Chinese Journal of Magnetic Resonance ›› 2015, Vol. 32 ›› Issue (2): 181-194.doi: 10.11938/cjmr20150204
Previous Articles Next Articles
PENG Jun-hui，ZHAO De-biao，WEN Bin，ZHANG Zhi-yong*
Received:2015-02-06
Revised:2015-05-08
Online:2015-06-05
Published:2015-06-05
About author:PENG Jun-hui (1989-), male, born in Jiangxi, PhD., his research focuses on Computational Biology, Tel: +86-551-63600854, E-mail: jhpanda@mail.ustc.edu.cn.
*Corresponding author.: ZHANG Zhi-yong, Tel: +86-551-63600854, E-mail: zzyzhang@ustc.edu.cn.
Supported by:The National Key Basic Research Program of China (2013CB910203), the National Natural Science Foundation of China (31270760), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB08030102), the Specialized Research Fund for the Doctoral Program of Higher Education (20113402120013).
CLC Number:
PENG Jun-hui，ZHAO De-biao，WEN Bin，ZHANG Zhi-yong*. Determining Structural Models of Biomolecular Complexes Integrating Nuclear Magnetic Resonance, Small-Angle X-ray Scattering and Computational Simulations[J]. Chinese Journal of Magnetic Resonance, 2015, 32(2): 181-194.
| [1] Robinson C V, Sali A, Baumeister W. The molecular sociology of the cell[J]. Nature, 2007, 450: 973－982.[2] Alberts B. Molecular Biology of the Cell (4th ed)[M]. New York: Garland Science; 2002.[3] Kuehlbrandt W. Cryo-em enters a new era[J]. Elife, 2014, 3.[4] Mertens H D T, Svergun D I. Structural characterization of proteins and complexes using small-angle X-ray solution scattering[J]. J Struct Biol, 2010, 172: 128－141.[5] Graewert M A, Svergun D I. Impact and progress in small and wide angle X-ray scattering (saxs and waxs) [J]. Curr Opin Struc Biol, 2013, 23: 748－754.[6] Ward A B, Sali A, Wilson I A. Integrative structural biology[J]. Science, 2013, 339: 913－915.[7] Dominguez C, Boelens R, Bonvin A M. Haddock: A protein-protein docking approach based on biochemical or biophysical information[J]. J Am Chem Soc, 2003, 125: 1 731－1 737.[8] De Vries S J, van Dijk M, Bonvin A M J J. The haddock web server for data-driven biomolecular docking[J]. Nat Protoc, 2010, 5: 883－897.[9] Russel D, Lasker K, Webb B, et al. Putting the pieces together: Integrative modeling platform software for structure determination of macromolecular assemblies[J]. PLoS Biol, 2012, 10.[10] Zhao D B, Wang X J, Peng J H, et al. Structural investigation of the interaction between the tandem sh3 domains of c-cbl-associated protein and vinculin[J]. J Struct Biol, 2014, 187: 194－205.[11] Zuiderweg E R P. Mapping protein-protein interactions in solution by nmr spectroscopy[J]. Biochemistry-us, 2002, 41: 1－7.[12] Pellecchia M, Montgomery D L, Stevens S Y, et al. Structural insights into substrate binding by the molecular chaperone dnak[J]. Nat Struct Biol, 2000, 7: 298－303.[13] Nguyen C, Haushalter R W, Lee D J, et al. Trapping the dynamic acyl carrier protein in fatty acid biosynthesis[J]. Nature, 2014, 505: 427－431. [14] Chou J J, Gaemers S, Howder B, et al. A simple apparatus for generating stretched polyacrylamide gels, yielding uniform alignment of proteins and detergent micelles[J]. J Biomol NMR, 2001, 21: 377－382.[15] Ruckert M, Otting G. Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments[J]. J Am Chem Soc, 2000, 122: 7 793－7 797.[16] Fushman D, Varadan R, Assfalg M, et al. Determining domain orientation in macromolecules by using spin-relaxation and residual dipolar coupling measurements[J]. Prog Nucl Mag Res Spectrosc, 2004, 44: 189－214.[17] Dosset P, Hus J C, Marion D, et al. A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings[J]. J Biomol NMR, 2001, 20: 223－231.[18] Valafar H, Prestegard J H. Redcat: A residual dipolar coupling analysis tool[J]. J Magn Reson, 2004, 167: 228－241.[19] Ramirez B E, Bax A. Modulation of the alignment tensor of macromolecules dissolved in a dilute liquid crystalline medium[J]. J Am Chem Soc, 1998, 120: 9 106－9 107.[20] Liu Z, Tang C. Paramagnetic relaxation enhancement——A tool for visualizing transient protein structures[J]. Chinese J Magn Reson, 2011, 28(3): 301－316.[21] Yang Y, Chen J L, Su X C. Paramagnetic labeling of proteins and pseudocontact shift in structural biology[J]. Chinese J Magn Reson, 2014, 31(2): 155－171.[22] Iwahara J, Tang C, Clore G M. Practical aspects of 1H transverse paramagnetic relaxation enhancement measurements on macromolecules[J]. J Magn Reson, 2007, 184: 185－195.[23] Clore G M, Iwahara J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes[J]. Chem Rev, 2009, 109: 4 108－4 139.[24] Hass M A S, Ubbink M. Structure determination of protein-protein complexes with long-range anisotropic paramagnetic nmr restraints[J]. Curr Opin Struc Biol, 2014, 24: 45－53.[25] Saio T, Yokochi M, Kumeta H, et al. Pcs-based structure determination of protein-protein complexes[J]. J Biomol NMR, 2010, 46: 271－280.[26] Kay L E. Solution nmr spectroscopy of supra-molecular systems, why bother? A methyl-trosy view[J]. J Magn Reson, 2011, 210: 159－170.[27] Sprangers R, Velyvis A, Kay L E. Solution nmr of supramolecular complexes: Providing new insights into function[J]. Nat Methods, 2007, 4: 697－703.[28] Tugarinov V, Kay L E. An isotope labeling strategy for methyl trosy spectroscopy[J]. J Biomol NMR, 2004, 28: 165－172.[29] Ayala I, Sounier R, Use N, et al. An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein[J]. J Biomol NMR, 2009, 43: 111－119.[30] Gans P, Hamelin O, Sounier R, et al. Stereospecific isotopic labeling of methyl groups for nmr spectroscopic studies of high-molecular-weight proteins[J]. Angew Chem Int Ed, 2010, 49: 1 958－1 962.[31] Tugarinov V, Hwang P M, Ollerenshaw J E, et al. Cross-correlated relaxation enhanced 1H-13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes[J]. J Am Chem Soc, 2003, 125: 10 420－10 428.[32] Shi L C, Kay L E. Tracing an allosteric pathway regulating the activity of the hslv protease[J]. Proc Natl Acad Sci, 2014, 111: 2 140－2 145.[33] Velyvis A, Kay L E. Measurement of active site ionization equilibria in the 670 kda proteasome core particle using methyl-trosy NMR[J]. J Am Chem Soc, 2013, 135: 9 259－9 262.[34] Velyvis A, Schachman H K, Kay L E. Application of methyl-trosy NMR to test allosteric models describing effects of nucleotide binding to aspartate transcarbamoylase[J]. J Mol Biol, 2009, 387: 540－547.[35] Lipfert J, Doniach S. Small-angle X-ray scattering from rna, proteins, and protein complexes[J]. Annu Rev Biophys Biomol Struct, 2007, 36: 307－327.[36] Schneidman-Duhovny D, Kim S J, Sali A. Integrative structural modeling with small angle X-ray scattering profiles[J]. BMC Struct Biol, 2012, 12.[37] Putnam C D, Hammel M, Hura G L, et al. X-ray solution scattering (SAXS) combined with crystallography and computation: Defining accurate macromolecular structures, conformations and assemblies in solution[J]. Q Rev Biophys, 2007, 40: 191－285.[38] Rambo R P, Tainer J A. Characterizing flexible and intrinsically unstructured biological macromolecules by sas using the porod-debye law[J]. Biopolymers, 2011, 95: 559－571.[39] Forster F, Webb B, Krukenberg K A, et al. Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies[J]. J Mol Biol, 2008, 382: 1 089－1 106.[40] Svergun D I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing[J]. Biophys J, 1999, 76(6): 2 879－2 886; 1999, 77(5): 2 896.[41] Franke D, Svergun D I. Dammif, a program for rapid ab-initio shape determination in small-angle scattering[J]. J Appl Crystallogr, 2009, 42: 342－346.[42] Svergun D I, Petoukhov M V, Koch M H J. Determination of domain structure of proteins from X-ray solution scattering[J]. Biophys J, 2001, 80: 2 946－2 953.[43] Zheng W J, Doniach S. Fold recognition aided by constraints from small angle X-ray scattering data[J]. Protein Eng Des Sel, 2005, 18: 209－219.[44] Petoukhov M V, Svergun D I. Global rigid body modeling of macromolecular complexes against small-angle scattering data[J]. Biophys J, 2005, 89: 1 237－1 250.[45] Bernado P, Mylonas E, Petoukhov M V, et al. Structural characterization of flexible proteins using small-angle X-ray scattering[J]. J Am Chem Soc, 2007, 129: 5 656－5 664.[46] Zheng W J, Tekpinar M. Accurate flexible fitting of high-resolution protein structures to small-angle X-ray scattering data using a coarse-grained model with implicit hydration shell[J]. Biophys J, 2011, 101: 2 981－2 991.[47] Wen B, Peng J H, Zuo X B, et al. Characterization of protein flexibility using small-angle X-ray scattering and amplified collective motion simulations[J]. Biophys J, 2014, 107: 956－964.[48] Guinier A. La diffraction des rayons X aux très petits angles: Application à l'étude de phénomènes ultramicroscopiques[J]. Ann Phys, 1939, 12: 161－237.[49] Svergun D I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria[J]. Appl Crystallogr, 1992, 25: 495－503.[50] Fischer H, Neto M D, Napolitano H B, et al. Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale[J]. J Appl Crystallogr, 2010, 43: 101－109.[51] Svergun D, Barberato C, Koch M H J. CRYSOL — A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates[J]. J Appl Crystallogr, 1995, 28: 768－773.[52] Grishaev A, Wu J, Trewhella J, et al. Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and nmr data[J]. J Am Chem Soc, 2005, 127: 16 621－16 628.[53] Yang S, Park S, Makowski L, et al. A rapid coarse residue-based computational method for X-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes[J]. Biophys J, 2009, 96: 4 449－4 463.[54] Grishaev A, Guo L A, Irving T, et al. Improved fitting of solution X-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling[J]. J Am Chem Soc, 2010, 132: 15 484－15 486.[55] Schneidman-Duhovny D, Hammel M, Sali A. Foxs: A web server for rapid computation and fitting of saxs profiles[J]. Nucleic Acids Res, 2010, 38: W540－W544.[56] Schwieters C D, Suh J Y, Grishaev A, et al. Solution structure of the 128 kda enzyme i dimer from escherichia coli and its 146 kda complex with hpr using residual dipolar couplings and small- and wide-angle X-ray scattering[J]. J Am Chem Soc, 2010, 132: 13 026－13 045.[57] Chacon P, Moran F, Diaz J F, et al. Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm[J]. Biophys J, 1998, 74: 2 760－2 775.[58] Kozin M B, Svergun D I. Automated matching of high- and low-resolution structural models[J]. J Appl Crystallogr, 2001, 34: 33－41.[59] Wriggers W, Milligan R A, McCammon J A. Situs: A package for docking crystal structures into low-resolution maps from electron microscopy[J]. J Struct Biol, 1999, 125: 185－195.[60] Wriggers W, Chacon P. Using situs for the registration of protein structures with low-resolution bead models from X-ray solution scattering[J]. J Appl Crystallogr, 2001, 34: 773－776.[61] Konarev P V, Petoukhov M V, Volkov V V, et al. Atsas 2.1, a program package for small-angle scattering data analysis[J]. J Appl Crystallogr, 2006, 39: 277－286.[62] Pons C, D'Abramo M, Svergun D I, et al. Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data[J]. J Mol Biol, 2010, 403: 217－230.[63] Schneidman-Duhovny D, Hammel M, Sali A. Macromolecular docking restrained by a small angle X-ray scattering profile[J]. J Struct Biol, 2011, 173: 461－471.[64] Webb B, Lasker K, Schneidman-Duhovny D, et al. Modeling of proteins and their assemblies with the integrative modeling platform[J]. Methods Mol Biol, 2011, 781: 377－397.[65] de Vries S J, Bonvin A M. Cport: A consensus interface predictor and its performance in prediction-driven docking with HADDOCK[J]. PLoS One, 2011, 6(3): e17695.[66] Gorba C, Miyashita O, Tama F. Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data[J]. Biophys J, 2008, 94: 1 589－1 599.[67] Pelikan M, Hura G L, Hammel M. Structure and flexibility within proteins as identified through small angle X-ray scattering[J]. Gen Physiol Biophys, 2009, 28: 174－189.[68] Yang S C, Blachowicz L, Makowski L, et al. Multidomain assembled states of hck tyrosine kinase in solution[J]. Proc Natl Acad Sci, 2010, 107: 15 757－15 762.[69] Ró?ycki B, Kim Y C, Hummer G. Saxs ensemble refinement of escrt-iii chmp3 conformational transitions[J]. Structure, 2011, 19: 109－116.[70] Carisey A, Ballestrem C. Vinculin, an adapter protein in control of cell adhesion signalling[J]. Eur J Cell Biol, 2011, 90: 157－163.[71] Borgon R A, Vonrhein C, Bricogne G, et al. Crystal structure of human vinculin[J]. Structure, 2004, 12: 1 189－1 197.[72] Baumann C A, Ribon V, Kanzaki M, et al. Cap defines a second signalling pathway required for insulin-stimulated glucose transport[J]. Nature, 2000, 407: 202－207.[73] Zhang M, Liu J, Cheng A, et al. Identification of cap as a costameric protein that interacts with filamin c[J]. Mol Biol Cell, 2007, 18: 4 731－4 740.[74] Mandai K, Nakanishi H, Satoh A, et al. Ponsin/sh3p12: An 1-afadin- and vinculin-binding protein localized at cell-cell and cell-matrix adherens junctions[J]. J Cell Biol, 1999, 144: 1 001－1 017. [75] Eswar N, Webb B, Marti-Renom M A, et al. Comparative protein structure modeling using MODELLER: Chapter 5: Unit 5.6[M]. Curr Protoc Bioinformatics, John Wiley & Sons Inc, 2006.[76] Brunger A T. Version 1.2 of the crystallography and NMR system[J]. Nat Protoc, 2007, 2: 2 728－2 733.[77] Schwieters C D, Kuszewski J J, Tjandra N, et al. The xplor-nih NMR molecular structure determination package[J]. J Magn Reson, 2003, 160: 65－73.[78] Takamoto K, Chance M R. Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes[J]. Annu Rev Bioph Biom Struct, 2006, 35: 251－276.[79] Vandermarliere E, Stes E, Gevaert K, et al. Resolution of protein structure by mass spectrometry[J]. Mass Spectrom Rev, 2014.[80] Lasker K, Phillips J L, Russel D, et al. Integrative structure modeling of macromolecular assemblies from proteomics data[J]. Mol Cell Proteomics, 2010, 9: 1 689－1 702.[81] Alber F, Dokudovskaya S, Veenhoff L M, et al. Determining the architectures of macromolecular assemblies[J]. Nature, 2007, 450 :683－694. |
| [1] | LIU Wen-qing, SONG Yan-hong, WANG Xue-lu, YAO Ye-feng. In Operando Nuclear Magnetic Resonance Spectroscopy Study on Photocatalytic Methanol Reforming [J]. Chinese Journal of Magnetic Resonance, 2019, 36(3): 298-308. |
| [2] | YIN Tian-peng, WANG Ya-rong, WANG Min, SHI Wen-zhi, ZHANG Zheng-qian, HE Sha-sha. Complete Assignments of NMR Spectral Data of Three C19-Diterpenoid Alkaloids [J]. Chinese Journal of Magnetic Resonance, 2019, 36(3): 331-340. |
| [3] | YANG Yun-han, DU Yao, YING Fei-xiang, YANG Jun-li, XIA Da-zhen, XIA Fu-ting, YANG Li-juan. Inclusion Behavior of Naringenin/β-Cyclodextrin Supramolecular Complex [J]. Chinese Journal of Magnetic Resonance, 2019, 36(3): 319-330. |
| [4] | HU Kun, SUN Han-dong, PUNO Pema-tenzin. Application of Quantum Chemical Calculation of Nuclear Magnetic Resonance Parameters in the Structure Elucidation of Natural Products [J]. Chinese Journal of Magnetic Resonance, 2019, 36(3): 359-376. |
| [5] | WANG Ya-lan, WANG Xiao-jing, WANG Zhi-wei. Spectral Analyses and Structural Elucidation of Azilsartan [J]. Chinese Journal of Magnetic Resonance, 2019, 36(3): 350-358. |
| [6] | LIU Ji-hong, JIN Kun, WANG Ping, LUO Gen. An NMR Study on Esculetin and It's Derivatives [J]. Chinese Journal of Magnetic Resonance, 2019, 36(3): 341-349. |
| [7] | WAN Zhi-bin, SONG Jian-hui, GUO Ming-ming. The Application of in Operando Liquid State NMR on Macromolecular Material Characterization [J]. Chinese Journal of Magnetic Resonance, 2019, 36(3): 408-424. |
| [8] | TANG Ming-xue, SCHMIDT Claudia. Estimation of Nematic Order Parameters via Haller Analysis of 1H NMR Spectra of Liquid Crystals [J]. Chinese Journal of Magnetic Resonance, 2019, 36(2): 138-147. |
| [9] | CAO Yuan, WU Yong-ping, CHEN Dong-jun. A Spectroscopic Study on Tautomerism of Selaginellins from Selaginella [J]. Chinese Journal of Magnetic Resonance, 2019, 36(2): 155-163. |
| [10] | TANG Heng, Gilbert NSHOGOZA, LIU Ming-qing, LIU Ya-qian, RUAN Ke, MA Rong-sheng, GAO Jia. Identification of Novel Hits of the NSD1 SET Domain by NMR Fragment-Based Screening [J]. Chinese Journal of Magnetic Resonance, 2019, 36(2): 148-154. |
| [11] | XIAO Xiong-jie, HU Mary, ZHANG Xu, HU Jian-zhi. An NMR-Based Metabolomics Study of Kidneys from Mice Exposed to Ionizing Radiation [J]. Chinese Journal of Magnetic Resonance, 2019, 36(2): 172-181. |
| [12] | XU Xiao-jun, WANG Shen-lin. Probing Membrane Protein Interactions by 19F Solid-State NMR [J]. Chinese Journal of Magnetic Resonance, 2019, 36(2): 238-251. |
| [13] | KOU Xin-hui, LIU Yi-xiang, LIU Xing-hong, LI Cong-gang, LIU Mai-li, JIANG Ling. Visualizing the Pre-Active Conformation of Response Regulator PhoBNF20D in Its apo State [J]. Chinese Journal of Magnetic Resonance, 2019, 36(2): 164-171. |
| [14] | CHEN Xiao-ying, YU Gang-jin, MAO Shi-zhen, LIU Mai-li, DU You-ru. Mixing-Induced Decreases in Critical Micelle Concentration in Aqueous Solution of Surfactants:Probing into the Mechanisms with 1H NMR Spectroscopy [J]. Chinese Journal of Magnetic Resonance, 2019, 36(2): 219-224. |
| [15] | WANG Shuang-hong, ZENG Pei, PAN Si-na, WANG Jia, WANG Shu-mei, YANG Yong-xia. Effects of Gegen Qinlian Decoction on the Fecal Metabonome of High Fructose-Induced Insulin Resistance Rats Studied by 1H NMR Spectroscopy [J]. Chinese Journal of Magnetic Resonance, 2019, 36(2): 182-194. |
| Viewed | ||||||
|
Full text |
|
|||||
|
Abstract |
|
|||||
