Contact Information

copie

Office: Room 111A 

Lab: Room 144 and 146

NMR Center Instrumentation room: Room 18

Chemistry and Biochemistry Building
P.O. Box 173400
Bozeman, MT 59717

Phone: 406-994-7244
Fax: 406-994-5407
Email: vcopie@montana.edu

Education

  • B. Sci. Biochemistry, 1983 University of Minnesota, Minneapolis, MN
  • PhD, Physical Chemistry, 1990, Massachusetts Institute of Technology, Cambridge MA
  • Postdoc: 1990-1992, University of California, Berkeley, CA
  • Postoc: 1992-1997, National Institutes of Health, Bethesda, MD

Courses

  • BCH 526 ADVANCED PROTEIN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
  • BCH 543 PROTEINS
  • BCH 544 MOLECULAR BIOLOGY

Awards and Professional Activities

  • 2000-2005:National Science Foundation Career Advancement Award recipient.
  • 1993-1997: Intramural NIH IRTA fellow.
  • 1990-1993: Recipient of an extramural NIH post-doctoral fellowship.

Copié Group Overview

Our collaborative and inter-disciplinary research program is focused on two main research areas: (1) protein structural biology and (2) metabolomics (e.g. the global profiling of small molecule metabolites as direct readouts of cellular phenotypes) – and utilizes technical approaches based on solution nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and complementary biophysical techniques including: protein structure-function assays; in vitro protein expression and purification techniques (e.g. cDNA cloning, site-directed mutagenesis, prokaryotic and eukaryotic cell cultures, etc); circular dichroism (CD); surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), and others. Our NMR metabolomics approach is integrated with LC-MS-based metabolomics analyses, and involves of a Systems Biology-wide global analysis and profiling of small molecule metabolites as characteristic markers of cellular phenotypes and cellular responses to environmental stress. All the research conducted in the Copié lab involves undergraduate and graduate students (and post-doc) training, which is a key component of the teaching mission of Montana State University.

Protein Structural Biology


 

Employing multidimensional (2D, 3D, 4D, nD), heteronuclear (1H, 15N, 13C and 2H) solution NMR techniques, our laboratory has been interested in solving, to high-resolution, the 3D structures of under- or poorly-characterized proteins of biological interest. We aim to better understand the molecular, functional mechanisms of several proteins of interest, including: (1) Isd proteins (Iron-regulated Surface Determinant proteins) that are part of the heme iron acquisition machinery of pathogens such as Staphylococcus aureus; (2) Crenarchaeal viral proteins infecting extremophilic hosts such as Sulfolobus archaea, which live in extreme environments such as the hot (T > 80oC) and acidic  (pH < 4) thermal pools of Yellowstone National Park; and (3) RNA-binding proteins regulating leaf senescence in barley plants.

We have also been interested in employing 15N (and 13C) NMR relaxation experiments to characterize protein internal motions that modulate, for example, the DNA-binding property of repressor proteins such as the tryptophan repressor (TrpR) and associated variants.


Structural Biology: Project 1: Iron acquisition in pathogenic bacteria- Structural and functional studies of the heme iron acquisition machinery of S. aureus.

 Overview:

The long-term goal of the research is to generate a comprehensive understanding of the heme acquisition process in the Gram-positive bacterium Staphylococcus aureus. We aim to determine the molecular mechanisms and structural basis of the heme transfer reactions along the S. aureus heme uptake pathway. The heme acquisition machinery of S. aureus consists of the iron-regulated surface determinants (Isd) proteins, including three surface proteins, IsdA, IsdB, and IsdC, and an ATP-binding cassette-type ABC transporter.

Heme capture from hemoglobin (Hb) is accomplished by IsdB and IsdH that are anchored at the cell surface of S. aureus. The acquired heme is subsequently transferred through the cell wall via a relay system of proteins exhibiting different affinities for heme, and involves heme transfer from IsdB to IsdA and IsdC, which in turn relay heme to IsdE, the lipoprotein component of the ATP-binding cassette (ABC) transporter IsdEDF. From there, heme is transported across the cytoplasmic membrane by action of this ABC transporter system and oxidized in the cytoplasm by IsdG and IsdI to release iron from heme for cellular use by S.aureus. (a schematic of the heme iron acquisition machinery of S. aureus is depicted in Figure 1).

Figure 1: Schematic representation of S. aureus heme acquisition pathway and of the Isd proteins involved.

fig1

The IsdB protein plays a unique role in the S. aureus Isd-mediated heme uptake process, capturing heme from human hemoglobin (metHb), assimilating heme from metHb, and transferring heme to the downstream proteins of the S. aureus heme acquisition machinery, IsdA and IsdC. Despite extensive progress on the structural biology of Isd proteins, the molecular mechanism and structural basis of IsdB’s heme uptake and transfer functions remains poorly understood. Over the past several years, our lab has been collaborating with Professor Benfang Lei’s laboratory (MSU’s Department of Immunology and Microbiology) to enhance our understanding of how IsdB functions and to establish a clearer understanding of the structural basis underlying heme acquisition and transfer from metHb to IsdB.

Structural Investigations of IsdB by NMR:

As mentioned, IsB is one of two hemoglobin (Hb) receptors in S. aureus, and is comprised of two NEAr transporter (NEAT) domains, which allow for the rapid capture of heme from hemoglobin. NEAT domains are structurally conserved, comprised of ∼ 120 amino acids, and adopt characteristic immunoglobulin-like β -sandwich folds.  The single NEAT domains of IsdA and IsdC, and the C-terminal NEAT domain of IsdB (e.g. IsdB-N2) have been shown to bind heme, and contain a hydrophobic heme-binding site which envelops the heme within the protein’s 3D architecture with a 6-stranded antiparallel β -sheet on one side and a short α -helix of the other side of the heme binding pocket.

Interestingly and despite their close structural similarities, NEAT domains have evolved different functions, even within the same protein. For example, within the modular architecture of IsdB and unlike IsdB-N2 domain, IsdB’s N-terminal NEAT domain (e.g. IsdB-N1) does not bind heme, but seems instead responsible for mediating protein-protein or protein-domain interactions, which we have aimed to characterize at the molecular level.

Another intriguing aspect of IsdB is the protein’s ability to efficiently capture heme from hemoglobin (in spite of Hb’s very strong affinity for heme), while also being capable of quick transfer of IsdB-bound heme to IsdB’s downstream protein partner IsdA or IsdC. The dual heme capture-heme transfer function of IsdB suggests the existence of a heme-binding “affinity switch” mechanism whereby conformational changes within the protein (or changes within its protein-protein or protein-domain interaction network) modulate IsdB’s affinity for heme, enabling both efficient and rapid heme capture from Hb, and efficient heme transfer to downstream protein acceptors.

Our NMR structural studies have thus far been focused on elucidating the molecular basis of this potential “heme-binding affinity switch.” Toward this goal, we have undertaken structural studies of individual functional domains of the IsB protein (as the full-length 645-residue long protein is too large for solution NMR), and have engineered protein variants with single and double amino acid substitutions aimed at perturbing heme-IsdB or metHb-IsdB interactions, to identify critical residues involved in protein-protein or protein-heme ligand interactions.

3D-structure of IsdB-N1: We recently solved the 3D structure of the NEAT-1 domain of IsdB by NMR (IsdB-N1), a domain that spans residues 125-272 of the full-length protein (& published in Fonner et al. (2014) Biochemistry, Vol. 53, pp. 3922-3933).

The structure revealed a canonical NEAT domain fold with particular structural similarity to the NEAT 1 and NEAT 2 domains of IsdH, which also interact with Hb. IsdB-N1 is also comprised of a short N-terminal helix, which has not previously been observed in other NEAT domain structures. Interestingly, the Hb binding region (e.g. loop 2 of IsdB-N1) is disordered in solution in the uncomplexed protein (Figure 2).

Figure 2: 3D solution structure of IsdB-N1 as determined by multidimensional heteronuclear NMR

vcfig2

Analysis of Hb binding demonstrated that IsdB-N1 can bind metHb weakly, and that the affinity of this interaction is further increased by the presence of IsdB linker domain (e.g. a region spanning residues ~ 270 -339 of the full-length protein). Engineered variants of IsdB-N1, with amino acid substitutions within the loop 2 region of the protein revealed that phenylalanine 164 (F164) of IsdB is necessary for Hb binding and rapid heme transfer from metHb to IsdB. Together, these findings provide a structural role for IsdB-N1 in enhancing the rate of extraction of metHb heme by the IsdB NEAT 2 domain.

Structural Biology - Project 2:Extremophiles’ Adaptation – Investigations ofcrenarchaeal viral proteins, and characterization of virus- hyperthermophilic Sulfolobus archaeal-host interactions.

This research is in collaboration with Dr. Martin Lawrence (expert in protein X-ray crystallography, and Professor of Biochemistry in MSU’s Department of Chemistry and Biochemistry). This protein structural biology project focuses on better understanding the function and life cycles of archeal viruses infecting extremophilic archaea such as Sulfolobus such as Sulfolobus spindle-shaped virus 1 (SSV-1) and related members.

While archaea were first isolated from extreme environments, more recent work has revealed their abundance throughout the biosphere, including soils and oceans, where archaea are thought to constitute ~30% of the pelagic prokaryotic diversity, and 20% of the overall global biomass. Because viruses are thought to catalyze the turnover of 20% of the oceanic biomass per day, archaeal viruses significantly impact global carbon and nitrogen cycles. Yet despite their abundance and environmental impact, little is known about the life cycles of archaeal viruses and virus-host interactions. One of the most advanced model systems of crenarchaeal viruses is SSV1 (Figure 3), which inhabits extreme thermal and acidic environments (T > 80 degrees C; 4.0 > pH > 1.0) as found in the hot thermal pools of Yellowstone National Park.

However, even our understanding of this better studied SSV1 “model system” remains limited. Initial sequence analyses of SSV genomes largely failed to suggest functions for most of the encoded proteins. And while recent genetic, biochemical and structural studies of viral particles and viral cellular proteins have provided much insight, the functions for more than half of each of these viral proteomes remains a mystery.

Figure 3: Cryo-EM images of crenarchaeal viruses, such as Sulfolobus spindle shaped virus 1 (SSV-1).

fig3

3D NMR structure of SSV-RH E73. As a collaboration with the Lawrence lab, the Copié lab solved the 3D solution structure of SSV-RH E73, which originates from the SSV1 viral homolog SSV-Ragged Hills, and whose protein appears to serve as a structural proxy for the SSV1 E-51 protein (Schlenker et al (2012) Biochemistry, Vol. 51, pp. 2899-2910).

We found that E73 is assembled as a dimeric ribbon-helix-helix (RHH) protein, which is structurally homologous to the RHH domains of many transcriptional regulators. E73 is, however, notably distinct from other RHHs in containing a third helix that forms a structural cleft which we suspect mediates protein-protein interactions and/or contribute to the high thermal stability of E73. Analysis of backbone amide dynamics via 15N NMR relaxation measurements provided evidence for a rigid protein core with fast ps-ns timescale NH bond vector motions in the proposed DNA-binding domain, and motions on a slower μs to ms timescale for residues in the a1-a2 loop. In vitro nucleic acid-binding experiments demonstrated that E73 can bind dsDNA in a non-specific manner consistent with our docking model (see Figure 4). Overall, the work suggests a potential role for E73 as a transcriptional regulator of viral or host gene expression.

fig4

 

Figure 4: 3Dstructure of SSV-RH E73 as determined by NMR (here docked on DNA) reveals a tightly intertwined homodimer containing an “RH3” DNA binding motif

NMR Metabolomics and Systems Biology

Metabolomics refers to the quantitative and qualitative assessment of low molecular weight compounds (metabolites) present inside cells (e.g. intracellular) or secreted by cells (e.g. extracellular)25. Cellular metabolomes consist of diverse groups of small molecules (polar, non polar) spanning a wide range of concentrations, and include compounds required for growth, metabolic energy, cellular maintenance and function. Small organic molecules that can be identified (i.e. “profiled”) by NMR and mass spectrometry (MS) approaches include amino acids, fatty acids, carbohydrates (sugars), vitamins, lipids, and in some cases, some inorganic, elemental species.

Metabolite levels are closely related to cellular phenotypes. Further, in cells, the number of metabolites is much lower than the number of genes or proteins (Figure 5). Analyses of cellular metabolism have thus the potential to reveal biological properties that are much closer to cells’ phenotypes than investigations at the protein or gene levels. While metabolic changes are regulated by gene expression, they are widely influenced by environmental factors, such as stress. Thus we view system biology-wide metabolomics research as a potentially extremely useful approach to help identify small molecule markers of cellular responses to environmental conditions and cellular stress.

Figure 5: Reduced complexity of metabolome composition compared to profiling genomes or proteomes (reproduced from Wishart et al. 2009)

The field of metabolomic analysis is becoming increasingly important and is at the forefront of providing deeper understanding of health, disease, and cells’ interactions with the environment. New metabolites, that were previously unknown, are increasingly being discovered to reveal new insights into many biological mechanisms. While NMR has relatively low sensitivity, it is very powerful to identify and quantify metabolites and to characterize previously unknown compounds. LC-MS is extremely sensitive for studies of metabolism, but is not effective at revealing the structures of metabolites that are not annotated in mass spectral databases. NMR and LC-MS are highly complementary approaches and enhance the coverage of metabolites that can be extracted, identified, and quantified from complex cellular environments.

Figure 6: Untargeted (e.g. global profiling of metabolite mixtures) metabolomics workflow using NMR (top) or LC-MS (bottom).

The NMR metabolomics research efforts in the Copié’s lab are highly interdisciplinary and combine 1D, 2D (and possibly 3D) 1H/13C NMR with LC-MS metabolite analysis. The research involves a strong commitment to project design (e.g. ensuring that the proposed metabolomics studies are based on strong and rigorous biochemical or microbiological principles). Project design ahead of data collection and NMR/MS measurements is essential to ensure that observed changes in metabolite profiles can be interpreted unambiguously in terms of the biological phenomenon being probed and of interest. Metabolomics studies also require careful optimization of sample preparations and metabolite protocols (as each cell types appear to “behave” differently, requiring optimization of cell lysis, metabolism quenching, and metabolite recovery protocols).

Dr. Copié and colleagues were instrumental in securing federal funding to develop NMR metabolomics at MSU as a component of Professor Dratz’s P20  “Center for Analysis of Cellular Mechanisms and Systems Biology” and to upgrade MSU’s 600 MHz NMR with a new console and helium-cooled TCI cryoprobe. The P20 Systems Biology Center was designed to build proteomics and systems biology infrastructure at MSU, taking advantage of existing genomics and computational facilities, and was focused on investigations of host-pathogen interactions. The additional support permitted to take the next step in systems biology infrastructure development at MSU by adding nuclear magnetic resonance (NMR) metabolomics capabilities to the parent P20 CoBRE Center.

These funds permitted to equip MSU’s 600 MHz NMR spectrometer with an AVANCE III console, cryoprobe, an automatic sample loading system (SampleJetTM), and ChenomxTM software licenses for high throughput NMR metabolomics research and NMR metabolite spectra analysis and NMR metabolite identification (Figure 7).

    

Figure 7:(LHS panel) 600 MHz NMR setup with SampleJet and TCI cryoprobe configuration. (RHS panel) Illustration of metabolite ID via spectral pattern matching (i.e. screen display) using the ChenomxTM software and its associated 600 MHz NMR spectral database of reference small molecules.

Most recently, Dr. Copié and colleagues were successful in obtaining support to purchase a state-of-the-art integrated LC-SPE-NMR-MS instrument, involving the acquisition of a new Prodigy-equipped (e.g. X-nucleus detection optimized) 500 NMR system, which will be coupled to a mass spectrometer instrument for simultaneous MS and NMR analysis (i.e. MS and NMR analysis of the same LC analyte fractions) of metabolites. During operation of the LC-SPE-NMR-MS, a tiny fraction of the liquid chromatography (LC) effluent (1-5%) will be directed to the MS system that detects and commands which fractions of the LC flow appear to contain interesting compounds; those will be captured on a fraction collection system for most of the LC sample stream, using a movable array of solid phase extraction (SPE) cartridges.  The compounds trapped on the SPE cartridges will then be eluted following the LC run, and dried in NMR sample tubes. NMR solvents will be subsequently added and racks of tubes moved to the automatic sample loading system (autosampler) of the NMR instrument, where a variety of 1D and 2D NMR experiments will be used for small molecule identification and structure determination.

A major component of Dr. Copié’s metabolomics research program thus involves bioinformatics approaches to metabolic pathway analyses, to identify key biomarkers of cellular phenotypes and cellular responses to environmental stresses. Results from the metabolite profiling experiments are analyzed within a Systems Biology framework (in collaboration with MSU colleagues Drs. Ross Carlson, Brian Bothner, and others) that examines the impact of cellular phenotypes on metabolic pathways and cellular networks. The goal is to integrate metabolomics data with available proteomics and transcriptomics knowledge to develop in silico models of metabolic pathway requirements, and metabolic energy flux as a function of nutrient availability favoring, for example, microbial growth and adaptive metabolic strategies. These metabolic network models can then be used to generate new hypotheses regarding host-microbe interactions and to guide new study in animal models of disease (for example).

Metabolomics research projects of interest in the Copié lab include: (1) a global metabolic analysis of pathogenic microbial biofilms involved in antibiotic resistance and the chronicity of poorly healing wounds; (2) the probing of metabolic networks modulating Ignicoccus and Nanoarcheum archaeal host-symbiont interactions, as a model system of host-microbe interactions; (3) the impact of nutrients (copper and fructose) on the metabolic profiles of non-alcoholic fatty liver disease (NAFLD) animal models; (4) NMR metabolomics studies of Agrobacterium tumefaciens-arsenite interactions, to better understand the mechanisms by which this soil bacterium detoxifies arsenic and toxic arsenate byproducts; and (5) the metabolic profiling of extremophiles, including deciphering metabolic strategies employed by hyperthermophilic Sulfolobus archaea to survive in extreme environments;

Project 1:Metabolomics investigations of pathogenic bacteria and microbial biofilms

The goal of this research is to provide fundamental biochemical insights into adaptive metabolic strategies employed by bacterial biofilms that contribute to their enhanced persistence in human wounds, and to enhance our understanding of human skin cell responses to biofilm environment exposure. The underlying hypothesis is that a global systems analysis of metabolic changes can be used to identify key small molecule biomarkers of microbial biofilm colonization of skin tissue.

Metabolomics and Systems Biology Framework for the investigations of host- bacterial microbe interactions 

 

The research involves a highly interdisciplinary, systems-wide, and fundamental biochemical analysis of small molecule metabolites of Staphylococcus aureus bacterial biofilms and planktonic (free floating) cell cultures using NMR and liquid-chromatography-coupled mass spectrometry (LC-MS/MS) metabolomics research approaches.

The goal is to integrate acquired NMR and LC-MS/MS metabolomics data into a global “system” analysis including identification of impacted metabolic pathways and cellular networks, and in silico modeling of metabolic energy flux characterizing microbial biofilms and microbes-human skin cells interactions.  Another key objective of this project is to establish the potential this integrated “omics” approach to generate a deeper understanding of underlying biochemical mechanisms contributing to the persistence and phenotype of bacterial biofilms, and metabolic strategies employed by bacteria to colonize host such as human skin tissue.

The long-term goal would be to employ resulting biochemical knowledge to develop accurate small molecule-based prognostics of the likelihood of bacterial biofilm-colonized wounds to heal, less invasive diagnostics of biofilm-colonization of wounds or implants, or tools to assess the effectiveness of treatments based on the development of new bacterial biofilm-targeting therapeutics.

 

Project 2: From Genomes to Metabolomes: Studying Mechanisms of Interspecies Interactions Using the Archaeal System Ignicoccus-Nanoarchaeum (Collaborative project with Drs. Bothner (MSU), Podar and Hettich (ORNL)

A fundamental change in how human-microbe interactions are perceived is underway. In disciplines from immunology to nutrition, the physiological boundaries between “us” and “them” are beginning to blur. For example, sequencing of various human body site microbiomes has revealed the dynamic nature of these communities and the influence on nutrient and drug metabolism and tuning of the immune system. Perhaps this should come as no surprise, given the co-evolutionary history of host-microbe interactions. Just as humans do not live in isolation, microorganisms rarely live in functional or spatial isolation. The nature of the various types of inter-species interactions can be complex and dynamic, ranging from competition, to parasitism, or to mutualism. In complex microbial communities, such interactions influence community structure and dynamics and, in associations with a plant or animal host, can significantly impact its physiology.

            There is limited understanding of fundamental mechanisms of interspecies recognition and communication, how they impact genome evolution, what genetic regulatory mechanisms control metabolic/energetic coupling between species in response to environmental factors. We are using the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans (Figure 8) to address such questions. With a combined genomic complement of less than 2000 genes and an obligate chemolithoautotrophic metabolism, this system represents one of the simplest specific microbial associations, and allows fundamental system level investigations and modeling of symbiosis.

 

 

We have been employing a Systems Biology approach to understand fundamental cellular, genomic and metabolic principles of specific inter-organism interactions, integrating comparative evolutionary genomics, transcriptomics, proteomics, metabolomics and cellular network reconstruction. We aim to apply the integrated “omics” approach and the results of this project to investigations of more complex host-microbe systems.

We have been testing the specific hypothesis that the physical interaction between Ignicoccus hospitalis and Nanoarchaeum in laboratory cultures is induced and controlled by specific temporal gene expression, metabolic events and surface protein-protein interactions. We have identified candidate genes, proteins, and small molecules regulating the metabolic/energetic coupling network shared by the two organisms, which should allow us to establish a model of symbiosis at the genomic and metabolic level.

 

Metabolomics profiling studies of host-microbe interactions – Future Directions

A new direction for this research (initiated with several MSU colleagues) is to better understand human and animal microbiomes, host-microbe interactions, microbial processes in soil, and microbial adaptation to extreme environments. For example, microbial processes control many components of sustainable energy systems, including production of methane, hydrogen, alcohols, lipids, hydrocarbons, while reducing CO2 emissions to the atmosphere. These key roles strongly suggest that an integrated approach including system-wide NMR and LC-MS metabolomics to studying microbial function at different levels of organization (cellular to community) has the potential to generate broad benefits.

In addition to examining the metabolome of microbes for sustainable energy processes and health, metabolomics can be applied to better understand the environmental adaptations of extremophiles. For example, thermal ecosystems maintain a significant and strategic role in the search for biocatalysts for novel bioprocesses. Hot springs are a model environment for isolating relevant and robust microorganisms for biotechnology and energy applications. We are working with TBI colleagues to help develop a more complete understanding of archaeal populations that populate thermoalkaline ecosystems, and to uncover some of their biotechnological potential.  These studies are valuable to better understand the biodiversity and biochemistry of these relatively uncharacterized systems, and lay the fundamental groundwork for potential applications that range from renewable fuel processing to biodegradation of toxic compounds.

Figure 8: Electron micrograph of a thin section of a Nanoarchaeum equitans cell attached to an Ignicoccus hospitalis host cell (solid bar represent 1 mm scale).  Key features: I. hospitalis possesses a unique cell envelope, lacking an S layer, and is the only known archaea with 2 cell membranes. Ignicoccus is an anaerobic, obligate chemolithoautotropic (H2/So respiration, CO2 fixation), hyperthermophile (90C, pH 5.5, 1.8% NaCl), which grows by reduction of elemental sulfur (So) using molecular hydrogen (H2) as electron donor; it also contains a novel CO2 fixation pathway: dicarboxylate/4-hydroxybutyrate pathway (see Moissl-Eichinger & Huber (2011) Curr. Opin. Microbiol 14, 364-370)


Recent Publications

(1) L. Taubner*, E. Bienkiewicz, V. Copié, and B. Caughey (2010) Structure of the flexible amino terminal domain of prion protein bound to a sulfated glycan. J. Mol. Biol. 395, p.475-490

(2) A. Goel, B. P. Tripet, R.C. Tyler, L.D. Nebert, and V. Copié* (2010) Backbone amide dynamics studies of apo-L75F-TrpR, a temperature-sensitive mutant of the tryptophan repressor protein (TrpR): comparison with the 15N relaxation profiles of wild-type and A77V mutant apo-TrpR repressors, Biochemistry,49(37), pp 8006-8019.

(3) N. G. Lintner, K.A. Frankel, S.E Tsutakawa, D.L. Alsbury, V. Copié, M.J. Young, J.A. Tainer, and C.M Lawrence* (2010) Structural insight into the CRISPR/CAS system from SSO1445, a CRISPR associated Csa3 protein from Sulfolobus solfataricus, J. Mol. Biol., 405(4) pp 939-955

(4) N. G. Lintner, M. Kerou, S.K. Brumfield, S. Graham, H. Liu, Naismith, J.H., M. Sdano, N. Peng, Q. She, V.Copié, M.J. Young, M.F. White, and C.M. Lawrence* (2011) Structural and Functional Characterization of an Archaeal CASCADE complex for CRISPR-mediated viral defense, J. Biol. Chem., Vol 286 pp. 21643-21656

(5) B. P. Tripet, A. Goel, and V. Copié* (2011) Internal dynamics of the tryptophan repressor (TrpR) and two functionally distinct TrpR variants, L75F-TrpR and A77V-TrpR, in their L-Trp-bound forms, Biochemistry, Vol. 50 pp. 5140-5153

(6) C. Schlenker, A. Goel, B. Tripet, S. Menon, C.M. Lawrence, and V. Copié* (2012) Structure and Dynamics of the E73 protein from the hyperthermophilic archeal virus SSV-RH: Identification of an extended RHH structural motif whose DNA-binding function suggests a role in gene transcription regulation. Biochemistry, Vol 51, pp 2899-2910. PMCID: PMC3326356

(7) K. Mason, B. Tripet, Parrott, D., Fischer A.M, and Copié* V. (2014) 1H, 13C, 15N backbone and side chain NMR resonance assignments for the N-terminal RNA recognition motif of the HvGR-RBP1 protein involved in the regulation of barley (Hordeum vulgare L.) senescence. Biomol. NMR Assignments. Vol. 8, pp. 149-153. PMCID: PMC3672310

(8) MC Ammons*, and V. Copié* (2013) Mini-review: Lactoferrin: a bioinspired, anti-biofilm therapeutic. Biofouling, Vol. 29(4), 443-455. PMCID: PMC3648868

(9) B. Fonner, B. Tripet, M. Lui, H. Zhu, B. Lei, and V. Copié* (2014) 1H, 13C, 15N backbone and side chain NMR resonance assignments of the N-terminal NEAr iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of S. aureus. Biomol. NMR Assignments. Vol. 8, pp 201-205. PMCID: PMC3796148

(10) M.C. Ammons*, B.P Tripet, R. Carlson, K. Kirker, M. Gross, J. Stanisich, and V. Copié* (2014) Quantitative NMR metabolite profiling of methicillin-resistant and methicillin-susceptible S. aureus discriminates between biofilm and planktonic phenotypes. J. Proteome Res. Vol. 13 (6), pp.2973-85. PMCID: PMC4059261

(11) Fonner, B.A., Tripet, B.P., Eilers, B.J., Stanisich, J., Sullivan-Springhetti, R.K., Moore, R., Liu, M., Lei, B., and V. Copié* (2014) Solution structure and molecular determinants of hemoglobin binding of the first NEAT domain of IsdB in Staphylococcus aureus. Biochemistry. Vol 53(24) pp 3922-3933. PMCID: PMC4072347

(12) Zhu, H., Li, D., Copié, V. and Lei*, B. (2014) Non-heme-binding domains and segments of the Staphylococcus aureus IsdB protein critically contribute to the kinetics and equilibrium of heme acquisition from methemoglobin. PLoS ONE, Vol 9(6):e100744. PMCID: PMC4069089

(13) Tripet, B.P., Mason, K.E., Eilers, B.J., Burns, J.,Powell, P., Fischer, A., and Copié*, V. (2014) Structural and Biochemical Analysis of the Hordeum vulgare L. HvGR-RBP1 Protein, a Glycine-Rich RNA-Binding Protein Involved in the Regulation of Barley Plant Development and Stress Response. Biochemistry. Vol 53 (50), pp. 7945-7960. PMCID: PMC4278681

(14) Ammons*, M.C., Morrisey, K., Tripet, B.P., Van Leuven, J.Y., Han, A., Lazarus, G.S., Zenilman, J.M., Stewart, P.S., and Copié*, V. (2015) Biochemical association of metabolic profile and microbiome in chronic pressure ulcer wounds. PLoS One, 2015 May 15;10(5):e0126735.

(15) Hamerly, T., Tripet, B.P., Tigges, M., Giannone, R.J., Wurch, L., Hettich, R.L., Podar, M., Copié*, V., and Bothner*, B. (2015) Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis. Metabolomics. Vol 11(4), pp 895-907.

(16) Hamerly, T., Tripet, B.P., Giannone, R.J., Wurch, L., Hettich, R.L., Podar, M., Bothner*, B., and Copié*, V., (2015) Characterization of fatty acids in Crenarchaeota by GC-MS and NMR. Archaea – Dec31 2015:472726.doi

(17) Fuchs, A., Tripet, B.P., Ammons*, M.C., and Copié* V. (2016)  Optimization of metabolite extraction protocols for the identification and profiling of small molecule metabolites from planktonic and biofilm Pseudomonas aeruginosa cell cultures. Current Metabolomics Vol. 3 (1), pp 1-8


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