are stabilized by both electrostatic interactions between CPT lateral cations and DNA phosphodiesters and van der Waals interactions between the CPT backbone and the DNA grooves. Simulated circular dichroism (CD) spectra show that the induced CD signal stems from a conserved geometrical feature across the replicated simulations, i. e. the presence of segments of syn configurations between thiophene units along the CPT chain. At the macromolecular scale, we inspected the different shapes related to the CPT binding modes around the DNA through symmetry metrics. Altogether, molecular dynamics (MD) simulations, model Hamiltonian calculations of the CD spectra, and symmetry indices provide insights into the origin of induced chirality from the atomic to the macromolecular scale. Our multidisciplinary approach points out the hierarchical aspect of CPT chiral organization induced by DNA.
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Affiliation(s)
- Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 20 Place du Parc, Mons, 7000, Belgium
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - David Beljonne
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 20 Place du Parc, Mons, 7000, Belgium
| | | | | | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 20 Place du Parc, Mons, 7000, Belgium
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8
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Kaspi-Kaneti AW, Barroso J, Merino G, Avnir D, Garzón IL, Tuvi-Arad I. Head to Tail Distortion Wave Characterizes the Enantiomerization of Helicenes. J Org Chem 2020; 85:15415-15421. [PMID: 33210538 DOI: 10.1021/acs.joc.0c02196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A fresh look on helicenes' enantiomerization process with a focus on ring conformation reveals that it can be described as a step-by-step mechanism in which maximal distortion is consecutively transferred along the helicene skeleton, head to tail. Density functional theory methods were used to compute the enantiomerization pathway, and continuous symmetry measures were applied to quantify the distortion of even-number helicenes with 8-14 rings. Our findings show that the distortion wave is additive-the process always starts from one edge of the helicene and progresses along the rings until the other edge is reached. As more rings are added to the helicene, extra steps are appended to the distortion wave. Implications of this fundamental process are discussed in light of similar natural phenomena from polymer dynamics to snake locomotion.
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Affiliation(s)
- Ariela W Kaspi-Kaneti
- Department of Natural Sciences, The Open University of Israel, Raanana 4353701, Israel.,Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Jorge Barroso
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, Mérida, Yucatán 97310, México
| | - Gabriel Merino
- Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida, Mérida, Yucatán 97310, México
| | - David Avnir
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ignacio L Garzón
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana 4353701, Israel
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9
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Ghanbarpour A, Santos EM, Pinger C, Assar Z, Hossaini Nasr S, Vasileiou C, Spence D, Borhan B, Geiger JH. Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering. Chembiochem 2020; 21:3192-3196. [PMID: 32608180 PMCID: PMC8220890 DOI: 10.1002/cbic.202000405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 06/29/2020] [Indexed: 11/07/2022]
Abstract
Domain-swapping is a mechanism for evolving new protein structure from extant scaffolds, and has been an efficient protein-engineering strategy for tailoring functional diversity. However, domain swapping can only be exploited if it can be controlled, especially in cases where various folds can coexist. Herein, we describe the structure of a domain-swapped trimer of the iLBP family member hCRBPII, and suggest a mechanism for domain-swapped trimerization. It is further shown that domain-swapped trimerization can be favored by strategic installation of a disulfide bond, thus demonstrating a strategy for fold control. We further show the domain-swapped trimer to be a useful protein design template by installing a high-affinity metal binding site through the introduction of a single mutation, taking advantage of its threefold symmetry. Together, these studies show how nature can promote oligomerization, stabilize a specific oligomer, and generate new function with minimal changes to the protein sequence.
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Affiliation(s)
- Alireza Ghanbarpour
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
- Yale University Medical School, Department of Cell Biology, 333 S. Cedar Street, New Haven, CT 06510, USA
| | - Elizabeth M Santos
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
- Dow Performance Silicones, 2200W Salzburg Road, Midland, MI 48686, USA
| | - Cody Pinger
- Department of Biomedical Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, MI 48823, USA
| | - Zahra Assar
- Cayman Chemical, 1180 East Ellsworth Road, Ann Arbor, MI 48108, USA
| | - Seyedmehdi Hossaini Nasr
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Dana Spence
- Department of Biomedical Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, MI 48823, USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - James H Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
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10
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Shalit Y, Tuvi-Arad I. Side chain flexibility and the symmetry of protein homodimers. PLoS One 2020; 15:e0235863. [PMID: 32706779 PMCID: PMC7380632 DOI: 10.1371/journal.pone.0235863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
A comprehensive analysis of crystallographic data of 565 high-resolution protein homodimers comprised of over 250,000 residues suggests that amino acids form two groups that differ in their tendency to distort or symmetrize the structure of protein homodimers. Residues of the first group tend to distort the protein homodimer and generally have long or polar side chains. These include: Lys, Gln, Glu, Arg, Asn, Met, Ser, Thr and Asp. Residues of the second group contribute to protein symmetry and are generally characterized by short or aromatic side chains. These include: Ile, Pro, His, Val, Cys, Leu, Trp, Tyr, Phe, Ala and Gly. The distributions of the continuous symmetry measures of the proteins and the continuous chirality measures of their building blocks highlight the role of side chain geometry and the interplay between entropy and symmetry in dictating the conformational flexibility of proteins.
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Affiliation(s)
- Yaffa Shalit
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
- * E-mail:
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11
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Bonjack M, Avnir D. The near-symmetry of protein oligomers: NMR-derived structures. Sci Rep 2020; 10:8367. [PMID: 32433550 PMCID: PMC7239866 DOI: 10.1038/s41598-020-65097-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
The majority of oligomeric proteins form clusters which have rotational or dihedral symmetry. Despite the many advantages of symmetric packing, protein oligomers are only nearly symmetric, and the origin of this phenomenon is still in need to be fully explored. Here we apply near-symmetry analyses by the Continuous Symmetry Measures methodology of protein homomers to their natural state, namely their structures in solution. NMR-derived structural data serves us for that purpose. We find that symmetry deviations of proteins are by far higher in solution, compared to the crystalline state; that much of the symmetry distortion is due to amino acids along the interface between the subunits; that the distortions are mainly due to hydrophilic amino acids; and that distortive oligomerization processes such as the swap-domain mechanism can be identified by the symmetry analysis. Most of the analyses were carried out on distorted C2-symmetry dimers, but C3 and D2 cases were analyzed as well. Our NMR analysis supports the idea that the crystallographic B-factor represents non-classical crystals, in which different conformers pack in the crystal, perhaps from the conformers which the NMR analysis provides.
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Affiliation(s)
- Maayan Bonjack
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - David Avnir
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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12
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Tuvi-Arad I, Alon G. Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis. J Cheminform 2019; 11:39. [PMID: 31172379 PMCID: PMC6551912 DOI: 10.1186/s13321-019-0360-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
Symmetry of proteins, an important source of their elegant structure and unique functions, is not as perfect as it may seem. In the framework of continuous symmetry, in which symmetry is no longer a binary yes/no property, such imperfections can be quantified and used as a global descriptor of the three-dimensional structure. We present an improved algorithm for calculating the continuous symmetry measure for proteins that takes into account their complete set of atoms including all side chains. Our method takes advantage of the protein sequence and the division into peptides in order to improve the accuracy and efficiency of the calculation over previous methods. The Hungarian algorithm is applied to solve the assignment problem and find the permutation that defines the symmetry operation. Analysis of the symmetry of several sets of protein homomers, with various degrees of rotational symmetry is presented. The new methodology lays the foundations for accurate, efficient and reliable large scale symmetry analysis of protein structure and can be used as a collective variable that describes changes of the protein geometry along various processes, both at the backbone level and for the complete protein structure.
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Affiliation(s)
- Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, 4353701, Raanana, Israel.
| | - Gil Alon
- Department of Mathematics and Computer Science, The Open University of Israel, 4353701, Raanana, Israel.
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13
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Carreras A, Bernuz E, Marugan X, Llunell M, Alemany P. Effects of Temperature on the Shape and Symmetry of Molecules and Solids. Chemistry 2018; 25:673-691. [DOI: 10.1002/chem.201801682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/17/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Abel Carreras
- Donostia International Physics Center (DIPC) Paseo Manuel de Lardizabal 4 20018 Donostia, Euskadi Spain
| | - Efrem Bernuz
- Departament de Ciència dels Materials i Química Física andInstitut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona Diagonal 647 08028 Barcelona, Catalunya Spain
| | - Xavier Marugan
- Departament de Ciència dels Materials i Química Física andInstitut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona Diagonal 647 08028 Barcelona, Catalunya Spain
| | - Miquel Llunell
- Departament de Ciència dels Materials i Química Física andInstitut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona Diagonal 647 08028 Barcelona, Catalunya Spain
| | - Pere Alemany
- Departament de Ciència dels Materials i Química Física andInstitut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona Diagonal 647 08028 Barcelona, Catalunya Spain
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14
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Affiliation(s)
- Julian T. Brennecke
- Department of Theoretical and Computational Biophysics, Computational Biomolecular, Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L. de Groot
- Department of Theoretical and Computational Biophysics, Computational Biomolecular, Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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15
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Hannon C, Cruz-Migoni A, Platonova O, Owen RL, Nettleship JE, Miller A, Carr SB, Harris G, Rabbitts TH, Phillips SEV. Cloning, purification and structure determination of the HIV integrase-binding domain of lens epithelium-derived growth factor. Acta Crystallogr F Struct Biol Commun 2018; 74:143-149. [PMID: 29497017 PMCID: PMC5947699 DOI: 10.1107/s2053230x18001553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/23/2018] [Indexed: 12/04/2022] Open
Abstract
Lens epithelium-derived growth factor (LEDGF)/p75 is the dominant binding partner of HIV-1 integrase in human cells. The crystal structure of the HIV integrase-binding domain (IBD) of LEDGF has been determined in the absence of ligand. IBD was overexpressed in Escherichia coli, purified and crystallized by sitting-drop vapour diffusion. X-ray diffraction data were collected at Diamond Light Source to a resolution of 2.05 Å. The crystals belonged to space group P21, with eight polypeptide chains in the asymmetric unit arranged as an unusual octamer composed of four domain-swapped IBD dimers. IBD exists as a mixture of monomers and dimers in concentrated solutions, but the dimers are unlikely to be biologically relevant.
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Affiliation(s)
- Clare Hannon
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
- West Suffolk Hospital, Hardwick Lane, Bury St Edmunds IP33 2QZ, England
| | - Abimael Cruz-Migoni
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
| | - Olga Platonova
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
| | - Robin L. Owen
- Diamond Light Source, Rutherford Appleton Laboratory, Didcot OX11 0DE, England
| | - Joanne E. Nettleship
- Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Ami Miller
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
| | - Stephen B. Carr
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Terence H. Rabbitts
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, England
| | - Simon E. V. Phillips
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
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