1
|
Griffiths D, Anderson M, Richardson K, Inaba-Inoue S, Allen WJ, Collinson I, Beis K, Morris M, Giles K, Politis A. Cyclic Ion Mobility for Hydrogen/Deuterium Exchange-Mass Spectrometry Applications. Anal Chem 2024; 96:5869-5877. [PMID: 38561318 PMCID: PMC11024883 DOI: 10.1021/acs.analchem.3c05753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localization of dynamic changes. Consequently, the HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase the data quality by providing an orthogonal mode of peptide ion separation in the gas phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multipass IM separations. Using one-pass and multipass cIM routines, we use the recently commercialized SELECT SERIES Cyclic IM spectrometer for HDX-MS analyses of four detergent solubilized IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multipass cIM data. Interestingly, use of one-pass and multipass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM that has the potential to enable the analysis of more complex systems with greater accuracy and speed.
Collapse
Affiliation(s)
- Damon Griffiths
- Faculty
of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, Princess
Street, Manchester M1 7DN, United Kingdom
| | - Malcolm Anderson
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Keith Richardson
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Satomi Inaba-Inoue
- Department
of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford
Appleton Laboratory, Research Complex at Harwell, Oxfordshire, Didcot OX11 0FA, United Kingdom
- Diffraction
and Scattering Division, Japan Synchrotron
Radiation Research Institute, SPring-8, 1-1-1, Kouto, Sayo, Hyogo 679-5198, Japan
| | - William J. Allen
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Ian Collinson
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Konstantinos Beis
- Department
of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom
- Rutherford
Appleton Laboratory, Research Complex at Harwell, Oxfordshire, Didcot OX11 0FA, United Kingdom
| | - Michael Morris
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Kevin Giles
- Waters
Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United
Kingdom
| | - Argyris Politis
- Faculty
of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, Princess
Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
2
|
Crossley JA, Allen WJ, Watkins DW, Sabir T, Radford SE, Tuma R, Collinson I, Fessl T. Dynamic coupling of fast channel gating with slow ATP-turnover underpins protein transport through the Sec translocon. EMBO J 2024; 43:1-13. [PMID: 38177311 PMCID: PMC10883268 DOI: 10.1038/s44318-023-00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024] Open
Abstract
The Sec translocon is a highly conserved membrane assembly for polypeptide transport across, or into, lipid bilayers. In bacteria, secretion through the core channel complex-SecYEG in the inner membrane-is powered by the cytosolic ATPase SecA. Here, we use single-molecule fluorescence to interrogate the conformational state of SecYEG throughout the ATP hydrolysis cycle of SecA. We show that the SecYEG channel fluctuations between open and closed states are much faster (~20-fold during translocation) than ATP turnover, and that the nucleotide status of SecA modulates the rates of opening and closure. The SecY variant PrlA4, which exhibits faster transport but unaffected ATPase rates, increases the dwell time in the open state, facilitating pre-protein diffusion through the pore and thereby enhancing translocation efficiency. Thus, rapid SecYEG channel dynamics are allosterically coupled to SecA via modulation of the energy landscape, and play an integral part in protein transport. Loose coupling of ATP-turnover by SecA to the dynamic properties of SecYEG is compatible with a Brownian-rachet mechanism of translocation, rather than strict nucleotide-dependent interconversion between different static states of a power stroke.
Collapse
Affiliation(s)
- Joel A Crossley
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK
| | - Tara Sabir
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, BS8 1QU, UK.
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic.
| |
Collapse
|
3
|
Schimunek J, Seidl P, Elez K, Hempel T, Le T, Noé F, Olsson S, Raich L, Winter R, Gokcan H, Gusev F, Gutkin EM, Isayev O, Kurnikova MG, Narangoda CH, Zubatyuk R, Bosko IP, Furs KV, Karpenko AD, Kornoushenko YV, Shuldau M, Yushkevich A, Benabderrahmane MB, Bousquet-Melou P, Bureau R, Charton B, Cirou BC, Gil G, Allen WJ, Sirimulla S, Watowich S, Antonopoulos N, Epitropakis N, Krasoulis A, Itsikalis V, Theodorakis S, Kozlovskii I, Maliutin A, Medvedev A, Popov P, Zaretckii M, Eghbal-Zadeh H, Halmich C, Hochreiter S, Mayr A, Ruch P, Widrich M, Berenger F, Kumar A, Yamanishi Y, Zhang KYJ, Bengio E, Bengio Y, Jain MJ, Korablyov M, Liu CH, Marcou G, Glaab E, Barnsley K, Iyengar SM, Ondrechen MJ, Haupt VJ, Kaiser F, Schroeder M, Pugliese L, Albani S, Athanasiou C, Beccari A, Carloni P, D'Arrigo G, Gianquinto E, Goßen J, Hanke A, Joseph BP, Kokh DB, Kovachka S, Manelfi C, Mukherjee G, Muñiz-Chicharro A, Musiani F, Nunes-Alves A, Paiardi G, Rossetti G, Sadiq SK, Spyrakis F, Talarico C, Tsengenes A, Wade RC, Copeland C, Gaiser J, Olson DR, Roy A, Venkatraman V, Wheeler TJ, Arthanari H, Blaschitz K, Cespugli M, Durmaz V, Fackeldey K, Fischer PD, Gorgulla C, Gruber C, Gruber K, Hetmann M, Kinney JE, Padmanabha Das KM, Pandita S, Singh A, Steinkellner G, Tesseyre G, Wagner G, Wang ZF, Yust RJ, Druzhilovskiy DS, Filimonov DA, Pogodin PV, Poroikov V, Rudik AV, Stolbov LA, Veselovsky AV, De Rosa M, De Simone G, Gulotta MR, Lombino J, Mekni N, Perricone U, Casini A, Embree A, Gordon DB, Lei D, Pratt K, Voigt CA, Chen KY, Jacob Y, Krischuns T, Lafaye P, Zettor A, Rodríguez ML, White KM, Fearon D, Von Delft F, Walsh MA, Horvath D, Brooks CL, Falsafi B, Ford B, García-Sastre A, Yup Lee S, Naffakh N, Varnek A, Klambauer G, Hermans TM. A community effort in SARS-CoV-2 drug discovery. Mol Inform 2024; 43:e202300262. [PMID: 37833243 DOI: 10.1002/minf.202300262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/15/2023]
Abstract
The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against COVID-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.
Collapse
|
4
|
Robinson ML, Hahn PG, Inouye BD, Underwood N, Whitehead SR, Abbott KC, Bruna EM, Cacho NI, Dyer LA, Abdala-Roberts L, Allen WJ, Andrade JF, Angulo DF, Anjos D, Anstett DN, Bagchi R, Bagchi S, Barbosa M, Barrett S, Baskett CA, Ben-Simchon E, Bloodworth KJ, Bronstein JL, Buckley YM, Burghardt KT, Bustos-Segura C, Calixto ES, Carvalho RL, Castagneyrol B, Chiuffo MC, Cinoğlu D, Cinto Mejía E, Cock MC, Cogni R, Cope OL, Cornelissen T, Cortez DR, Crowder DW, Dallstream C, Dáttilo W, Davis JK, Dimarco RD, Dole HE, Egbon IN, Eisenring M, Ejomah A, Elderd BD, Endara MJ, Eubanks MD, Everingham SE, Farah KN, Farias RP, Fernandes AP, Fernandes GW, Ferrante M, Finn A, Florjancic GA, Forister ML, Fox QN, Frago E, França FM, Getman-Pickering AS, Getman-Pickering Z, Gianoli E, Gooden B, Gossner MM, Greig KA, Gripenberg S, Groenteman R, Grof-Tisza P, Haack N, Hahn L, Haq SM, Helms AM, Hennecke J, Hermann SL, Holeski LM, Holm S, Hutchinson MC, Jackson EE, Kagiya S, Kalske A, Kalwajtys M, Karban R, Kariyat R, Keasar T, Kersch-Becker MF, Kharouba HM, Kim TN, Kimuyu DM, Kluse J, Koerner SE, Komatsu KJ, Krishnan S, Laihonen M, Lamelas-López L, LaScaleia MC, Lecomte N, Lehn CR, Li X, Lindroth RL, LoPresti EF, Losada M, Louthan AM, Luizzi VJ, Lynch SC, Lynn JS, Lyon NJ, Maia LF, Maia RA, Mannall TL, Martin BS, Massad TJ, McCall AC, McGurrin K, Merwin AC, Mijango-Ramos Z, Mills CH, Moles AT, Moore CM, Moreira X, Morrison CR, Moshobane MC, Muola A, Nakadai R, Nakajima K, Novais S, Ogbebor CO, Ohsaki H, Pan VS, Pardikes NA, Pareja M, Parthasarathy N, Pawar RR, Paynter Q, Pearse IS, Penczykowski RM, Pepi AA, Pereira CC, Phartyal SS, Piper FI, Poveda K, Pringle EG, Puy J, Quijano T, Quintero C, Rasmann S, Rosche C, Rosenheim LY, Rosenheim JA, Runyon JB, Sadeh A, Sakata Y, Salcido DM, Salgado-Luarte C, Santos BA, Sapir Y, Sasal Y, Sato Y, Sawant M, Schroeder H, Schumann I, Segoli M, Segre H, Shelef O, Shinohara N, Singh RP, Smith DS, Sobral M, Stotz GC, Tack AJM, Tayal M, Tooker JF, Torrico-Bazoberry D, Tougeron K, Trowbridge AM, Utsumi S, Uyi O, Vaca-Uribe JL, Valtonen A, van Dijk LJA, Vandvik V, Villellas J, Waller LP, Weber MG, Yamawo A, Yim S, Zarnetske PL, Zehr LN, Zhong Z, Wetzel WC. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science 2023; 382:679-683. [PMID: 37943897 DOI: 10.1126/science.adh8830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023]
Abstract
Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.
Collapse
Affiliation(s)
- M L Robinson
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Department of Biology, Utah State University, Logan, UT, USA
| | - P G Hahn
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
| | - B D Inouye
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - N Underwood
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - S R Whitehead
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - K C Abbott
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA
| | - E M Bruna
- Center for Latin American Studies, University of Florida, Gainesville, FL, USA
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - N I Cacho
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - L A Dyer
- Biology Department, University of Nevada, Reno, Reno, NV, USA
| | - L Abdala-Roberts
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - W J Allen
- Bio-Protection Research Centre, University of Canterbury, Christchurch, New Zealand
| | - J F Andrade
- Departamento de Sistemática e Ecologia Universidade Federal da Paraíba, João Pessoa, Brazil
| | - D F Angulo
- Centro de Investigación Científica de Yucatán, Departamento de Recursos Naturales, Mérida, Yucatán, México
| | - D Anjos
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - D N Anstett
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - R Bagchi
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - S Bagchi
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - M Barbosa
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - S Barrett
- Department of Biodiversity Conservation & Attractions Western Australia, Albany, Western Australia, Australia
| | - C A Baskett
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - E Ben-Simchon
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization - Volcani Institute, Rishon Le Tzion, Israel
- Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - K J Bloodworth
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - J L Bronstein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Y M Buckley
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland
| | - K T Burghardt
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - C Bustos-Segura
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - E S Calixto
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
| | - R L Carvalho
- Institute of Advanced Studies, University of São Paulo, São Paulo, Brazil
| | | | - M C Chiuffo
- Grupo de Ecología de Invasiones, INIBIOMA, Universidad Nacional del Comahue, CONICET, San Carlos de Bariloche, Río Negro, Argentina
| | - D Cinoğlu
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - E Cinto Mejía
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - M C Cock
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa, Santa Rosa, La Pampa, Argentina
| | - R Cogni
- Department of Ecology, University of São Paulo, São Paulo, Brazil
| | - O L Cope
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Department of Biology, Whitworth University, Spokane, WA, USA
| | - T Cornelissen
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - D R Cortez
- Department of Biology, California State University San Bernardino, San Bernardino, CA, USA
| | - D W Crowder
- Department of Entomology, Washington State University, Pullman, WA, USA
| | - C Dallstream
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - W Dáttilo
- Red de Ecoetología, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | - J K Davis
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - R D Dimarco
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
- Grupo de Ecología de Poblaciones de Insectos, IFAB, San Carlos de Bariloche, Río Negro, Argentina
| | - H E Dole
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - I N Egbon
- Department of Animal and Environmental Biology, University of Benin, Benin City, Nigeria
| | - M Eisenring
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - A Ejomah
- Department of Animal and Environmental Biology, University of Benin, Benin City, Nigeria
| | - B D Elderd
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - M-J Endara
- Grupo de Investigación en Ecología y Evolución en los Trópicos-EETROP, Universidad de las Américas, Quito, Ecuador
| | - M D Eubanks
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - S E Everingham
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Evolution & Ecology Research Centre, University of New South Wales Sydney, Sydney, Australia
| | - K N Farah
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - R P Farias
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, Brasil
| | - A P Fernandes
- Department of Botany, Ganpat Parsekar College of Education Harmal, Pernem, Goa, India
| | - G W Fernandes
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Knowledge Center for Biodiversity, Brazil
| | - M Ferrante
- Faculty of Agricultural Sciences and Environment, University of the Azores, Ponta Delgada, Portugal
- Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | - A Finn
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland
| | - G A Florjancic
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - M L Forister
- Biology Department, University of Nevada, Reno, Reno, NV, USA
| | - Q N Fox
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - E Frago
- CIRAD, UMR CBGP, INRAE, Institut Agro, IRD, Université Montpellier, Montpellier, France
| | - F M França
- School of Biological Sciences, University of Bristol, Bristol, UK
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Pará, Belém, Pará, Brasil
| | | | - Z Getman-Pickering
- Department of Mechanical and Industrial Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - E Gianoli
- Departamento de Biología, Universidad de La Serena, La Serena, Chile
| | - B Gooden
- CSIRO Black Mountain Laboratories, CSIRO Health and Biosecurity, Canberra, Australia
| | - M M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - K A Greig
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - S Gripenberg
- School of Biological Sciences, University of Reading, Reading, UK
| | - R Groenteman
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
| | - P Grof-Tisza
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - N Haack
- Independent Institute for Environmental Issues, Halle, Germany
| | - L Hahn
- Molecular Evolution and Systematics of Animals, University of Leipzig, Leipzig, Germany
| | - S M Haq
- Wildlife Crime Control Division, Wildlife Trust of India, Noida, Uttar Pradesh, India
| | - A M Helms
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - J Hennecke
- Systematic Botany and Functional Biodiversity, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - S L Hermann
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - L M Holeski
- Department of Biological Sciences and Center for Adaptive Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - S Holm
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - M C Hutchinson
- Department of Life and Environmental Sciences, University of California, Merced, Merced, CA, USA
| | - E E Jackson
- School of Biological Sciences, University of Reading, Reading, UK
| | - S Kagiya
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - A Kalske
- Department of Biology, University of Turku, Turku, Finland
| | - M Kalwajtys
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - R Karban
- Department of Entomology and Nematology, University of California Davis, Davis, CA, USA
| | - R Kariyat
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - T Keasar
- Department of Biology and the Environment, University of Haifa - Oranim, Oranim, Tivon, Israel
| | - M F Kersch-Becker
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - H M Kharouba
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - T N Kim
- Department of Entomology, Kansas State University, Manhattan, KS, USA
| | - D M Kimuyu
- Department of Natural Resources, Karatina University, Karatina, Kenya
| | - J Kluse
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - S E Koerner
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - K J Komatsu
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
- Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - S Krishnan
- Center for Sustainable Future, Amrita University and EIACP RP, Amrita Viswa Vidyapeetham, Coimbatore, India
| | - M Laihonen
- Biodiversity Unit, University of Turku, Turku, Finland
| | - L Lamelas-López
- Faculty of Agricultural Sciences and Environment, University of the Azores, Ponta Delgada, Portugal
| | - M C LaScaleia
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - N Lecomte
- Canada Research Chair in Polar and Boreal Ecology, Department of Biology and Centre d'Études Nordiques, Université de Moncton, Moncton, Canada
| | - C R Lehn
- Biological Sciences Course, Instituto Federal Farroupilha, Panambi, RS, Brazil
| | - X Li
- College of Resources and Environmental sciences, Jilin Agricultural University, Changchun, China
| | - R L Lindroth
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - E F LoPresti
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - M Losada
- Department of Soil Science and Agricultural Chemistry, University of Santiago de Compostela, Santiago de Compostela, A Coruña, Spain
| | - A M Louthan
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - V J Luizzi
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - S C Lynch
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - J S Lynn
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| | - N J Lyon
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - L F Maia
- Bio-Protection Research Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - R A Maia
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - T L Mannall
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - B S Martin
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - T J Massad
- Department of Scientific Services, Gorongosa National Park, Sofala, Mozambique
| | - A C McCall
- Biology Department, Denison University, Granville, OH, USA
| | - K McGurrin
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - A C Merwin
- Department of Biology and Geology, Baldwin Wallace University, Berea, OH, USA
| | - Z Mijango-Ramos
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - C H Mills
- Evolution & Ecology Research Centre, University of New South Wales Sydney, Sydney, Australia
| | - A T Moles
- Evolution & Ecology Research Centre, University of New South Wales Sydney, Sydney, Australia
| | - C M Moore
- Department of Biology, Colby College, Waterville, ME, USA
| | - X Moreira
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Galicia, Spain
| | - C R Morrison
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - M C Moshobane
- South African National Biodiversity Institute, Pretoria National Botanical Garden, Brummeria, Silverton, South Africa
- Centre for Functional Biodiversity, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - A Muola
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Tromsø, Norway
| | - R Nakadai
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - K Nakajima
- Insitute of Science and Engineering, Chuo University, Tokyo, Japan
- Institute of Cave Research, Shimohei-guun, Iwate Prefecture, Japan
| | - S Novais
- Red de Interacciones Multitróficas, Instituto de Ecología A.C., Xalapa, Veracruz, Mexico
| | - C O Ogbebor
- Nigerian Institute for Oil Palm Research, Benin City, Edo State, Nigeria
| | - H Ohsaki
- Department of Biological Sciences, Hirosaki University, Hirosaki, Aomori, Japan
| | - V S Pan
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - N A Pardikes
- Department of Biology, Utah State University, Logan, UT, USA
| | - M Pareja
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, Brazil
| | - N Parthasarathy
- Department of Ecology and Evironmental Sciences, Pondicherry University, Puducherry, India
| | | | - Q Paynter
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - I S Pearse
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - R M Penczykowski
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - A A Pepi
- Department of Biology, Tufts University, Medford, MA, USA
| | - C C Pereira
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - S S Phartyal
- School of Ecology & Environment Studies, Nalanda University, Rajgir, India
| | - F I Piper
- Millennium Nucleus of Patagonian Limit of Life and Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Institute of Ecology and Biodiversity, Ñuñoa, Santiago
| | - K Poveda
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - E G Pringle
- Biology Department, University of Nevada, Reno, Reno, NV, USA
| | - J Puy
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - T Quijano
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - C Quintero
- INIBIOMA, CONICET - Universidad Nacional del Comahue, San Carlos de Bariloche, Río Negro, Argentina
| | - S Rasmann
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - C Rosche
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - L Y Rosenheim
- Department of Entomology and Nematology, University of California Davis, Davis, CA, USA
| | - J A Rosenheim
- Department of Entomology and Nematology, University of California Davis, Davis, CA, USA
| | - J B Runyon
- Rocky Mountain Research Station, USDA Forest Service, Bozeman, MT, USA
| | - A Sadeh
- Department of Natural Resources, Newe Ya'ar Research Center, Volcani Institute, Ramat Yishay, Israel
| | - Y Sakata
- Department of Biological Environment, Akita Prefectural University, Shimoshinjyo-Nakano, Akita, Japan
| | - D M Salcido
- Biology Department, University of Nevada, Reno, Reno, NV, USA
| | - C Salgado-Luarte
- Instituto de Investigación Multidisciplinario en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - B A Santos
- Departamento de Sistemática e Ecologia Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Y Sapir
- The Botanic Garden, School of Plant Sciences and Food Security, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Y Sasal
- INIBIOMA, CONICET - Universidad Nacional del Comahue, San Carlos de Bariloche, Río Negro, Argentina
| | - Y Sato
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - M Sawant
- Department of Ecology, University of Pune, Maharashtra, India
| | - H Schroeder
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - I Schumann
- Department of Human Genetics, University of Leipzig, Leipzig, Germany
| | - M Segoli
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - H Segre
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization - Volcani Institute, Rishon Le Tzion, Israel
- Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- Department of Natural Resources, Newe Ya'ar Research Center, Volcani Institute, Ramat Yishay, Israel
| | - O Shelef
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization - Volcani Institute, Rishon Le Tzion, Israel
| | - N Shinohara
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - R P Singh
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - D S Smith
- Department of Biology, California State University San Bernardino, San Bernardino, CA, USA
| | - M Sobral
- Department of Soil Science and Agricultural Chemistry, University of Santiago de Compostela, Santiago de Compostela, A Coruña, Spain
| | - G C Stotz
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - A J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - M Tayal
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - J F Tooker
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - D Torrico-Bazoberry
- Laboratorio de Comportamiento Animal y Humano, Centro de Investigación en Complejidad Social, Universidad del Desarrollo, Las Condes, Chile
| | - K Tougeron
- Écologie et Dynamique des Systèmes Anthropisés, Université de Picardie Jules Verne, UMR 7058 CNRS, Amiens, France
- Ecology of Interactions and Global Change, Institut de Recherche en Biosciences, Université de Mons, Mons, Belgium
| | - A M Trowbridge
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI, USA
| | - S Utsumi
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - O Uyi
- Department of Animal and Environmental Biology, University of Benin, Benin City, Nigeria
- Department of Entomology, University of Georgia, Tifton, GA, USA
| | - J L Vaca-Uribe
- Programa de ingeniría agroecológica, Corporación Universitaria Minuto de Dios, Bogotá, Colombia
| | - A Valtonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - L J A van Dijk
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - V Vandvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - J Villellas
- Department of Life Sciences, University of Alcalá, Madrid, Spain
| | - L P Waller
- Bioprotection Aotearoa, Lincoln University, Lincoln, New Zealand
| | - M G Weber
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - A Yamawo
- Department of Biological Sciences, Hirosaki University, Hirosaki, Aomori, Japan
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - S Yim
- Biology Department, University of Nevada, Reno, Reno, NV, USA
| | - P L Zarnetske
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - L N Zehr
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Z Zhong
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology, Ministry of Education/Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, Jilin Province, China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China
| | - W C Wetzel
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
- Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| |
Collapse
|
5
|
Allen WJ, Collinson I. A unifying mechanism for protein transport through the core bacterial Sec machinery. Open Biol 2023; 13:230166. [PMID: 37643640 PMCID: PMC10465204 DOI: 10.1098/rsob.230166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but they also pose a challenge: how to partition the molecules that perform biological functions-the proteins-across impermeable barriers into sub-cellular organelles, and to the outside. The solution lies in the evolution of specialized machines, translocons, found in every biological membrane, which act both as gate and gatekeeper across and into membrane bilayers. Understanding how these translocons operate at the molecular level has been a long-standing ambition of cell biology, and one that is approaching its denouement; particularly in the case of the ubiquitous Sec system. In this review, we highlight the fruits of recent game-changing technical innovations in structural biology, biophysics and biochemistry to present a largely complete mechanism for the bacterial version of the core Sec machinery. We discuss the merits of our model over alternative proposals and identify the remaining open questions. The template laid out by the study of the Sec system will be of immense value for probing the many other translocons found in diverse biological membranes, towards the ultimate goal of altering or impeding their functions for pharmaceutical or biotechnological purposes.
Collapse
Affiliation(s)
- William J. Allen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| |
Collapse
|
6
|
Prentis LE, Singleton CD, Bickel JD, Allen WJ, Rizzo RC. A molecular evolution algorithm for ligand design in DOCK. J Comput Chem 2022; 43:1942-1963. [PMID: 36073674 PMCID: PMC9623574 DOI: 10.1002/jcc.26993] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/13/2022] [Accepted: 08/03/2022] [Indexed: 01/11/2023]
Abstract
As a complement to virtual screening, de novo design of small molecules is an alternative approach for identifying potential drug candidates. Here, we present a new 3D genetic algorithm to evolve molecules through breeding, mutation, fitness pressure, and selection. The method, termed DOCK_GA, builds upon and leverages powerful sampling, scoring, and searching routines previously implemented into DOCK6. Three primary experiments were used during development: Single-molecule evolution evaluated three selection methods (elitism, tournament, and roulette), in four clinically relevant systems, in terms of mutation type and crossover success, chemical properties, ensemble diversity, and fitness convergence, among others. Large scale benchmarking assessed performance across 651 different protein-ligand systems. Ensemble-based evolution demonstrated using multiple inhibitors simultaneously to seed growth in a SARS-CoV-2 target. Key takeaways include: (1) The algorithm is robust as demonstrated by the successful evolution of molecules across a large diverse dataset. (2) Users have flexibility with regards to parent input, selection method, fitness function, and molecular descriptors. (3) The program is straightforward to run and only requires a single executable and input file at run-time. (4) The elitism selection method yields more tightly clustered molecules in terms of 2D/3D similarity, with more favorable fitness, followed by tournament and roulette.
Collapse
Affiliation(s)
- Lauren E. Prentis
- Department of Biochemistry & Cell BiologyStony Brook UniversityStony BrookNew YorkUSA
| | | | - John D. Bickel
- Department of ChemistryStony Brook UniversityStony BrookNew YorkUSA
| | - William J. Allen
- Department of Applied Mathematics & StatisticsStony Brook UniversityStony BrookNew YorkUSA
| | - Robert C. Rizzo
- Department of Applied Mathematics & StatisticsStony Brook UniversityStony BrookNew YorkUSA,Institute of Chemical Biology & Drug DiscoveryStony Brook UniversityStony BrookNew YorkUSA,Laufer Center for Physical & Quantitative BiologyStony Brook UniversityStony BrookNew YorkUSA
| |
Collapse
|
7
|
Ford HC, Allen WJ, Pereira GC, Liu X, Dillingham MS, Collinson I. Towards a molecular mechanism underlying mitochondrial protein import through the TOM and TIM23 complexes. eLife 2022; 11:75426. [PMID: 35674314 PMCID: PMC9255969 DOI: 10.7554/elife.75426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/07/2022] [Indexed: 12/27/2022] Open
Abstract
Nearly all mitochondrial proteins need to be targeted for import from the cytosol. For the majority, the first port of call is the translocase of the outer membrane (TOM complex), followed by a procession of alternative molecular machines, conducting transport to their final destination. The pre-sequence translocase of the inner membrane (TIM23-complex) imports proteins with cleavable pre-sequences. Progress in understanding these transport mechanisms has been hampered by the poor sensitivity and time resolution of import assays. However, with the development of an assay based on split NanoLuc luciferase, we can now explore this process in greater detail. Here, we apply this new methodology to understand how ∆ψ and ATP hydrolysis, the two main driving forces for import into the matrix, contribute to the transport of pre-sequence-containing precursors (PCPs) with varying properties. Notably, we found that two major rate-limiting steps define PCP import time: passage of PCP across the outer membrane and initiation of inner membrane transport by the pre-sequence - the rates of which are influenced by PCP size and net charge. The apparent distinction between transport through the two membranes (passage through TOM is substantially complete before PCP-TIM engagement) is in contrast with the current view that import occurs through TOM and TIM in a single continuous step. Our results also indicate that PCPs spend very little time in the TIM23 channel - presumably rapid success or failure of import is critical for maintenance of mitochondrial fitness.
Collapse
Affiliation(s)
- Holly C Ford
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Gonçalo C Pereira
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Xia Liu
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | | | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
8
|
Allen WJ, Corey RA, Watkins DW, Oliveira ASF, Hards K, Cook GM, Collinson I. Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion. eLife 2022; 11:77586. [PMID: 35486093 PMCID: PMC9110029 DOI: 10.7554/elife.77586] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/24/2022] Open
Abstract
Transport of proteins across and into membranes is a fundamental biological process with the vast majority being conducted by the ubiquitous Sec machinery. In bacteria, this is usually achieved when the SecY-complex engages the cytosolic ATPase SecA (secretion) or translating ribosomes (insertion). Great strides have been made towards understanding the mechanism of protein translocation. Yet, important questions remain – notably, the nature of the individual steps that constitute transport, and how the proton-motive force (PMF) across the plasma membrane contributes. Here, we apply a recently developed high-resolution protein transport assay to explore these questions. We find that pre-protein transport is limited primarily by the diffusion of arginine residues across the membrane, particularly in the context of bulky hydrophobic sequences. This specific effect of arginine, caused by its positive charge, is mitigated for lysine which can be deprotonated and transported across the membrane in its neutral form. These observations have interesting implications for the mechanism of protein secretion, suggesting a simple mechanism through which the PMF can aid transport by enabling a 'proton ratchet', wherein re-protonation of exiting lysine residues prevents channel re-entry, biasing transport in the outward direction.
Collapse
Affiliation(s)
- William J Allen
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | | | - Kiel Hards
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Duneding, New Zealand
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
9
|
Beato M, De Keijzer KL, Leskauskas Z, Allen WJ, Dello Iacono A, McErlain-Naylor SA. Effect of Postactivation Potentiation After Medium vs. High Inertia Eccentric Overload Exercise on Standing Long Jump, Countermovement Jump, and Change of Direction Performance. J Strength Cond Res 2021; 35:2616-2621. [PMID: 31232831 DOI: 10.1519/jsc.0000000000003214] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
ABSTRACT Beato, M, De Keijzer, KL, Leskauskas, Z, Allen, WJ, Dello Iacono, A, and McErlain-Naylor, SA. Effect of postactivation potentiation after medium vs. high inertia eccentric overload exercise on standing long jump, countermovement jump, and change of direction performance. J Strength Cond Res 35(9): 2616-2621, 2021-This study aimed to evaluate the postactivation potentiation (PAP) effects of an eccentric overload (EOL) exercise on vertical and horizontal jumps and change of direction (COD) performance. Twelve healthy physically active male subjects were involved in a crossover study. The subjects performed 3 sets of 6 repetitions of EOL half squats for maximal power using a flywheel ergometer. Postactivation potentiation using an EOL exercise was compared between a medium (M-EOL) vs. high inertia (H-EOL) experimental condition. Long jump (LJ) was recorded at 30 seconds, 3, and 6 minutes after both EOL exercises and compared with baseline values (control). The same procedure was used to assess countermovement jump (CMJ) height and peak power and 5-m COD test (COD-5m). A fully Bayesian statistical approach to provide probabilistic statements was used in this study. Long jump performance reported improvements after M-EOL and H-EOL exercise (Bayes factor [BF10] = 32.7, strong; BF10 = 9.2, moderate), respectively. Countermovement jump height (BF10 = 135.6, extreme; BF10 > 200, extreme), CMJ peak power (BF10 > 200, extreme; BF10 = 56.1, very strong), and COD-5m (BF10 = 55.7, very strong; BF10 = 16.4, strong) reported improvements after M-EOL and H-EOL exercise, respectively. Between analysis did not report meaningful differences in performance between M-EOL and H-EOL exercises. The present outcomes highlight that PAP using an EOL (M-EOL and H-EOL) improves LJ, CMJ height, CMJ peak power, and COD-5m in male athletes. The optimal time window for the PAP effect was found for both EOL conditions from 3 to 6 minutes. However, M-EOL and H-EOL produce similar PAP effect on LJ, CMJ, and COD-5m tasks.
Collapse
Affiliation(s)
- Marco Beato
- School of Science, Technology and Engineering, University of Suffolk, Ipswich, United Kingdom; and
| | - Kevin L De Keijzer
- School of Science, Technology and Engineering, University of Suffolk, Ipswich, United Kingdom; and
| | - Zygimantas Leskauskas
- School of Science, Technology and Engineering, University of Suffolk, Ipswich, United Kingdom; and
| | - William J Allen
- School of Science, Technology and Engineering, University of Suffolk, Ipswich, United Kingdom; and
| | - Antonio Dello Iacono
- Institute of Clinical Exercise and Health Science, School of Health and Life Sciences, University of the West of Scotland, Hamilton, United Kingdom
| | - Stuart A McErlain-Naylor
- School of Science, Technology and Engineering, University of Suffolk, Ipswich, United Kingdom; and
| |
Collapse
|
10
|
Abstract
Signaling bias is a feature of many G protein-coupled receptor (GPCR) targeting drugs with potential clinical implications. Whether it is therapeutically advantageous for a drug to be G protein biased or β-arrestin biased depends on the context of the signaling pathway. Here, we explored GPCR ligands that exhibit biased signaling to gain insights into scaffolds and pharmacophores that lead to bias. More specifically, we considered BiasDB, a database containing information about GPCR biased ligands, and focused our analysis on ligands which show either a G protein or β-arrestin bias. Five different machine learning models were trained on these ligands using 15 different sets of features. Molecular fragments which were important for training the models were analyzed. Two of these fragments (number of secondary amines and number of aromatic amines) were more prevalent in β-arrestin biased ligands. After training a random forest model on HierS scaffolds, we found five scaffolds, which demonstrated G protein or β-arrestin bias. We also conducted t-SNE clustering, observing correspondence between unsupervised and supervised machine learning methods. To increase the applicability of our work, we developed a web implementation of our models, which can predict bias based on user-provided SMILES, drug names, or PubChem CID. Our web implementation is available at: drugdiscovery.utep.edu/biasnet.
Collapse
Affiliation(s)
- Jason E Sanchez
- Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Govinda B Kc
- Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Julian Franco
- Mechanical Engineering, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - William J Allen
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, Texas 78758, United States
| | - Jesus David Garcia
- Computer Science, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Suman Sirimulla
- Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, United States.,Computer Science, The University of Texas at El Paso, El Paso, Texas 79968, United States.,Department of Pharmaceutical Science, The University of Texas at El Paso, El Paso, Texas 79968, United States
| |
Collapse
|
11
|
Muthusivarajan R, Allen WJ, Pehere AD, Sokolov KV, Fuentes D. Role of alkylated residues in the tetrapeptide self-assembly-A molecular dynamics study. J Comput Chem 2020; 41:2634-2640. [PMID: 32930440 DOI: 10.1002/jcc.26419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/05/2020] [Accepted: 08/28/2020] [Indexed: 12/17/2022]
Abstract
Designing peptide sequences that self-assemble into well-defined nanostructures can open a new venue for the development of novel drug carriers and molecular contrast agents. Current approaches are often based on a linear block-design of amphiphilic peptides where a hydrophilic peptide chain is terminated by a hydrophobic tail. Here, a new template for a self-assembling tetrapeptide (YXKX, Y = tyrosine, X = alkylated tyrosine, K = lysine) is proposed with two distinct sides relative to the peptide's backbone: alkylated hydrophobic residues on one side and hydrophilic residues on the other side. Using all-atom molecular dynamics simulations, the self-assembly pathway of the tetrapeptide is analyzed for two different concentrations. At both concentrations, tetrapeptides self-assembled into a nanosphere structure. The alkylated tyrosines initialize the self-assembly process via a strong hydrophobic effect and to reduce exposure to the aqueous solvent, they formed a hydrophobic core. The hydrophilic residues occupied the surface of the self-assembled nanosphere. Ordered arrangement of tetrapeptides within the nanosphere with the backbone hydrogen bonding led to a beta sheet formation. Alkyl chain length constrained the size and shape of the nanosphere. This study provides foundation for further exploration of self-assembling structures that are based on peptides with hydrophobic and hydrophilic moieties located on the opposite sides of a peptide backbone.
Collapse
Affiliation(s)
| | - William J Allen
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, Texas, USA
| | - Ashok D Pehere
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Konstantin V Sokolov
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Bioengineering, Rice University, Houston, Texas, USA.,Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - David Fuentes
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
12
|
Alvira S, Watkins DW, Troman LA, Allen WJ, Lorriman JS, Degliesposti G, Cohen EJ, Beeby M, Daum B, Gold VAM, Skehel JM, Collinson I. Inter-membrane association of the Sec and BAM translocons for bacterial outer-membrane biogenesis. eLife 2020; 9:e60669. [PMID: 33146611 PMCID: PMC7695460 DOI: 10.7554/elife.60669] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
The outer-membrane of Gram-negative bacteria is critical for surface adhesion, pathogenicity, antibiotic resistance and survival. The major constituent - hydrophobic β-barrel Outer-Membrane Proteins (OMPs) - are first secreted across the inner-membrane through the Sec-translocon for delivery to periplasmic chaperones, for example SurA, which prevent aggregation. OMPs are then offloaded to the β-Barrel Assembly Machinery (BAM) in the outer-membrane for insertion and folding. We show the Holo-TransLocon (HTL) - an assembly of the protein-channel core-complex SecYEG, the ancillary sub-complex SecDF, and the membrane 'insertase' YidC - contacts BAM through periplasmic domains of SecDF and YidC, ensuring efficient OMP maturation. Furthermore, the proton-motive force (PMF) across the inner-membrane acts at distinct stages of protein secretion: (1) SecA-driven translocation through SecYEG and (2) communication of conformational changes via SecDF across the periplasm to BAM. The latter presumably drives efficient passage of OMPs. These interactions provide insights of inter-membrane organisation and communication, the importance of which is becoming increasingly apparent.
Collapse
Affiliation(s)
- Sara Alvira
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Daniel W Watkins
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Luca A Troman
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - William J Allen
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - James S Lorriman
- School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Gianluca Degliesposti
- Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Eli J Cohen
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Morgan Beeby
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Bertram Daum
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- College of Life and Environmental Sciences, University of ExeterExeterUnited Kingdom
| | - Vicki AM Gold
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- College of Life and Environmental Sciences, University of ExeterExeterUnited Kingdom
| | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ian Collinson
- School of Biochemistry, University of BristolBristolUnited Kingdom
| |
Collapse
|
13
|
Allen WJ, Collinson I. A molecular dual carriageway. eLife 2020; 9:61148. [PMID: 32840481 PMCID: PMC7447420 DOI: 10.7554/elife.61148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 11/29/2022] Open
Abstract
In order to enter a cell, an ammonium ion must first dissociate to form an ammonia molecule and a hydrogen ion (a proton), which then pass through the cell membrane separately and recombine inside.
Collapse
Affiliation(s)
- William J Allen
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
14
|
Gabr RE, Coronado I, Robinson M, Sujit SJ, Datta S, Sun X, Allen WJ, Lublin FD, Wolinsky JS, Narayana PA. Brain and lesion segmentation in multiple sclerosis using fully convolutional neural networks: A large-scale study. Mult Scler 2019; 26:1217-1226. [PMID: 31190607 DOI: 10.1177/1352458519856843] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To investigate the performance of deep learning (DL) based on fully convolutional neural network (FCNN) in segmenting brain tissues in a large cohort of multiple sclerosis (MS) patients. METHODS We developed a FCNN model to segment brain tissues, including T2-hyperintense MS lesions. The training, validation, and testing of FCNN were based on ~1000 magnetic resonance imaging (MRI) datasets acquired on relapsing-remitting MS patients, as a part of a phase 3 randomized clinical trial. Multimodal MRI data (dual-echo, FLAIR, and T1-weighted images) served as input to the network. Expert validated segmentation was used as the target for training the FCNN. We cross-validated our results using the leave-one-center-out approach. RESULTS We observed a high average (95% confidence limits) Dice similarity coefficient for all the segmented tissues: 0.95 (0.92-0.98) for white matter, 0.96 (0.93-0.98) for gray matter, 0.99 (0.98-0.99) for cerebrospinal fluid, and 0.82 (0.63-1.0) for T2 lesions. High correlations between the DL segmented tissue volumes and ground truth were observed (R2 > 0.92 for all tissues). The cross validation showed consistent results across the centers for all tissues. CONCLUSION The results from this large-scale study suggest that deep FCNN can automatically segment MS brain tissues, including lesions, with high accuracy.
Collapse
Affiliation(s)
- Refaat E Gabr
- Department of Diagnostic and Interventional Imaging, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Ivan Coronado
- Department of Diagnostic and Interventional Imaging, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Melvin Robinson
- Department of Electrical Engineering, The University of Texas at Tyler, Houston, TX, USA
| | - Sheeba J Sujit
- Department of Diagnostic and Interventional Imaging, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Sushmita Datta
- Department of Diagnostic and Interventional Imaging, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Xiaojun Sun
- Department of Diagnostic and Interventional Imaging, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - William J Allen
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA
| | | | - Jerry S Wolinsky
- Department of Neurology, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Ponnada A Narayana
- Department of Diagnostic and Interventional Imaging, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| |
Collapse
|
15
|
Allen WJ, Collinson I, Römisch K. Post-Translational Protein Transport by the Sec Complex. Trends Biochem Sci 2019; 44:481-483. [PMID: 30962027 DOI: 10.1016/j.tibs.2019.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 11/28/2022]
Abstract
Although it has been studied for 30 years, the mechanism by which secretory proteins are transported post-translationally into the endoplasmic reticulum (ER) has not yet been fully resolved. Recently published structures (Itskanov and Park, Science 2019;363:84-87; Wu, X. et al. Nature 2019;566:136-139) of the heptameric secretory (Sec) complex which mediates post-translational import into the yeast ER shed new light on the process.
Collapse
Affiliation(s)
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Karin Römisch
- Faculty of Natural Sciences and Technology, Saarland University, Saarbruecken, Germany.
| |
Collapse
|
16
|
Allen WJ, Gabr RE, Tefera GB, Pednekar AS, Vaughn MW, Narayana PA. Platform for Automated Real-Time High Performance Analytics on Medical Image Data. IEEE J Biomed Health Inform 2019; 22:318-324. [PMID: 29505399 DOI: 10.1109/jbhi.2017.2771299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Biomedical data are quickly growing in volume and in variety, providing clinicians an opportunity for better clinical decision support. Here, we demonstrate a robust platform that uses software automation and high performance computing (HPC) resources to achieve real-time analytics of clinical data, specifically magnetic resonance imaging (MRI) data. We used the Agave application programming interface to facilitate communication, data transfer, and job control between an MRI scanner and an off-site HPC resource. In this use case, Agave executed the graphical pipeline tool GRAphical Pipeline Environment (GRAPE) to perform automated, real-time, quantitative analysis of MRI scans. Same-session image processing will open the door for adaptive scanning and real-time quality control, potentially accelerating the discovery of pathologies and minimizing patient callbacks. We envision this platform can be adapted to other medical instruments, HPC resources, and analytics tools.
Collapse
|
17
|
Corey RA, Ahdash Z, Shah A, Pyle E, Allen WJ, Fessl T, Lovett JE, Politis A, Collinson I. ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery. eLife 2019; 8:41803. [PMID: 30601115 PMCID: PMC6335059 DOI: 10.7554/elife.41803] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/01/2019] [Indexed: 11/13/2022] Open
Abstract
Transport of proteins across membranes is a fundamental process, achieved in every cell by the 'Sec' translocon. In prokaryotes, SecYEG associates with the motor ATPase SecA to carry out translocation for pre-protein secretion. Previously, we proposed a Brownian ratchet model for transport, whereby the free energy of ATP-turnover favours the directional diffusion of the polypeptide (Allen et al., 2016). Here, we show that ATP enhances this process by modulating secondary structure formation within the translocating protein. A combination of molecular simulation with hydrogendeuterium-exchange mass spectrometry and electron paramagnetic resonance spectroscopy reveal an asymmetry across the membrane: ATP-induced conformational changes in the cytosolic cavity promote unfolded pre-protein structure, while the exterior cavity favours its formation. This ability to exploit structure within a pre-protein is an unexplored area of protein transport, which may apply to other protein transporters, such as those of the endoplasmic reticulum and mitochondria.
Collapse
Affiliation(s)
- Robin A Corey
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Zainab Ahdash
- Department of Chemistry, King's College London, London, United Kingdom
| | - Anokhi Shah
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, Scotland, United Kingdom
| | - Euan Pyle
- Department of Chemistry, King's College London, London, United Kingdom.,Department of Chemistry, Imperial College London, London, United Kingdom
| | - William J Allen
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Tomas Fessl
- University of South Bohemia in Ceske Budejovice, České Budějovice, Czech Republic
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, Scotland, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, London, United Kingdom
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
18
|
Fuentes D, Muñoz NM, Guo C, Polak U, Minhaj AA, Allen WJ, Gustin MC, Cressman ENK. A molecular dynamics approach towards evaluating osmotic and thermal stress in the extracellular environment. Int J Hyperthermia 2018; 35:559-567. [PMID: 30303437 DOI: 10.1080/02656736.2018.1512161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/13/2018] [Accepted: 08/12/2018] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE A molecular dynamics approach to understanding fundamental mechanisms of combined thermal and osmotic stress induced by thermochemical ablation (TCA) is presented. METHODS Structural models of fibronectin and fibronectin bound to its integrin receptor provide idealized models for the effects of thermal and osmotic stress in the extracellular matrix. Fibronectin binding to integrin is known to facilitate cell survival. The extracellular environment produced by TCA at the lesion boundary was modelled at 37 °C and 43 °C with added sodium chloride (NaCl) concentrations (0, 40, 80, 160, and 320 mM). Atomistic simulations of solvated proteins were performed using the GROMOS96 force field and TIP3P water model. Computational results were compared with the results of viability studies of human hepatocellular carcinoma (HCC) cell lines HepG2 and Hep3B under matching thermal and osmotic experimental conditions. RESULTS Cell viability was inversely correlated with hyperthermal and hyperosmotic stresses. Added NaCl concentrations were correlated with a root mean square fluctuation increase of the fibronectin arginylglycylaspartic acid (RGD) binding domain. Computed interaction coefficients demonstrate preferential hydration of the protein model and are correlated with salt-induced strengthening of hydrophobic interactions. Under the combined hyperthermal and hyperosmotic stress conditions (43 °C and 320 mM added NaCl), the free energy change required for fibronectin binding to integrin was less favorable than that for binding under control conditions (37 °C and 0 mM added NaCl). CONCLUSION Results quantify multiple measures of structural changes as a function of temperature increase and addition of NaCl to the solution. Correlations between cell viability and stability measures suggest that protein aggregates, non-functional proteins, and less favorable cell attachment conditions have a role in TCA-induced cell stress.
Collapse
Affiliation(s)
- David Fuentes
- a Department of Imaging Physics , M. D. Anderson Cancer Center, The University of Texas , Houston , TX , USA
| | - Nina M Muñoz
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
| | - Chunxiao Guo
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
| | - Urzsula Polak
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
| | - Adeeb A Minhaj
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
| | - William J Allen
- c Texas Advanced Computing Center , The University of Texas at Austin , Austin , TX , USA
| | - Michael C Gustin
- d Department of Biosciences , Rice University , Houston , TX , USA
| | - Erik N K Cressman
- b Department of Interventional Radiology , M. D. Anderson Cancer Center, The University of Texas, Houston , TX , USA
| |
Collapse
|
19
|
Allen WJ, Fochtman BC, Balius TE, Rizzo RC. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. J Comput Chem 2017; 38:2641-2663. [PMID: 28940386 DOI: 10.1002/jcc.25052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/03/2017] [Indexed: 12/12/2022]
Abstract
De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from-scratch construction of molecules is not limited to compounds in pre-existing vendor catalogs. Here, we present an iterative fragment growth method, integrated into the program DOCK, in which new molecules are built using rules for allowable connections based on known molecules. The method leverages DOCK's advanced scoring and pruning approaches and users can define very specific criteria in terms of properties or features to customize growth toward a particular region of chemical space. The code was validated using three increasingly difficult classes of calculations: (1) Rebuilding known X-ray ligands taken from 663 complexes using only their component parts (focused libraries), (2) construction of new ligands in 57 drug target sites using a library derived from ∼13M drug-like compounds (generic libraries), and (3) application to a challenging protein-protein interface on the viral drug target HIVgp41. The computational testing confirms that the de novo DOCK routines are robust and working as envisioned, and the compelling results highlight the potential utility for designing new molecules against a wide variety of important protein targets. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- William J Allen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794
| | - Brian C Fochtman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Trent E Balius
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, 94158
| | - Robert C Rizzo
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794.,Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York, 11794.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, 11794
| |
Collapse
|
20
|
McGee TD, Yi HA, Allen WJ, Jacobs A, Rizzo RC. Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer. Bioorg Med Chem Lett 2017; 27:3177-3184. [PMID: 28558972 DOI: 10.1016/j.bmcl.2017.05.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/04/2017] [Accepted: 05/06/2017] [Indexed: 10/19/2022]
Abstract
The viral protein HIVgp41 is an attractive and validated drug target that proceeds through a sequence of conformational changes crucial for membrane fusion, which facilitates viral entry. Prior work has identified inhibitors that interfere with the formation of a required six-helix bundle, composed of trimeric C-heptad (CHR) and N-heptad (NHR) repeat elements, through blocking association of an outer CHR helix or obstructing formation of the inner NHR trimer itself. In this work, we employed similarity-based scoring to identify and experimentally characterize 113 compounds, related to 2 small-molecule inhibitors recently reported by Allen et al. (Bioorg. Med. Chem Lett.2015, 25 2853-59), proposed to act via the NHR trimer obstruction mechanism. The compounds were first tested in an HIV cell-cell fusion assay with the most promising evaluated in a second, more biologically relevant viral entry assay. Of the candidates, compound #11 emerged as the most promising hit (IC50=37.81µM), as a result of exhibiting activity in both assays with low cytotoxicity, as was similarly seen with the known control peptide inhibitor C34. The compound also showed no inhibition of VSV-G pseudotyped HIV entry compared to a control inhibitor suggesting it was specific for HIVgp41. Molecular dynamics simulations showed the predicted DOCK pose of #11 interacts with HIVgp41 in an energetic fashion (per-residue footprints) similar to the four native NHR residues (IQLT) which candidate inhibitors were intended to mimic.
Collapse
Affiliation(s)
- T Dwight McGee
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States
| | - Hyun Ah Yi
- Department of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, NY 14214, United States
| | - William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States
| | - Amy Jacobs
- Department of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, NY 14214, United States
| | - Robert C Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States; Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY 11794, United States; Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| |
Collapse
|
21
|
Collinson I, Corey RA, Allen WJ. Channel crossing: how are proteins shipped across the bacterial plasma membrane? Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0025. [PMID: 26370937 PMCID: PMC4632601 DOI: 10.1098/rstb.2015.0025] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The structure of the first protein-conducting channel was determined more than a decade ago. Today, we are still puzzled by the outstanding problem of protein translocation—the dynamic mechanism underlying the consignment of proteins across and into membranes. This review is an attempt to summarize and understand the energy transducing capabilities of protein-translocating machines, with emphasis on bacterial systems: how polypeptides make headway against the lipid bilayer and how the process is coupled to the free energy associated with ATP hydrolysis and the transmembrane protein motive force. In order to explore how cargo is driven across the membrane, the known structures of the protein-translocation machines are set out against the background of the historic literature, and in the light of experiments conducted in their wake. The paper will focus on the bacterial general secretory (Sec) pathway (SecY-complex), and its eukaryotic counterpart (Sec61-complex), which ferry proteins across the membrane in an unfolded state, as well as the unrelated Tat system that assembles bespoke channels for the export of folded proteins.
Collapse
Affiliation(s)
- Ian Collinson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Robin A Corey
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - William J Allen
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| |
Collapse
|
22
|
Corey RA, Allen WJ, Komar J, Masiulis S, Menzies S, Robson A, Collinson I. Unlocking the Bacterial SecY Translocon. Structure 2016; 24:518-527. [PMID: 26973090 PMCID: PMC4826270 DOI: 10.1016/j.str.2016.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 11/25/2022]
Abstract
The Sec translocon performs protein secretion and membrane protein insertion at the plasma membrane of bacteria and archaea (SecYEG/β), and the endoplasmic reticular membrane of eukaryotes (Sec61). Despite numerous structures of the complex, the mechanism underlying translocation of pre-proteins, driven by the ATPase SecA in bacteria, remains unresolved. Here we present a series of biochemical and computational analyses exploring the consequences of signal sequence binding to SecYEG. The data demonstrate that a signal sequence-induced movement of transmembrane helix 7 unlocks the translocon and that this conformational change is communicated to the cytoplasmic faces of SecY and SecE, involved in SecA binding. Our findings progress the current understanding of the dynamic action of the translocon during the translocation initiation process. The results suggest that the converging effects of the signal sequence and SecA at the cytoplasmic face of SecYEG are decisive for the intercalation and translocation of pre-protein through the SecY channel. Validation of previously observed signal sequence-induced “unlocking” of SecYEG Conformational changes upon SecYEG unlocking are relayed to SecA binding site Unlocking the translocon perturbs the interaction between SecY and SecE Conformational changes distinct between secretion and membrane protein insertion
Collapse
Affiliation(s)
- Robin A Corey
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - William J Allen
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Joanna Komar
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Simonas Masiulis
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Sam Menzies
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Alice Robson
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK.
| |
Collapse
|
23
|
Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. J Comput Chem 2015; 36:1132-56. [PMID: 25914306 DOI: 10.1002/jcc.23905] [Citation(s) in RCA: 429] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 03/01/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) → 5.4 (65.2%) → 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% → 13.6% → 9.1% and scoring 24.4% → 21.1% → 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/.
Collapse
Affiliation(s)
- William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, 11794
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Airola MV, Allen WJ, Pulkoski-Gross MJ, Obeid LM, Rizzo RC, Hannun YA. Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase. Structure 2015; 23:1482-1491. [PMID: 26190575 PMCID: PMC4830088 DOI: 10.1016/j.str.2015.06.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/03/2015] [Accepted: 06/11/2015] [Indexed: 01/07/2023]
Abstract
Neutral ceramidase (nCDase) catalyzes conversion of the apoptosis-associated lipid ceramide to sphingosine, the precursor for the proliferative factor sphingosine-1-phosphate. As an enzyme regulating the balance of ceramide and sphingosine-1-phosphate, nCDase is emerging as a therapeutic target for cancer. Here, we present the 2.6-Å crystal structure of human nCDase in complex with phosphate that reveals a striking, 20-Å deep, hydrophobic active site pocket stabilized by a eukaryotic-specific subdomain not present in bacterial ceramidases. Utilizing flexible ligand docking, we predict a likely binding mode for ceramide that superimposes closely with the crystallographically observed transition state analog phosphate. Our results suggest that nCDase uses a new catalytic strategy for Zn(2+)-dependent amidases, and generates ceramide specificity by sterically excluding sphingolipids with bulky headgroups and specifically recognizing the small hydroxyl head group of ceramide. Together, these data provide a foundation to aid drug development and establish common themes for how proteins recognize the bioactive lipid ceramide.
Collapse
Affiliation(s)
- Michael V Airola
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Stony Brook Cancer Center, Stony Brook, NY 11794, USA
| | - William J Allen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Lina M Obeid
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Stony Brook Cancer Center, Stony Brook, NY 11794, USA; Department of Medicine, Northport Veterans Affairs Medical Center, Northport, NY 11768, USA
| | - Robert C Rizzo
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yusuf A Hannun
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; Department of Medicine, Stony Brook Cancer Center, Stony Brook, NY 11794, USA.
| |
Collapse
|
25
|
Allen WJ, Yi HA, Gochin M, Jacobs A, Rizzo RC. Small molecule inhibitors of HIVgp41 N-heptad repeat trimer formation. Bioorg Med Chem Lett 2015; 25:2853-9. [PMID: 26013847 DOI: 10.1016/j.bmcl.2015.04.067] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/16/2015] [Accepted: 04/20/2015] [Indexed: 10/23/2022]
Abstract
Identification of mechanistically novel anti-HIV fusion inhibitors was accomplished using a computer-aided structure-based design approach with the goal of blocking the formation of the N-heptad repeat (NHR) trimer of the viral protein gp41. A virtual screening strategy that included per-residue interaction patterns (footprints) was employed to identify small molecules compatible with putative binding pockets at the internal interface of the NHR helices at the core native viral six-helix bundle. From a screen of ∼2.8 million compounds using the DOCK program, 120 with favorable energetic and footprint overlap characteristics were purchased and experimentally tested leading to two compounds with favorable cell-cell fusion (IC50) and cytotoxicity profiles. Importantly, both hits were identified on the basis of scores containing footprint overlap terms and would not have been identified using the standard DOCK energy function alone. To our knowledge, these compounds represent the first reported small molecules that inhibit viral entry via the proposed NHR-trimer obstruction mechanism.
Collapse
Affiliation(s)
- William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States
| | - Hyun Ah Yi
- Department of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, NY 14214, United States
| | - Miriam Gochin
- Department of Basic Sciences, Touro University-California, Mare Island, Vallejo, CA 94592, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94143, United States
| | - Amy Jacobs
- Department of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, NY 14214, United States
| | - Robert C Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States; Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY 11794, United States; Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| |
Collapse
|
26
|
Allen WJ, Wiley MR, Myles KM, Adelman ZN, Bevan DR. Steered molecular dynamics identifies critical residues of the Nodamura virus B2 suppressor of RNAi. J Mol Model 2014; 20:2092. [PMID: 24549790 DOI: 10.1007/s00894-014-2092-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 11/25/2013] [Indexed: 11/30/2022]
Abstract
Nearly all RNA viruses produce double-stranded RNA (dsRNA) during their replication cycles--an important pathogen-associated molecular pattern recognized by the RNA interference (RNAi) pathway in invertebrates and plants. Nodamura virus (NoV) encodes a suppressor of RNA silencing termed B2, which binds to dsRNA and prevents the initiation of RNAi as well as the loading of silencing complexes. Using the published crystal structure of NoV-B2, we performed a series of molecular dynamics (MD) simulations to determine the relative electrostatic and van der Waals contributions of various residues in binding dsRNA, identifying four novel potential interactors: R56, E48, P68 and R69. Additionally, steered MD was used to simulate the binding affinity of NoV-B2 sequences bearing substitutions at positions F49, R56 or R59 to dsRNA, with F49S and R56L/R59L substitutions found to have a significant negative impact on the ability of NoV-B2 to bind dsRNA. NoV RNA1 variants were tested for self-directed replication in both vertebrate (RNAi⁻) and invertebrate (RNAi⁺) cultured cells. Consistent with a role in dsRNA binding, NoV replication in F49C and F49S variant constructs was affected negatively only in RNAi⁺ cells. Thus, we used a combination of MD simulations and experimental mutagenesis to further characterize residues important for NoV-dsRNA interactions.
Collapse
Affiliation(s)
- William J Allen
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061-0308, USA,
| | | | | | | | | |
Collapse
|
27
|
Abstract
![]()
False
negative docking outcomes for highly symmetric molecules
are a barrier to the accurate evaluation of docking programs, scoring
functions, and protocols. This work describes an implementation of
a symmetry-corrected root-mean-square deviation (RMSD) method into
the program DOCK based on the Hungarian algorithm for solving the
minimum assignment problem, which dynamically assigns atom correspondence
in molecules with symmetry. The algorithm adds only a trivial amount
of computation time to the RMSD calculations and is shown to increase
the reported overall docking success rate by approximately 5% when
tested over 1043 receptor–ligand systems. For some families
of protein systems the results are even more dramatic, with success
rate increases up to 16.7%. Several additional applications of the
method are also presented including as a pairwise similarity metric
to compare molecules during de novo design, as a scoring function
to rank-order virtual screening results, and for the analysis of trajectories
from molecular dynamics simulation. The new method, including source
code, is available to registered users of DOCK6 (http://dock.compbio.ucsf.edu).
Collapse
Affiliation(s)
- William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University , Stony Brook, New York 11794, United States
| | | |
Collapse
|
28
|
Holden PM, Allen WJ, Gochin M, Rizzo RC. Strategies for lead discovery: application of footprint similarity targeting HIVgp41. Bioorg Med Chem 2013; 22:651-61. [PMID: 24315195 DOI: 10.1016/j.bmc.2013.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 10/08/2013] [Accepted: 10/17/2013] [Indexed: 10/26/2022]
Abstract
A highly-conserved binding pocket on HIVgp41 is an important target for development of anti-viral inhibitors. Holden et al. (Bioorg. Med. Chem. Lett.2012, 22, 3011) recently reported 7 experimentally-verified leads identified through a computational screen to the gp41 pocket in conjunction with a new DOCK scoring method (termed FPS scoring) developed in our laboratory. The method employs molecular footprints based on per-residue van der Waals interactions, electrostatic interactions, or the sum. In this work, we critically examine the gp41 screening results, prioritized using different scoring methods, in terms of two main criteria: (1) ligand pose properties which include footprint and energy score decompositions, MW, number of rotatable bonds, ligand efficiency, formal charge, and volume overlap, and (2) ligand pose stability which includes footprint stability (changes in footprint overlap) and rmsd stability (changes in geometry). Relative to standard DOCK scoring, pose property analyses demonstrate how FPS scoring can be used to identify ligands that mimic a known reference (derived here from the native gp41 substrate), while pose stability analyses demonstrate how FPS scoring can be used to enrich for compounds with greater overall stability during molecular dynamics (MD) simulations. Compellingly, of the 115 compounds tested experimentally, the 7 active compounds, as a group, more closely mimic the footprints made by the reference and show greater MD stability compared to the inactive group. Extensive studies using 116 protein-ligand complexes as controls reveal that ligands in their crystallographic binding pose also maintain higher FPS scores and smaller rmsds than do accompanying decoys, confirming that native poses are indeed 'stable' under the same conditions and that monitoring FPS variability during compound prioritization is likely to be beneficial. Overall, the results suggest the new scoring method will complement current virtual screening approaches for both the identification (FPS-ranking) and prioritization (FPS-stability) of target-compatible molecules in a quantitative and logical way.
Collapse
Affiliation(s)
- Patrick M Holden
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States
| | - William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States
| | - Miriam Gochin
- Department of Basic Sciences, Touro University-California, Mare Island, Vallejo, CA 94592, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, CA 94143, United States
| | - Robert C Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY 11794, United States; Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY 11794, United States; Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| |
Collapse
|
29
|
Furt F, Allen WJ, Widhalm JR, Madzelan P, Rizzo RC, Basset G, Wilson MA. Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis. Acta Crystallogr D Biol Crystallogr 2013; 69:1876-88. [PMID: 24100308 PMCID: PMC3792638 DOI: 10.1107/s0907444913015771] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/06/2013] [Indexed: 11/10/2022]
Abstract
The synthesis of phylloquinone (vitamin K1) in photosynthetic organisms requires a thioesterase that hydrolyzes 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to release 1,4-dihydroxy-2-naphthoate (DHNA). Cyanobacteria and plants contain distantly related hotdog-fold thioesterases that catalyze this reaction, although the structural basis of these convergent enzymatic activities is unknown. To investigate this, the crystal structures of hotdog-fold DHNA-CoA thioesterases from the cyanobacterium Synechocystis (Slr0204) and the flowering plant Arabidopsis thaliana (AtDHNAT1) were determined. These enzymes form distinct homotetramers and use different active sites to catalyze hydrolysis of DHNA-CoA, similar to the 4-hydroxybenzoyl-CoA (4-HBA-CoA) thioesterases from Pseudomonas and Arthrobacter. Like the 4-HBA-CoA thioesterases, the DHNA-CoA thioesterases contain either an active-site aspartate (Slr0204) or glutamate (AtDHNAT1) that are predicted to be catalytically important. Computational modeling of the substrate-bound forms of both enzymes indicates the residues that are likely to be involved in substrate binding and catalysis. Both enzymes are selective for DHNA-CoA as a substrate, but this selectivity is achieved using divergent predicted binding strategies. The Slr0204 binding pocket is predominantly hydrophobic and closely conforms to DHNA, while that of AtDHNAT1 is more polar and solvent-exposed. Considered in light of the related 4-HBA-CoA thioesterases, these structures indicate that hotdog-fold thioesterases using either an active-site aspartate or glutamate diverged into distinct clades prior to the evolution of strong substrate specificity in these enzymes.
Collapse
Affiliation(s)
- Fabienne Furt
- Center for Plant Science Innovation and Departments of Agronomy and Horticulture and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - William J. Allen
- Department of Applied Mathematics and Statistics, Stony Brook University, Math Tower 1-111, Stony Brook, NY 11794, USA
| | - Joshua R. Widhalm
- Center for Plant Science Innovation and Departments of Agronomy and Horticulture and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Peter Madzelan
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, N118 Beadle Center, Lincoln, NE 68588, USA
| | - Robert C. Rizzo
- Department of Applied Mathematics and Statistics, Stony Brook University, Math Tower 1-111, Stony Brook, NY 11794, USA
| | - Gilles Basset
- Center for Plant Science Innovation and Departments of Agronomy and Horticulture and Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, N118 Beadle Center, Lincoln, NE 68588, USA
| |
Collapse
|
30
|
Rothwell PJ, Allen WJ, Sisamakis E, Kalinin S, Felekyan S, Widengren J, Waksman G, Seidel CAM. dNTP-dependent conformational transitions in the fingers subdomain of Klentaq1 DNA polymerase: insights into the role of the "nucleotide-binding" state. J Biol Chem 2013; 288:13575-91. [PMID: 23525110 DOI: 10.1074/jbc.m112.432690] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Conformational selection plays a key role in the polymerase cycle. RESULTS Klentaq1 exists in conformational equilibrium between three states (open, closed, and “nucleotide-binding”) whose level of occupancy is determined by the bound substrate. CONCLUSION The “nucleotide-binding” state plays a pivotal role in the reaction pathway. SIGNIFICANCE Direct evidence is provided for the role of a conformationally distinct “nucleotide-binding” state during dNTP incorporation. DNA polymerases are responsible for the accurate replication of DNA. Kinetic, single-molecule, and x-ray studies show that multiple conformational states are important for DNA polymerase fidelity. Using high precision FRET measurements, we show that Klentaq1 (the Klenow fragment of Thermus aquaticus DNA polymerase 1) is in equilibrium between three structurally distinct states. In the absence of nucleotide, the enzyme is mostly open, whereas in the presence of DNA and a correctly base-pairing dNTP, it re-equilibrates to a closed state. In the presence of a dNTP alone, with DNA and an incorrect dNTP, or in elevated MgCl2 concentrations, an intermediate state termed the "nucleotide-binding" state predominates. Photon distribution and hidden Markov modeling revealed fast dynamic and slow conformational processes occurring between all three states in a complex energy landscape suggesting a mechanism in which dNTP delivery is mediated by the nucleotide-binding state. After nucleotide binding, correct dNTPs are transported to the closed state, whereas incorrect dNTPs are delivered to the open state.
Collapse
Affiliation(s)
- Paul J Rothwell
- Chair for Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstraβe 1, 40225 Düsseldorf, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Balius TE, Allen WJ, Mukherjee S, Rizzo RC. Grid-based molecular footprint comparison method for docking and de novo design: application to HIVgp41. J Comput Chem 2013; 34:1226-1240. [PMID: 23436713 DOI: 10.1002/jcc.23245] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/24/2012] [Accepted: 01/06/2013] [Indexed: 11/06/2022]
Abstract
Scoring functions are a critically important component of computer-aided screening methods for the identification of lead compounds during early stages of drug discovery. Here, we present a new multigrid implementation of the footprint similarity (FPS) scoring function that was recently developed in our laboratory which has proven useful for identification of compounds which bind to a protein on a per-residue basis in a way that resembles a known reference. The grid-based FPS method is much faster than its Cartesian-space counterpart, which makes it computationally tractable for on-the-fly docking, virtual screening, or de novo design. In this work, we establish that: (i) relatively few grids can be used to accurately approximate Cartesian space footprint similarity, (ii) the method yields improved success over the standard DOCK energy function for pose identification across a large test set of experimental co-crystal structures, for crossdocking, and for database enrichment, and (iii) grid-based FPS scoring can be used to tailor construction of new molecules to have specific properties, as demonstrated in a series of test cases targeting the viral protein HIVgp41. The method is available in the program DOCK6.
Collapse
Affiliation(s)
- Trent E Balius
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York 11794, USA
| | - William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sudipto Mukherjee
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Robert C Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York 11794, USA.,Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794, USA.,Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| |
Collapse
|
32
|
Allen WJ, Phan G, Hultgren SJ, Waksman G. Dissection of pilus tip assembly by the FimD usher monomer. J Mol Biol 2013; 425:958-67. [PMID: 23295826 PMCID: PMC3650583 DOI: 10.1016/j.jmb.2012.12.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/21/2012] [Accepted: 12/22/2012] [Indexed: 01/08/2023]
Abstract
Type 1 pili are representative of a class of bacterial surface structures assembled by the conserved chaperone/usher pathway and used by uropathogenic Escherichia coli to attach to bladder cells during infection. The outer membrane assembly platform-the usher-is critical for the formation of pili, catalysing the polymerisation of pilus subunits and enabling the secretion of the nascent pilus. Despite extensive structural characterisation of the usher, a number of questions about its mechanism remain, notably its oligomerisation state, and how it orchestrates the ordered assembly of pilus subunits. We demonstrate here that the FimD usher is able to catalyse in vitro pilus assembly effectively in its monomeric form. Furthermore, by establishing the kinetics of usher-catalysed reactions between various pilus subunits, we establish a complete kinetic model of tip fibrillum assembly, able to account for the order of subunits in native type 1 pili.
Collapse
Affiliation(s)
- William J. Allen
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Gilles Phan
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Scott J. Hultgren
- Center for Women's Infectious Disease Research, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8230, St. Louis, MO 63110, USA
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
- Corresponding author.
| |
Collapse
|
33
|
Whitehouse S, Gold VAM, Robson A, Allen WJ, Sessions RB, Collinson I. Mobility of the SecA 2-helix-finger is not essential for polypeptide translocation via the SecYEG complex. ACTA ACUST UNITED AC 2012; 199:919-29. [PMID: 23209305 PMCID: PMC3518217 DOI: 10.1083/jcb.201205191] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Polypeptide translocation in bacteria, once underway, requires only one copy each of SecA and SecYEG and does not require the mobility of the SecA 2-helix-finger. The bacterial ATPase SecA and protein channel complex SecYEG form the core of an essential protein translocation machinery. The nature of the conformational changes induced by each stage of the hydrolytic cycle of ATP and how they are coupled to protein translocation are not well understood. The structure of the SecA–SecYEG complex revealed a 2-helix-finger (2HF) of SecA in an ideal position to contact the substrate protein and push it through the membrane. Surprisingly, immobilization of this finger at the edge of the protein channel had no effect on translocation, whereas its imposition inside the channel blocked transport. This analysis resolves the stoichiometry of the active complex, demonstrating that after the initiation process translocation requires only one copy each of SecA and SecYEG. The results also have important implications on the mechanism of energy transduction and the power stroke driving transport. Evidently, the 2HF is not a highly mobile transducing element of polypeptide translocation.
Collapse
Affiliation(s)
- Sarah Whitehouse
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, England, UK
| | | | | | | | | | | |
Collapse
|
34
|
Morrissey B, Leney AC, Toste Rêgo A, Phan G, Allen WJ, Verger D, Waksman G, Ashcroft AE, Radford SE. The role of chaperone-subunit usher domain interactions in the mechanism of bacterial pilus biogenesis revealed by ESI-MS. Mol Cell Proteomics 2012; 11:M111.015289. [PMID: 22371487 PMCID: PMC3394950 DOI: 10.1074/mcp.m111.015289] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 01/23/2012] [Indexed: 01/12/2023] Open
Abstract
The PapC usher is a β-barrel outer membrane protein essential for assembly and secretion of P pili that are required for adhesion of pathogenic E. coli, which cause the development of pyelonephritis. Multiple protein subunits form the P pilus, the highly specific assembly of which is coordinated by the usher. Despite a wealth of structural knowledge, how the usher catalyzes subunit polymerization and orchestrates a correct and functional order of subunit assembly remain unclear. Here, the ability of the soluble N-terminal (UsherN), C-terminal (UsherC2), and Plug (UsherP) domains of the usher to bind different chaperone-subunit (PapDPapX) complexes is investigated using noncovalent electrospray ionization mass spectrometry. The results reveal that each usher domain is able to bind all six PapDPapX complexes, consistent with an active role of all three usher domains in pilus biogenesis. Using collision induced dissociation, combined with competition binding experiments and dissection of the adhesin subunit, PapG, into separate pilin and adhesin domains, the results reveal why PapG has a uniquely high affinity for the usher, which is consistent with this subunit always being displayed at the pilus tip. In addition, we show how the different soluble usher domains cooperate to coordinate and control efficient pilus assembly at the usher platform. As well as providing new information about the protein-protein interactions that determine pilus biogenesis, the results highlight the power of noncovalent MS to interrogate biological mechanisms, especially in complex mixtures of species.
Collapse
MESH Headings
- Adhesins, Escherichia coli/chemistry
- Adhesins, Escherichia coli/genetics
- Adhesins, Escherichia coli/metabolism
- Bacterial Adhesion
- Binding Sites
- Binding, Competitive
- Escherichia coli/pathogenicity
- Escherichia coli/physiology
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Fimbriae Proteins/chemistry
- Fimbriae Proteins/genetics
- Fimbriae Proteins/metabolism
- Fimbriae, Bacterial/chemistry
- Fimbriae, Bacterial/genetics
- Fimbriae, Bacterial/metabolism
- Models, Molecular
- Molecular Chaperones/chemistry
- Molecular Chaperones/genetics
- Molecular Chaperones/metabolism
- Periplasmic Proteins/chemistry
- Periplasmic Proteins/genetics
- Periplasmic Proteins/metabolism
- Porins/chemistry
- Porins/genetics
- Porins/metabolism
- Protein Binding
- Protein Structure, Tertiary
- Protein Subunits/chemistry
- Protein Subunits/genetics
- Protein Subunits/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Spectrometry, Mass, Electrospray Ionization
Collapse
Affiliation(s)
- Bethny Morrissey
- From the ‡Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, The University of Leeds, Leeds, LS2 9JT, UK
| | - Aneika C. Leney
- From the ‡Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, The University of Leeds, Leeds, LS2 9JT, UK
| | - Ana Toste Rêgo
- §Institute of Structural and Molecular Biology, Birkbeck College and University College London, London, WC1E 7HX, UK
| | - Gilles Phan
- §Institute of Structural and Molecular Biology, Birkbeck College and University College London, London, WC1E 7HX, UK
| | - William J. Allen
- §Institute of Structural and Molecular Biology, Birkbeck College and University College London, London, WC1E 7HX, UK
| | - Denis Verger
- §Institute of Structural and Molecular Biology, Birkbeck College and University College London, London, WC1E 7HX, UK
| | - Gabriel Waksman
- §Institute of Structural and Molecular Biology, Birkbeck College and University College London, London, WC1E 7HX, UK
| | - Alison E. Ashcroft
- From the ‡Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, The University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E. Radford
- From the ‡Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, The University of Leeds, Leeds, LS2 9JT, UK
| |
Collapse
|
35
|
Allen WJ, Phan G, Waksman G. Pilus biogenesis at the outer membrane of Gram-negative bacterial pathogens. Curr Opin Struct Biol 2012; 22:500-6. [PMID: 22402496 DOI: 10.1016/j.sbi.2012.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 02/16/2012] [Accepted: 02/17/2012] [Indexed: 11/24/2022]
Abstract
Pili belong to a broad class of bacterial surface structures that play a key role in infection and pathogenicity. The largest and best characterised pilus biogenesis system--the chaperone-usher pathway--is particularly remarkable in its ability to synthesise and display highly organised structures at the outer membrane without any input from endogenous energy sources. The past few years have heralded exciting new developments in our understanding of the structural biology and mechanism of pilus assembly, which are discussed in this review. Such knowledge will be particularly important in the future, as we approach an era of widespread resistance to common antibiotics and require new targets.
Collapse
Affiliation(s)
- William J Allen
- Institute of Structural and Molecular Biology, University College London and Birkbeck, Malet Street, WC1E 7HX London, UK
| | | | | |
Collapse
|
36
|
Allen WJ, Bevan DR. Steered Molecular Dynamics Simulations Reveal Important Mechanisms in Reversible Monoamine Oxidase B Inhibition. Biochemistry 2011; 50:6441-54. [DOI: 10.1021/bi200446w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- William J. Allen
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - David R. Bevan
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| |
Collapse
|
37
|
Phan G, Remaut H, Wang T, Allen WJ, Pirker KF, Lebedev A, Henderson NS, Geibel S, Volkan E, Yan J, Kunze MBA, Pinkner JS, Ford B, Kay CWM, Li H, Hultgren SJ, Thanassi DG, Waksman G. Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate. Nature 2011; 474:49-53. [PMID: 21637253 PMCID: PMC3162478 DOI: 10.1038/nature10109] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 04/13/2011] [Indexed: 11/29/2022]
Abstract
Type 1 pili are the archetypal representative of a widespread class of adhesive multisubunit fibres in Gram-negative bacteria. During pilus assembly, subunits dock as chaperone-bound complexes to an usher, which catalyzes their polymerization and mediates pilus translocation across the outer membrane. We report the crystal structure of the full-length FimD usher bound to the FimC:FimH chaperone:adhesin complex and that of the unbound form of the FimD translocation domain. The FimD:FimC:FimH structure shows FimH inserted inside the FimD 24-stranded β-barrel translocation channel. FimC:FimH is held in place through interactions with the two C-terminal periplasmic domains of FimD, a binding mode confirmed in solution by electron paramagnetic resonance spectroscopy. To accommodate FimH, the usher plug domain is displaced from the barrel lumen to the periplasm, concomitant with a dramatic conformational change in the β-barrel. The N-terminal domain of FimD is observed in an ideal position to catalyse incorporation of a newly recruited chaperone:subunit complex. The FimD:FimC:FimH structure provides unique insights into the pilus subunit incorporation cycle, and captures the first view of a protein transporter in the act of secreting its cognate substrate.
Collapse
Affiliation(s)
- Gilles Phan
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Grimm ML, Allen WJ, Finn M, Castagnoli N, Tanko JM. Reaction of benzophenone triplet with aliphatic amines. What a potent neurotoxin can tell us about the reaction mechanism. Bioorg Med Chem 2011; 19:1458-63. [DOI: 10.1016/j.bmc.2011.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/28/2010] [Accepted: 01/01/2011] [Indexed: 10/18/2022]
|
39
|
Allen WJ, Capelluto DGS, Finkielstein CV, Bevan DR. Modeling the relationship between the p53 C-terminal domain and its binding partners using molecular dynamics. J Phys Chem B 2011; 114:13201-13. [PMID: 20873738 DOI: 10.1021/jp1011445] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Fifty percent of all cancer cases result from mutations of the TP53 gene, which encodes the tumor suppressor p53, and it is hypothesized that the p53-mediated checkpoint pathway is compromised in most of the remaining cases. The p53 C-terminal domain (CTD) is an important site of p53 regulation but by nature is difficult to study, as it is intrinsically disordered. In this study, we performed molecular dynamics simulations on the p53 CTD and five known regulatory binding partners. We identified distinct trends in fluctuation within and around the p53 CTD binding site on each partner demonstrating a behavior that facilitates association. Further, we present evidence that the size of the hydrophobic pocket in each p53 CTD binding site governs the secondary structure of the p53 CTD when in the bound state. This information will be useful for predicting new binding partners for the p53 CTD, identifying interacting regions within other known partners, and discovering inhibitors that provide additional points of control over p53 activity.
Collapse
Affiliation(s)
- William J Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, 111 Engel Hall (0308), Blacksburg, Virginia 24061, United States
| | | | | | | |
Collapse
|
40
|
Abstract
Molecular dynamics simulations are being applied to increasingly complex systems, including those involving small endogenous compounds and drug molecules. In order to obtain meaningful and accurate data from these simulations, high-quality topologies for small molecules must be generated in a manner that is consistent with the derivation of the force field applied to the system. Often, force fields are designed for use with macromolecules such as proteins, making their transferability to other species challenging. Investigators are increasingly attracted to automated topology generation programs, although the quality of the resulting topologies remains unknown. Here we assess the applicability of the popular PRODRG server that generates small-molecule topologies for use with the GROMOS family of force fields. We find that PRODRG does not reproduce topologies for even the most well-characterized species in the force field due to inconsistent charges and charge groups. We assessed the effects of PRODRG-derived charges on several systems: pure liquids, amino acids at a hydrophobic-hydrophilic interface, and an enzyme-cofactor complex. We found that partial atomic charges generated by PRODRG are largely incompatible with GROMOS force fields, and the behavior of these systems deviates substantially from that of simulations using GROMOS parameters. We conclude by proposing several points as "best practices" for parametrization of small molecules under the GROMOS force fields.
Collapse
Affiliation(s)
- Justin A Lemkul
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | | | | |
Collapse
|
41
|
Abstract
Proteins often require specific helper proteins, chaperones, to assist with their correct folding and to protect them from denaturation and aggregation. The cell envelope of Gram-negative bacteria provides a particularly challenging environment for chaperones to function in as it lacks readily available energy sources such as adenosine 5' triphosphate (ATP) to power reaction cycles. Periplasmic chaperones have therefore evolved specialized mechanisms to carry out their functions without the input of external energy and in many cases to transduce energy provided by protein folding or ATP hydrolysis at the inner membrane. Structural and biochemical studies have in recent years begun to elucidate the specific functions of many important periplasmic chaperones and how these functions are carried out. This includes not only specific carrier chaperones, such as those involved in the biosynthesis of adhesive fimbriae in pathogenic bacteria, but also more general pathways including the periplasmic transport of outer membrane proteins and the extracytoplasmic stress responses. This chapter aims to provide an overview of protein chaperones so far identified in the periplasm and how structural biology has assisted with the elucidation of their functions.
Collapse
Affiliation(s)
- William J Allen
- Institute of Structural and Molecular Biology, Birkbeck and University College London, London WC1E 7HX, UK
| | | | | |
Collapse
|
42
|
|
43
|
Abstract
A major goal of polymerase research is to determine the mechanism through which a nucleotide complementary to a templating DNA base is selected and delivered to the polymerase active site. Structural evidence suggests a large open-to-closed conformational change affecting the fingers subdomain as being crucial to the process. We previously designed a FRET system capable of measuring the rate of fingers subdomain closure in the presence of correct nucleotide. However, this FRET system was limited in that it could not directly measure the rate of fingers subdomain opening by FRET after polymerization or in the absence of DNA. Here we report the development of a new system capable of measuring both fingers subdomain closure and reopening by FRET, and show that the rate of fingers subdomain opening is limited only by the rate of polymerization. We anticipate that this system will scale down to the single molecule level, allowing measurement of fingers subdomain movements in the presence of incorrect nucleotide and in the absence of DNA.
Collapse
Affiliation(s)
- William J Allen
- Institute of Structural Molecular Biology, UCL and Birkbeck, London WC1E 7HX, United Kingdom
| | | | | |
Collapse
|
44
|
Abstract
BACKGROUND This investigation evaluates the potential of using a novel suturing device to achieve mitral valve repair (Alfieri type) on a beating heart without cardiopulmonary bypass. METHODS Eight healthy adult sheep were anesthetized and the chest was opened via a left thoracotomy. The suture device was directly inserted into the appendage of the left atrium. Suction ports on the distal tip of the device grasped and approximated the mitral leaflets while the heart was beating. Two-dimensional echocardiography and intracardiac pressure monitoring at the tip of the device were utilized to guide the procedure. The device was used to place two single sutures across the two leaflets at the center of the mitral valve. A knot pusher with integrated cutter was used to tie the sutures and cut the suture ends. RESULTS In all animals, the free margins of the mitral leaflets were successfully grasped and approximated by this device. Echocardiography confirmed successful deployment of the sutures in all cases, with a figure-of-eight appearance of the valve and normal valve hemodynamic function after placement of the sutures. Mid-leaflet approximation was verified at autopsy immediately after the procedure. No tissue damage was observed. CONCLUSIONS This study demonstrates that mitral valve repair (Alfieri type) can be performed safely and consistently on a beating heart without cardiopulmonary bypass using this new tissue approximation suture device. This technique may be applicable to the treatment of ischemic mitral regurgitation in conjunction with revascularization procedures or to mitral regurgitation in heart failure patients.
Collapse
|
45
|
Bosch OJH, Allen WJ, Williams JM, Ensor AH. An Integrated Approach for Maximising Local and Scientific Knowledge for Land Management Decision-Making in the New Zealand High Country. Rangel J 1996. [DOI: 10.1071/rj9960023] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper describes the development of a process to facilitate the identification and introduction of
sustainable land management practices in the high country of New Zealand. The process was designed
to gather and structure community knowledge (both local and scientific) into a single, accessible
decision support system (DSS). The development and provision of appropriate, and user-friendly
monitoring tools is supported. An outline is given of how this integrated system can be used to
integrate monitoring with adaptive management. Special reference is made to how this process is
used as a large-scale ecological 'experiment', to enhance continually the knowledge base available
for land use decision-making in the South Island high country of New Zealand.
Collapse
|
46
|
Allen WJ. Somebody Help Me!--a new film. J Audiov Media Med 1982; 5:145-7. [PMID: 7175091 DOI: 10.3109/17453058209154352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
47
|
McGuiness AF, Allen WJ, Knox SJ. Psychiatric training and the development of insight. Nurs Times 1969; 65:555-6. [PMID: 5780654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
48
|
Allen WJ, Barcroft H, Edholm OG. On the action of adrenaline on the blood vessels in human skeletal muscle. J Physiol 1946; 105:255-67. [PMID: 16991726 PMCID: PMC1393638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
|
49
|
Anderson DP, Allen WJ, Barcroft H, Edholm OG, Manning GW. Circulatory changes during fainting and coma caused by oxygen lack. J Physiol 1946; 104:426-34. [PMID: 16991699 PMCID: PMC1393573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
|