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.
Eli Lilly Young Investigator Award, 2013
National Science Foundation CAREER Award, 2013
American Society for Mass Spectrometry Research Award, 2011
Ralph E. Powe Junior Faculty Enhancement Award, 2011
Waters Research Fellowship, University of Cambridge, 2009
Tomas A. Hirschfeld Award for Outstanding Graduate Research, 2003
Leopold Marcus Award for Undergraduate Research Excellence, 1999
I.M. Kolthoff Enrichment Award for Excellence in Undergraduate Analytical Chemistry, 1998
Evidence for Macromolecular Protein Rings in the Absence of Bulk Water” Brandon T. Ruotolo, Kevin Giles, Iain Campuzano, Alan M. Sandercock, Robert H. Bateman, Carol V. Robinson Science (2005) 310, 1658-1661.
“Aspects of Native Protein Structure are Retained in Vacuum” Brandon T. Ruotolo and Carol V. Robinson Curr. Opin. Chem. Biol. (2006) 10, 402-408.
“Protein Complexes in the Gas Phase: Technology for Structural Genomics and Proteomics” Justin L. P. Benesch, Brandon T. Ruotolo, Douglas A. Simmons, Carol V. Robinson Chem. Rev. (2007) 107, 3544-3567.
“Ion Mobility-Mass Spectrometry Analysis of Large Protein-Protein Complexes” Brandon T. Ruotolo, Justin L. P. Benesch, Alan M. Sandercock, Suk-Joon Hyung, Carol V. Robinson Nature Prot. (2008), 3, 139-1152.
“Subunit architecture of intact protein complexes from mass spectrometry and homology modeling” Thomas Taverner, Helena Hernández, Michal Sharon, Brandon T. Ruotolo, Damien Davos, Robert Russell, Carol V. Robinson Acc. Chem. Res. (2008), 41, 617-627.
“Ion Mobility-Mass Spectrometry: A New Paradigm for Proteomics” John A. McLean, Brandon T. Ruotolo, Kent J. Gillig, David H. Russell Int. J. Mass Spectrom. (2005) 240, 301-315.