个人简介

1999-2001: Hal and Alma Reagan Fellowship for academic excellence in the field of cancer research. Distinguished Member of The National Society of Collegiate Scholars, 2006.

研究领域

Proteomics, Protein Dynamics, Supramolecular Complexes

Metabolomics and Biomarker Discovery Metabolomics refers to the parallel analysis of all the small molecules of biological origin (the metabolome) in a sample. A wide range of samples can be analyzed using this approach including cells, tissues, hot springs, and bodily fluids. Quantitative analysis of the metabolome provides a systems view of the biochemical status of a cell or organism. Metabolomics is particularly attractive for gaining insight into the complex biological processes that together define a system at a given time point because, it provides a direct read-out of cellular physiology and biochemical activity. In contrast, transcriptomics and proteomics only provide information on biological potential. Comparative analysis of metabolomes provides a powerful and sensitive indicator of a biological system’s response to external stimuli. Our approach is motivated by the hypothesis that a comprehensive gauge of the metabolic state of an organism is the most complete and sensitive measure of physiology and will enhance the development of network models of cellular function. We are currently using LCMS, GCMS, and NMR to addressstudy cellular response to stress in archaea, bacteria, and eukaryotic model systems, along with biomarker discovery efforts in support of emergency clinical care. Stress Response in an Extremophile The idea that life is a delicate balance of chemical processes that can occur only within a narrow range of conditions is changing as scientists continue to discover life in extreme environments. The thermal features of Yellowstone National Park are one example. Pools of nearly boiling acid, once thought to be void of life, are now known to contain thriving populations of unicellular organisms and their viruses. Of the three domains of life (Eukarya, Bacteria, and Archaea), the Archaea are the least understood. Many of the organisms that are classified as extremophiles are members the archaeal domain of life. Currently these organisms are the focus of intense research because of our lack of understanding their ability to thrive in conditions once thought uninhabitable and the possibility of isolating enzymes that can with stand harsh industrial conditions. The specific objectives of this project are two-fold: 1) learn about viruses from extreme environments. 2) understand the Sulfolbus solfataricus response to stress. Cutting edge proteomics and activity-based protein profiling (ABPP) are being applied to these studies. Among the many exciting findings from this work is the extensive use of protein post-translational modification in Archaea. The relatively small genome size of Sulfolobus makes this an ideal organism for systems biology studies. This is being pursued in conjunction with other MSU research groups within the Thermal Biology Institute. Proteomics of Viral-Host Interaction Viruses are obligate cellular pathogens and therefore many cellular proteins are critical for viral infection, replication, and release from a host cell. Using cutting edge proteomics approaches, we are seeking to identify cellular pathways that are involved with the infection process. The significance of this work is two-fold: the basic biology of viruses can be elucidated and novel targets for antiviral agents can be identified. Noroviruses are a serious health and economic concern world-wide and are responsible for > 23 million infections per year in the USA alone. Despite the obvious importance of this group of viruses, much remains to be learned about their biology. This is largely due to a lack of animal and tissue culture model systems. The recent development of a murine norovirus (MNV) that can be cultured was a major breakthrough. We have adopted this system and are using a two-level proteomics approach to elucidate pathways and proteins involved with MNV infection. At the systems level, 2D differential gel electrophoresis (2D-DIGE) is being applied to generate an overview of the global changes in the host proteome during infection. This is being complemented by activity-based screening of enzyme classes. Activity-based protein profiling (ABPP) is currently the only technique that can directly measure specific protein activity across a biological system. Current research is directed toward understanding the role of apoptosis in MNV infected cells at the level of the system and individual proteins that become activated during programmed cell death. Protein Dynamics The solution-phase protein motion that is part of a multi-component complex can not always be inferred from the three-dimensional structure. For example, in contrast to the still-life representation of viral capsids in models based on cryo-electron microscopy and X-ray crystallography, these supramolecular protein complexes are highly dynamic in solution. The range and frequency of capsid protein dynamics are poorly understood, despite evidence that the infectivity of animal viruses requires conformational freedom. Protein function is intimately connected to dynamics and therefore knowledge of the frequency, range, and coordination of motion by supramolecular complexes is critical to understanding how they function. Our lab uses viruses as a paradigm for studying protein dynamics in supramolecular complexes. With the use of kinetic hydrolysis and quantitative mass spectrometry, we are determining the free energy and rates of large scale protein motion within viral particles. These are the first quantitative measurements for protein dynamics in a megadalton complex. Hydrogen-deuterium exchange, chemical labeling, and quartz crystal microbalance measurements are a few of the additional methods applied to the quantitative analysis of virus particle stability and dynamics. Protein Cages as Nanomaterials Nature has evolved active bio-architectures that are both dynamic and responsive individually as well as collectively when assembled into hierarchical structures. In fact, dynamic protein regions are responsible for biological mineral nucleation, surface recognition, chemical reactivity, and targeting. The concerted protein motion that is part of a multi-component biomolecular complex is rarely obvious from the high resolution three-dimensional structure. Protein function is intimately connected to dynamics and therefore knowledge of the frequency, range, and coordination of motion by supramolecular complexes is critical to understanding function and the development of bio-inspired nanomaterials. The extremely large size and icosahedral architecture of virus capsids limit the use of many standard techniques for studying protein motion such as NMR and FRET. To overcome these problems, we employ an array of biophysical techniques to study the solution phase behavior of viruses. Kinetic hydrolysis, an approach being developed in our lab, is a straight-forward and powerful technique for identifying the dynamic regions within a single protein or in the context of a multi-component complex. Protein dynamics is being investigated at three levels: the dynamics of the subunit, the assembled cage architecture, and the dynamics associated with higher order particle/particle and surface/particle interactions. The long-term goal of this effort is to understand dynamics of the nanoparticle/cage system at each distinct level of complexity so that the underlying mechanism of nucleation, recognition, and functionality can be elucidated and exploited. This work is being conducted in collaboration with other research groups in the Center for Bio-Inspired Nanomaterials.

近期论文

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Comparative analysis of adeno-associated virus capsid stability and dynamics ;Journal of Virology;Rayaprolu V, Kruse S, Kant R, Venkatakrishnan B, Movahed N, Brooke D, Lins B, Bennett A, Potter T, McKenna R, Agbandje-McKenna M, Bothner B;2013; Expanding the paradigm of thiol redox in the thermophilic root of life ;Biochimica et Biophysica Acta (BBA) - General Subjects;Heinemann J, Hamerly T, Maaty WS, Movahed N, Steffens JD, Reeves BD, Hilmer JK, Therien J, Grieco PA, Peters JW, Bothner B;2013; Enhanced sensitivity employing zwitterionic and pI balancing dyes (Z-CyDyes) optimized for 2D-gel electrophoresis based on side chain modifications of CyDye fluorophores. New tools for use in proteomics and diagnostics ;Bioconjugate Chemistry;Epstein MG, Reeves BD, Maaty WS, Fouchard D, Dratz EA, Bothner B, Grieco PA;2013; Identification of C-terminal phosphorylation sites of N-formyl peptide receptor-1 (FPR1) in human blood neutrophils ;Journal of Biological Chemistry;Maaty WS, Lord CI, Gripentrog JM, Riesselman M, Keren-Aviram G, Liu T, Dratz EA, Bothner B, Jesaitis AJ;2013; Nutrient resupplementation arrests bio-oil accumulation in Phaeodactylum tricornutum ;Applied Microbiology and Biotechnology;Valenzuela J, Carlson RP, Gerlach R, Cooksey K, Peyton BM, Bothner B, Fields MW;2013; Virus assembly and maturation: auto-regulation through allosteric molecular switches ;Journal of Molecular Biology; Domitrovic T, Movahed N, Bothner B, Matsui T, Wang Q, Doerschuk PC, Johnson JE;2013; Structure and dynamics of adeno-associated virus serotype 1 VP1-unique N-terminal domain and its role in capsid trafficking ;Journal of Virology;Venkatakrishnan B, Yarbrough J, Domsic J, Bennett A, Bothner B, Kozyreva OG, Samulski RJ, Muzyczka N, McKenna R, Agbandje-McKenna M;2013; Global analysis of viral infection in anarchaeal model system ;Frontiers in Microbiology;Maaty WS, Steffens JD, Heinemann J, Ortmann AC, Reeves BD, Biswas SK, Dratz EA, Grieco PA, Young MJ, Bothner B;2012; Integrated co-regulation of bacterial arsenic and phosphorus metabolisms ;Environmental Microbiology;Kang YS, Heinemann J, Bothner B, Rensing C, McDermott TR;2012; Phevalin (aureusimine B) production by Staphylococcus aureus biofilm and impacts on human keratinocyte gene expression ;PLoS One;Secor PR, Jennings LK, James GA, Kirker KR, Pulcini ED, McInnerney K, Gerlach R, Livinghouse T, Hilmer JK, Bothner B, Fleckman P, Olerud JE, Stewart PS;2012; Involvement of RpoN in regulating bacterial arsenite oxidation ;Applied Environmental Microbiology;Kang YS, Bothner B, Rensing C, McDermott TR;2012; A periplasmic arsenite-binding protein involved in regulating arsenite oxidation ;Environmental Microbiology;Liu G, Liu M, Kim EH, Maaty WS, Bothner B, Lei B, Rensing C, Wang G, McDermott TR;2011; The nucleotide exchange factor Ric-8A is a chaperone for the conformationally dynamic nucleotide-free state of Gαi1 ;PLoS One;Thomas CJ, Briknarová K, Hilmer JK, Movahed N, Bothner B, Sumida JP, Tall GG,;2011; Rotavirus infection activates the UPR but modulates its activity ;Journal of Virology;Zambrano JL, Ettayebi K, Maaty WS, Faunce NR, Bothner B, Hardy ME ;2011; Virus particles as active nanomaterials that can rapidly change their viscoelastic properties in response to dilute solutions ;Soft MatterRoyal Society of Chemistry;Rayaprolu V, Manning BM, Douglas T, Bothner B ;2010; Trehalose 6-phosphate phosphatase is required for cell wall integrity and fungal virulence but not trehalose biosynthesis in the human fungal pathogen Aspergillus fumigatus ;Molecular Microbiology;Puttikamonkul S, Willger SD, Grahl N, Perfect JR, Movahed N, Bothner B, Park S, Paderu P, Perlin DS, Cramer RA Jr ;2010; Structure and function of a genetically engineered mimic of a nonenveloped virus entry intermediate ;Journal of Virology;Banerjee M, Speir JA, Kwan MH, Huang R, Aryanpur PP, Bothner B, Johnson JE ;2010; Dynamics and stability in the maturation of a T=4 virus ;Journal of Molecular Biology;Tang J, Lee KK, Bothner B, Baker TS, Yeager M, Johnson JE ;2009; Cysteine protease activation and apoptosis in Murine Norovirus infection ;Virology Journal;Furman LM, Maaty WSA, Lena C Petersen, Khalil Ettayebi, Hardy ME, and Bothner B ;2009; Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress. ;PLoS One;Maaty WSA, Weidenheft B, Tarlykov P, Schaff N, Heinemann J, Robison-Cox J, Valenzuela J, Dougherty A, Blum P, Lawrence CM, DouglasT, Young M, and Bothner B ;2009; Viral capsid structures in solution ;Structural Virology Royal Society of Chemistry;Bothner B and Hilmer JK ;2009; Drosophila A virus is an unusual RNA virus with a T=3 icosahedral core and permuted RNA-dependent RNA-polymerase ;Journal of General Virology;Ambrose RL, Lander GC, Maaty WS, Bothner B, Johnson JE, and Johnson KN ;2009; Structural and functional studies of archaeal viruses ;Journal of Biological Chemistry;Lawrence CM, Menon S, Eilers BJ, Bothner B, Khayat R, Douglas T, and Young MJ ;2009; Genetics, biochemistry and structure of the archaeal virus STIV ;Biochemical Society Transactions;Fulton J, Bothner B, Lawrence M, Johnson JE, Douglas T, Young M ;2009; Intrinsically Unstructured Domains of Arf and Hdm2 Form Bi-molecular Oligomeric Structures In Vitro and In Vivo ;Journal of Molecular Biology;Sivakolundu SG, Nourse A, Moshiach S, Bothner B, Ashley C, Satumba J, Lahti J, Kriwacki RW ;2008; Detecting small changes and additional peptides in the canine parvovirus capsid structure ;Journal of Virology;Nelson CD, Minkkinen E, Bergkvist M, Hoelzer K, Fisher M, Bothner B, Parrish CR ;2008; Cysteine usage in Sulfolobus spindle-shaped virus 1 and extension to hyperthermophilic viruses in general ;Virology;Menon SK, Maaty WS, Corn GJ, Kwok SC, Eilers BJ, Kraft P, Gillitzer E, Young MJ, Bothner B, Lawrence CM ;2008; Transcriptome analysis of infection of the archaeon Sulfolobus solfataricus with STIV ;Journal of Virology;Ortmann, AC, Brumfield SK, Walther J, McInnerney K, Brouns SJ, van de Werken HJ, Bothner B, Douglas T, van de Oost J, Young MJ ;2008; Conformational equilibria and rates of localized motion within Hepatitis B Virus capsids ;Journal of Molecular Biology;Hilmer JK, Zlotnick A, and Bothner, B ;2008