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Aleksandrova AA, Sarti E, Forrest LR. EncoMPASS: An encyclopedia of membrane proteins analyzed by structure and symmetry. Structure 2024; 32:492-504.e4. [PMID: 38367624 PMCID: PMC11251422 DOI: 10.1016/j.str.2024.01.011] [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: 08/24/2018] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/19/2024]
Abstract
Protein structure determination and prediction, active site detection, and protein sequence alignment techniques all exploit information about protein structure and structural relationships. For membrane proteins, however, there is limited agreement among available online tools for highlighting and mapping such structural similarities. Moreover, no available resource provides a systematic overview of quaternary and internal symmetries, and their orientation relative to the membrane, despite the fact that these properties can provide key insights into membrane protein function and evolution. Here, we describe the Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry (EncoMPASS), a database for relating integral membrane proteins of known structure from the points of view of sequence, structure, and symmetry. EncoMPASS is accessible through a web interface, and its contents can be easily downloaded. This allows the user not only to focus on specific proteins, but also to study general properties of the structure and evolution of membrane proteins.
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Affiliation(s)
- Antoniya A Aleksandrova
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edoardo Sarti
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
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2
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Sun J, Kulandaisamy A, Liu J, Hu K, Gromiha MM, Zhang Y. Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications. Comput Struct Biotechnol J 2023; 21:1205-1226. [PMID: 36817959 PMCID: PMC9932300 DOI: 10.1016/j.csbj.2023.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
Membrane proteins mediate a wide spectrum of biological processes, such as signal transduction and cell communication. Due to the arduous and costly nature inherent to the experimental process, membrane proteins have long been devoid of well-resolved atomic-level tertiary structures and, consequently, the understanding of their functional roles underlying a multitude of life activities has been hampered. Currently, computational tools dedicated to furthering the structure-function understanding are primarily focused on utilizing intelligent algorithms to address a variety of site-wise prediction problems (e.g., topology and interaction sites), but are scattered across different computing sources. Moreover, the recent advent of deep learning techniques has immensely expedited the development of computational tools for membrane protein-related prediction problems. Given the growing number of applications optimized particularly by manifold deep neural networks, we herein provide a review on the current status of computational strategies mainly in membrane protein type classification, topology identification, interaction site detection, and pathogenic effect prediction. Meanwhile, we provide an overview of how the entire prediction process proceeds, including database collection, data pre-processing, feature extraction, and method selection. This review is expected to be useful for developing more extendable computational tools specific to membrane proteins.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Headington, Oxford OX3 7LD, UK
| | - Arulsamy Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India
| | - Jacklyn Liu
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Kai Hu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India,Corresponding authors.
| | - Yuan Zhang
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China,Corresponding authors.
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3
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Ernst M, Ozturk TN, Robertson JL. A single-molecule method for measuring fluorophore labeling yields for the study of membrane protein oligomerization in membranes. PLoS One 2023; 18:e0280693. [PMID: 36662827 PMCID: PMC9858377 DOI: 10.1371/journal.pone.0280693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Membrane proteins are often observed as higher-order oligomers, and in some cases in multiple stoichiometric forms, raising the question of whether dynamic oligomerization can be linked to modulation of function. To better understand this potential regulatory mechanism, there is an ongoing effort to quantify equilibrium reactions of membrane protein oligomerization directly in membranes. Single-molecule photobleaching analysis is particularly useful for this as it provides a binary readout of fluorophores attached to protein subunits at dilute conditions. However, any quantification of stoichiometry also critically requires knowing the probability that a subunit is fluorescently labeled. Since labeling uncertainty is often unavoidable, we developed an approach to estimate labeling yields using the photobleaching probability distribution of an intrinsic dimeric control. By iterative fitting of an experimental dimeric photobleaching probability distribution to an expected dimer model, we estimate the fluorophore labeling yields and find agreement with direct measurements of labeling of the purified protein by UV-VIS absorbance before reconstitution. Using this labeling prediction, similar estimation methods are applied to determine the dissociation constant of reactive CLC-ec1 dimerization constructs without prior knowledge of the fluorophore labeling yield. Finally, we estimate the operational range of subunit labeling yields that allows for discrimination of monomer and dimer populations across the reactive range of mole fraction densities. Thus, our study maps out a practical method for quantifying fluorophore labeling directly from single-molecule photobleaching data, improving the ability to quantify reactive membrane protein stoichiometry in membranes.
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Affiliation(s)
- Melanie Ernst
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tugba N. Ozturk
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Janice L. Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
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4
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Burata OE, Yeh TJ, Macdonald CB, Stockbridge RB. Still rocking in the structural era: A molecular overview of the small multidrug resistance (SMR) transporter family. J Biol Chem 2022; 298:102482. [PMID: 36100040 PMCID: PMC9574504 DOI: 10.1016/j.jbc.2022.102482] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
The small multidrug resistance (SMR) family is composed of widespread microbial membrane proteins that fulfill different transport functions. Four functional SMR subtypes have been identified, which variously transport the small, charged metabolite guanidinium, bulky hydrophobic drugs and antiseptics, polyamines, and glycolipids across the membrane bilayer. The transporters possess a minimalist architecture, with ∼100-residue subunits that require assembly into homodimers or heterodimers for transport. In part because of their simple construction, the SMRs are a tractable system for biochemical and biophysical analysis. Studies of SMR transporters over the last 25 years have yielded deep insights for diverse fields, including membrane protein topology and evolution, mechanisms of membrane transport, and bacterial multidrug resistance. Here, we review recent advances in understanding the structures and functions of SMR transporters. New molecular structures of SMRs representing two of the four functional subtypes reveal the conserved structural features that have permitted the emergence of disparate substrate transport functions in the SMR family and illuminate structural similarities with a distantly related membrane transporter family, SLC35/DMT.
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Affiliation(s)
- Olive E Burata
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Trevor Justin Yeh
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Randy B Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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5
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Staritzbichler R, Yaklich E, Sarti E, Ristic N, Hildebrand PW, Forrest LR. AlignMe: an update of the web server for alignment of membrane protein sequences. Nucleic Acids Res 2022; 50:W29-W35. [PMID: 35609986 PMCID: PMC9252776 DOI: 10.1093/nar/gkac391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/19/2022] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
The AlignMe web server is dedicated to accurately aligning sequences of membrane proteins, a particularly challenging task due to the strong evolutionary divergence and the low compositional complexity of hydrophobic membrane-spanning proteins. AlignMe can create pairwise alignments of either two primary amino acid sequences or two hydropathy profiles. The web server for AlignMe has been continuously available for >10 years, supporting 1000s of users per year. Recent improvements include anchoring, multiple submissions, and structure visualization. Anchoring is the ability to constrain a position in an alignment, which allows expert information about related residues in proteins to be incorporated into an alignment without manual modification. The original web interface to the server limited the user to one alignment per submission, hindering larger scale studies. Now, batches of alignments can be initiated with a single submission. Finally, to provide structural context for the relationship between proteins, sequence similarity can now be mapped onto one or more structures (or structural models) of the proteins being aligned, by links to MutationExplorer, a web-based visualization tool. Together with a refreshed user interface, these features further enhance an important resource in the membrane protein community. The AlignMe web server is freely available at https://www.bioinfo.mpg.de/AlignMe/.
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Affiliation(s)
- René Staritzbichler
- University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Emily Yaklich
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Edoardo Sarti
- Algorithms, Biology, Structure Unit Inria Sophia Antipolis - Méditerranée, 06902 Valbonne, France
| | - Nikola Ristic
- University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Peter W Hildebrand
- University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany.,Charité -Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, 10117 Berlin, Germany
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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Fu T, Li F, Zhang Y, Yin J, Qiu W, Li X, Liu X, Xin W, Wang C, Yu L, Gao J, Zheng Q, Zeng S, Zhu F. VARIDT 2.0: structural variability of drug transporter. Nucleic Acids Res 2021; 50:D1417-D1431. [PMID: 34747471 PMCID: PMC8728241 DOI: 10.1093/nar/gkab1013] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/08/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022] Open
Abstract
The structural variability data of drug transporter (DT) are key for research on precision medicine and rational drug use. However, these valuable data are not sufficiently covered by the available databases. In this study, a major update of VARIDT (a database previously constructed to provide DTs' variability data) was thus described. First, the experimentally resolved structures of all DTs reported in the original VARIDT were discovered from PubMed and Protein Data Bank. Second, the structural variability data of each DT were collected by literature review, which included: (a) mutation-induced spatial variations in folded state, (b) difference among DT structures of human and model organisms, (c) outward/inward-facing DT conformations and (d) xenobiotics-driven alterations in the 3D complexes. Third, for those DTs without experimentally resolved structural variabilities, homology modeling was further applied as well-established protocol to enrich such valuable data. As a result, 145 mutation-induced spatial variations of 42 DTs, 1622 inter-species structures originating from 292 DTs, 118 outward/inward-facing conformations belonging to 59 DTs, and 822 xenobiotics-regulated structures in complex with 57 DTs were updated to VARIDT (https://idrblab.org/varidt/ and http://varidt.idrblab.net/). All in all, the newly collected structural variabilities will be indispensable for explaining drug sensitivity/selectivity, bridging preclinical research with clinical trial, revealing the mechanism underlying drug-drug interaction, and so on.
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Affiliation(s)
- Tingting Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenqi Qiu
- Department of Surgery, HKU-SZH & Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xuedong Li
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Xingang Liu
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Wenwen Xin
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Chengzhao Wang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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7
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Yin J, Li F, Li Z, Yu L, Zhu F, Zeng S. Feature, Function, and Information of Drug Transporter Related Databases. Drug Metab Dispos 2021; 50:76-85. [PMID: 34426411 DOI: 10.1124/dmd.121.000419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/20/2021] [Indexed: 11/22/2022] Open
Abstract
With the rapid progress in pharmaceutical experiments and clinical investigations, extensive knowledge of drug transporters (DTs) has accumulated, which is valuable data for the understanding of drug metabolism and disposition. However, such data is largely dispersed in the literature, which hampers its utility and significantly limits its possibility for comprehensive analysis. A variety of databases have, therefore, been constructed to provide DT-related data, and they were reviewed in this study. First, several knowledge bases providing data regarding clinically important drugs and their corresponding transporters were discussed, which constituted the most important resources of DT-centered data. Second, some databases describing the general transporters and their functional families were reviewed. Third, various databases offering transporter information as part of their entire data collection were described. Finally, customized database functions that are available to facilitate DT-related research were discussed. This review provided an overview of the whole collection of DT-related databases, which might facilitate research on precision medicine and rational drug use. Significance Statement A collection of well-established databases related to DTs were comprehensively reviewed, which were organized according to their importance in drug ADME research. These databases could collectively contribute to the research on rational drug use.
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Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, China
| | - Zhaorong Li
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, China
| | | | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, China
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8
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Staritzbichler R, Sarti E, Yaklich E, Aleksandrova A, Stamm M, Khafizov K, Forrest LR. Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors. PLoS One 2021; 16:e0239881. [PMID: 33930031 PMCID: PMC8087094 DOI: 10.1371/journal.pone.0239881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/15/2021] [Indexed: 01/08/2023] Open
Abstract
The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution, and in the generation of homology-based models. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently, if those positions are not correctly matched by a standard pairwise sequence alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner, with manual adjustments. However, such modifications are problematic because they reduce the robustness and reproducibility of the aligned regions either side of the newly matched positions. Previous studies have introduced restraints as a means to impose the matching of positions during sequence alignments, originally in the context of genome assembly. Here we introduce position restraints, or "anchors" as a feature in our alignment tool AlignMe, providing an aid to pairwise global sequence alignment of alpha-helical membrane proteins. Applying this approach to realistic scenarios involving distantly-related and low complexity sequences, we illustrate how the addition of anchors can be used to modify alignments, while still maintaining the reproducibility and rigor of the rest of the alignment. Anchored alignments can be generated using the online version of AlignMe available at www.bioinfo.mpg.de/AlignMe/.
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Affiliation(s)
- René Staritzbichler
- ProteinFormatics Group, Institute of Biophysics and Medical Physics, University of Leipzig, Leipzig, Germany
| | - Edoardo Sarti
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris Seine, Sorbonne Université, Paris, France
| | - Emily Yaklich
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Antoniya Aleksandrova
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
| | - Marcus Stamm
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, National Research University, Moscow, Russia
| | - Lucy R. Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States of America
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9
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Merski M, Młynarczyk K, Ludwiczak J, Skrzeczkowski J, Dunin-Horkawicz S, Górna MW. Self-analysis of repeat proteins reveals evolutionarily conserved patterns. BMC Bioinformatics 2020; 21:179. [PMID: 32381046 PMCID: PMC7204011 DOI: 10.1186/s12859-020-3493-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/15/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Protein repeats can confound sequence analyses because the repetitiveness of their amino acid sequences lead to difficulties in identifying whether similar repeats are due to convergent or divergent evolution. We noted that the patterns derived from traditional "dot plot" protein sequence self-similarity analysis tended to be conserved in sets of related repeat proteins and this conservation could be quantitated using a Jaccard metric. RESULTS Comparison of these dot plots obviated the issues due to sequence similarity for analysis of repeat proteins. A high Jaccard similarity score was suggestive of a conserved relationship between closely related repeat proteins. The dot plot patterns decayed quickly in the absence of selective pressure with an expected loss of 50% of Jaccard similarity due to a loss of 8.2% sequence identity. To perform method testing, we assembled a standard set of 79 repeat proteins representing all the subgroups in RepeatsDB. Comparison of known repeat and non-repeat proteins from the PDB suggested that the information content in dot plots could be used to identify repeat proteins from pure sequence with no requirement for structural information. Analysis of the UniRef90 database suggested that 16.9% of all known proteins could be classified as repeat proteins. These 13.3 million putative repeat protein chains were clustered and a significant amount (82.9%) of clusters containing between 5 and 200 members were of a single functional type. CONCLUSIONS Dot plot analysis of repeat proteins attempts to obviate issues that arise due to the sequence degeneracy of repeat proteins. These results show that this kind of analysis can efficiently be applied to analyze repeat proteins on a large scale.
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Affiliation(s)
- Matthew Merski
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Krzysztof Młynarczyk
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Jakub Skrzeczkowski
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Stanisław Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maria W. Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
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10
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An Interfacial Sodium Ion is an Essential Structural Feature of Fluc Family Fluoride Channels. J Mol Biol 2020; 432:1098-1108. [PMID: 31945374 DOI: 10.1016/j.jmb.2020.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/17/2022]
Abstract
Fluc family fluoride channels are assembled as primitive antiparallel homodimers. Crystallographic studies revealed a cation bound at the center of the protein, where it is coordinated at the dimer interface by main chain carbonyl oxygen atoms from the midmembrane breaks in two corresponding transmembrane helices. Here, we show that this cation is a stably bound sodium ion, and although it is not a transported substrate, its presence is required for the channel to adopt an open, fluoride-conducting conformation. The interfacial site is selective for sodium over other cations, except for Li+, which competes with Na+ for binding, but does not support channel activity. The strictly structural role fulfilled by this sodium provides new context to understand the structures, mechanisms, and evolutionary origins of widespread Na+-coupled transporters.
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11
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Juračka J, Šrejber M, Melíková M, Bazgier V, Berka K. MolMeDB: Molecules on Membranes Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5523873. [PMID: 31250015 PMCID: PMC6597476 DOI: 10.1093/database/baz078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/16/2022]
Abstract
Biological membranes act as barriers or reservoirs for many compounds within the human body. As such, they play an important role in pharmacokinetics and pharmacodynamics of drugs and other molecular species. Until now, most membrane/drug interactions have been inferred from simple partitioning between octanol and water phases. However, the observed variability in membrane composition and among compounds themselves stretches beyond such simplification as there are multiple drug–membrane interactions. Numerous experimental and theoretical approaches are used to determine the molecule–membrane interactions with variable accuracy, but there is no open resource for their critical comparison. For this reason, we have built Molecules on Membranes Database (MolMeDB), which gathers data about over 3600 compound–membrane interactions including partitioning, penetration and positioning. The data have been collected from scientific articles published in peer-reviewed journals and complemented by in-house calculations from high-throughput COSMOmic approach to set up a baseline for further comparison. The data in MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method or dataset and we offer the collected data openly for further reuse and we are open to further additions. MolMeDB can be a powerful tool that could help researchers better understand the role of membranes and to compare individual approaches used for the study of molecule/membrane interactions.
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Affiliation(s)
- Jakub Juračka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Martin Šrejber
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michaela Melíková
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Václav Bazgier
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Tř. 17, listopadu 12, 771 46 Olomouc, Czech Republic
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12
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Rigden DJ, Fernández X. The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. Nucleic Acids Res 2019; 47:D1-D7. [PMID: 30626175 PMCID: PMC6323895 DOI: 10.1093/nar/gky1267] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The 2019 Nucleic Acids Research (NAR) Database Issue contains 168 papers spanning molecular biology. Among them, 64 are new and another 92 are updates describing resources that appeared in the Issue previously. The remaining 12 are updates on databases most recently published elsewhere. This Issue contains two Breakthrough articles, on the Virtual Metabolic Human (VMH) database which links human and gut microbiota metabolism with diet and disease, and Vibrism DB, a database of mouse brain anatomy and gene (co-)expression with sophisticated visualization and session sharing. Major returning nucleic acid databases include RNAcentral, miRBase and LncRNA2Target. Protein sequence databases include UniProtKB, InterPro and Pfam, while wwPDB and RCSB cover protein structure. STRING and KEGG update in the section on metabolism and pathways. Microbial genomes are covered by IMG/M and resources for human and model organism genomics include Ensembl, UCSC Genome Browser, GENCODE and Flybase. Genomic variation and disease are well-covered by GWAS Catalog, PopHumanScan, OMIM and COSMIC, CADD being another major newcomer. Major new proteomics resources reporting here include iProX and jPOSTdb. The entire database issue is freely available online on the NAR website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 506 entries, adding 66 new resources and eliminating 147 discontinued URLs, bringing the current total to 1613 databases. It is available at http://www.oxfordjournals.org/nar/database/c.
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Affiliation(s)
- Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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