Topf, Maya - Birkbeck, University of London - Department of Biological Sciences

研究领域

Our research is focused on the development of computational methods that combine experimental data with bioinformatics and modelling techniques to characterise the structure of macromolecular machines. Structural models are further analysed to understand their function, thereby help designing new experiments. The group is particularly interested in applying these methods using data from cryo electron microscopy and mass spectrometry. In collaboration with experimentalists, specific systems we are interested in include herpes virus sub-complexes, bacterial secretion systems, ligand-gated ion channels, and kinesin motors bound to microtubules.

近期论文

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Meyer, E. and Carss, K.J and Rankin, J. and Nichols, J.M.E and Grozeva, D. and Joseph, A.P and Mencacci, N.E. and Papandreou, A. and Ng, J. and Barral, S. and Ngoh, A. and Ben-Pazi, H. and Willemsen, M.A. and Arkadir, D. and Barnicoat, A. and Bergman, H. and Bhate, S. and Boys, A. and Darin, N. and Foulds, N. and Gutowski, N. and Hills, A. and Houlden, H. and Hurst, J.A. and Israel, Z. and Kaminska, M. and Limousin, P. and Lumsden, D. and McKee, S. and Misra, S. and Mohammed, S.S. and Nakou, V. and Nicolai, J. and Nilsson, M. and Pall, H. and Peall, K.J. and Peters, G.B. and Prabhakar, P. and Reuter, M.S. and Rump, P. and Segel, R. and Sinnema, M. and Smith, M. and Turnpenny, P. and White, S.M. and Wieczorek, D. and Wiethoff, S. and Wilson, B.T. and Winter, G. and Wragg, C. and Pope, S. and Heales, S.J.H. and Morrogh, D. and Pittman, A. and Carr, L. J. and Perez-Dueñas, B. and Lin, J.-P. and Reis, A. and Gahl, W.A. and Toro, C. and Bhatia, K.P. and Wood, N.W. and Kamsteeg, E.-J. and Chong, W.K. and Gissen, P. and Topf, Maya and Dale, R.C. and Chubb, J.R. and Raymond, F.L. and Kurian, M.A. (2016) Mutations in the histone methyltransferase gene KMT2B cause complex early-onset dystonia. Nature Genetics 49 , pp. 223-237. ISSN 1061-4036. Ashford, Paul and Hernandez duran, Anna and Greco, T.M. and Buch, A. and Sodeik, B. and Cristea, I.M. and Grünewald, K. and Shepherd, Adrian and Topf, Maya (2016) HVint: a strategy for identifying novel protein-protein interactions in Herpes Simplex Virus Type 1. Molecular & Cellular Proteomics 15 (9), pp. 2939-2953. ISSN 1535-9476. Bullock, Joshua and Schwab, J. and Thalassinos, Kostas and Topf, Maya (2016) The importance of non-accessible crosslinks and solvent accessible surface distance in modelling proteins with restraints from crosslinking mass spectrometry. Molecular & Cellular Proteomics 15 (7), pp. 2491-2500. ISSN 1535-9476. Pilorge, M. and Fassier, C. and Le Corronc, H. and Potey, A. and Bai, J. and De Gois, S. and Delaby, E. and Assouline, B. and Guinchat, V. and Devillard, F. and Delorme, R. and Nygren, G. and Råstam, M. and Meier, J.C. and Otani, S. and Cheval, H. and James, V.M. and Topf, Maya and Dear, T.N. and Gillberg, C. and Leboyer, M. and Giros, B. and Gautron, S. and Hazan, J. and Harvey, R.J. and Legendre, P. and Betancur, C. (2016) Genetic and functional analyses demonstrate a role for abnormal glycinergic signaling in autism. Molecular Psychiatry 21 , pp. 936-945. ISSN 1359-4184. Joseph, Agnal Praveen and Malhotra, S. and Burnley, T. and Wood, C. and Clare, D.K. and Winn, M. and Topf, Maya (2016) Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment. Methods 100 , pp. 42-49. ISSN 1046-2023. Kalscheuer, V.M. and James, V.M. and Himelright, M.L. and Long, P. and Oegema, R. and Jensen, C. and Bienek, M. and Hu, H. and Haas, S.A. and Topf, Maya and Hoogeboom, A.J.M. and Harvey, K. and Walikonis, R. and Harvey, R.J. (2016) Novel Missense Mutation A789V in IQSEC2 underlies X-Linked intellectual disability in the MRX78 family. Frontiers in Molecular Neuroscience 8 , ISSN 1662-5099. Zeev-Ben-Mordehai, T. and Vasishtan, D. and Hernández Durán, A. and Vollmer, B. and White, P. and Prasad Pandurangan, A. and Siebert, C.A. and Topf, Maya and Grünewald, K. (2016) Two distinct trimeric conformations of natively membrane-anchored full-length herpes simplex virus 1 glycoprotein B. Proceedings of the National Academy of Sciences of the United States of America 113 (15), pp. 4176-4181. ISSN 0027-8424. Pandurangan, Arun and Vasishtan, D. and Alber, F. and Topf, Maya (2015) γ-TEMPy: simultaneous fitting of components in 3D-EM maps of their assembly using a genetic algorithm. Structure 23 (12), pp. 2365-2376. ISSN 0969-2126. Stödberg, T. and McTague, A. and Ruiz, A.J. and Hirata, H. and Zhen, J. and Long, P. and Farabella, Irene and Meyer, E. and Kawahara, A. and Vassallo, G. and Stivaros, S.M. and Bjursell, M.K. and Stranneheim, H. and Tigerschiöld, S. and Persson, B. and Bangash, I. and Das, K. and Hughes, D. and Lesko, N. and Lundeberg, J. and Scott, R.C. and Poduri, A. and Scheffer, I.E. and Smith, H. and Gissen, P. and Schorge, S. and Reith, M.E.A. and Topf, Maya and Kullmann, D.M. and Harvey, R.J. and Wedell, A. and Kurian, M.A. (2015) Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures. Nature Communications 6 , p. 8038. ISSN 2041-1723. Farabella, I. and Vasishtan, D. and Joseph, Agnel Praveen and Pandurangan, Arun Prasad and Sahota, Harpal and Topf, Maya (2015) TEMPy: a Python library for assessment of 3D electron microscopy density fits. Journal of Applied Crystallography 48 , pp. 1314-1323. ISSN 0021-8898. Sali, A. and Berman, H.M. and Schwede, T. and Trewhella, J. and Kleywegt, G. and Burley, S.K. and Markley, J. and Nakamura, H. and Adams, P. and Bonvin, A.M.J.J. and Wah, C. and Dal Peraro, M. and Di Maio, F. and Ferrin, T.E. and Grünewald, K. and Gutmanas, A. and Henderson, R. and Hummer, G. and Iawsaki, K. and Johnson , G. and Lawson, C.L. and Meiler, J. and Marti-Renom, M.A. and Montelione, G.T. and Nilges, M. and Nussinov, R. and Patwardhan, A. and Rappsilber, J. and Read, R.J. and Saibil, Helen R. and Schröder, G.F. and Schwieters, C. and Seidel, C.A.M. and Svergun, D. and Topf, Maya and Ulrich, E.L. and Velankar, S. and Westbrook, J.D. (2015) Outcome of the First wwPDB Hybrid / Integrative Methods Task Force Workshop. Structure 23 (7), pp. 1156-1167. ISSN 0969-2126. Lukoyanova, Natalya and Kondos, S.C. and Farabella, Irene and Law, R.H.P. and Reboul, C.F. and Caradoc-Davies, T.T. and Spicer, B.A. and Kleifeld, O. and Traore, D.A.K. and Ekkel, S.M. and Voskoboinik, I. and Trapani, J.A. and Hatfaludi, T. and Oliver, K. and Hotze, E.M. and Tweten, R.K. and Whisstock, J.C. and Topf, Maya and Saibil, Helen R. and Dunstone, M.A. (2015) Conformational changes during pore formation by the perforin-related protein pleurotolysin. PLOS Biology 13 (2), e1002049. ISSN 1545-7885. Wood, C. and Burnley, T. and Patwardhan, A. and Scheres, S. and Topf, Maya and Roseman, A. and Winn, M. (2015) Collaborative computational project for electron cryo-microscopy. Acta Crystallographica Section D Biological Crystallography 71 (1), pp. 123-126. ISSN 1399-0047. Leung, C. and Dudkina, N.V. and Lukoyanova, Natalya and Hodel, A.W. and Farabella, I. and Pandurangan, A.P. and Jahan, N. and Pires Damaso, M. and Osmanović, D. and Reboul, C.F. and Dunstone, M.A. and Andrew, P.W. and Lonnen, R. and Topf, Maya and Saibil, Helen R. and Hoogenboom, B.W. (2014) Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin. eLife 3 , ISSN 2050-084X. Farabella, Irene and Pham, T. and Henderson, N.S. and Geibel, Sebastien and Phan, Gilles and Thanassi, D.G. and Delcour, A.H. and Waksman, Gabriel and Topf, Maya (2014) Allosteric signalling in the outer membrane translocation domain of PapC usher. eLife 3 , ISSN 2050-084X. Atherton, Joseph and Farabella, Irene and Yu, I-M. and Rosenfeld, S.S. and Houdusse, A. and Topf, Maya and Moores, Carolyn A. (2014) Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins. eLife 3 , ISSN 2050-084X. Mortensen, M. and Iqbal, F. and Pandurangan, Arun and Hannan, S. and Huckvale, R. and Topf, Maya and Baker, J.R. and Smart, T.G. (2014) Photo-antagonism of the GABAA receptor. Nature Communications 5 , ISSN 2041-1723. Ganser, L.R. and Yan, Q. and James, Victoria M. and Kozol, R. and Topf, Maya and Harvey, R.J. and Dallman, J.E. (2013) Distinct phenotypes in zebrafish models of human startle disease. Neurobiology of Disease 60 , pp. 139-151. ISSN 0969-9961. Thalassinos, Konstantinos and Pandurangan, Arun and Xu, M. and Alber, F. and Topf, Maya (2013) Conformational states of macromolecular assemblies explored by integrative structure calculation. Structure 21 (9), pp. 1500-1508. ISSN 0969-2126. Maurer, U.E. and Zeev-Ben-Mordehai, T. and Pandurangan, Arun and Cairns, T.M. and Hannah, B.P. and Whitbeck, J.C. and Eisenberg, R.J. and Cohen, G.H. and Topf, Maya and Huiskonen, J.T. and Grünewald, K. (2013) The structure of Herpesvirus Fusion Glycoprotein B-Bilayer Complex reveals the protein-membrane and lateral protein-protein interaction. Structure 21 (8), pp. 1396-1405. ISSN 0969-2126. Redzej, Adam and Ilangovan, Aravindan and Lang, S. and Gruber, C.J. and Topf, Maya and Zangger, K. and Zechner, E.L. and Waksman, Gabriel (2013) Structure of a translocation signal domain mediating conjugative transfer by Type IV secretion systems. Molecular Microbiology 89 (2), pp. 324-333. ISSN 0950-382X. James, Victoria M. and Bode, A. and Chung, S.-K. and Gill, J.L. and Nielsen, M. and Cowan, Frances M. and Vujic, M. and Thomas, R.H. and Rees, M.I. and Harvey, K. and Keramidas, A. and Topf, Maya and Ginjaar, I. and Lynch, J.W. and Harvey, R.J. (2013) Novel missense mutations in the glycine receptor β subunit gene (GLRB) in startle disease. Neurobiology of Disease 52 , pp. 137-149. ISSN 0969-9961. Yuan, Shujun and Topf, Maya and Reubold, T.F. and Eschenburg, S. and Akey, C.W. (2013) Changes in Apaf-1 conformation that drive apoptosome assembly. Biochemistry 52 (13), pp. 2319-2327. ISSN 0006-2960. Pandurangan, A.P. and Shakeel, S. and Butcher, S. and Topf, Maya (2013) Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change. Journal of Structural Biology 185 (3), pp. 427-439. ISSN 1047-8477. Pandurangan, Arun and Topf, Maya (2012) RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps. Bioinformatics 28 (18), pp. 2391-2393. ISSN 1367-4803.