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Tolbatov I, Marrone A, Shepard W, Chiaverini L, Upadhyay Kahaly M, La Mendola D, Marzo T, Ciccone L. Inorganic Drugs as a Tool for Protein Structure Solving and Studies on Conformational Changes. Chemistry 2023; 29:e202202937. [PMID: 36477932 DOI: 10.1002/chem.202202937] [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: 09/20/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
Inorganic drugs are capable of tight interactions with proteins through coordination towards aminoacidic residues, and this feature is recognized as a key aspect for their pharmacological action. However, the "protein metalation process" is exploitable for solving the phase problem and structural resolution. In fact, the use of inorganic drugs bearing specific metal centers and ligands capable to drive the binding towards the desired portions of the protein target could represent a very intriguing and fruitful strategy. In this context, a theoretical approach may further contribute to solve protein structures and their refinement. Here, we delineate the main features of a reliable experimental-theoretical integrated approach, based on the use of metallodrugs, for protein structure solving.
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Affiliation(s)
- Iogann Tolbatov
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Alessandro Marrone
- Department of Pharmacy, University "G. D'Annunzio" Chieti-Pescara, Via dei Vestini, 31, 66100, Chieti, Italy
| | - William Shepard
- Department PROXIMA2 A, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
| | - Lorenzo Chiaverini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | | | - Diego La Mendola
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Tiziano Marzo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Lidia Ciccone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy
- Department PROXIMA2 A, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
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Marchetti A, Pizzi A, Bergamaschi G, Demitri N, Stollberg U, Diederichsen U, Pigliacelli C, Metrangolo P. Fibril Structure Demonstrates the Role of Iodine Labelling on a Pentapeptide Self‐Assembly. Chemistry 2022; 28:e202104089. [PMID: 35084787 PMCID: PMC9306938 DOI: 10.1002/chem.202104089] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Alessandro Marchetti
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Andrea Pizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Greta Bergamaschi
- Istituto di Scienze e Tecnologie Chimiche National Research Council of Italy Via M. Bianco 9 20131 Milano Italy
| | - Nicola Demitri
- Elettra – Sincrotrone Trieste S.S. 14 Km 163.5 in Area Science Park 34149 Basovizza Trieste Italy
| | - Ulrike Stollberg
- Institute for Organic and Biomolecular Chemistry Georg-August-University Göttingen Tammannstr. 2 37077 Göttingen Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry Georg-August-University Göttingen Tammannstr. 2 37077 Göttingen Germany
| | - Claudia Pigliacelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab) Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta” Politecnico di Milano Via L. Mancinelli 7 20131 Milano Italy
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Kermani AA. A guide to membrane protein X‐ray crystallography. FEBS J 2020; 288:5788-5804. [DOI: 10.1111/febs.15676] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/17/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Ali A. Kermani
- Department of Molecular, Cellular, and Developmental Biology University of Michigan Ann Arbor MI USA
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Pike ACW, Garman EF, Krojer T, von Delft F, Carpenter EP. An overview of heavy-atom derivatization of protein crystals. Acta Crystallogr D Struct Biol 2016; 72:303-18. [PMID: 26960118 PMCID: PMC4784662 DOI: 10.1107/s2059798316000401] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 01/08/2016] [Indexed: 11/11/2022] Open
Abstract
Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.
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Affiliation(s)
- Ashley C. W. Pike
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
- Department of Biochemistry, University of Johannesburg, Aukland Park 2006, South Africa
| | - Elisabeth P. Carpenter
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
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Li D, Pye VE, Caffrey M. Experimental phasing for structure determination using membrane-protein crystals grown by the lipid cubic phase method. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:104-22. [PMID: 25615865 PMCID: PMC4304691 DOI: 10.1107/s1399004714010360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/07/2014] [Indexed: 03/02/2023]
Abstract
Despite the marked increase in the number of membrane-protein structures solved using crystals grown by the lipid cubic phase or in meso method, only ten have been determined by SAD/MAD. This is likely to be a consequence of the technical difficulties associated with handling proteins and crystals in the sticky and viscous hosting mesophase that is usually incubated in glass sandwich plates for the purposes of crystallization. Here, a four-year campaign aimed at phasing the in meso structure of the integral membrane diacylglycerol kinase (DgkA) from Escherichia coli is reported. Heavy-atom labelling of this small hydrophobic enzyme was attempted by pre-labelling, co-crystallization, soaking, site-specific mercury binding to genetically engineered single-cysteine mutants and selenomethionine incorporation. Strategies and techniques for special handling are reported, as well as the typical results and the lessons learned for each of these approaches. In addition, an assay to assess the accessibility of cysteine residues in membrane proteins for mercury labelling is introduced. The various techniques and strategies described will provide a valuable reference for future experimental phasing of membrane proteins where crystals are grown by the lipid cubic phase method.
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Affiliation(s)
- Dianfan Li
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Valerie E. Pye
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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