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2009

October 7, 2009
2009 Nobel Winner Was Early User of BioCARS

One of the three winners of the 2009 Nobel Prize in Chemistry, Thomas Steitz, has conducted research at BioCARS. Steitz of Yale University, Ada Yonath of Israel's Weizmann Institute, and Venkatraman Ramakrishnan of Cambridge, England's Medical Research Center shared the award for their study of the structure and function of the ribosome. The following are publications by Steitz based on data taken at BioCARS.

October 6, 2009, Proceedings of the National Academy of Sciences
Natural and recombinant prion structure from X-ray fiber diffraction

A collaboration between scientists at Vanderbilt University and the University of California, San Francisco has led to the first direct information about the molecular structure of prions. Prions are the infectious proteins responsible for human Creutzfeldt-Jakob disease, bovine spongiform encephalopathy, or "mad cow" disease, scrapie in sheep and several other related nervous system disorders in mammals.

In addition, the study has revealed surprisingly large structural differences between natural prions and the closest analogs that scientists have created in the lab. Artificial prions do not show the same degree of infectious behavior as their natural counterparts. "We expected to find subtle [structural] differences, but we found major differences instead," said Gerald Stubbs, professor of biological sciences at Vanderbilt University. "Although we cannot say for certain that the differences we've seen can explain why natural prions are so infectious, there is a good chance that they are closely related." The work was conducted at BioCARS biosafety level 2 (BSL-2) facilities under an agreement with BioCAT (APS sector 18).

May 2009 - The Scientist
Article Traces Development of Research on Photoactive Proteins

An article entitled "LOV Story" in The Scientist features the work of the first researchers to study biological signaling based on the LOV domain--a segment of protein sensitive to light, oxygen, and voltage. The role of early BioCARS user Sean Crosson and sector PI Keith Moffat are highlighted.

May 2009 - The Scientist
BioCARS Principal Investigator Keith Moffat Profiled in The Scientist

In a companion "Careers" piece, The Scientist profiled Keith Moffat, whose interest in physics led to pioneering x-ray techniques for studying how protein molecules respond to light.  

February 8, 2009 - lightsources.org
Scientists Create First Crystal Structure of an Intermediate Particle in Virus Assembly

A research team at the Scripps Research Institute has been able to produce the first crystal structure of a virus particle caught in the midst of assembling its impenetrable outer protein coat. The structure, described February 8 in an advance online publication of the journal Nature, provides fresh insights into the elegant dance that viral proteins perform to create the infectious structure that causes all manner of misery and disease. The work is based in part on data taken at BioCARS beamline 14-BM-C.

2008

October 8, 2008 - lightsources.org
Scripps researchers seek to understand, and improve, virus that can
infect lung cancer cells

The structure of a virus that is harmless to normal human cells but an enemy of certain cancer cells has been determined by Scripps researchers. This new knowledge may help drug designers tweak the pathogen enough so that it can attack other tumor subtypes.

  • Sangita Venkataraman, Seshidhar P. Reddy, Jackie Loo, Neeraja Idamakanti, Paul L. Hallenbeck, and Vijay S. Reddy
    Structure of Seneca Valley Virus-001: An Oncolytic Picornavirus Representing a New Genus
    Structure 16, 1555 (08 October 2008) | DOI: 10.1016/j.str.2008.07.013 

August 11, 2008 - lightsources.org
Australian scientists unravel Leukemia link

Scientists have unravelled the structure of a cell signalling receptor in the blood control system that, when damaged, is responsible for diseases such as leukemia. Their discovery helps to explain, for the first time, how this receptor is activated and will form the springboard for the development of new treatments.

  • 14-BM-C
  • Guido Hansen, Timothy R. Hercus, Barbara J. McClure, Frank C. Stomski, Mara Dottore, Jason Powell, Hayley Ramshaw, Joanna M. Woodcock, Yibin Xu, Mark Guthridge, William J. McKinstry, Angel F. Lopez, and Michael W. Parke
    The Structure of the GM-CSF Receptor Complex Reveals a Distinct Mode of Cytokine Receptor Activation
    Cell 134, 496-507 (2008)

May 4, 2008 (online)
Molecular clues to variable response of cancer patients to the common anti-cancer drug chlorambucil

The commonly used anti-cancer drug chlorambucil is the primary treatment for patients with chronic lymphocytic leukaemia. Chlorambucil has been shown to be detoxified by human glutathione transferase Pi (GST P1-1), an enzyme that is often found over-expressed in cancer tissues. The allelic variants of GST P1-1 are associated with differing susceptibilities to leukaemia and differ markedly in their efficiency in catalysing glutathione (GSH) conjugation reactions. Here, we perform detailed kinetic studies of the allelic variants with the aid of three representative co-substrates. We show that the differing catalytic properties of the variants are highly substrate-dependent. We show also that all variants exhibit the same temperature stability in the range 10 °C to 45 °C. We have determined the crystal structures of GST P1-1 in complex with chlorambucil and its GSH conjugate for two of these allelic variants that have different residues at positions 104 and 113. Chlorambucil is found to bind in a non-productive mode to the substrate-binding site (H-site) in the absence of GSH. This result suggests that under certain stress conditions where GSH levels are low, GST P1-1 can inactivate the drug by sequestering it from the surrounding medium. However, in the presence of GSH, chlorambucil binds in the H-site in a productive mode and undergoes a conjugation reaction with GSH present in the crystal. The crystal structure of the GSH–chlorambucil complex bound to the *C variant is identical with the *A variant ruling out the hypothesis that primary structure differences between the variants cause structural changes at the active site. Finally, we show that chlorambucil is a very poor inhibitor of the enzyme in contrast to ethacrynic acid, which binds to the enzyme in a similar fashion but can act as both substrate and inhibitor.

  • L.J. Parker, S. Ciccone, L.C. Italiano, A. Primavera, A.J. Oakley, C.J. Morton, N.C. Hancock, M. Lo Bello, M.W. Parker
    The Anti-Cancer Drug Chlorambucil as a Substrate for the Human Polymorphic Enzyme Glutathione Transferase P1-1: Kinetic Properties and Crystallographic Characterisation of Allelic Variants
    J. Mol. Biol. 380 (1) 131-144 (2008) | doi:10.1016/j.jmb.2008.04.066 

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April 23, 2008
Researchers reveal structure of protein that repairs damage to cancer cells

A team of University of Chicago scientists has shown how two proteins locate and repair damaged genetic material inside cells. One protein detects and repairs damage in malignant cells that may result from a certain type of cancer therapy. In a paper published in the April 24 issue of the journal Nature, the team raised the possibility of designing a molecule that could interfere with the repair process, making cancer treatment more effective.

March 14, 2008
Study shows how new antibody recognizes and binds Alzheimer's peptide

Alzheimer's disease (AD) is the most common form of dementia. Amyloid-β (Aβ) peptide, generated by proteolytic cleavage of the amyloid precursor protein, is central to AD pathogenesis. Most pharmaceutical activity in AD research has focused on Aβ, its generation and clearance from the brain. In particular, there is much interest in immunotherapy approaches with a number of anti-Aβ antibodies in clinical trials. We have developed a monoclonal antibody, called WO2, which recognises the Aβ peptide. To this end, we have determined the three-dimensional structure, to near atomic resolution, of both the antibody and the complex with its antigen, the Aβ peptide. The structures reveal the molecular basis for WO2 recognition and binding of Aβ. The Aβ peptide adopts an extended, coil-like conformation across its major immunodominant B-cell epitope between residues 2 and 8. We have also studied the antibody-bound Aβ peptide in the presence of metals known to affect its aggregation state and show that WO2 inhibits these interactions. Thus, antibodies that target the N-terminal region of Aβ, such as WO2, hold promise for therapeutic development.

  • L.A. Miles, S.W. Kwok, G.A.N. Crespi, M.T. Fodero-Tavoletti, D. Galatis, C.J. Bagley, K. Beyreuther, C.L. Masters, R. Cappai, W.J. McKinstry, K.J. Barnham, M.W. Parker
    Amyloid-β–Anti-Amyloid-β Complex Structure Reveals an Extended Conformation in the Immunodominant B-Cell Epitope
    J. Mol. Biol. 377 (1) 181-192 (14 March 2008))

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March 2008 (online January 9, 2008)
Crystal structure of unliganded influenza B virus hemagglutinin

Here we report the crystal structure of hemagglutinin (HA) from influenza B/HK/8/73 virus determined to 2.8 Å. At a sequence identity of 25% to influenza A virus HAs, B/HK HA shares a similar overall structure and domain organization. More than two dozen of amino acid substitutions have been identified on influenza B virus HAs to cause antigenicity alteration in site-specific mutants, monoclonal antibody-escape mutants or field isolates. Mapping these substitutions on the structure of B/HK HA reveals four major epitopes, the 120-loop, 150-loop, 160-loop and 190-helix, that are located close in space to form a large, continuous antigenic site. Moreover, a systematic comparison of known HA structures across the entire influenza virus family reveals evolutionarily conserved ionizable residues at all regions along chain and subunit interface. These ionizable residues are likely the structural basis for the pH-dependence and sensitivity to ionic strength of influenza HA and HEF proteins.

February 26, 2008
CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling

RAF kinase functions in the mitogen-activated protein kinase (MAPK) pathway to transmit growth signals to the downstream kinases MEK and ERK. Activation of RAF catalytic activity is facilitated by a regulatory complex comprising the proteins CNK (Connector enhancer of KSR), HYP (Hyphen), and KSR (Kinase Suppressor of Ras). The sterile α-motif (SAM) domain found in both CNK and HYP plays an essential role in complex formation. Here, we have determined the x-ray crystal structure of the SAM domain of CNK in complex with the SAM domain of HYP. The structure reveals a single-junction SAM domain dimer of 1:1 stoichiometry in which the binding mode is a variation of polymeric SAM domain interactions. Through in vitro and in vivo mutational analyses, we show that the specific mode of dimerization revealed by the crystal structure is essential for RAF signaling and facilitates the recruitment of KSR to form the CNK/HYP/KSR regulatory complex. We present two docking-site models to account for how SAM domain dimerization might influence the formation of a higher-order CNK/HYP/KSR complex.

  • T. Rajakulendran, M. Sahmi, I. Kurinov, M. Tyers, M. Therrien, F. Sicheri
    CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling
    PNAS 105 (8) 2836-2841 (2008)

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February 2008
Impact of clonal competition for peptide-MHC complexes on the CD8+ T-cell repertoire selection in a persistent viral infection

CD8+ T-cell responses to persistent viral infections are characterized by the accumulation of an oligoclonal T-cell repertoire and a reduction in the naive T-cell pool. However the precise mechanism for this phenomenon remains elusive. Here we show that human cytomegalovirus (HCMV)-specific CD8+ T-cells recognizing distinct epitopes from the pp65 protein and restricted through an identical HLA class I allele (HLA B*3508) exhibited either a highly conserved public T-cell repertoire or a private yet diverse T-cell response, which was uniquely altered in each donor following in vitro antigen exposure. Selection of a public TCR was coincident with an atypical MHC-peptide structure, in that the epitope adopted a helical conformation that bulged from the Ag-binding groove, whilst a diverse TCR profile was observed in response to the epitope that formed a flatter, more "featureless" landscape. Clonotypes with biased TCR usage demonstrated more efficient recognition of virus-infected cells, a greater CD8 dependency, and were more terminally differentiated in their phenotype when compared to the T-cells expressing diverse TCR. These findings provide new insights into our understanding on how the biology of antigen presentation in addition to the structural features of the pMHC-I might shape the T-cell repertoire and its phenotype.

  • K.K. Wynn, Z. Marland, L. Cooper, S.L. Silins, S. Gras, J.K. Archbold, F.E. Tynan, J.J. Miles, J. McCluskey, S.R. Burrows, J. Rossjohn, R. Khanna
    Blood 111 (8) 4283-4292 (2008)

January 2008
Structure–activity relationships of C6-uridine derivatives targeting Plasmodia orotidine monophosphate decarboxylase

Malaria, caused by Plasmodia parasites, has re-emerged as a major problem, imposing its fatal effects on human health, especially due to multidrug resistance. In Plasmodia, orotidine 5′ monophosphate decarboxylase (ODCase) is an essential enzyme for the de novo synthesis of uridine 5′-monophosphate. Impairing ODCase in these pathogens is a promising strategy to develop novel classes of therapeutics. Encouraged by our recent discovery that 6-iodo uridine is a potent inhibitor of P. falciparum, we investigated the structure–activity relationships of various C6 derivatives of UMP. 6-Cyano, 6-azido, 6-amino, 6-methyl, 6-N-methylamino, and 6-N,N-dimethylamino derivatives of uridine were evaluated against P. falciparum. The mononucleotides of 6-cyano, 6-azido, 6-amino, and 6-methyl uridine derivatives were studied as inhibitors of plasmodial ODCase. 6-Azidouridine 5′-monophosphate is a potent covalent inhibitor of P. falciparum ODCase. 6-Methyluridine exhibited weak antimalarial activity against P. falciparum 3D7 isolate. 6-N-Methylamino and 6-N,N-dimethylamino uridine derivatives exhibited moderate antimalarial activities.

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2007

October 2007
Structural basis for the recruitment of profilin–actin complexes during filament elongation by Ena/VASP

Cells sustain high rates of actin filament elongation by maintaining a large pool of actin monomers above the critical concentration for polymerization. Profilin–actin complexes constitute the largest fraction of polymerization-competent actin monomers. Filament elongation factors such as Ena/VASP and formin catalyze the transition of profilin–actin from the cellular pool onto the barbed end of growing filaments. The molecular bases of this process are poorly understood. Here we present structural and energetic evidence for two consecutive steps of the elongation mechanism: the recruitment of profilin–actin by the last poly-Pro segment of vasodilator-stimulated phosphoprotein (VASP) and the binding of profilin–actin simultaneously to this poly-Pro and to the G-actin-binding (GAB) domain of VASP. The actin monomer bound at the GAB domain is proposed to be in position to join the barbed end of the growing filament concurrently with the release of profilin.

October 2007
Molecular basis for passive immunotherapy of Alzheimer's disease

Amyloid aggregates of the amyloid-β (Aβ) peptide are implicated in the pathology of Alzheimer's disease. Anti-Aβ monoclonal antibodies (mAbs) have been shown to reduce amyloid plaques in vitro and in animal studies. Consequently, passive immunization is being considered for treating Alzheimer's, and anti-Aβ mAbs are now in phase II trials. We report the isolation of two mAbs (PFA1 and PFA2) that recognize Aβ monomers, protofibrils, and fibrils and the structures of their antigen binding fragments (Fabs) in complex with the Aβ(1–8) peptide DAEFRHDS. The immunodominant EFRHD sequence forms salt bridges, hydrogen bonds, and hydrophobic contacts, including interactions with a striking WWDDD motif of the antigen binding fragments. We also show that a similar sequence (AKFRHD) derived from the human protein GRIP1 is able to cross-react with both PFA1 and PFA2 and, when cocrystallized with PFA1, binds in an identical conformation to Aβ(1–8). Because such cross-reactivity has implications for potential side effects of immunotherapy, our structures provide a template for designing derivative mAbs that target Aβ with improved specificity and higher affinity.

  • Anna S. Gardberg, Lezlee T. Dice, Susan Ou, Rebecca L. Rich, Elizabeth Helmbrecht, Jan Ko, Ronald Wetzel, David G. Myszka, Paul H. Patterson, Chris Dealwis
    PNAS 104 15659-15664 (2007)

June 2007
The N terminus of the serpin, tengpin, functions to trap the metastable native state

Serpins fold to a metastable native state and are susceptible to undergoing spontaneous conformational change to more stable conformers, such as the latent form. We investigated conformational change in tengpin, an unusual prokaryotic serpin from the extremophile Thermoanaerobacter tengcongensis. In addition to the serpin domain, tengpin contains a functionally uncharacterized 56-amino-acid amino-terminal region. Deletion of this domain creates a variant—tengpinΔ51—which folds past the native state and readily adopts the latent conformation. Analysis of crystal structures together with mutagenesis studies show that the N terminus of tengpin protects a hydrophobic patch in the serpin domain and functions to trap tengpin in its native metastable state. A 13-amino-acid peptide derived from the N terminus is able to mimick the role of the N terminus in stabilizing the native state of tengpinΔ51. Therefore, the function of the N terminus in tengpin resembles protein cofactors that prevent mammalian serpins from spontaneously adopting the latent conformation.

  • Qingwei Zhang, Ashley M. Buckle, Ruby H.P. Law, Mary C. Pearce, Lisa D. Cabrita, Gordon J. Lloyd, James A. Irving, A. Ian Smith, Katya Ruzyla, Jamie Rossjohn, Stephen P. Bottomley, James C. Whisstock
    EMBO Reports 8 658-663 (2007)

June 2007
An atomic model of the interferon-β enhanceosome

Transcriptional activation of the interferon-β (IFN-β) gene requires assembly of an enhanceosome containing ATF-2/c-Jun, IRF-3/IRF-7, and NFκB. These factors bind cooperatively to the IFN-β enhancer and recruit coactivators and chromatin-remodeling proteins to the IFN-β promoter. We describe here a crystal structure of the DNA-binding domains of IRF-3, IRF-7, and NFκB, bound to one half of the enhancer, and use a previously described structure of the remaining half to assemble a complete picture of enhanceosome architecture in the vicinity of the DNA. Association of eight proteins with the enhancer creates a continuous surface for recognizing a composite DNA-binding element. Paucity of local protein-protein contacts suggests that cooperative occupancy of the enhancer comes from both binding-induced changes in DNA conformation and interactions with additional components such as CBP. Contacts with virtually every nucleotide pair account for the evolutionary invariance of the enhancer sequence.

July 2007
Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion

Bacteriophytochromes RpBphP2 and RpBphP3 from the photosynthetic bacterium Rhodopseudomonas palustris work in tandem to modulate synthesis of the light-harvesting complex LH4 in response to light. Although RpBphP2 and RpBphP3 share the same domain structure with 52% sequence identity, they demonstrate distinct photoconversion behaviors. RpBphP2 exhibits the "classical" phytochrome behavior of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states, whereas RpBphP3 exhibits novel photoconversion between Pr and a near-red (Pnr) light-absorbing states. We have determined the crystal structure at 2.2-Å resolution of the chromophore binding domains of RpBphP3, covalently bound with chromophore biliverdin IXα. By combining structural and sequence analyses with site-directed mutagenesis, we identify key residues that directly modulate the photochemical properties of RpBphP3 and RpBphP2. Remarkably, we identify a region spanning residues 207-212 in RpBphP3, in which a single mutation, L207Y, causes this unusual bacteriophytochrome to revert to the classical phenotype that undergoes reversible photoconversion between the Pr and Pfr states. The reverse mutation, Y193L, in the corresponding region in RpBphP2 significantly diminishes the formation of the Pfr state. We propose that residues 207-212 and the spatially adjacent conserved residues, Asp-216 and Tyr-272, interact with the chromophore and form part of the interface between the chromophore binding domains and the PHY domain that modulates photoconversion.

March 2007
Time-resolved crystallographic studies of the heme domain of the oxygen sensor FixL: Structural dynamics of ligand rebinding and their relation to signal transduction

The FixL protein of Bradyrhizobium japonicum is a dimeric oxygen sensor responsible for initiating regulation of transcription of genes encoding proteins involved in nitrogen fixation and oxidative stress. It consists of an N-terminal heme-bound PAS domain, denoted bjFixLH, and a C-terminal histidine kinase domain whose enzymatic activity depends on the ligation state of the heme. To investigate the molecular basis for this dependence and the dynamics associated with conversion between ligated and unligated states, we have conducted time-resolved Laue diffraction studies of CO recombination in bjFixLH. Time-dependent difference Fourier maps from 1 ms to 10 ms after photolysis of the heme-CO bond show movement of the side chain of Leu236 and the H and I β-strands into the ligand binding pocket formerly occupied by CO. Long-range conformational changes are evident in the protein, driven by relaxation of steric interactions between the bound ligand and amino acid side chains and/or changes in heme stereochemistry. These structural changes fully reverse as CO rebinds to the heme. Spectroscopic measurements of CO recombination kinetics in bjFixLH crystals relate the behavior of crystalline bjFixLH to solution and provide a framework for our time-resolved crystallographic experiments. Analysis of the time-dependent difference Fourier maps by singular value decomposition reveals that only one significant singular value accounts for the data. Thus only two structural states are present, the photolyzed and the CO-bound states. The first left singular vector represents the difference in density between these two states and shows features common to difference maps calculated from the static CO and deoxy states. The first right singular vector represents the time course of this difference density and agrees well with the CO recombination kinetics measured spectroscopically. We refine the structure of the photolyzed state present in the early-microsecond time range and find that it does not differ significantly in conformation from static, deoxy bjFixLH. Thus, structural relaxation from CO-bound to deoxy bjFixLH is complete in less than 1m s.

March 22, 2007 - lightsources.org
Biologists learn structure of enzyme needed to power "molecular motor"

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2006

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2005

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