CPFM: Center for Protein Folding Machinery

Publications Supported all or in Part by the NDC Award

Chen, D. H., Song, J. L., Chuang, D. T., Chiu, W. Ludtke, S. J. (2006). An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate. Structure 14: 1711-22.
Pubmed: 17098196
Speiss, C., Miller, E. J., McClellan, A. J., and Frydman, J. (2006). Identification of the TRIC/CCT substrate binding sites uncovers the function of subunit diversity in eukaryotic chaperonins. Molecular Cell 23(1):25-37.
Pubmed: 17018290
Marsh, M. P., Chang, J. T., Booth, C. R., Liang, N. L., Schmid, M. F., and Chiu, W. (2007). Modular software platform for low-dose electron microscopy and tomography. J Microsc 228: 384-389.
Pubmed: 18045333
Reissman, S., Parnot, C., Booth, C. R., Chiu, W., and Frydman, J. (2007). Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins. Nat Struct Mol Biol, 14: 432-40.
Pubmed: 17460696
Lucent, D. V., Vishal, V., and Pande, V. S. (2007). Protein folding under confinement: A new role for solvent. Proc Natl Acad Sci U S A, 104: 10430-10434.
Schroder, G., Brunger, A., and Levitt, M. (2007) Deformable elastic network model to combine initial structural information with low resolution data: application to real-space refinement. Structure, 15:1630-1641.
Ludtke, S., Baker, M.L., Chen, D.H., Song, J., Chuang, D. and Chiu, W. (2008) De Novo Backbone Trace of GroEL from Single Particle Electron Cryo-Microscopy. Structure, 16: 441-8.
Pubmed: 18334219
Topf, M., Lasker, K., Webb, B., Wolfson, H., Chiu, W. and Sali, A.(2008). Protein Structure Fitting and Refinement Guided by Cryo-EM Density. Structure 16: 295-307.
Pubmed: 18275820
England, J., Park, S., and Pande, V. S. (2008) Theory for an order-driven disruption of the liquid state in water. J Chem Physics, 128:044503.
Pubmed: 18247965
Booth, C. R., Meyer, A. S., Cong, Y., Topf, M., Sali, A., Ludtke, S, J., Chiu, W. and Frydman, J. (2008). Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nature Struct & Molec Biol, 15:746-53.
Pubmed: 18536725
England, J. L., Lucent, D., and Pande, V. S. (2008). A Role for Confined Water in Chaperonin Function. J Am Chem Soc, 130:11838-9.
Pubmed: 18710231
F�rster, F., Webb B., Krukenberg, K.A., Tsuruta, H., Agard, D. A., Sali, A. Integration of small angle X-ray scattering data into structural modeling of proteins and assemblies, J. Mol Biol., 382(4):1089-106.
Pubmed: 18694757
Cohen, A. E., and Moerner, W. E. (2008). Controlling Brownian motion of single protein molecules and single fluorophores in aqueous buffer. Optics Express 16: 6941-6956.
Pubmed: 18545398
Chen, DH, Luke, K., Zhang, J., Chiu, W., and Wittung-Stafshede, P. (2008). Location and flexibility of the unique C-terminal tail of Aquifex aeolicus co-chaperonin protein10 as derived by cryo-EM and biophysical techniques. J Mol Biol, 381:707-17.
Pubmed: 18588898
England, J. and Pande, V. S. (2008). Potential for modulation of the hydrophobic effect inside chaperonins. Biophysical J, 95 3391-9
Pubmed: 18599630
Jiang, Y., Q. Wang, A. E. Cohen, N. Douglas, J. Frydman, and W. E. Moerner (2008), Hardware-based anti-Brownian electrokinetic trap (ABEL trap) for single molecules: Control loop simulations and application to ATP binding stoichiometry in multi-subunit enzymes, Proc. SPIE 7038, 1-12.
PubMed Central: 2759103.
England, J., Lucent, D., and Pande, V. S. (2008). Rattling the cage: computational models of chaperonin-mediated protein folding. Current Opin in Struct Biol, 18:163-9.
Pubmed: 18291636
Lucent, D. Lucent, England, J., Pande, V. S. (2008). Inside the Chaperonin toolbox: Theoretical and computational models for chaperonin mechanism, Physical Biology 6:15003.
Pubmed: 19208937
Zhang, J., Nakamura, N., Shimizu, Y., Liang, N. L., Liu, X., Jakana, J., Marsh, M. P., Booth, C. R.. Shinkawa, T., Nakata, M. And Chiu, W. (2009). JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles. J Struct Biol, 165: 1-9.
Pubmed: 18926912
Baker, M. L., Marsh, M. P., and Chiu, W. (2009). Cryo-EM of molecular nanomachines and cells. Nanotechnology, ed. Viola Vogel, Wiley VCH, 5:91-111.
Zhang, R., X. Hu, H. Khant, S. J. Ludtke, W. Chiu, M. F. Schmid, C. Frieden, J.M. Lee (2009). Inter-protofilament interactions between Alzheimer's Aβ1-42 peptides in amyloid fibrils revealed by cryo-EM. PNAS 106: 4653-4658.
Tam, S., Spiess, C., Auyeung, W., Joachimiak, L., Chen, B., Poirier, M.A. and Frydman, J. (2009). The Chaperonin TRIC Blocks a Huntingtin Sequence Element that promotes the Conformational Switch to Aggregation. Nature Struct & Mol Biol 16: 1279-85.
PubMed Central: 2788664.
Kelley, N. W., X. Huang, S. Tam, C. Spies, J. Frydman, and V. S. Pande (2009). The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation, J Mol Biol, 388: 919-927.
PubMed Central: 2677131.
Mandell DJ, Coutsias EA, Kortemme T. (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nature Methods 6:551-2. NIHMS183260
Babor M, and Kortemme T. (2009). Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. Proteins 75(4):846-58. NIHMS 131227.
DiMaio, F., Tyka, M. D., Baker, M.L, Chiu, W. and Baker, D. (2009). Refinement of protein structures into low-resolution density maps using Rosetta. J Mol Biol 392: 181-90. NIHMS144804.
Pintilie, G., J. Zhang, W. Chiu, D. Gossard (2009). Identifying Components in 3-D Density maps of protein nanomachines by multi-scale segmentation, IEEE, Proc. of LISSA, 44-47. PMC to be assigned.
Zhang, J., Baker, M.L., Schr�eder, G.F., Douglas, N.R., Reissmann, S., Jakana, J., Dougherty, M., Fu, C.F., Levitt, M., Ludtke, S.J., Frydman, J. and Chiu, W. (2010). Mechanism of folding chamber closure in a group II chaperonin. Nature 463: 379-383.
PubMed Central: 2834796.
Cong, Y., Baker, M. L., Jakana, J., Woolford, D., Miller, E.J., Reissmann, S., Kumar, R. N., Redding-Johanson, A. M., Batth, T.S., Mukhopadhyay, A., Ludtke, S. J., Frydman, J. and Chiu, W. (2010). 4.0 � resolution cryo‐EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Proc Natl Acad Sci U S A 107: 4967-4972.

PMC to be assigned.

Kalisman, N. and Levitt, M. (2010). Insights into the Intra-Ring Subunit Order of TRiC/CCT: A Structural and Evolutionary Analysis. Pacific. Symp. Biocomputing. 252-259. PMC to be assigned.
Schr�der, G. Levitt, M. and Brunger, A. (2010). Super-resolution biomolecular crystallography with low-resolution data, Nature, in press. PMCID to be assigned.
Suha, M. Levitt, M. and Chiu, W. (2010). MOTIF-EM: an Automated Computational Tool for Identifying Conserved Regions in Cryo-EM Structures. ISMB 2010. In press. PMC to be assigned.
Pintilie, G., Zhang, J., Chiu, W., Gossard, D. (2010) Segmentation and fitting of molecular components in cryo-EM density maps: quantitative analysis of a multi-scale region-based approach. Submitted to J Struc Biol. In press. PMC to be assigned.

NDC Related Publications Benefited from the Technologies Available in the NDC or the Collaborative Network

Krukenberg, K. A., F�rster, F., Rice, L. M., Sali, A., Agard, D.A. (2008). A novel conformation of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure 16, 755-765.
Pubmed: 18462680
Cong, Y., Topf, M., Sali, A., Matsudaira, P., Dougherty, M., Chiu, W. and Schmid, M.F. (2008). Crystallographic conformers of actin in a biologically active bundle of filaments. J Mol Biol 375: 331-6.
Pubmed: 18022194
Chandramouli, P., Topf, M., M�n�tret, J. F., Eswar, N., Gutell, R. R., Sali, A., Akey, C. W. (2008). Structure of the Mammalian 80S Ribosome at 8.7 � Resolution. Structure 16, 535-548.
Pubmed: 18400176
Jiang, W., Baker, M.L., Jakana, J., Weigele, P. R., King, J. and Chiu, W. (2008). Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature 451: 1130-4.
Pubmed: 18305544
Serysheva, I. I., Ludtke, S. J., Baker, M. L., Cong, Y., Topf, M., Eramian, D., Sali, A., Hamilton, S. L., and Chiu, W. (2008). Subnanometer resolution cryo-EM based domain models for the cytoplasmic region of skeletal muscle RyR channel. PNAS, 105:9610-5.
Pubmed: 18621707
Schwede, T., A. Sali, B. Honig, M. Levitt, H.M. Berman, D. Jones, S.E. Brenner, S.K. Burley, R. Das, N.V. Dokholyan, R.L. Dunbrack, Jr., K. Fidelis, A. Fiser, A. Godzik, Y.J. Huang, C. Humblet, M.P. Jacobson, A. Joachimiak, S.R. Krystek, Jr., T. Kortemme, A. Kryshtafovych, G.T. Montelione, J. Moult, D. Murray, R. Sanchez, T.R. Sosnick, D.M. Standley, T. Stouch, S. Vajda, M. Vasquez, J.D. Westbrook, and I.A. Wilson (2009). Outcome of a workshop on applications of protein models in biomedical research. Structure 17: 151-159.
Pubmed: 19217386
Mandell DJ, Kortemme T. (2009). Backbone flexibility in computational protein design. Curr Opin Biotechnol 20(4):420-8.
Cong, Y., Q. Zhang, D. Woolford, T. Schweikardt, H. Khant, M. Dougherty, S. J. Ludtke, W. Chiu and H. Decker (2009). Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy. Structure 17(5): 749-58.
PubMed Central: 2705691.
Alber, F., Chait, B. T., Rout, M. P., & Sali, A. (2008) Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints. Protein-protein interactions and networks: identification, characterization and prediction., eds Panchenko A & Przytycka T (Springer-Verlag, London, UK), pp 99-114.
Lasker, K., Topf, M., Sali, A., & Wolfson, H. (2009) Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. J Mol Biol. 388 (1):180-194
PubMed Central: 2680734.
Russel, D., Lasker, K., Phillips, J., Schneidman-Duhovny, D., Velazquez-Muriel, J., & Sali, A. (2009) The structural dynamics of macromolecular processes. Curr Opin Cell Biol. 21 97-108
PubMed Central: 2774249.
Nickell, S., Beck, F., Scheres, S. H. W., Korinek, A., F�rster, F., Lasker, K., Mihalache, O., Sun, N., Nagy, I., Sali, A., Plitzko, J., Carazo, J.-M., Mann, M., & Baumeister, W. (2009) Insights into the Molecular Architecture of the 26S Proteasome. Proc Natl Acad Sci USA. 29 (104):11943-11947
PubMed Central: 2715492.
F�rster, F., Lasker, K., Beck, F., Nickell, S., Sali, A., & Baumeister, W. (2009) An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome. Biochem Biophys Res Commun. 388 228-233
PubMed Central: 2771176.
Taylor, D. J., Devkota, B., Huang, A. D., Topf, M., Eswar, N., Sali, A., Harvey, S. C., & Frank, J. (2009) Comprehensive Molecular Structure of the Eukaryotic Ribosome. Structure. 17 1591-1604.
PubMed Central: 2814252.
F�rster, F., Lasker, K., Nickell, S., Sali, A., & Baumeister, W. (2010) Towards an integrated structural model of the 26S proteasome. Molecular & Celullar Proteomics. in press.
Bammes, B.E., Jakana, J., Schmid, M.F., and Chiu, W. (2010). Radiation damage effects at four specimen temperatures from 4 to 100K. J Struct Biol 169: 331-341.
PubMed Central: 2826528.