研究领域

Analytical Chemistry/Bioanalytical Chemistry/Biophysical Chemistry/Chemical Biology

Proteins act as the molecular machinery of cellular biology, executing numerous critical functions in the life cycle of every known organism. To perform their biological function, individual proteins associate, often in a transient manner, to form complexes. In some cases, proteins form vast interaction networks capable of performing intricate cellular tasks. Understanding the function of such protein assemblies is an important scientific goal for disciplines ranging from molecular medicine to physical chemistry. However, one of the chief bottle-necks in such scientific endeavors is the available technology for determining the structure and architecture of large protein complexes. While high-detail structural information can be obtained by X-ray diffraction analysis, this experiment requires the availability of a sufficient quantity of homogenous material and definition of suitable crystallization parameters. Both conditions are often difficult to meet and the number of atomic structures for multi-subunit complexes deposited in structural databases remains relatively low. Alternative methodologies such as electron microscopy (EM) and small angle X-ray scattering (SAXS) allow the determination of the surface envelope of complexes of sufficient dimensions, but interpretation of these data is aided by detailed knowledge of complex composition and is limited to homogeneous complexes. Consequently, there is a need to develop new approaches capable of defining the subunit stoichiometry, composition, and shape of heterogeneous macromolecular complexes of biological importance. Our group is primarily focused on developing ion mobility-mass spectrometry (IM-MS), an emerging technology that can determine the composition, size, and topological organization of protein assemblies from a small amount of sample, in the presence of impurities and structural heterogeneity, as a tool for structural biology. This focus necessitates research projects that span a wide range of topics. Some of these projects are focused on classical analytical chemistry, including IM-MS instrument development (in collaboration with Waters Corporation) and the development of computational tools for IM-MS data analysis and 3D model generation (in collaboration with researchers at Lawrence Livermore National Laboratory and the University of Cambridge). Other projects focus on the study of protein quaternary structure stability in the gas-phase, including elucidating the role of small molecules in stabilizing protein structure in the absence of bulk solvent. Still others involve the study of protein self-assembly, aggregation and amyloid formation. Our long-term aim is utilize IM-MS data alongside other protein structure determination approaches to support the emerging field of integrative structural biology – where many pieces of data derived from disparate techniques are combined to generate a more-complete picture of the assembly than was possible with any one tool.

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"Collisional and Coulombic Unfolding of Gas-Phase Proteins: High Correlation to Their Domain Structures in Solution." Yueyang Zhong, Linjie Han, Brandon T. Ruotolo Angew. Chem. Int. Ed. (2014), doi: 10.1002/anie.201403784 "Integrative modelling coupled with ion mobility mass spectrometry reveals structural features of the clamp loader in complex with single-stranded DNA binding protein." Argyris Politis, Ah Young Park, Zoe Hall, Brandon T. Ruotolo, Carol V. Robinson. J Mol Biol. (2013), doi: 10.1016/j.jmb.2013.04.006. "Robotically assisted titration coupled to ion mobility-mass spectrometry reveals the interface structures and analysis parameters critical for multiprotein topology mapping" Yueyang Zhong, Jun Feng, Brandon T. Ruotolo. Anal Chem. (2013), doi: 85(23):11360-8 "Ion mobility-mass spectrometry of intact protein-ligand complexes for pharmaceutical drug discovery and development" Shuai Niu, Jessica N. Rabuck, Brandon T. Ruotolo. Current Opinion in Chemical Biology (2013), doi:10.1016/j.cbpa.2013.06.019 "An Activation State-Selective Kinase Inhibitor Assay Based on Ion Mobility-Mass Spectrometry." Jessica N. Rabuck, Suk-Joon Hyung, Kristin S. Ko, Christel C. Fox, Matthew B. Soellner, Brandon T. Ruotolo. Anal. Chem. (2013), doi:10.1021/ac4012655 "Hofmeister Salts Recover a Misfolded Multiprotein Complex for Subsequent Structural Measurements in the Gas Phase" Linjie Han, Brandon T. Ruotolo. Angew. Chem. Int. Ed. (2013), doi: 10.1002/anie.201301893 "Analysis of a Soluble (UreD:UreF:UreG)2 Accessory Protein Complex and Its Interactions with Klebsiella aerogenes Urease by Mass Spectrometry" Mark A. Farrugia, Linjie Han, Yueyang Zhong, Jodi L. Boer, Brandon T. Ruotolo, Robert P. Hausinger. Journal of The American Society for Mass Spectrometry (2013), doi:10.1007/s13361-013-0677-y "Amyloid-b-neuropeptide interactions assessed by ion mobility-mass spectrometry" Molly T. Soper, Alaina S. DeToma, Suk-Joon Hyung, Mi Hee Lim, Brandon T. Ruotolo. Phys. Chem. Chem. Phys.(2013), doi: 10.1039/C3CP50721A "Traveling-wave ion mobility-mass spectrometry reveals additional mechanistic details in the stabilization of protein complex ions through tuned salt additives" Linjie Han, Brandon T. Ruotolo. International Journal for Ion Mobility Spectrometry. (2013), doi: 10.1007/s12127-013-0121-9 "Resolution of Oligomeric Species during the Aggregation of Ab1-40 Using 19F NMR." Yuta Suzuki, Jeffrey R. Brender, Molly T. Soper, Janarthanan Krishnamoorthy, Yunlong Zhou, Brandon T. Ruotolo, Nicholas A. Kotov, Ayyalusamy Ramamoorthy, E Neil G. Marsh. Biochemistry (2013), doi:10.1021/bi400027y "Insights into antiamyloidogenic properties of the green tea extract (-)-epigallocatechin-3-gallate toward metal-associated amyloid-beta species" Suk-Joon Hyung, Alaina S. DeToma, Jeffrey R. Brender, Sanghyun Lee, Subramanian Vivekanandan, Akiko Kochi, Jung-Suk Choi, Ayyalusamy Ramamoorthy, Brandon T. Ruotolo, and Mi Hee Lim. Proc. Natl. Acad. Sci. (2013), doi: 10.1073/pnas.1220326110 "Dramatically stabilizing multiprotein complex structure in the absence of bulk water using tuned Hofmeister salts" Linjie Han, Suk-Joon Hyung, Brandon T. Ruotolo. Faraday Discuss. (2013)160, 371-388 "Bound cations significantly stabilize the structure of multiprotein complexes in the gas phase" Linjie Han, Suk-Joon Hyung, Brandon T. Ruotolo. Angew. Chem. Int. Ed. (2012)51, 5692-5695. "Investigation of Flavonoid Compounds as Modulators for Metal-Associated Amyloid-b Species" Xiaoming He, Hyun Min Park, Suk-Joon Hyung, Alaina S. DeToma, Cheal Kim, Brandon T. Ruotolo, Mi Hee Lim Dalton Trans. (2012) 41, 6558-6566. "Reactivity of Diphenylpropynone Derivatives Toward Metal-Associated Amyloid-b Species" Amit S. Pithadia, Akiko Kochi, Molly T. Soper, Michael W. Beck, Yuzhong Liu, Sanghyun Lee, Alaina S. Detoma, Brandon T. Ruotolo, Mi Hee Lim. Inorg. Chem. (2012)51, 12959-12967 "Integrating mass spectrometry of intact protein complexes into structural proteomics" Suk-Joon Hyung, Brandon T. Ruotolo. Proteomics. (2012)12, 1547-64 "Ion mobility-mass spectrometry for structural proteomics" Yueyang Zhong, Suk-Joon Hyung, Brandon T. Ruotolo. Expert Rev. Proteomics (2012)9, 47-58 "Gas-Phase Protein Assemblies: Unfolding Landscapes and Preserving Native-Like Structures using Noncovalent Adducts" Joanna Freeke, Matthew F Bush, Carol V Robinson*, Brandon T. Ruotolo* (joint corresponding authors) Chem. Phys. Lett.(2012)524, 1-9 "Mass spectrometry: come of age for structural and dynamical biology" Justin LP Benesch, Brandon T Ruotolo. Curr Opin Struct Biol. (2011)21, 641-9 "Ion Mobility-Mass Spectrometry Reveals Conformational Changes in Charge Reduced Multiprotein Complexes" Russell E. Bornschein, Suk-Joon Hyung and Brandon T. Ruotolo J. Am. Soc. Mass. Spectrom. (2011)22, 1690-8