Simulation data related to the shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters Article Swipe

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Alves da Silva, Leticia , Clarke, Amy , Senning, Niklas , Stockner Thomas , Konstantinos Beis , Slotboom, Dirk ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.5281/zenodo.17544057

This record contains the MD simulation dataset for the paper with the title: Shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters Authors Thijs W. Ettema ^1#, Satomi Inaba-Inoue ^2,3,#,^†, Chancievan Thangaratnarajah ^1,#,‡, Leticia Alves da Silva ⁴, Nikas Senning ⁴,Amy Clarke ⁴, Piotr Stepien ^5,^§, Anokhi Shah ^6,7, Yue Ma ^6,7, Katie Hardman ⁸, Sophia David ⁹, Hassane El Mkami ¹⁰, Jonathan G. Heddle ^5,^§, Norimichi Nomura ¹¹, Satoshi Ogasawara ¹¹, So Iwata ¹¹, Dmitry Ghilarov ^5,12,*, Christos Pliotas ^6,7,*, Thomas Stockner ^4,*,Dirk J. Slotboom ^1,*, Konstantinos Beis ^2,3,* Affiliations ¹ Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands ² Department of Life Sciences, Imperial College London; Exhibition Road, London, South Kensington, SW7 2AZ, UK. ³ Rutherford Appleton Laboratory, Research Complex at Harwell; Didcot, Oxfordshire OX11 0FA, UK. ⁴ Institute of Pharmacology, Medical University of Vienna; 1090 Vienna, Austria ⁵ Malopolska Centre of Biotechnology, Jagiellonian University; Krakow, Poland. ⁶BioEmPiRe Centre for Structural Biological EPR Spectroscopy, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK. ⁷Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK ⁸Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK. ⁹ Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, OX3 7DQ, UK. ¹⁰School of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK ¹¹ Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan. ¹²Department of Molecular Microbiology, John Innes Centre; Norwich Research Park, Norwich NR4 7UH, UK

Related Topics

Biology

Research Institute

Library Science

The Transporter Refueled

Atp-Binding Cassette Transporter

Actinopterygii

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Biological sciences Research centre Library science University hospital Coronavirus disease 2019 (COVID-19) Transporter Exhibition Medical school National laboratory Chemistry Cell-penetrating peptide Human immunodeficiency virus (HIV) Medicine Cell survival ATP-binding cassette transporter Fish <Actinopterygii> Biology Columbia university

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Landing Page: https://doi.org/10.5281/zenodo.17544057
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DOI: https://doi.org/10.5281/zenodo.17544057

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Title: Simulation data related to the shared structural mechanisms of alternating access between the secondary peptide transporter SbmA and ABC transporters

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Language: en

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Publication year: 2025

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Publication date: 2025-12-01

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Authors: Alves da Silva, Leticia, Clarke, Amy, Senning, Niklas, Stockner Thomas, Konstantinos Beis, Slotboom, Dirk

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Landing page: https://doi.org/10.5281/zenodo.17544057

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Concepts: Biological sciences, Research centre, Library science, University hospital, Coronavirus disease 2019 (COVID-19), Transporter, Exhibition, Medical school, National laboratory, Chemistry, Cell-penetrating peptide, Human immunodeficiency virus (HIV), Medicine, Cell survival, ATP-binding cassette transporter, Fish , Biology, Columbia university

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abstract_inverted_index.Institute,	236
abstract_inverted_index.Malopolska	163
abstract_inverted_index.Manchester	192, 204
abstract_inverted_index.Rutherford	139
abstract_inverted_index.Structural	175, 212
abstract_inverted_index.University	114, 156, 189, 201, 219, 237, 250
abstract_inverted_index.mechanisms	15
abstract_inverted_index.simulation	5
abstract_inverted_index.structural	14
abstract_inverted_index.Inaba-Inoue	34
abstract_inverted_index.Kensington,	134
abstract_inverted_index.Laboratory,	141
abstract_inverted_index.Manchester,	191, 203
abstract_inverted_index.Oxfordshire	147
abstract_inverted_index.University,	269
abstract_inverted_index.University;	168
abstract_inverted_index.alternating	17
abstract_inverted_index.transporter	23
abstract_inverted_index.Biomolecular	107
abstract_inverted_index.Engineering,	105
abstract_inverted_index.Jagiellonian	167
abstract_inverted_index.Konstantinos	95
abstract_inverted_index.UK</p>	207, 258, 289
abstract_inverted_index.<p>This	0
abstract_inverted_index.Microbiology,	279
abstract_inverted_index.Pharmacology,	154
abstract_inverted_index.Spectroscopy,	178
abstract_inverted_index.Surveillance,	233
abstract_inverted_index.UK.</p>	137, 150, 195, 227, 243
abstract_inverted_index.<p>Thijs	29
abstract_inverted_index.Biotechnology,	110, 166, 200
abstract_inverted_index.</sup>Amy	47
abstract_inverted_index.</sup>Dirk	91
abstract_inverted_index.Japan.</p>	274
abstract_inverted_index.Thangaratnarajah	37
abstract_inverted_index.title:</p>	12
abstract_inverted_index.Austria</p>	161
abstract_inverted_index.Poland.</p>	170
abstract_inverted_index.</sup>School	245
abstract_inverted_index.Yoshida-Konoe-cho,	270
abstract_inverted_index.</sup>Astbury	209
abstract_inverted_index.</sup>BioEmPiRe	172
abstract_inverted_index.<p><sup>6	171
abstract_inverted_index.<p><sup>7	196
abstract_inverted_index.<p><sup>8	208
abstract_inverted_index.Netherlands</p>	121
abstract_inverted_index.</sup>Department	276
abstract_inverted_index.</sup>Manchester	197
abstract_inverted_index.<p><sup>10	244
abstract_inverted_index.<p><sup>12	275
abstract_inverted_index.<p> </p>	98
abstract_inverted_index.<sup>4</sup>,	43, 49
abstract_inverted_index.<sup>8</sup>,	61
abstract_inverted_index.<sup>9</sup>,	64
abstract_inverted_index.<p>Authors</p>	28
abstract_inverted_index.<sup>1#</sup>,	32
abstract_inverted_index.<sup>10</sup>,	68
abstract_inverted_index.<sup>11</sup>,	75, 78, 81
abstract_inverted_index.<sup>1,*</sup>,	94
abstract_inverted_index.<sup>6,7</sup>,	55, 58
abstract_inverted_index.<p><strong>Shared	13
abstract_inverted_index.<sup>6,7,*</sup>,	87
abstract_inverted_index.<sup>5,12,*</sup>,	84
abstract_inverted_index.<p>Affiliations</p>	99
abstract_inverted_index.<p><sup>1</sup>	100
abstract_inverted_index.<p><sup>2</sup>	122
abstract_inverted_index.<p><sup>3</sup>	138
abstract_inverted_index.<p><sup>4</sup>	151
abstract_inverted_index.<p><sup>5</sup>	162
abstract_inverted_index.<p><sup>9</sup>	228
abstract_inverted_index.<p><sup>11</sup>	259
abstract_inverted_index.<sup>1,#,&Dagger;</sup>,	38
abstract_inverted_index.<sup>4</sup>,<sup>	46
abstract_inverted_index.transporters</strong></p>	27
abstract_inverted_index.<sup>2,3,*</sup></p>	97
abstract_inverted_index.<sup>4,*</sup>,<sup>	90
abstract_inverted_index.<sup>5,</sup><sup>§</sup>,	52, 72
abstract_inverted_index.<sup>2,3,#,</sup><sup>&dagger;</sup>,	35
cited_by_percentile_year
countries_distinct_count	3
institutions_distinct_count	6
citation_normalized_percentile