Affiliation: University of London
- Protein structure fitting and refinement guided by cryo-EM densityMaya Topf
School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
Structure 16:295-307. 2008..At approximately 10 A resolution, Calpha rmsd between the initial and final structures was reduced on average by approximately 53%. The method is automated and can refine both experimental and predicted atomic structures...
- RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM mapsArun Prasad Pandurangan
Department of Crystallography Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
Bioinformatics 28:2391-3. 2012..Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component...
- ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperoninDaniel K Clare
Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
Cell 149:113-23. 2012..The extended conformation also provides a potential docking site for GroES, to trigger the final, 100° domain rotation constituting the "power stroke" that ejects substrate into the folding chamber...
- Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM mapsArun Prasad Pandurangan
Institute of Structural and Molecular Biology, Crystallography Department of Biological Sciences, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
J Struct Biol 177:520-31. 2012..The method is stand-alone and could serve as a general interactive tool for guiding flexible fitting into EM maps...
- Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational changeArun Prasad Pandurangan
Institute of Structural and Molecular Biology, Department of Biological Sciences Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom
J Struct Biol 185:427-39. 2014..The protocol could be applied not only to viral capsids but also to many other complexes characterised by a combination of atomic structure modelling and cryoEM density fitting. ..
- Scoring functions for cryoEM density fittingDaven Vasishtan
Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, University of London, London WC1E7HX, UK
J Struct Biol 174:333-43. 2011..Finally, we show that our score-testing method, when combined with the Laplacian CCF or the mutual information scores, can be used as a statistical tool for improving cryoEM density fitting...
- CHOYCE: a web server for constrained homology modelling with cryoEM mapsReda Rawi
Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, University of London, London, UK
Bioinformatics 26:1673-4. 2010..It provides an interactive approach to improving the selection of models based on the quality of their fit into the EM map...
- Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCTChristopher R Booth
Graduate Program in Structural and Computational Biology and Molecular Biophysics, One Baylor Plaza, Baylor College of Medicine, Houston, Texas 77030, USA
Nat Struct Mol Biol 15:746-53. 2008..Our findings show how different mechanical switches can evolve from a common structural framework through modification of allosteric networks...
- Structure of the mammalian 80S ribosome at 8.7 A resolutionPreethi Chandramouli
Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA
Structure 16:535-48. 2008..Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation...
- Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channelIrina I Serysheva
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
Proc Natl Acad Sci U S A 105:9610-5. 2008..Taken together, these results provide a structural context for both channel gating and the consequences of certain malignant hyperthermia and central core disease-associated mutations in RyR1...
- Mapping a molecular link between allosteric inhibition and activation of the glycine receptorPaul S Miller
Department of Pharmacology, University College London, Gower Street, London WC1E 6BT, UK
Nat Struct Mol Biol 15:1084-93. 2008..We provide a new view for the activation of a Cys-loop receptor where, following agonist binding, the hydrophobic core and interfacial loops reorganize in a concerted fashion to induce downstream gating...
- Crystallographic conformers of actin in a biologically active bundle of filamentsYao Cong
National Center for Macromolecular Imaging and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
J Mol Biol 375:331-6. 2008..The scruin and bundle packing forces appear to influence the tertiary and quaternary conformations of actin in the filament of this biologically active bundle...
- Refinement of protein structures by iterative comparative modeling and CryoEM density fittingMaya Topf
Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3, 1700 4th Street, Suite 503B, University of California at San Francisco, San Francisco, CA 94143 2552, USA
J Mol Biol 357:1655-68. 2006..The method is being implemented in our program MODELLER for protein structure modeling by satisfaction of spatial restraints and will be applicable to the rapidly increasing number of cryoEM density maps of macromolecular assemblies...
- Combining electron microscopy and comparative protein structure modelingMaya Topf
Department of Biopharmaceutical Sciences, University of California San Francisco, San Francisco, CA 94143, USA
Curr Opin Struct Biol 15:578-85. 2005..Also, comparative modeling can benefit from electron microscopy through the use of intermediate-resolution density maps in fold recognition, template selection and sequence-structure alignment...
- Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopyMaya Topf
Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California, San Francisco, CA 94143, USA
J Struct Biol 149:191-203. 2005..Moreover, a pseudo-atomic model of a component in an assembly may be built better with comparative models of the native subunit sequences than with experimentally determined structures of their homologs...
- PREDICT modeling and in-silico screening for G-protein coupled receptorsSharon Shacham
Predix Pharmaceuticals Ltd, Ramat Gan, Israel
Proteins 57:51-86. 2004..Namely, the PREDICT models can be used to identify active small-molecule ligands embedded in large compound libraries with an efficiency comparable to that obtained using crystal structures for non-GPCR targets...
- Crystal structure of carbapenem synthase (CarC)Ian J Clifton
Oxford Centre for Molecular Sciences and the Dyson Perrins Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
J Biol Chem 278:20843-50. 2003..The combined work will stimulate further mechanistic studies and aid in the engineering of carbapenem biosynthesis...