Publications
2024
Kleywegt GJ, Adams PD, Butcher SJ, Lawson C, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Bernard Heymann J, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok S-M, Ludtke SJ, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. (2024) IUCrJ 11. Community recommendations on cryoEM data archiving and validation. doi.org/10.1107/S2052252524001246.
Manalastas-Cantos K, Adoni KR, Pfeifer M, Märtens B, Grünewald K, Thalassinos K, Topf M. (2024) Mol Cell Proteomics 23:100724. Modeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry. doi.org/10.1016/j.mcpro.2024.100724.
Beton JG*, Mulvaney T*, Cragnolini T, Topf M. (2024) Nat Commun 15:444. Cryo-EM structure and B-factor refinement with ensemble representation. (*co-first authors) doi.org/10.1038/s41467-023-44593-1.
Sweeney A, Mulvaney T, Maiorca M, Topf M. (2024) ChemEM: Flexible Docking of Small Molecules in Cryo-EM Structures. J. Med. Chem. 67(1):199–212. doi.org/10.1021/acs.jmedchem.3c01134.
2023
Mulvaney T, Kretsch RC, Elliott L, Beton JG, Kryshtafovych A, Rigden DJ, Das R, Topf M. (2023) Proteins 91:1935–1951. CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps. doi.org/10.1002/prot.26644.
Genz LR, Mulvaney T, Nair S, Topf, M. (2023) Bioinformatics (online ahead of print). PICKLUSTER: A protein-interface clustering and analysis plug-in for UCSF ChimeraX. doi.org/10.1093/bioinformatics/btad629.
Kryshtafovych A, Schwede T., Topf M, Fidelis K, Moult J (2023) Proteins: Struct Funct Bioinf. Critical assessment of methods of protein structure prediction (CASP)—Round XV. doi.org/10.1002/prot.26617.
Malhotra S*, Mulvaney T*, Cragnolini T, Sidhu H, Joseph AP, Beton JG, Topf M. (2023) Nucleic Acids Res. 51: 9567-9575. RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures. (*co-first authors) doi.org/10.1093/nar/gkad721.
Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN Jr, Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. (2023)
Proteins. (online ahead of print). Protein target highlights in CASP15: Analysis of models by structure providers. doi.org/10.1002/prot.26545.
Kryshtafovych A, Antczak M, Szachniuk M, Zok T, Kretsch RC, Rangan R, Pham P, Das R, Robin X, Studer G, Durairaj J, Eberhardt J, Sweeney A, Topf M, Schwede T, Fidelis K, Moult J. (2023) Proteins (online ahead of print). New prediction categories in CASP15. doi.org/10.1002/prot.26515.
Das R, Kretsch RC, Simpkin A, Mulvaney T, Pham P, Rangan R, Bu F, Keegan R, Topf M, Rigden D, Miao Z, Westhof E. (2023) Proteins. (online ahead of print). Assessment of three-dimensional RNA structure prediction in CASP15. doi.org/10.1002/prot.26602.
Beton JG, Cragnolini T, Kaleel M, Mulvaney T, Sweeney A, Topf M. (2023) WIREs Comput Mol Sci.2023;13:e1642. Integrating model simulation tools and cryo‐electron microscopy. doi.org/10.1002/wcms.1642.
Marini G, Poland B, Leininger C, Lukoyanova N, Spielbauer D, Barry J, Altier D, Lum A, Scolaro E, Pérez Ortega C, Yalpani N, Sandahl G, Mabry T, Klever J, Nowatzki T, Zhao J-Z, Sethi A, Kassa A, Crane V, Lu A, Nelson ME*, Eswar N*, Topf M*, Saibil HR*. (2023) Nat. Commun 14(1):4171. Structural journey of an insecticidal pore-forming protein targeting western corn rootworm. doi.org/10.1038/s41467-023-39891-7.
Dyne Steel DB, Danti FR, Abunada M, Kamien B, Malhotra S, Topf M, Kaliakatsos M, Valentine J, Nemeth AH, Jayawant S, Reid KM, Mankad K, Sudhakar S, Ben-Pazi H, Barwick K, Kurian MA. (2023) Neurology Clinical Phenotype in Individuals With Birk-Landau-Perez Syndrome Associated With Biallelic SLC30A9 Pathogenic Variants. doi.org/10.1212/WNL.0000000000207241.
Reid KM, Steel D, Nair S, Bhate S, Biassoni L, Sudhakar S, Heys M, Burke E, Kamsteeg E-J, Genomics England Research Consortium, Hameed B, Zech M, Mencacci NE, Barwick K, Topf M, Kurian MA. (2023) Cells 12:1046. Loss-of-Function Variants in DRD1 in Infantile Parkinsonism-Dystonia. doi.org/10.3390/cells12071046.
2022
Polubothu S, Bender N, Muthiah S, Zecchin D, Demetriou C, Martin SB, Malhotra S, Travnickova J, Zeng Z, Böhm M, Barbarot S, Cottrell C, Davies O, Baselga E, Burrows NP, Carmignac V, Diaz JS, Fink C, Haenssle HA, Happle R, Harland M, Majerowski J, Vabres P, Vincent M, Newton-Bishop JA, Bishop DT, Siegel D, Patton EE, Topf M, Rajan N, Drolet B, Kinsler VA. (2022) J Invest Dermatol. PTPN11 mosaicism causes a spectrum of pigmentary and vascular neurocutaneous disorders and predisposes to melanoma. doi.org/10.1016/j.jid.2022.09.661.
Bremer JP, Baumdick ME, Knorr MS, Wegner LHM, Wesche J, Jordan-Paiz A, Jung JM, Highton AJ, Jäger J, Hinrichs O, Brias S, Niersch J, Müller L, Schreurs RRC, Koyro T, Löbl S, Mensching L, Konczalla L, Niehrs A, Vondran FWR, Schramm C, Hölzemer A, Oldhafer K, Königs I, Kluge S, Perez D, Reinshagen K, Pals ST, Gagliani N, Joosten SP, Topf M, Altfeld M, Bunders MJ. (2022) bioRxiv 2022.09.06.506648. GOAT: Deep learning-enhanced Generalized Organoid Annotation Tool. doi.org/10.1101/2022.09.06.506648.
Reid KM, Spaull R, Salian S, Barwick K, Meyer E, Zhen J, Hirata H, Sheipouri D, Benkerroum H, Gorman KM, Papandreou A, Simpson MA, Hirano Y, Farabella I, Topf M, Grozeva D, Carss K, Smith M, Pall H, Lunt P, De Gressi S, Kamsteeg E-J, Haack TB, Carr L, Guerreiro R, Bras J, Maher ER, Scott RH, Vandenberg RJ, Raymond FL, Chong WK, Sudhakar S, Mankad K, Reith ME, Campeau PM, Harvey RJ, Kurian MA. (2022) Mov Disord 37(10):2139–2146. MED27, SLC6A7, and MPPE1 Variants in a Complex Neurodevelopmental Disorder with Severe Dystonia. doi.org/10.1002/mds.29147.
Sanders VR, Sweeney A, Topf M, Millar NS. (2022) ACS Chem Neurosci 13:1805–1817. Stoichiometry-Selective Antagonism of α4β2 Nicotinic Acetylcholine Receptors by Fluoroquinolone Antibiotics. doi.org/10.1021/acschemneuro.2c00200.
Soloviev Z, Bullock JMA, James JMB, Sauerwein AC, Nettleship JE, Owens RJ, Hansen DF, Topf M, Thalassinos K. (2022) Biochim Biophys Acta Proteins Proteom 1870:140759. Structural mass spectrometry decodes domain interaction and dynamics of the full-length Human Histone Deacetylase 2. doi.org/10.1016/j.bbapap.2022.140759.
Ivanova ME, Lukoyanova N, Malhotra S, Topf M, Trapani JA, Voskoboinik I, Saibil HR. (2022) Sci Adv 8:eabk3147. The pore conformation of lymphocyte perforin. doi.org/10.1126/sciadv.abk3147.
2021
Topf M, Rosta E, Bowman GR, Bonomi M. (2021) Frontiers in molecular biosciences 8:799406. Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function. doi.org/10.3389/fmolb.2021.799406.
Cragnolini T, Kryshtafovych A, Topf M. (2021) Proteins 89:1949–1958. Cryo-EM targets in CASP14. doi.org/10.1002/prot.26216.
Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J (2021) Proteins 89:1607–1617. Critical assessment of methods of protein structure prediction (CASP)-Round XIV. doi.org/10.1002/prot.26237.
Cook AD, Roberts AJ, Atherton J, Tewari R, Topf M, Moores CA. (2021) J Biol Chem 297(5):101063. Cryo-EM structure of a microtubule-bound parasite kinesin motor and implications for its mechanism and inhibition. doi.org/10.1016/j.jbc.2021.101063.
Malhotra S, Joseph AP, Thiyagalingam J, Topf M. (2021) Nat Commun 12:3399. Assessment of protein-protein interfaces in cryo-EM derived assemblies. doi.org/s41467-021-23692-x.
Malhotra S, Joseph A-P, Topf M. (2021) In: Single particle Cryo-EM. IOP Publishing 244–247. Using known components or homologs: model building. doi.org/10.1088/978-0-7503-3039-8.
Beton JG, Moorehead R, Helfmann L, Gray R, Hoogenboom BW, Praveen Joseph A, Topf M, Pyne ALB. (2021) Methods 193:68-79. TopoStats – a program for automated tracing of biomolecules from AFM images. doi.org/10.1016/j.ymeth.2021.01.008.
Cragnolini T, Sahota H, Joseph AP, Sweeney A, Malhotra S, Vasishtan D, Topf M. (2021) Acta Cryst Section D. 77:41-47. TEMPy2: A python library with improved 3D electron microscopy density fitting and validation workflows. doi.org/10.1107/S2059798320014928.
2020
Cif L, Demailly D, Lin J-P, Barwick KE, Sa M, Abela L, Malhotra S, Chong WK, Steel D, Sanchis-Juan A, Ngoh A, Trump N, Meyer E, Vasques X, Rankin J, Allain MW, Applegate CD, Attaripour Isfahani S, Baleine J, Balint B, Bassetti JA, Baple EL, Bhatia KP, Blanchet C, Burglen L, Cambonie G, Seng EC, Bastaraud SC, Cyprien F, Coubes C, d’Hardemare V, Deciphering Developmental Disorders Study, Doja A, Dorison N, Doummar D, Dy-Hollins ME, Farrelly E, Fitzpatrick DR, Fearon C, Fieg EL, Fogel BL, Forman EB, Fox RG, Genomics England Research Consortium, Gahl WA, Galosi S, Gonzalez V, Graves TD, Gregory A, Hallett M, Hasegawa H, Hayflick SJ, Hamosh A, Hully M, Jansen S, Jeong SY, Krier JB, Krystal S, Kumar KR, Laurencin C, Lee H, Lesca G, François LL, Lynch T, Mahant N, Martinez-Agosto JA, Milesi C, Mills KA, Mondain M, Morales-Briceno H, NIHR BioResource, Ostergaard JR, Pal S, Pallais JC, Pavillard F, Perrigault P-F, Petersen AK, Polo G, Poulen G, Rinne T, Roujeau T, Rogers C, Roubertie A, Sahagian M, Schaefer E, Selim L, Selway R, Sharma N, Signer R, Soldatos AG, Stevenson DA, Stewart F, Tchan M, Undiagnosed Diseases Network, Verma IC, de Vries BBA, Wilson JL, Wong DA, Zaitoun R, Zhen D, Znaczko A, Dale RC, de Gusmão CM, Friedman J, Fung VSC, King MD, Mohammad SS, Rohena L, Waugh JL, Toro C, Raymond FL, Topf M, Coubes P, Gorman KM, Kurian MA. (2020) Brain, awaa304. KMT2B-related disorders: Expansion of the phenotypic spectrum and long-term efficacy of deep brain stimulation. doi.org/10.1093/brain/awaa304.
Vollmer B, Pražák V, Vasishtan D, Jefferys EE, Hernandez-Duran A, Vallbracht M, Klupp B, Mettenleiter TC, Backovic B, Rey FA, Topf M, Grünewald K. (2020) Sci Adv 6: eabc1726. The pre-fusion structure of Herpes simplex virus glycoprotein B. doi.org/10.1126/sciadv.abc1726.
Cragnolini T, Sweeney A, Topf M. (2020) In: CryoEM Methods and Protocols. Met Mol Biology 2225: 189-223. Automated modelling and validation of protein complexes in cryo-EM maps. doi.org/10.1007/978-1-0716-0966-8_9.
Sinnott M, Malhotra S, Madhusudhan MS, K. Thalassinos K, Topf M. (2020) Structure 28:1-10. Combining Information from Crosslinks and Monolinks in the Modelling of Protein Structures. doi.org/10.1016/j.str.2020.05.012
Joseph AP, Lagerstedt I, Jakobi, A, Burnley, T, Patwardhan A, Topf M, Winn M. (2020) J Chem Inf Model. 60:2552–2560. Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit using Difference Maps. doi.org/10.1021/acs.jcim.9b01103.
Peña A, Sweeney A, Cook AD, Topf M, Moores CA. (2020) Structure 28:450-457. Mechanism of microtubule-trapped human kinesin-5 inhibition revealed using cryo-EM. doi.org/10.1016/j.str.2020.01.013.
2019
Kryshtafovych A*, Schwede T, Topf M, Fidelis K, Moult J. (2019) Proteins 87:1011-1020. Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XIII. doi.org/10.1002/prot.25823.
Ignatiou E, Brasiles S, Sadek Fadel ME, Bürger J, Mielke T, Topf M, Tavares P. Orlova E, (2019) Nat Commun 10:4840. Structural Transitions during the Scaffolding-Driven Assembly of a Viral Capsid. doi.org/10.1038/s41467-019-12790-6.
Kryshtafovych A*, Malhotra S*, Monastyrskyy B, Cragnolini T, Joseph AP, Chiu W, Topf M. (2019) Proteins 87:1128-1140. Cryo-EM targets in CASP13: overview and evaluation of results. doi.org/10.1002/prot.25817.
Hernández Durán A, Grünewald K, Topf M (2019) mSystems pii: e00295-19. A conserved central intraviral protein interactome of the Herpesviridae family. doi.org/10.1128/mSystems.00295-19.
Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN Jr, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. (2019) Proteins 87:1037-1057. Target highlights in CASP13: experimental target structures through the eyes of their authors. doi.org/10.1002/prot.25805.
Malhotra S, Träger S, Dal Peraro M, Topf M. (2019) Curr Op Struct Biol 58:105–114. Modelling structures in cryo-EM maps. doi.org/10.1016/j.sbi.2019.05.024.
Demetriou C, Chanudet E, GOSgene, Joseph A, Topf M, Thomas AC, Bitner-Glindzicz M, Regan L, Stanier P, Moore GE. (2019) Hum Mol Genet, 28:3466–3474. Exome sequencing identifies variants in FKBP4 that are associated with recurrent fetal loss in humans doi.org/10.1093/hmg/ddz203.
Carecchio M, Invernizzi F, Panteghini C, Zorzi G, Romito L. Leuzzi V, Galosi S, Reale C, Zibordi F, Topf M, Joseph AP ... Kurian MA, Garavaglia B, Mencacci NE, Lubbe S, Nardocci N. (2019) Movement Disorders. 34:1516-1527. Frequency and phenotypic spectrum of kmt2b dystonia in childhood: a single-centre cohort study. doi.org/10.1002/mds.27771.
Hernández Durán A, Greco TM, Vollmer B, Cristea IM, Grünewald K, Topf M. (2019) PLoS Biol 17(6):e3000316. Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. doi.org/10.1371/journal.pbio.3000316.
Fumagalli M, Diekmann Y, Camus SM, Burke A, Norman PJ, Joseph AP, Abi-Rached L, Benazzo A, Rasteiro R, Mathieson I, Topf M, Parham P, Thomas MG, Brodsky FM. (2019) eLife pii: e41517. Evolution of the CLTCL1 gene encoding CHC22 clathrin reveals selection influencing CHC22's role in human glucose metabolism. doi.org/10.7554/eLife.41517.
Pereira R, Gendron T, Sanghera C, Greenwood H, Newcombe J, McCormick P, Sander, K; Topf, M; Årstad, E; Witney, T (2019) Chemistry A European Journal, 25:1–8. Mapping Aldehyde Dehydrogenase 1A1 Activity using an [18F] Substrate‐based Approach. doi.org/10.1002/chem.201805473.
2018
Menny A, Serna M, Boyd CM, Scott Gardner, Joseph AP, Morgan BP, Topf M, Brooks NJ, Bubeck D. (2018) Nat Commun. 9:5316. CryoEM reveals how the complement membrane attack complex ruptures lipid bilayers. doi.org/10.1038/s41467-018-07653-5.
Smelt CLC, Sanders VR, Newcombe J, Burt RP, Sheppard TD, Topf M, Millar NS (2018) Neuropharmacology. 139:194-
Identification by virtual screening and functional characterisation of novel positive and negative allosteric modulators of the α7 nicotinic acetylcholine receptor. doi.org/10.1016/j.neuropharm.2018.07.009.
Bullock JMA, Thalassinos K, Topf M. (2018) Bioinformatics 34:3584–3585. Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry. doi.org/10.1093/bioinformatics/bty366.
Bullock JMA, Sen N, Thalassinos K, Topf M. (2018) Structure 26:1015-1024.e2. Modelling protein complexes using restraints from cross-linking mass spectrometry. doi.org/10.1016/j.str.2018.04.016.
Al-Olabi L, Polubothu S, Dowsett K, Andrews KA, Stadnik P, Joseph AP, Knox R, Pittman A, Clark G, Baird W, Bulstrode N, Glover M, Gordon K, Hargrave D, Huson SM, Jacques TS, James G, Kondolf H, Kangesu L, Keppler-Noreuil KM, Khan A, Lindhurst MJ, Lipson M, Mansour S, O’Hara J, Mahon C, Mosica A, Moss C, Murthy A, Ong J, Parker VE, Rivière J-B, Sapp JC, Sebire NJ, Shah R, Sivakumar B, Thomas A, Virasami A, Waelchli R, Zeng Z, Biesecker LG, Barnacle A, Topf M, Semple RK, Patton EE, Kinsler VA. (2018) J Clin Invest 128:1496-1508. Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy. doi.org/10.1172/JCI98589.
Fedele L, Newcombe J, Topf M, Gibb A, Harvey RJ, Smart TG. (2018) Nat Commun 9:957. Disease-associated missense mutations in GluN2B subunit alter NMDA receptor ligand binding and ion channel properties. doi.org/10.1038/s41467-018-02927-4.
2017
Tweedy JG, Escriva E, Topf M, and Gompels UA. (2017) Viruses 10:16. Analyses of Tissue Culture Adaptation of Human Herpesvirus-6A by Whole Genome Deep Sequencing Redefines the Reference Sequence and Identifies Virus Entry Complex Changes. doi.org/10.3390/v10010016
Newcombe J, Chatzidaki A, Sheppard TD, Topf M+ and Millar NS+. (2017) Mol Pharm 93:128-140. Diversity of nicotinic acetylcholine receptor positive allosteric modulators revealed by mutagenesis and a revised structural model. doi.org/10.1124/mol.117.110551.
Locke J, Joseph AP, Peña A, Möckel M, Mayer TU, Topf M, Moores CA. (2017) Proc Natl Acad Sci USA 114:E9539-E9548. Structural basis of human kinesin-8 function and inhibition. doi.org/10.1073/pnas.1712169114.
McTague A, Nair U, Malhotra S, Meyer E, Trump N, Gazina EV, Papandreou A, Ngoh A, Ackermann S, Ambegaonkar G, Appleton R, Desurkar A, Eltze C, Kneen R, Kumar AV, Lascelles K, Montgomery T, Ramesh V, Samanta R, Scott RH, Tan J, Whitehouse W, Poduri A, Scheffer IE, Chong WKK, Cross JH, Topf M, Petrou S, Kurian MA. (2017) Neurology 90:e55-e66. Clinical and molecular characterisation of KCNT1-related severe early onset epilepsy. doi.org/10.1212/WNL.0000000000004762.
Wright ZVF, McCarthy S, Dickman R, Reyes FE, Sanchez-Martinez S, Cryar A, Kilford I5, Hall A5, Takle AK, Topf M, Gonen T, Thalassinos K, Tabor AB. (2017) J Am Chem Soc 139:13063-13075. The Role of Disulfide Bond Replacements in Analogues of the Tarantula Toxin ProTx-II and Their Effects on Inhibition of the Voltage-Gated Sodium Ion Channel Nav1.7. doi.org/10.1021/jacs.7b06506.
Atherton J, Jiang K, Stangier MM, Luo Y, Hua S, Houben K, van Hooff JJE, Joseph AP, Scarabelli G, Grant BJ, Roberts AJ, Topf M, Steinmetz MO, Baldus M, Moores CA, Akhmanova A. (2017) Nat Struct Mol Biol 24:931-943. A structural model for microtubule minus-end recognition and protection by CAMSAP proteins. doi.org/10.1038/nsmb.3483.
Atherton J, Yu I, Cook A, Muretta JM, Joseph A, Major J, Souriques Y, Clause J, Topf M, Rosenfeld SS, Houdusse A, Moores C. (2017) eLife 6:e27793. The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry. doi.org/10.7554/eLife.27793.
Deville C., Carroni M, Franke KB, Topf M, Bukau B, Mogk A Saibil HR. (2017) Sci Adv 3, e1701726. Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase. doi.org/10.1126/sciadv.1701726.
Joseph AP, Polles G, Alber F, Topf M. (2017) Curr Opin Struct Biol 46:102–109. Integrative modelling of cellular assemblies. (review). doi.org/10.1016/j.sbi.2017.07.001.
Schaefer N, Berger A, v.Brederode H, Zheng F, Zhang Y, Leacock S, Littau L, Jablonka S, Malhotra S, Topf M, Winter F, Davydova D, Lynch J, Paige C, Alzheimer C, Harvey RJ, Villmann C. (2017) J Neuroscience 37:7948-7961. Disruption of an extracellular glycine receptor structurally important element leads to decreased synaptic integration and strength resulting in severe startle disease. doi.org/10.1523/JNEUROSCI.0009-17.2017.
Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M. (2017) J Struct Biol 199:12–26. Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy. doi.org/10.1016/j.jsb.2017.05.007.
Meyer E*, Carss KJ*, Rankin J*, Nichols J, Grozeva D, Joseph AP, Mencacci NE, Papandreou A, Ng J, 1Barral S, Ngoh A, Ben-Pazi H, Willemsen MA, Arkadir D, Barnicoat A, Bergman H, Bhate S, Boys A, Darin N, Foulds N, Gutowski N, Hills A, Houlden H, Hurst J, Israel Z, Kaminska M, Limousin P, Lumsden D, McKee S, Misra S, Mohammed SS, Nakou V, Nicolai J, Nilsson M, Pall H, Peall KJ, Peters GB, Prabhakar P, Reuter MS, Rump P, Segel R, Sinnema M, Smith M, Turnpenny P, White S, Wieczorek D, Wilson B, Winter G, Wragg C, Pope S, Heales SJH, Morrogh D, The UK10K Consortium, DDD study, NIHR Bioresource Rare Diseases Consortium, Pittman A, Carr LJ, Perez-Dueñas B, Lin JP, Reis A, Gahl WA, Toro C, Bhatia KB, Wood NW, Kamsteeg EJ, Chong WK, Gissen P, Topf M, Dale RC, Chubb JR, Raymond FL+, Kurian MA+. (2017) Nat Gen 49:223-237. Mutations in the Histone Methyltransferase Gene KMT2B Cause Complex Early Onset Dystonia. doi.org/10.1038/ng.3740.
2016
Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grünewald K, Shepherd A, Topf M. (2016) Mol Cell Proteomics 15:10.1074/mcp.M116.058552, 2939-2953. HVint: A strategy for identifying novel protein-protein interactions in herpes simplex virus type 1. doi.org/10.1074/mcp.M116.058552.
Matthew Allen Bullock J, Schwab J, Thalassinos K, Topf M. The Importance of Non-accessible Crosslinks and Solvent Accessible Surface Distance in Modeling Proteins with Restraints From Crosslinking Mass Spectrometry. Mol. Cell. Proteomics 2016;15(7):2491–2500. doi.org/10.1074/mcp.M116.058560.
Joseph AP, Malhotra S, Burnley T, Wood C, Clare DK, Winn M, Topf M. (2016) Methods 100:42-49. Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment. doi.org/10.1016/j.ymeth.2016.03.007.
Zeev-Ben-Mordehai T, Vasishtan D, Hernandez A, Vollmer B, White P, Pandurangan AP, Siebert A, Topf M, Grünewald K. (2016) Proc Natl Acad Sci USA 113:4176–4181. Two distinct trimeric conformations of natively membrane-anchored full-length Herpes simplex virus 1 glycoprotein B. doi.org/10.1073/pnas.1523234113.
2015
Kalscheuer VM, James VM, Himelright ML, Long P, Oegema R, Jensen C, Bienek M, Hu H, Haas SA, Topf M, Hoogeboom AJM, Harvey K, Walikonis R, Harvey RJ (2015) Front. Mol. Neurosci 8:85. Novel missense mutation A789V in IQSEC2 underlies X-linked intellectual disability in the MRX78 family. 10.3389/fnmol.2015.00085. doi.org/10.3389/fnmol.2015.00085.
Pandurangan AP, Vasishtan D, Alber F, Topf M (2015) Structure, 23:2365–2376. γ-TEMPy: simultaneous fitting of components in 3D-EM maps of their assembly using a genetic algorithm. doi.org/10.1016/j.str.2015.10.013.
Pilorge M, Fassier C, Le Corronc H, Potey A, Bai J, De Gois S, Delaby E, Assouline B, Guinchat V, Devillard F, Delorme R, Nygren G, Rastam M, Meier JC, Otani S, Cheval H, James VM, Topf M, Dear TN, Gillberg C, Leboyer M, Giros B, Gautron S, Hazan J, Harvey RJ, Legendre P, Betancur C. (2015) Molec Psych 21:936-45. Genetic and functional analyses demonstrate a role for abnormal glycinergic signaling in autism. doi.org/10.1038/mp.2015.139.
Farabella I, Vasishtan D, Joseph AP, Pandurangan AP, Sahota H, Topf M (2015) J Appl Cryst 48:1314-1323. TEMPy: a Python Library for Assessment of 3D Electron Microscopy Density Fits. doi.org/10.1107/S1600576715010092.
Stödberg T, McTague A, Ruiz AJ, Hirata H, Zhen J, Long P, Farabella I, Meyer E, Kawahara A, Vassallo G, Stivaros SM, Bjursell MK, Stranneheim H, Tigerschiöld S, Persson B, Bangash I, Das K, Hughes D, Lesko N, Lundeberg J, Scott RC, Poduri A, Scheffer IE, Smith H, Gissen P, Schorge S, Reith MEA, Topf M, Kullmann DM, Harvey RJ, Wedell A, Kurian MA. (2015) Nat Commun 6:8038. Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures. doi.org/10.1038/ncomms9038.
Sali A, Berman, H, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. (2015) Structure 23:1156-67. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. doi.org/10.1016/j.str.2015.05.013.
Lukoyanova N, Kondos SC, Farabella I, Law, RHP, Reboul CF, Caradoc-Davies TT, Spicer BA, Kleifeld O, Traore D, Ekke SM, Voskoboinik I, Trapani, JA, Hatfaludi T, Oliver K, Hotze EM, Tweten RK, Whisstock JC, Topf M, Saibil HR, Dunstone MA. (2015) PLoS Biol 13:e1002049. Conformational changes during pore formation by the perforin-related protein pleurotolysin. doi.org/10.1371/journal.pbio.1002049.
Wood C, Tom Burnley T, Patwardhan A, Scheres S, Topf M, Roseman A, Winn M. (2015) Acta Cryst Section D D71:123–
Collaborative Computational Project for Electron cryo-Microscopy. doi.org/10.1107/S1399004714018070.
2014
Leung C, Dudkina NV, Lukoyanova N, Hodel AW, Farabella I, Pandurangan AP, Jahan N, Pires Damaso M, Osmanović D, Reboul CF, Dunstone MA, Andrew PW, Lonnen R, Topf M, Saibil HR, Hoogenboom BW (2014) eLife 10.7554/eLife.04247. Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin. doi.org/10.7554/eLife.04247.
Farabella I, Pham T, Henderson NS, Geibel S, Phan G, Thanassi DG, Delcour AH, Waksman G, Topf M (2014) eLife 3:e0332. Allosteric Signalling in the Outer Membrane Translocation Domain of PapC Usher. doi.org/10.7554/eLife.21585
Atherton J, Farabella I, Yu I, Rosenfeld SS, Houdusse A, Topf M, Moores C. (2014) eLife 3:e03680. Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins. doi.org/10.7554/eLife.03680.
Mortensen M, Iqbal F, Pandurangan AP, Hannan S, Huckvale R, Topf M, Baker JR, Smart TG. (2014) Nat Commun 5:4454. Photo-antagonism of the GABAA receptor. doi.org/10.1038/ncomms5454.
Pandurangan AP, Shakeel S, Butcher SJ, Topf M. (2014) J Struct Biol 185: 427–439. Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change. doi.org/10.1016/j.jsb.2013.12.003.
2013
Ganser LR, Yan Q, James VM, Kozol R, Topf M, Harvey RJ, Dallman J. (2013) Neurobiol Dis 60:139-51. Distinct phenotypes in zebrafish models of human startle disease. doi.org/10.1016/j.nbd.2013.09.002.
Thalassinos K, Pandurangan AP, Xu M, Alber F, Topf M. (2013) Structure 21:1500-8. Conformational States of macromolecular assemblies explored by integrative structure calculation. doi.org/10.1016/j.str.2013.08.006.
Maurer UE, Zeev-Ben-Mordehai T, Pandurangan AP, Cairns TM, Hannah BP, Whitbeck JC, Eisenberg RJ, Cohen GH, Topf M, Huiskonen JT, Grünewald K. (2013) Structure 21:1-10. The structure of herpesvirus fusion glycoprotein B-bilayer complex reveals the protein-membrane and lateral protein-protein interaction. doi.org/10.1016/j.str.2013.05.018.
Redzej A, Ilangovan A, Lang S, Gruber CJ, Topf M, Zangger K, Zechner EL, Waksman G. (2013) Mol Microbiol 89:324-33. Structure of a translocation signal domain mediating conjugative transfer by type IV secretion systems. doi.org/10.1111/mmi.12275.
Yuan S, Topf M, Reubold TF, Eschenburg S, Akey CW. (2013) Biochemistry 52:2319-27. Changes in Apaf-1 conformation that drive apoptosome assembly. doi.org/10.1021/bi301721g.
James VM, Bode A, Chung S-K, Gil JL, Nielsen M, Cowan FM, Vujic M, Thomas RH, Rees MI, Harvey K, Keramidas A, Topf M, Ginjaar L, Lynch JW, Harvey RJ. (2013) Neurobiol Dis 52:137-49. Novel missense mutations in the glycine receptor ß subunit gene (GLRB) in startle disease. doi.org/10.1016/j.nbd.2012.12.001.
2012
Pandurangan AP, Topf M. (2012) Bioinformatics 28:2391-3. RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps. doi.org/10.1016/j.jsb.2013.12.003.
Giménez C, Pérez-Siles G, Martínez-Villarreal J, Arribas-González E, Jiménez E, Núñez E, de Juan-Sanz J, Fernández-Sánchez E, García-Tardón N, Ibáñez I, Romanelli V, Nevado J, James VM, Topf M, Chung SK, Thomas RH, Desviat LR, Aragón C, Zafra F, Rees MI, Lapunzina P, Harvey RJ, López-Corcuera B. (2012) J Biol Chem 287:28986-9002. A novel dominant hyperekplexia mutation y705c alters trafficking and biochemical properties of the presynaptic glycine transporter glyt2. doi.org/10.1074/jbc.M111.319244.
Carta E, Chung SK, James VM, Robinson A, Gill JL, Remy N, Vanbellinghen JF, Drew CJ, Cagdas S, Cameron D, Cowan FM, Del Toro M, Graham GE, Manzur AY, Masri A, Rivera S, Scalais E, Shiang R, Sinclair K, Stuart CA, Tijssen MA, Wise G, Zuberi SM, Harvey K, Pearce BR, Topf M, Thomas RH, Supplisson S, Rees MI, Harvey RJ. (2012) J Biol Chem 287:28975-85. Mutations in the GlyT2 gene (SLC6A5) are a second major cause of startle disease. doi.org/10.1074/jbc.M112.372094.
Seitsonen JJ, Shakeel S, Susi P, Pandurangan AP, Sinkovits RS, Hyvönen, Laurinmäki P, Ylä-Pelto J, Topf M, Hyypiä T, Butcher SJ. (2012) J Virol 86:7207-15. Structural analysis of coxsackievirus A7 reveals conformational changes associated with uncoating. doi.org/10.1074/jbc.M112.372094.
Clare DK, Vasishtan D, Stagg S, Quispe J, Farr GW, Topf M, Horwich AL, Saibil HR. (2012) Cell 149:113-23. ATP-triggered molecular mechanics of the chaperonin GroEL. doi.org/10.1016/j.cell.2012.02.047.
James VM, Gill JL, Topf M, Harvey RJ. (2012) Biol Chem 393:283–289. Molecular mechanisms of glycine transporter GlyT2 mutations in startle disease. doi.org/10.1515/BC-2011-232.
Pandurangan AP, Topf M. (2012) J Struct Biol 177:520-531. Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps. doi.org/10.1016/j.jsb.2011.10.011.
Gill JL, James VM, Carta E, Harris D, Topf M, Scholes SFE, Hateley G, Harvey RJ. (2012) Animal Genetics 43(3):267-70. Identification of congenital muscular dystonia 2 associated with an inherited GlyT2 defect in Belgian Blue cattle from the United Kingdom. doi.org/10.1111/j.1365-2052.2011.02255.x.
2011
Vasishtan D, Topf M. (2011) J Struct Biol 174:333-343. Scoring functions for cryoEM density fitting. doi.org/10.1016/j.jsb.2011.01.012.
Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW. (2011) Structure 19:128-140. Structure of the Drosophila apoptosome at 6.9 Å resolution. doi.org/10.1016/j.str.2010.10.009.
Beck M, Topf M, Frazier Z, Tjong, Xu M, Zhang S, Alber F. (2011) J Struct Biol 173:483-96. Exploring the spatial and temporal organization of a cell’s proteome. doi.org/10.1016/j.jsb.2010.11.011.
2010
Malet H, Topf M, Clare DK, Ebert J, Bonneau F, Basquin J, Drazkowska K, Tomecki R, Dziembowski A, Conti E, Saibil HR, Lorentzen E. (2010) EMBO Rep 11:936-942. RNA channelling by the eukaryotic exosome. (Cover). doi.org/10.1038/embor.2010.164.
Kumar RA, Pilz DT, Babatz TD, Cushion T, Harvey K, Topf M, Uyanik G, Rees MI, Harvey RJ, Dobyns WB. (2010) Hum Mol Genet 19:2817-2827. TUBA1A mutations cause wide spectrum lissencephaly (smooth brain) and suggest that multiple neuronal migration pathways converge on alpha tubulins. doi.org/10.1093/hmg/ddq182.
Rawi R, Whitmore L, Topf M. (2010) Bioinformatics 26:1673-4. CHOYCE – A web server for constrained homology modelling with cryoEM maps. doi.org/10.1093/bioinformatics/btq237.
Zhang S, Vasishtan D, Xu M, Topf M+, Alber F+ (2010) Bioinformatics [ISMB] 26:i261-i268. A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps. (+co-corresponding authors). doi.org/10.1093/bioinformatics/btq201.
Yuan S, Yu X, Topf M, Ludtke SJ, Wang X, Akey CW. (2010) Structure 18:571-583. Structure of the human apoptosome with prodomains of procaspase-9. doi.org/10.1016/j.str.2010.04.001.
Gartmann M, Blau M, Armache JP, Mielke T, Topf M, Beckmann R (2010) J Biol Chem 285:14848-14851. Mechanism of eIF6-mediated inhibition of ribosomal subunit joining. doi.org/10.1074/jbc.C109.096057.
2009
Taylor DJ, Devkota B, Huang AD, Topf M, Eswar N, Sali A, Harvey SC, Frank J. (2009) Structure 17:1591-604. Comprehensive Atomic Model of the Eukaryotic Ribosome. doi.org/10.1016/j.str.2009.09.015.
Lasker K, Topf M, Sali, A, Wolfson H. (2009) J Mol Biol 388:180-194. Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. doi.org/10.1016/j.jmb.2009.02.031.
2008
Connell SR*, Topf M*, Qin Y*, Wilson DN, Mielke T, Fucini P, Nierhaus KH, Spahn CMT. (2008) Nat Struct Mol Biol 15:910-915. A new tRNA-intermediate revealed on the ribosome during EF4-mediated back-translocation. (*co-first authors). doi.org/10.1038/nsmb.1469.
Miller PS, Topf M, Smart TG. (2008) Nat Struct Mol Biol 15:1084-1093. Mapping a molecular link between allosteric inhibition and activation of the glycine receptor. doi.org/10.1038/nsmb.1492.
Harvey RJ, Topf M, Harvey K, Rees MI. (2008) Trends in Genetics 24:439-447. The genetics of hyperekplexia: more than startle! doi.org/10.1016/j.tig.2008.06.005.
Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J. (2008) Nat Struct Mol Biol 15:746-
Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. doi.org/10.1038/nsmb.1436.
Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Guttell RR, Sali A, Akey C. (2008) Structure 16:535-
Structure of the mammalian 80S ribosome at 8.7 Å resolution. doi.org/10.1016/j.str.2008.01.007.
Alber F, Förster F, Korkin, D, Topf M, Sali A. (2008) Ann Rev Biochem 77:443-477. Integrating diverse data for structure determination of macromolecular assemblies. (Review). doi.org/10.1146/annurev.biochem.77.060407.135530.
Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. (2008) Structure 16:295-307. Protein structure fitting and refinement guided by CryoEM density. doi.org/10.1016/j.str.2007.11.016.
Cong Y, Topf M, Sali A, Matsudaira P, Dougherty MT, Chiu W, Schmid MF. (2008) J Mol Biol 375:331-336. Crystallographic conformers of actin in a biological context. doi.org/10.1016/j.jmb.2007.10.027.
Before 2008
Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, W Chiu. (2007) Proc Natl Acad Sci USA 105:9610-9615. Subnanometer resolution cryo-EM based domain models for the cytoplasmic region of skeletal muscle RYR channel. doi.org/10.1073/pnas.0803189105.
Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. (2006) J Mol Biol 357:1655-1668. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. doi.org/10.1016/j.jmb.2006.01.062.
Topf M, Sali A. (2005) Curr Opin Struct Biol 15:578-585. Combining electron microscopy and comparative protein structure modeling. (Review). doi.org/10.1016/j.sbi.2005.08.001.
Topf M, Baker ML, John B, Chiu W, Sali A. (2005) J Struct Biol 149:191-203. Structure characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. (Cover). Paper of the Year 2008, J Struct Biol. doi.org/10.1016/j.jsb.2004.11.004.
Topf M, Richards WG. (2004) J Am Chem Soc 126:14631-14641. Theoretical studies on the deacylation step of serine protease catalysis in the gas phase, in solution, and in elastase. doi.org/10.1021/ja047010a.
Topf M, Sandala GM, Smith DM, Schofield CJ, Easton CJ, Radom L. (2004) J Am Chem Soc 126:9932-9933. The unusual bifunctional catalysis of epimerization and desaturation by carbapenem synthase. doi.org/10.1021/ja047899v.
Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. (2004) Curr Opin Struct Biol 14:313-324. A structural perspective on protein-protein interactions. (Review). doi.org/10.1016/j.sbi.2004.04.006.
Shacham S, Marantz Y, Bar-Haim S, Kalid O, Warshaviak D, Avisar N, Inbal B, Heifetz A, Fichman M, Topf M, Naor Z, Noiman S, Becker OM. (2004) Proteins 57:51-86. PREDICT modeling and in-silico screening for G-protein coupled receptors. doi.org/10.1002/prot.20195.
Clifton IJ, Doan L, Sleeman MC, Topf M, Suzuki H, Wilmouth R, Schofield CJ. (2003) J Biol Chem 278:20843-20850. The crystal structure of Carbapenem synthase (CarC). doi.org/10.1074/jbc.M213054200.
Topf M, Várnai P, Richards WG. (2002) J Am Chem Soc 124:14780-14788. Ab initio QM/MM dynamics simulation of the tetrahedral intermediate of serine proteases: insights into the active site hydrogen-bonding network. doi.org/10.1021/ja026219q.
Topf M, Várnai P, Schofield CJ, Richards WG. (2002) Proteins 47:357-369. Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases. doi.org/10.1002/prot.10097.
Shacham S, Topf M, Avisar N, Glazer F, Marantz Y, Bar-Haim S, Noiman S, Naor Z, Becker OM. (2001) Med Res Rev 21:472-483. Modeling the 3D structure of GPCRs from sequence. (Review). doi.org/10.1002/med.1019.
Topf M, Várnai P, Richards WG. (2001) Theor Chem Acc 106:146-151. QM/MM study of three stationary points along the deacylation step of the catalytic mechanism of elastase. doi.org/10.1007/s002140000246.