1
|
Martin J, Robert X, Gouet P, Falson P, Chaptal V. Specific Xray diffraction patterns of membrane proteins caused by secondary structure collinearity. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184065. [PMID: 36206830 DOI: 10.1016/j.bbamem.2022.184065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/12/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
Diffraction anisotropy is a phenomenon that impacts more specifically membrane proteins, compared to soluble ones, but the reasons for this discrepancy remained unclear. Often, it is referred to a difference in resolution limits between highest and lowest diffraction limits as a signature for anisotropy. We show in this article that there is no single correlation between anisotropy and difference in resolution limits, with notably a substantial number of structures displaying various anisotropy with no difference in resolution limits. We further investigated diffraction intensity profiles, and observed a peak centred on 4.9 Å resolution more predominant in membrane proteins. Since this peak is in the region corresponding to secondary structures, we investigated the influence of secondary structure ratio. We showed that secondary structure content has little influence on this profile, while secondary structure collinearity in membrane proteins correlate with a stronger peak. Finally, we could further show that the presence of this peak is linked to higher diffraction anisotropy. These results bring to light a specific diffraction of membrane protein crystals, which calls for a specific handling by crystallographic software. It also brings an explanation for investigators struggling with their anisotropic data.
Collapse
Affiliation(s)
- Juliette Martin
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Xavier Robert
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France.
| |
Collapse
|
2
|
Abd El Salam HA, Moustafa G, Zayed EM, Mohamed GG. Isophthaloylbis (Azanediyl) Dipeptide Ligand and Its Complexes: Structural Study, Spectroscopic, Molecular Orbital, Molecular Docking, and Biological Activity Properties. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2097712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
| | - Gaber Moustafa
- Peptides Chemistry Department, National Research Centre, Dokki, Giza, Egypt
| | - Ehab M. Zayed
- Green Chemistry Department, National, Research Centre, Dokki, Giza, Egypt
| | - Gehad G. Mohamed
- Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
- Nanoscience Department, Basic and Applied Sciences Institute, Egypt-Japan University of Science and Technology, Alexandria, Egypt
| |
Collapse
|
3
|
Moustafa G, Sabry E, Zayed EM, Mohamed GG. Structural characterization, spectroscopic studies, and molecular docking studies on metal complexes of new hexadentate cyclic peptide ligand. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gaber Moustafa
- Peptides Chemistry Department National Research Centre Giza Egypt
| | - Eman Sabry
- Pesticide Chemistry Department National Research Centre Giza Egypt
| | - Ehab M. Zayed
- Green Chemistry Department National Research Centre Giza Egypt
| | - Gehad G. Mohamed
- Chemistry Department, Faculty of Science Cairo University Giza Egypt
| |
Collapse
|
4
|
X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins. Sci Rep 2017; 7:17013. [PMID: 29208950 PMCID: PMC5717104 DOI: 10.1038/s41598-017-17216-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/23/2017] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins are distinguished from soluble proteins by their insertion into biological membranes. This insertion is achieved via a noticeable arrangement of hydrophobic amino acids that are exposed at the surface of the protein, and renders the interaction with the aliphatic tails of lipids more energetically favorable. This important difference between these two categories of proteins is the source of the need for a specific handling of membrane proteins, which transpired in the creation of new tools for their recombinant expression, purification and even crystallization. Following this line, we show here that crystals of membrane proteins display systematically higher diffraction anisotropy than those of soluble proteins. This phenomenon dramatically hampers structure solution and refinement, and has a strong impact on the quality of electron-density maps. A farther search for origins of this phenomenon showed that the type of crystallization, and thus the crystal packing, has no impact on anisotropy, nor does the nature or function of the membrane protein. Membrane proteins fully embedded within the membrane display equal anisotropy compared to the ones with extra membranous domains or fusions with soluble proteins. Overall, these results overturn common beliefs and call for a specific handling of their diffraction data.
Collapse
|
5
|
Twinned CsLn2F7 compounds (Ln=Nd, Gd, Tb, Er, Yb): the role of a highly symmetrical cation lattice with an arrangement analogous to the Laves phase MgZn2. Z KRIST-CRYST MATER 2016. [DOI: 10.1515/zkri-2016-1972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The occurrence of twinning can often be related to higher symmetrical structures. Fluorides are frequently twinned due to their close relation to high symmetry structures like fluoride, tysonite or pyrochlores. The series of compounds CsLn2F7 is no exception. We refined the structures of the twinned compounds with Ln=Nd, Gd, Tb, Er, Yb in space group P1121/b. An analysis of the pseudosymmetry of the resulting structures shows a highly symmetrical cation partial structure with a cation distribution similar to the one in the hexagonal Laves phase MgZn2. Several other compounds ALn2F7, which have been described in the literature, show a similar cation array. The diversity of different space groups which have been reported for ALn2F7 compounds can be better understood using group-subgroup relationships assuming the hypothetical structure of the cation array with space group P63/mmc as aristotype. Furthermore, the twinning is easily understood on the basis of the lost symmetry operations in the symmetry reduction from point group 6/mmm, e.g. to 2/m in the case of the CsLn2F7 compounds.
Collapse
|
6
|
Scott C, Griffin S. Viroporins: structure, function and potential as antiviral targets. J Gen Virol 2015; 96:2000-2027. [PMID: 26023149 DOI: 10.1099/vir.0.000201] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The channel-forming activity of a family of small, hydrophobic integral membrane proteins termed 'viroporins' is essential to the life cycles of an increasingly diverse range of RNA and DNA viruses, generating significant interest in targeting these proteins for antiviral development. Viroporins vary greatly in terms of their atomic structure and can perform multiple functions during the virus life cycle, including those distinct from their role as oligomeric membrane channels. Recent progress has seen an explosion in both the identification and understanding of many such proteins encoded by highly significant pathogens, yet the prototypic M2 proton channel of influenza A virus remains the only example of a viroporin with provenance as an antiviral drug target. This review attempts to summarize our current understanding of the channel-forming functions for key members of this growing family, including recent progress in structural studies and drug discovery research, as well as novel insights into the life cycles of many viruses revealed by a requirement for viroporin activity. Ultimately, given the successes of drugs targeting ion channels in other areas of medicine, unlocking the therapeutic potential of viroporins represents a valuable goal for many of the most significant viral challenges to human and animal health.
Collapse
Affiliation(s)
- Claire Scott
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| |
Collapse
|
7
|
Duda DM, Olszewski JL, Schuermann JP, Kurinov I, Miller DJ, Nourse A, Alpi AF, Schulman BA. Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism. Structure 2013; 21:1030-41. [PMID: 23707686 DOI: 10.1016/j.str.2013.04.019] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 04/25/2013] [Accepted: 04/29/2013] [Indexed: 12/20/2022]
Abstract
A distinct mechanism for ubiquitin (Ub) ligation has recently been proposed for the RING1-IBR-RING2 (RBR) family of E3s: an N-terminal RING1 domain recruits a thioester-linked intermediate complex between Ub and the E2 UbcH7, and a structurally distinct C-terminal RING2 domain displays a catalytic cysteine required for Ub ligation. To obtain insights into RBR E3s, we determined the crystal structure of the human homolog of Ariadne (HHARI), which reveals the individual RING1, IBR, and RING2 domains embedded in superdomains involving sequences specific to the Ariadne RBR subfamily. The central IBR is flanked on one side by RING1, which is exposed and binds UbcH7. On the other side, a C-terminal autoinhibitory "Ariadne domain" masks the RING2 active site. Insights into RBR E3 mechanisms are provided by structure-based mutations that indicate distinct steps of relief from autoinhibition, Ub transfer from E2 to HHARI, and ligation from the HHARI cysteine to a terminal acceptor.
Collapse
Affiliation(s)
- David M Duda
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | | | | | | | | | | | | |
Collapse
|