Uncertainty in integrative structural modeling

Current Opinion in Structural Biology - Tập 28 - Trang 96-104 - 2014
Dina Schneidman-Duhovny1, Riccardo Pellarin1, Andrej Sali1,2
1Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
2Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA

Tài liệu tham khảo

Brünger, 1992, Free R value: a novel statistical quantity for assessing the accuracy of crystal structures, Nature, 355, 472, 10.1038/355472a0 Read, 2011, A new generation of crystallographic validation tools for the protein data bank, Structure, 19, 1395, 10.1016/j.str.2011.08.006 Montelione, 2013, Recommendations of the wwPDB NMR Validation Task Force, Structure, 21, 1563, 10.1016/j.str.2013.07.021 Henderson, 2012, Outcome of the first electron microscopy validation task force meeting, Structure, 205, 10.1016/j.str.2011.12.014 Jacques, 2012, Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution, Acta Crystallogr D Biol Crystallogr, 68, 620, 10.1107/S0907444912012073 Trewhella, 2013, Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB, Structure, 21, 875, 10.1016/j.str.2013.04.020 Schwede, 2009, Outcome of a workshop on applications of protein models in biomedical research, Structure, 151, 10.1016/j.str.2008.12.014 Berman, 2000, The Protein Data Bank, Nucl Acids Res, 28, 235, 10.1093/nar/28.1.235 Saxton, 1982, The correlation averaging of a regularly arranged bacterial cell envelope protein, J Microsc, 127, 127, 10.1111/j.1365-2818.1982.tb00405.x Harauz, 1986, Exact filters for general geometry three dimensional reconstruction, Proc IEEE Computer Vision Pattern Recogn, 78, 146 Henderson, 2011, Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy, J Mol Biol, 413, 1028, 10.1016/j.jmb.2011.09.008 Scheres, 2012, Prevention of overfitting in cryo-EM structure determination, Nat Methods, 9, 853, 10.1038/nmeth.2115 Chen, 2013, High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy, Ultramicroscopy, 135, 24, 10.1016/j.ultramic.2013.06.004 Stagg, 2014, ResLog plots as an empirical metric of the quality of cryo-EM reconstructions, J Struct Biol, 185, 418, 10.1016/j.jsb.2013.12.010 Rambo, 2013, Accurate assessment of mass, models and resolution by small-angle scattering, Nature, 496, 477, 10.1038/nature12070 Rambo, 2011, Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law, Biopolymers, 95, 559, 10.1002/bip.21638 Haas, 2013, The Protein Model Portal—a comprehensive resource for protein structure and model information, Database (Oxford), 2013, 10.1093/database/bat031 Kryshtafovych, 2014, Assessment of the assessment: evaluation of the model quality estimates in CASP10, Proteins, 82, 112, 10.1002/prot.24347 Sali, 2003, From words to literature in structural proteomics, Nature, 422, 216, 10.1038/nature01513 Alber, 2007, Determining the architectures of macromolecular assemblies, Nature, 450, 683, 10.1038/nature06404 Russel, 2012, Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies, PLoS Biol, 10, e1001244, 10.1371/journal.pbio.1001244 Ward, 2013, Biochemistry integrative structural biology, Science, 339, 913, 10.1126/science.1228565 Habeck, 2011, Statistical mechanics analysis of sparse data, J Struct Biol, 173, 541, 10.1016/j.jsb.2010.09.016 Borek, 2013, Everything happens at once—deconvolving systematic effects in X-ray data processing, Adv Methods Biomol Crystallogr, 105, 10.1007/978-94-007-6232-9_10 Guentert, 1989, Automated stereospecific proton NMR assignments and their impact on the precision of protein structure determinations in solution, J Am Chem Soc, 111, 3997, 10.1021/ja00193a036 Duhovny, 2002, Efficient unbound docking of rigid molecules, 185 Murtola, 2009, Multiscale modeling of emergent materials: biological and soft matter, Phys Chem Chem Phys, 11, 1869, 10.1039/b818051b Kahraman, 2011, Xwalk: computing and visualizing distances in cross-linking experiments, Bioinformatics, 27, 2163, 10.1093/bioinformatics/btr348 Burnley, 2012, Modelling dynamics in protein crystal structures by ensemble refinement, Elife, 1, e00311, 10.7554/eLife.00311 Lindorff-Larsen, 2005, Simultaneous determination of protein structure and dynamics, Nature, 433, 128, 10.1038/nature03199 Bernado, 2007, Structural characterization of flexible proteins using small-angle X-ray scattering, J Am Chem Soc, 129, 5656, 10.1021/ja069124n Pelikan, 2009, Structure and flexibility within proteins as identified through small angle X-ray scattering, Gen Physiol Biophys, 28, 174, 10.4149/gpb_2009_02_174 Różycki, 2011, SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions, Struct/Folding Design, 19, 109 Berlin, 2013, Recovering a representative conformational ensemble from underdetermined macromolecular structural data, J Am Chem Soc, 135, 16595, 10.1021/ja4083717 Shatsky, 2010, Automated multi-model reconstruction from single-particle electron microscopy data, J Struct Biol, 170, 98, 10.1016/j.jsb.2010.01.007 Rieping, 2005, Inferential structure determination, Science, 309, 303, 10.1126/science.1110428 Nilges, 2008, Accurate NMR structures through minimization of an extended hybrid energy, Struct/Folding Design, 16, 1305 Scheres, 2012, RELION: implementation of a Bayesian approach to cryo-EM structure determination, J Struct Biol, 180, 519, 10.1016/j.jsb.2012.09.006 Scheres, 2012, A Bayesian view on cryo-EM structure determination, J Mol Biol, 415, 406, 10.1016/j.jmb.2011.11.010 Rieping, 2008, ISD: a software package for Bayesian NMR structure calculation, Bioinformatics, 24, 1104, 10.1093/bioinformatics/btn062 Fernández, 2013, Molecular architecture of a eukaryotic translational initiation complex, Science, 342, 1240585, 10.1126/science.1240585 Bai, 2013, Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles, Elife, 2, e00461, 10.7554/eLife.00461 Sauerwald, 2013, Structure of active dimeric human telomerase, Nat Struct Mol Biol, 20, 454, 10.1038/nsmb.2530 Cossio, 2013, Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies, J Struct Biol, 184, 427, 10.1016/j.jsb.2013.10.006 Molnar, 2014, Cys-scanning Disulfide crosslinking and Bayesian modeling suggest scissoring motions in the histidine kinase, PhoQ, Structure, 22, 10.1016/j.str.2014.04.019 Street, 2014, Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone, J Mol Biol, 426, 2393, 10.1016/j.jmb.2014.04.001 Bonomi M, Muller EGD, Pellarin R, Kim SJ, Russel D, Ramsden R, Sundin BA, Davis TN, Sali A. Protein complex structures from Bayesian modeling of in vivo FRET data. Mol Cell Proteomics. Dong, 2013, Optimized atomic statistical potentials: assessment of protein interfaces and loops, Bioinformatics, 29, 3158, 10.1093/bioinformatics/btt560 Alber, 2007, The molecular architecture of the nuclear pore complex, Nature, 450, 695, 10.1038/nature06405 Efron B, Efron B. The jackknife, the bootstrap and other resampling plans. 1982 http://epubs.siam.org/doi/abs/10.1137/1.9781611970319.fm. Tjong, 2012, Physical tethering and volume exclusion determine higher-order genome organization in budding yeast, Genome Res, 22, 1295, 10.1101/gr.129437.111 Lasker, 2012, Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach, Proc Natl Acad Sci U S A, 109, 1380, 10.1073/pnas.1120559109 Loquet, 2012, Atomic model of the type III secretion system needle, Nature, 486, 276, 10.1038/nature11079 Murakami, 2013, Architecture of an RNA polymerase II transcription pre-initiation complex, Science, 342, 1238724, 10.1126/science.1238724 Kalisman, 2012, Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling, Proc Natl Acad Sci U S A, 109, 2884, 10.1073/pnas.1119472109 Tosi, 2013, Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex, Cell, 154, 1207, 10.1016/j.cell.2013.08.016 Ciferri, 2012, Molecular architecture of human polycomb repressive complex 2, Elife, 1, e00005, 10.7554/eLife.00005 Greber, 2014, Architecture of the large subunit of the mammalian mitochondrial ribosome, Nature, 505, 515, 10.1038/nature12890 Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Ayelett CH, Cimermančič P, Boehringer D, Sali A, Aebersold R, et al.: Molecular architecture of the 40S•eIF1•eIF3 translation initiation complex. Cell, 158 http://dx.doi.org/10.1016/j.cell.2014.07.044 (in press). Politis, 2014, A mass spectrometry-based hybrid method for structural modeling of protein complexes, Nat Methods, 10.1038/nmeth.2841 Boura, 2011, Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy, Proc Natl Acad Sci U S A, 108, 9437, 10.1073/pnas.1101763108 Huang, 2014, Transient electrostatic interactions dominate the conformational equilibrium sampled by multi-domain splicing factor U2AF65: a combined NMR and SAXS study, J Am Chem Soc, 10.1021/ja502030n Deshmukh, 2013, Structure and dynamics of full-length HIV-1 capsid protein in solution, J Am Chem Soc, 135, 16133, 10.1021/ja406246z Baù, 2011, The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules, Nat Struct Mol Biol, 18, 107, 10.1038/nsmb.1936 Baù, 2011, Structure determination of genomic domains by satisfaction of spatial restraints, Chromosome Res, 19, 25, 10.1007/s10577-010-9167-2 Kalhor, 2012, Genome architectures revealed by tethered chromosome conformation capture and population-based modeling, Nat Biotechnol, 30, 90, 10.1038/nbt.2057