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Xin L, Barrios M, Cohen JT, Chapman MS. Long-Lived Squeezed Ground States in a Quantum Spin Ensemble. Phys Rev Lett 2023; 131:133402. [PMID: 37832022 DOI: 10.1103/physrevlett.131.133402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/07/2023] [Indexed: 10/15/2023]
Abstract
We generate spin squeezed ground states in an atomic spin-1 Bose-Einstein condensate tuned near the quantum-critical point separating the different spin phases of the interacting ensemble using a novel nonadiabatic technique. In contrast to typical nonequilibrium methods for preparing atomic squeezed states by quenching through a quantum phase transition, squeezed ground states are time stationary with a constant quadrature squeezing angle. A squeezed ground state with 6-8 dB of squeezing and a constant squeezing angle is demonstrated. The long-term evolution of the squeezed ground state is measured and shows gradual decrease in the degree of squeezing over 2 s that is well modeled by a slow tuning of the Hamiltonian due to the loss of atomic density. Interestingly, modeling the gradual decrease does not require additional spin decoherence models despite a loss of 75% of the atoms.
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Affiliation(s)
- Lin Xin
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Maryrose Barrios
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Julia T Cohen
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Michael S Chapman
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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2
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Large EE, Chapman MS. Adeno-associated virus receptor complexes and implications for adeno-associated virus immune neutralization. Front Microbiol 2023; 14:1116896. [PMID: 36846761 PMCID: PMC9950413 DOI: 10.3389/fmicb.2023.1116896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Adeno-associated viruses (AAV) are among the foremost vectors for in vivo gene therapy. A number of monoclonal antibodies against several serotypes of AAV have previously been prepared. Many are neutralizing, and the predominant mechanisms have been reported as the inhibition of binding to extracellular glycan receptors or interference with some post-entry step. The identification of a protein receptor and recent structural characterization of its interactions with AAV compel reconsideration of this tenet. AAVs can be divided into two families based on which domain of the receptor is strongly bound. Neighboring domains, unseen in the high-resolution electron microscopy structures have now been located by electron tomography, pointing away from the virus. The epitopes of neutralizing antibodies, previously characterized, are now compared to the distinct protein receptor footprints of the two families of AAV. Comparative structural analysis suggests that antibody interference with protein receptor binding might be the more prevalent mechanism than interference with glycan attachment. Limited competitive binding assays give some support to the hypothesis that inhibition of binding to the protein receptor has been an overlooked mechanism of neutralization. More extensive testing is warranted.
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Affiliation(s)
- Edward E. Large
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
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Abstract
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Adeno-associated
virus (AAV) has a single-stranded DNA genome encapsidated
in a small icosahedrally symmetric protein shell with 60 subunits.
AAV is the leading delivery vector in emerging gene therapy treatments
for inherited disorders, so its structure and molecular interactions
with human hosts are of intense interest. A wide array of electron
microscopic approaches have been used to visualize the virus and its
complexes, depending on the scientific question, technology available,
and amenability of the sample. Approaches range from subvolume tomographic
analyses of complexes with large and flexible host proteins to detailed
analysis of atomic interactions within the virus and with small ligands
at resolutions as high as 1.6 Å. Analyses have led to the reclassification
of glycan receptors as attachment factors, to structures with a new-found
receptor protein, to identification of the epitopes of antibodies,
and a new understanding of possible neutralization mechanisms. AAV
is now well-enough characterized that it has also become a model system
for EM methods development. Heralding a new era, cryo-EM is now also
being deployed as an analytic tool in the process development and
production quality control of high value pharmaceutical biologics,
namely AAV vectors.
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Affiliation(s)
- Scott M Stagg
- Department of Biological Sciences, Florida State University, Tallahassee, Florida 32306, United States.,Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
| | - Craig Yoshioka
- Department of Biomedical Engineering, Oregon Health & Science University, Portland Oregon 97239, United States
| | - Omar Davulcu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Michael S Chapman
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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4
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Meyer NL, Chapman MS. Adeno-associated virus (AAV) cell entry: structural insights. Trends Microbiol 2021; 30:432-451. [PMID: 34711462 DOI: 10.1016/j.tim.2021.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/02/2021] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Adeno-associated virus (AAV) is the leading vector in emerging treatments of inherited diseases. Higher transduction efficiencies and cellular specificity are required for broader clinical application, motivating investigations of virus-host molecular interactions during cell entry. High-throughput methods are identifying host proteins more comprehensively, with subsequent molecular studies revealing unanticipated complexity and serotype specificity. Cryogenic electron microscopy (cryo-EM) provides a path towards structural details of these sometimes heterogeneous virus-host complexes, and is poised to illuminate more fully the steps in entry. Here presented, is progress in understanding the distinct steps of glycan attachment, and receptor-mediated entry/trafficking. Comparison with structures of antibody complexes provides new insights on immune neutralization with implications for the design of improved gene therapy vectors.
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Affiliation(s)
- Nancy L Meyer
- Pacific Northwest Cryo-EM Center, Oregon Health and Science University (OHSU) Center for Spatial Systems Biomedicine, Portland, OR, USA
| | - Michael S Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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5
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Silveria MA, Large EE, Zane GM, White TA, Chapman MS. The Structure of an AAV5-AAVR Complex at 2.5 Å Resolution: Implications for Cellular Entry and Immune Neutralization of AAV Gene Therapy Vectors. Viruses 2020; 12:E1326. [PMID: 33218165 PMCID: PMC7698955 DOI: 10.3390/v12111326] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/28/2022] Open
Abstract
Adeno-Associated Virus is the leading vector for gene therapy. Although it is the vector for all in vivo gene therapies approved for clinical use by the US Food and Drug Administration, its biology is still not yet fully understood. It has been shown that different serotypes of AAV bind to their cellular receptor, AAVR, in different ways. Previously we have reported a 2.4Å structure of AAV2 bound to AAVR that shows ordered structure for only one of the two AAVR domains with which AAV2 interacts. In this study we present a 2.5Å resolution structure of AAV5 bound to AAVR. AAV5 binds to the first polycystic kidney disease (PKD) domain of AAVR that was not ordered in the AAV2 structure. Interactions of AAV5 with AAVR are analyzed in detail, and the implications for AAV2 binding are explored through molecular modeling. Moreover, we find that binding sites for the antibodies ADK5a, ADK5b, and 3C5 on AAV5 overlap with the binding site of AAVR. These insights provide a structural foundation for development of gene therapy agents to better evade immune neutralization without disrupting cellular entry.
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Affiliation(s)
- Mark A. Silveria
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
| | - Edward E. Large
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
| | - Tommi A. White
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
- Electron Microscopy Core, University of Missouri, Columbia, MO 65211, USA
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
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Xie Q, Yoshioka CK, Chapman MS. Adeno-Associated Virus (AAV-DJ)-Cryo-EM Structure at 1.56 Å Resolution. Viruses 2020; 12:E1194. [PMID: 33092282 PMCID: PMC7589773 DOI: 10.3390/v12101194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 01/12/2023] Open
Abstract
Adeno-associated virus is the leading viral vector for gene therapy. AAV-DJ is a recombinant variant developed for tropism to the liver. The AAV-DJ structure has been determined to 1.56 Å resolution through cryo-electron microscopy (cryo-EM). Only apoferritin is reported in preprints at 1.6 Å or higher resolution, and AAV-DJ nearly matches the highest resolutions ever attained through X-ray diffraction of virus crystals. However, cryo-EM has the advantage that most of the hydrogens are clear, improving the accuracy of atomic refinement, and removing ambiguity in hydrogen bond identification. Outside of secondary structures where hydrogen bonding was predictable a priori, the networks of hydrogen bonds coming from direct observation of hydrogens and acceptor atoms are quite different from those inferred even at 2.8 Å resolution. The implications for understanding viral assembly mean that cryo-EM will likely become the favored approach for high resolution structural virology.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Craig K. Yoshioka
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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7
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Meyer N, Davulcu O, Xie Q, Silveria M, Zane GM, Large E, Chapman MS. Expression and Purification of Adeno-associated Virus Virus-like Particles in a Baculovirus System and AAVR Ectodomain Constructs in E. coli. Bio Protoc 2020; 10:e3513. [PMID: 33654738 PMCID: PMC7842819 DOI: 10.21769/bioprotoc.3513] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/16/2019] [Accepted: 12/30/2019] [Indexed: 11/02/2022] Open
Abstract
Adeno-associated virus (AAV) is a promising gene therapy vector and the biophysical characterization of its interactions with host proteins is a critical foundation for engineering tissue targeting and immune escape. Presented here are protocols for the production of: (a) the outer protein shells (virus-like particles or VLPs) for serotype 2 (AAV-2) and (b) two fragments from the binding ectodomain of AAV's cellular receptor, AAVR. His6PKD1-2 comprises the first two polycystic kidney disease (PKD) domains, the minimal required for efficient binding of AAV, expressed with an N-terminal histidine tag. MBP-PKD1-5 is a fusion of the maltose binding protein with all five of the PKD domains of the AAVR receptor. Presented are the expression and purification of milligram quantities, ample for in vitro analyses. For AAV-2, the protocol offers an alternative to the use of (infectious) wild-type virus or transducing vectors. One of the methods for producing transducing vector is in Sf9 cells, and the production of VLPs is based on this. For AAVR, the protocols enable biochemical and biophysical characterization of virus-binding. The minimal two-domain construct allows more saturated binding to symmetry-equivalent sites on the virus, while the larger construct might be better expected to reflect the native receptor.
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Affiliation(s)
- Nancy Meyer
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States
- Pacific Northwest Cryo-EM Center, OHSU Center for Spatial Systems Biomedicine, Portland, United States
| | - Omar Davulcu
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States
- Pfizer, Chesterfield, United States
| | - Qing Xie
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States
| | - Mark Silveria
- Department of Biochemistry, University of Missouri, Columbia, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, United States
| | - Edward Large
- Department of Biochemistry, University of Missouri, Columbia, United States
| | - Michael S. Chapman
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States
- Department of Biochemistry, University of Missouri, Columbia, United States
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8
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H M B, Boguslawski M, Barrios M, Xin L, Chapman MS. Exploring Non-Abelian Geometric Phases in Spin-1 Ultracold Atoms. Phys Rev Lett 2019; 123:173202. [PMID: 31702240 DOI: 10.1103/physrevlett.123.173202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Indexed: 06/10/2023]
Abstract
The spin vector of a spin-1 system, unlike that of a spin-1/2 system, can lie anywhere on or inside the Bloch sphere representing the phase space. As a consequence, the geometrical and topological properties of the spin-1 phase space of quantum states are richer and require a generalization of Berry's phase. For special trajectories passing through the center of the Bloch sphere (singular loops), the geometric phase has a non-Abelian nature. Here, we experimentally explore this geometric phase for singular loops in a spin-1 quantum system using ultracold ^{87}Rb atoms confined in an optical trap using microwave and rf control fields.
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Affiliation(s)
- Bharath H M
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
- Fakultät für Physik, Ludwig-Maximilians-Univesität München, 4 Schellingstraße, 80799 München, Germany
- Max-Planck-Institut für Quantenoptik, 85748 Garching, Germany
| | - Matthew Boguslawski
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
| | - Maryrose Barrios
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
| | - Lin Xin
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
| | - Michael S Chapman
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
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9
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Xie Q, Spear JM, Noble AJ, Sousa DR, Meyer NL, Davulcu O, Zhang F, Linhardt RJ, Stagg SM, Chapman MS. The 2.8 Å Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparinoid Pentasaccharide. Mol Ther Methods Clin Dev 2017; 5:1-12. [PMID: 28480299 PMCID: PMC5415311 DOI: 10.1016/j.omtm.2017.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 02/22/2017] [Indexed: 01/24/2023]
Abstract
Atomic structures of adeno-associated virus (AAV)-DJ, alone and in complex with fondaparinux, have been determined by cryoelectron microscopy at 3 Å resolution. The gene therapy vector, AAV-DJ, is a hybrid of natural serotypes that was previously derived by directed evolution, selecting for hepatocyte entry and resistance to neutralization by human serum. The structure of AAV-DJ differs from that of parental serotypes in two regions where neutralizing antibodies bind, so immune escape appears to have been the primary driver of AAV-DJ's directed evolution. Fondaparinux is an analog of cell surface heparan sulfate to which several AAVs bind during entry. Fondaparinux interacts with viral arginines at a known heparin binding site, without the large conformational changes whose presence was controversial in low-resolution imaging of AAV2-heparin complexes. The glycan density suggests multi-modal binding that could accommodate sequence variation and multivalent binding along a glycan polymer, consistent with a role in attachment, prior to more specific interactions with a receptor protein mediating entry.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA
| | - John M. Spear
- Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL 32306-4380, USA
| | - Alex J. Noble
- Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL 32306-4380, USA
| | - Duncan R. Sousa
- Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL 32306-4380, USA
| | - Nancy L. Meyer
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA
| | - Omar Davulcu
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA
| | - Fuming Zhang
- Departments of Chemical and Biological Engineering, Chemistry, and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Robert J. Linhardt
- Departments of Chemical and Biological Engineering, Chemistry, and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Scott M. Stagg
- Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL 32306-4380, USA
| | - Michael S. Chapman
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA
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10
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Davulcu O, Peng Y, Brüschweiler R, Skalicky JJ, Chapman MS. Elevated μs-ms timescale backbone dynamics in the transition state analog form of arginine kinase. J Struct Biol 2017; 200:258-266. [PMID: 28495594 DOI: 10.1016/j.jsb.2017.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/04/2017] [Accepted: 05/06/2017] [Indexed: 10/19/2022]
Abstract
Arginine kinase catalyzes reversible phosphoryl transfer between arginine and ATP. Crystal structures of arginine kinase in an open, substrate-free form and closed, transition state analog (TSA) complex indicate that the enzyme undergoes substantial domain and loop rearrangements required for substrate binding, catalysis, and product release. Nuclear magnetic resonance (NMR) has shown that substrate-free arginine kinase is rigid on the ps-ns timescale (average S2=0.84±0.08) yet quite dynamic on the µs-ms timescale (35 residues with Rex, 12%), and that movements of the N-terminal domain and the loop comprising residues I182-G209 are rate-limiting on catalysis. Here, NMR of the TSA-bound enzyme shows similar rigidity on the ps-ns timescale (average S2=0.91±0.05) and substantially increased μs-ms timescale dynamics (77 residues; 22%). Many of the residues displaying μs-ms dynamics in NMR Carr-Purcell-Meiboom-Gill (CPMG) 15N backbone relaxation dispersion experiments of the TSA complex are also dynamic in substrate-free enzyme. However, the presence of additional dynamic residues in the TSA-bound form suggests that dynamics extend through much of the C-terminal domain, which indicates that in the closed form, a larger fraction of the protein takes part in conformational transitions to the excited state(s). Conformational exchange rate constants (kex) of the TSA complex are all approximately 2500s-1, higher than any observed in the substrate-free enzyme (800-1900s-1). Elevated μs-ms timescale protein dynamics in the TSA-bound enzyme is more consistent with recently postulated catalytic networks involving multiple interconnected states at each step of the reaction, rather than a classical single stabilized transition state.
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Affiliation(s)
- Omar Davulcu
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, United States
| | - Yu Peng
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States; Department of Biological Chemistry and Pharmacology and Campus Chemical Instrument Center, The Ohio State University, OH 43210, United States
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - Michael S Chapman
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, United States.
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11
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Peng Y, Hansen AL, Bruschweiler-Li L, Davulcu O, Skalicky JJ, Chapman MS, Brüschweiler R. The Michaelis Complex of Arginine Kinase Samples the Transition State at a Frequency That Matches the Catalytic Rate. J Am Chem Soc 2017; 139:4846-4853. [PMID: 28287709 DOI: 10.1021/jacs.7b00236] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Arginine kinase (AK), which is a member of the phosphagen kinase family, serves as a model system for studying the structural and dynamic determinants of biomolecular enzyme catalysis of all major states involved of the enzymatic cycle. These states are the apo state (substrate free), the Michaelis complex analogue AK:Arg:Mg·AMPPNP (MCA), a product complex analogue AK:pAIE:Mg·ADP (PCA), and the transition state analogue AK:Arg:Mg·ADP:NO3- (TSA). The conformational dynamics of these states have been studied by NMR relaxation dispersion measurements of the methyl groups of the Ile, Leu, and Val residues at two static magnetic fields. Although all states undergo significant amounts of μs-ms time scale dynamics, only the MCA samples a dominant excited state that resembles the TSA, as evidenced by the strong correlation between the relaxation dispersion derived chemical shift differences Δω and the equilibrium chemical shift differences Δδ of these states. The average lifetime of the MCA is 36 ms and the free energy difference to the TSA-like form is 8.5 kJ/mol. It is shown that the conformational energy landscape of the Michaelis complex analogue is shaped in a way that at room temperature it channels passage to the transition state, thereby determining the rate-limiting step of the phosphorylation reaction of arginine. Conversely, relaxation dispersion experiments of the TSA reveal that it samples the structures of the Michaelis complex analogue or the apo state as its dominant excited state. This reciprocal behavior shows that the free energy of the TSA, with all ligands bound, is lower by only about 8.9 kJ/mol than that of the Michaelis or apo complex conformations with the TSA ligands present.
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Affiliation(s)
| | | | | | - Omar Davulcu
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239, United States
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - Michael S Chapman
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239, United States
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12
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Godsey MH, Davulcu O, Nix JC, Skalicky JJ, Brüschweiler RP, Chapman MS. The Sampling of Conformational Dynamics in Ambient-Temperature Crystal Structures of Arginine Kinase. Structure 2016; 24:1658-1667. [PMID: 27594681 DOI: 10.1016/j.str.2016.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 01/26/2023]
Abstract
Arginine kinase provides a model for functional dynamics, studied through crystallography, enzymology, and nuclear magnetic resonance. Structures are now solved, at ambient temperature, for the transition state analog (TSA) complex. Analysis of quasi-rigid sub-domain displacements show that differences between the two TSA structures average about 5% of changes between substrate-free and TSA forms, and they are nearly co-linear. Small backbone hinge rotations map to sites that also flex on substrate binding. Anisotropic atomic displacement parameters (ADPs) are refined using rigid-body TLS constraints. Consistency between crystal forms shows that they reflect intrinsic molecular properties more than crystal lattice effects. In many regions, the favored directions of thermal/static displacement are appreciably correlated with movements on substrate binding. Correlation between ADPs and larger substrate-associated movements implies that the latter approximately follow paths of low-energy intrinsic motions.
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Affiliation(s)
- Michael H Godsey
- Department of Math/Science, Concordia University, Portland, OR 97211, USA
| | - Omar Davulcu
- Department Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jay C Nix
- Molecular Biology Consortium, Lawrence Berkeley Natl. Lab., Berkeley, CA 94720, USA
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 8412, USA
| | - Rafael P Brüschweiler
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Michael S Chapman
- Department Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA.
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13
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Hoang TM, Bharath HM, Boguslawski MJ, Anquez M, Robbins BA, Chapman MS. Adiabatic quenches and characterization of amplitude excitations in a continuous quantum phase transition. Proc Natl Acad Sci U S A 2016; 113:9475-9. [PMID: 27503886 PMCID: PMC5003277 DOI: 10.1073/pnas.1600267113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spontaneous symmetry breaking occurs in a physical system whenever the ground state does not share the symmetry of the underlying theory, e.g., the Hamiltonian. This mechanism gives rise to massless Nambu-Goldstone modes and massive Anderson-Higgs modes. These modes provide a fundamental understanding of matter in the Universe and appear as collective phase or amplitude excitations of an order parameter in a many-body system. The amplitude excitation plays a crucial role in determining the critical exponents governing universal nonequilibrium dynamics in the Kibble-Zurek mechanism (KZM). Here, we characterize the amplitude excitations in a spin-1 condensate and measure the energy gap for different phases of the quantum phase transition. At the quantum critical point of the transition, finite-size effects lead to a nonzero gap. Our measurements are consistent with this prediction, and furthermore, we demonstrate an adiabatic quench through the phase transition, which is forbidden at the mean field level. This work paves the way toward generating entanglement through an adiabatic phase transition.
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Affiliation(s)
- Thai M Hoang
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430
| | - Hebbe M Bharath
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430
| | | | - Martin Anquez
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430
| | - Bryce A Robbins
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430
| | - Michael S Chapman
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430
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14
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Meyer NL, Pillay S, Xie Q, Davulcu O, Puschnik A, Diep J, Ishikawa Y, Jae L, Wosen J, Nagamine C, Noble A, Stagg S, Carette JE, Chapman MS. 478. An Essential and Ubiquitous Protein Receptor for AAV; Glycans as Attachment Receptors. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)33287-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Anquez M, Robbins BA, Bharath HM, Boguslawski M, Hoang TM, Chapman MS. Quantum Kibble-Zurek Mechanism in a Spin-1 Bose-Einstein Condensate. Phys Rev Lett 2016; 116:155301. [PMID: 27127974 DOI: 10.1103/physrevlett.116.155301] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 06/05/2023]
Abstract
The dynamics of a quantum phase transition are explored using slow quenches from the polar to the broken-axisymmetry phases in a small spin-1 ferromagnetic Bose-Einstein condensate. Measurements of the evolution of the spin populations reveal a power-law scaling of the temporal onset of excitations versus quench speed as predicted from quantum extensions of the Kibble-Zurek mechanism. The satisfactory agreement of the measured scaling exponent with the analytical theory and numerical simulations provides experimental confirmation of the quantum Kibble-Zurek model.
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Affiliation(s)
- M Anquez
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - B A Robbins
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - H M Bharath
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M Boguslawski
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - T M Hoang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M S Chapman
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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16
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Pillay S, Meyer NL, Puschnik AS, Davulcu O, Diep J, Ishikawa Y, Jae LT, Wosen JE, Nagamine CM, Chapman MS, Carette JE. An essential receptor for adeno-associated virus infection. Nature 2016; 530:108-12. [PMID: 26814968 PMCID: PMC4962915 DOI: 10.1038/nature16465] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 11/18/2015] [Indexed: 01/20/2023]
Affiliation(s)
- S Pillay
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, California 94305, USA
| | - N L Meyer
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health &Science University, 3181 Sam Jackson Park Road, Portland, Oregon 97239-3098, USA
| | - A S Puschnik
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, California 94305, USA
| | - O Davulcu
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health &Science University, 3181 Sam Jackson Park Road, Portland, Oregon 97239-3098, USA
| | - J Diep
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, California 94305, USA
| | - Y Ishikawa
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health &Science University, 3181 Sam Jackson Park Road, Portland, Oregon 97239-3098, USA.,Shriners Hospital for Children, 3101 Sam Jackson Park Road, Portland, Oregon 97239, USA
| | - L T Jae
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - J E Wosen
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, California 94305, USA
| | - C M Nagamine
- Department of Comparative Medicine, Stanford University School of Medicine, 287 Campus Drive, Stanford, California 94305, USA
| | - M S Chapman
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health &Science University, 3181 Sam Jackson Park Road, Portland, Oregon 97239-3098, USA
| | - J E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, California 94305, USA
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17
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Kanick SC, Davis SC, Zhao Y, Sheehan KL, Hasan T, Maytin EV, Pogue BW, Chapman MS. Pre-treatment protoporphyrin IX concentration in actinic keratosis lesions may be a predictive biomarker of response to aminolevulinic-acid based photodynamic therapy. Photodiagnosis Photodyn Ther 2015; 12:561-6. [PMID: 26480810 DOI: 10.1016/j.pdpdt.2015.10.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/14/2015] [Accepted: 10/12/2015] [Indexed: 01/23/2023]
Abstract
BACKGROUND Although aminolevulinic acid (ALA)-induced protoporphyrin IX (PpIX) photodynamic therapy (PDT) is an effective FDA-approved therapy for actinic keratosis (AK), a substantial fraction of patients (up to 25%) do not respond to treatment. This study examined the feasibility of using pre-treatment measurements of PpIX concentration in AK lesions to predict response of ALA-PpIX PDT. METHODS A non-invasive fiber-optic fluorescence spectroscopy system was used to measure PpIX concentration in patients undergoing standard-of-care ALA-PDT for AK. All patients provided assessments of pain at the time of treatment (n=70), and a subset reported pain and erythema 48-76 h after treatment (n=13). RESULTS PpIX concentration was significantly higher in lesions of patients reporting high levels of pain (VAS score ≥5) immediately after treatment vs. patients reporting pain scores below VAS=5 (p<0.022) (n=70). However, pain was not an exclusive indicator of PpIX concentration as many patients with low PpIX concentration reported high pain. In a subpopulation of patients surveyed in the days after treatment (n=13), PpIX concentration measured on the day of treatment was uncorrelated with pain-reported immediately after treatment (r=0.17, p<0.57), but positive correlations were found between PpIX concentration and patient-reported pain (r=0.55, p<0.051) and erythema (r=0.58, p<0.039) in the 48-72 h following treatment. CONCLUSIONS These data suggest that in vivo optical measurements of PpIX concentration acquired before light delivery may be an objective predictor of response to ALA-PpIX PDT. Identification of non-responding patients on the day of treatment could facilitate the use of interventions that may improve outcomes.
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Affiliation(s)
- S C Kanick
- Thayer School of Engineering, Dartmouth College, Hanover, USA; Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon NH, USA.
| | - S C Davis
- Thayer School of Engineering, Dartmouth College, Hanover, USA; Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon NH, USA
| | - Y Zhao
- Thayer School of Engineering, Dartmouth College, Hanover, USA
| | - K L Sheehan
- Department of Surgery, Dartmouth Hitchcock Medical Center, Lebanon, USA
| | - T Hasan
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, USA
| | - E V Maytin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, USA; Biomedical Engineering, Cleveland Clinic, Cleveland, USA
| | - B W Pogue
- Thayer School of Engineering, Dartmouth College, Hanover, USA; Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon NH, USA; Department of Surgery, Dartmouth Hitchcock Medical Center, Lebanon, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, USA
| | - M S Chapman
- Department of Surgery, Dartmouth Hitchcock Medical Center, Lebanon, USA
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18
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Spear JM, Noble AJ, Xie Q, Sousa DR, Chapman MS, Stagg SM. The influence of frame alignment with dose compensation on the quality of single particle reconstructions. J Struct Biol 2015; 192:196-203. [PMID: 26391007 DOI: 10.1016/j.jsb.2015.09.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 12/21/2022]
Abstract
As direct electron detection devices in cryo-electron microscopy become ubiquitous, the field is now ripe for new developments in image analysis techniques that take advantage of their increased SNR coupled with their high-throughput frame collection abilities. In approaching atomic resolution of native-like biomolecules, the accurate extraction of structural locations and orientations of side-chains from frames depends not only on the electron dose that a sample receives but also on the ability to accurately estimate the CTF. Here we use a new 2.8Å resolution structure of a recombinant gene therapy virus, AAV-DJ with Arixtra, imaged on an FEI Titan Krios with a DE-20 direct electron detector to probe new metrics including relative side-chain density and ResLog analysis for optimizing the compensation of electron beam damage and to characterize the factors that are limiting the resolution of the reconstruction. The influence of dose compensation on the accuracy of CTF estimation and particle classifiability are also presented. We show that rigorous dose compensation allows for better particle classifiability and greater recovery of structural information from negatively charged, electron-sensitive side-chains, resulting in a more accurate macromolecular model.
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Affiliation(s)
- John M Spear
- Institute of Molecular Biophysics, 91 Chieftan Way, Florida State University, Tallahassee, FL 32306-4380, United States
| | - Alex J Noble
- Department of Physics, 77 Chieftan Way, Florida State University, Tallahassee, FL 32306-4350, United States
| | - Qing Xie
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, United States
| | - Duncan R Sousa
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, United States
| | - Michael S Chapman
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, United States
| | - Scott M Stagg
- Institute of Molecular Biophysics, 91 Chieftan Way, Florida State University, Tallahassee, FL 32306-4380, United States; Departments of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306-4390, United States.
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19
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Chapman BK, Davulcu O, Skalicky JJ, Brüschweiler RP, Chapman MS. Parsimony in Protein Conformational Change. Structure 2015; 23:1190-8. [PMID: 26095029 DOI: 10.1016/j.str.2015.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/13/2015] [Accepted: 05/03/2015] [Indexed: 01/25/2023]
Abstract
Protein conformational change is analyzed by finding the minimalist backbone torsion angle rotations that superpose crystal structures within experimental error. Of several approaches for enforcing parsimony during flexible least-squares superposition, an ℓ(1)-norm restraint provided greatest consistency with independent indications of flexibility from nuclear magnetic resonance relaxation dispersion and chemical shift perturbation in arginine kinase and four previously studied systems. Crystallographic cross-validation shows that the dihedral parameterization describes conformational change more accurately than rigid-group approaches. The rotations that superpose the principal elements of structure constitute a small fraction of the raw (φ, ψ) differences that also reflect local conformation and experimental error. Substantial long-range displacements can be mediated by modest dihedral rotations, accommodated even within α helices and β sheets without disruption of hydrogen bonding at the hinges. Consistency between ligand-associated and intrinsic motions (in the unliganded state) implies that induced changes tend to follow low-barrier paths between conformational sub-states that are in intrinsic dynamic equilibrium.
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Affiliation(s)
- Brynmor K Chapman
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, School of Medicine L-224, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Omar Davulcu
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, School of Medicine L-224, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah, Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT 84112-5650, USA
| | - Rafael P Brüschweiler
- Department of Chemistry & Biochemistry, The Ohio State University, Newman and Wolfrom Laboratory, 100 West 18th Avenue, Columbus, OH 43210-1173, USA
| | - Michael S Chapman
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, School of Medicine L-224, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098, USA.
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20
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Davulcu O, Niu X, Brüschweiler-Li L, Brüschweiler R, Skalicky JJ, Chapman MS. Backbone resonance assignments of the 42 kDa enzyme arginine kinase in the transition state analogue form. Biomol NMR Assign 2014; 8:335-338. [PMID: 23893440 PMCID: PMC3906217 DOI: 10.1007/s12104-013-9512-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/21/2013] [Indexed: 06/02/2023]
Abstract
Nearly complete backbone resonance assignments for the 357 residue, 42 kDa enzyme arginine kinase in a transition state analogue (TSA) complex are presented. The TSA is a quaternary complex of arginine kinase, MgADP, arginine, and nitrate. About 93% (320 of 344) of the non-proline backbone amides were assigned using an enzyme enriched with (2)H, (13)C, and (15)N in combination with three enzyme samples prepared with a single (15)N-labeled amino acid (K, L, and R). The amide assignments will provide the foundation for investigating the dynamics of arginine kinase when in a TSA complex.
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Affiliation(s)
- Omar Davulcu
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, 97239-3098, USA
| | - Xiaogang Niu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
| | - Lei Brüschweiler-Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
| | - Jack J. Skalicky
- Department of Biochemistry, University of Utah, Salt Lake City, Utah, 84112-5650, USA
| | - Michael S. Chapman
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, 97239-3098, USA
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21
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Summerton JC, Martin GM, Evanseck JD, Chapman MS. Common hydrogen bond interactions in diverse phosphoryl transfer active sites. PLoS One 2014; 9:e108310. [PMID: 25238155 PMCID: PMC4169622 DOI: 10.1371/journal.pone.0108310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/27/2014] [Indexed: 11/18/2022] Open
Abstract
Phosphoryl transfer reactions figure prominently in energy metabolism, signaling, transport and motility. Prior detailed studies of selected systems have highlighted mechanistic features that distinguish different phosphoryl transfer enzymes. Here, a top-down approach is developed for comparing statistically the active site configurations between populations of diverse structures in the Protein Data Bank, and it reveals patterns of hydrogen bonding that transcend enzyme families. Through analysis of large samples of structures, insights are drawn at a level of detail exceeding the experimental precision of an individual structure. In phosphagen kinases, for example, hydrogen bonds with the O3β of the nucleotide substrate are revealed as analogous to those in unrelated G proteins. In G proteins and other enzymes, interactions with O3β have been understood in terms of electrostatic favoring of the transition state. Ground state quantum mechanical calculations on model compounds show that the active site interactions highlighted in our database analysis can affect substrate phosphate charge and bond length, in ways that are consistent with prior experimental observations, by modulating hyperconjugative orbital interactions that weaken the scissile bond. Testing experimentally the inference about the importance of O3β interactions in phosphagen kinases, mutation of arginine kinase Arg280 decreases kcat, as predicted, with little impact upon KM.
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Affiliation(s)
- Jean C. Summerton
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Gregory M. Martin
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Jeffrey D. Evanseck
- Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Michael S. Chapman
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
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22
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Boudko SP, Ishikawa Y, Nix J, Chapman MS, Bächinger HP. Structure of human peptidyl-prolyl cis-trans isomerase FKBP22 containing two EF-hand motifs. Protein Sci 2013; 23:67-75. [PMID: 24272907 DOI: 10.1002/pro.2391] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/23/2013] [Accepted: 10/24/2013] [Indexed: 11/09/2022]
Abstract
The FK506-binding protein (FKBP) family consists of proteins with a variety of protein-protein interaction domains and versatile cellular functions. It is assumed that all members are peptidyl-prolyl cis-trans isomerases with the enzymatic function attributed to the FKBP domain. Six members of this family localize to the mammalian endoplasmic reticulum (ER). Four of them, FKBP22 (encoded by the FKBP14 gene), FKBP23 (FKBP7), FKBP60 (FKBP9), and FKBP65 (FKBP10), are unique among all FKBPs as they contain the EF-hand motifs. Little is known about the biological roles of these proteins, but emerging genetics studies are attracting great interest to the ER resident FKBPs, as mutations in genes encoding FKBP10 and FKBP14 were shown to cause a variety of matrix disorders. Although the structural organization of the FKBP-type domain as well as of the EF-hand motif has been known for a while, it is difficult to conclude how these structures are combined and how it affects the protein functionality. We have determined a unique 1.9 Å resolution crystal structure for human FKBP22, which can serve as a prototype for other EF hand-containing FKBPs. The EF-hand motifs of two FKBP22 molecules form a dimeric complex with an elongated and predominantly hydrophobic cavity that can potentially be occupied by an aliphatic ligand. The FKBP-type domains are separated by a cleft and their putative active sites can catalyze isomerazation of two bonds within a polypeptide chain in extended conformation. These structural results are of prime interest for understanding biological functions of ER resident FKBPs containing EF-hand motifs.
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Affiliation(s)
- Sergei P Boudko
- Research Department, Shriners Hospital for Children, Portland, Oregon, 97239; Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, 97239
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23
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Xie Q, Spilman M, Meyer NL, Lerch TF, Stagg SM, Chapman MS. Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of adeno-associated virus. J Struct Biol 2013; 184:129-35. [PMID: 24036405 DOI: 10.1016/j.jsb.2013.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/02/2013] [Accepted: 09/04/2013] [Indexed: 12/19/2022]
Abstract
Mechanistic studies of macromolecular complexes often feature X-ray structures of complexes with bound ligands. The attachment of adeno-associated virus (AAV) to cell surface glycosaminoglycans (GAGs) is an example that has not proven amenable to crystallography, because the binding of GAG analogs disrupts lattice contacts. The interactions of AAV with GAGs are of interest in mediating the cell specificity of AAV-based gene therapy vectors. Previous electron microscopy led to differing conclusions on the exact binding site and the existence of large ligand-induced conformational changes in the virus. Conformational changes are expected during cell entry, but it has remained unclear whether the electron microscopy provided evidence of their induction by GAG-binding. Taking advantage of automated data collection, careful processing and new methods of structure refinement, the structure of AAV-DJ complexed with sucrose octasulfate is determined by electron microscopy difference map analysis to 4.8Å resolution. At this higher resolution, individual sulfate groups are discernible, providing a stereochemical validation of map interpretation, and highlighting interactions with two surface arginines that have been implicated in genetic studies. Conformational changes induced by the SOS are modest and limited to the loop most directly interacting with the ligand. While the resolution attainable will depend on sample order and other factors, there are an increasing number of macromolecular complexes that can be studied by cryo-electron microscopy at resolutions beyond 5Å, for which the approaches used here could be used to characterize the binding of inhibitors and other small molecule effectors when crystallography is not tractable.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health &v Science University, Portland, OR 97239-3098, USA
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24
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Zhang F, Aguilera J, Beaudet JM, Xie Q, Lerch TF, Davulcu O, Colón W, Chapman MS, Linhardt RJ. Characterization of interactions between heparin/glycosaminoglycan and adeno-associated virus. Biochemistry 2013; 52:6275-85. [PMID: 23952613 PMCID: PMC3859860 DOI: 10.1021/bi4008676] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Adeno-associated virus (AAV) is a key candidate in the development of gene therapy. In this work, we used surface plasmon resonance spectroscopy to study the interaction between AAV and heparin and other glycosaminoglycans (GAGs). Surface plasmon resonance results revealed that heparin binds to AAV with an extremely high affinity. Solution competition studies showed that binding of AAV to heparin is chain length-dependent. AAV prefers to bind full chain heparin. All sulfo groups (especially N-sulfo and 6-O-sulfo groups) on heparin are important for the AAV-heparin interaction. Higher levels of sulfo group substitution in GAGs enhance their binding affinities. Atomic force microscopy was also performed to image AAV-2 in a complex with heparin.
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Affiliation(s)
- Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Javier Aguilera
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Julie M. Beaudet
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Qing Xie
- Department of Biochemistry and Molecular Biology School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Thomas F. Lerch
- Department of Biochemistry and Molecular Biology School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Omar Davulcu
- Department of Biochemistry and Molecular Biology School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Wilfredo Colón
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Michael S. Chapman
- Department of Biochemistry and Molecular Biology School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Robert J. Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- Departments of Biology and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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25
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Hoang TM, Gerving CS, Land BJ, Anquez M, Hamley CD, Chapman MS. Dynamic stabilization of a quantum many-body spin system. Phys Rev Lett 2013; 111:090403. [PMID: 24033006 DOI: 10.1103/physrevlett.111.090403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Indexed: 06/02/2023]
Abstract
We demonstrate dynamic stabilization of a strongly interacting quantum spin system realized in a spin-1 atomic Bose-Einstein condensate. The spinor Bose-Einstein condensate is initialized to an unstable fixed point of the spin-nematic phase space, where subsequent free evolution gives rise to squeezing and quantum spin mixing. To stabilize the system, periodic microwave pulses are applied that rotate the spin-nematic many-body fluctuations and limit their growth. The stability diagram for the range of pulse periods and phase shifts that stabilize the dynamics is measured and compares well with a stability analysis.
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Affiliation(s)
- T M Hoang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332-0430, USA
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26
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Boudko SP, Ishikawa Y, Lerch TF, Nix J, Chapman MS, Bächinger HP. Crystal structures of wild-type and mutated cyclophilin B that causes hyperelastosis cutis in the American quarter horse. BMC Res Notes 2012; 5:626. [PMID: 23137129 PMCID: PMC3522003 DOI: 10.1186/1756-0500-5-626] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 11/01/2012] [Indexed: 11/30/2022] Open
Abstract
Background Hyperelastosis cutis is an inherited autosomal recessive connective tissue disorder. Affected horses are characterized by hyperextensible skin, scarring, and severe lesions along the back. The disorder is caused by a mutation in cyclophilin B. Results The crystal structures of both wild-type and mutated (Gly6->Arg) horse cyclophilin B are presented. The mutation neither affects the overall fold of the enzyme nor impairs the catalytic site structure. Instead, it locally rearranges the flexible N-terminal end of the polypeptide chain and also makes it more rigid. Conclusions Interactions of the mutated cyclophilin B with a set of endoplasmic reticulum-resident proteins must be affected.
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Affiliation(s)
- Sergei P Boudko
- Research Department, Shriners Hospital for Children, Portland, OR 97239, USA
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27
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Abstract
Density functional theory and natural bond orbital analysis are used to explore the impact of solvent on hyperconjugation in methyl triphosphate, a model for "energy rich" phosphoanhydride bonds, such as found in ATP. As expected, dihedral rotation of a hydroxyl group vicinal to the phosphoanhydride bond reveals that the conformational dependence of the anomeric effect involves modulation of the orbital overlap between the donor and acceptor orbitals. However, a conformational independence was observed in the rotation of a solvent hydrogen bond. As one lone pair orbital rotates away from an optimal antiperiplanar orientation, the overall magnitude of the anomeric effect is compensated approximately by the other lone pair as it becomes more antiperiplanar. Furthermore, solvent modulation of the anomeric effect is not restricted to the antiperiplanar lone pair; hydrogen bonds involving gauche lone pairs also affect the anomeric interaction and the strength of the phosphoanhydride bond. Both gauche and anti solvent hydrogen bonds lengthen nonbridging O-P bonds, increasing the distance between donor and acceptor orbitals and decreasing orbital overlap, which leads to a reduction of the anomeric effect. Solvent effects are additive with greater reduction in the anomeric effect upon increasing water coordination. By controlling the coordination environment of substrates in an active site, kinases, phosphatases, and other enzymes important in metabolism and signaling may have the potential to modulate the stability of individual phosphoanhydride bonds through stereoelectronic effects.
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Affiliation(s)
- Jean C Summerton
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Mail Code L224, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, USA
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Clark SA, Davulcu O, Chapman MS. Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs. Biochem Biophys Res Commun 2012; 427:212-7. [PMID: 22995310 DOI: 10.1016/j.bbrc.2012.09.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 09/09/2012] [Indexed: 11/29/2022]
Abstract
Arginine kinase catalyzes the reversible transfer of a phosphoryl group between ATP and l-arginine and is a monomeric homolog of the human enzyme creatine kinase. Arginine and creatine kinases belongs to the phosphagen kinase family of enzymes, which consists of eight known members, each of which is specific for its own phosphagen. Here, the source of phosphagen specificity in arginine kinase is investigated through the use of phosphagen analogs. Crystal structures have been determined for Limulus polyphemus arginine kinase with one of four arginine analogs bound in a transition state analog complex: l-ornithine, l-citrulline, imino-l-ornithine, and d-arginine. In all complexes, the enzyme achieves a closed conformation very similar to that of the cognate transition state analog complex, but differences are observed in the configurations of bound ligands. Arginine kinase exhibits no detectable activity towards ornithine, citrulline, or imino-l-ornithine, and only trace activity towards d-arginine. The crystal structures presented here demonstrate that phosphagen specificity is derived neither from a lock-and-key mechanism nor a modulation of induced-fit conformational changes, but potentially from subtle distortions in bound substrate configurations.
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Affiliation(s)
- Shawn A Clark
- Institute of Molecular Biophysics, Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306-4380, USA
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29
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Lerch TF, O’Donnell JK, Meyer NL, Xie Q, Taylor KA, Stagg SM, Chapman MS. Structure of AAV-DJ, a retargeted gene therapy vector: cryo-electron microscopy at 4.5 Å resolution. Structure 2012; 20:1310-20. [PMID: 22727812 PMCID: PMC3418430 DOI: 10.1016/j.str.2012.05.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/10/2012] [Accepted: 05/11/2012] [Indexed: 12/19/2022]
Abstract
AAV-DJ, a leading candidate vector for liver gene therapy, was created through random homologous recombination followed by directed evolution, selecting for in vivo liver tropism and resistance to in vitro immune neutralization. Here, the 4.5 Å resolution cryo-EM structure is determined for the engineered AAV vector, revealing structural features that illuminate its phenotype. The heparan sulfate receptor-binding site is little changed from AAV-2, and heparin-binding affinity is similar. A loop that is antigenic in other serotypes has a unique conformation in AAV-DJ that would conflict with the binding of an AAV-2 neutralizing monoclonal antibody. This is consistent with increased resistance to neutralization by human polyclonal sera, raising the possibility that changed tropism may be a secondary effect of altered immune interactions. The reconstruction exemplifies analysis of fine structural changes and the potential of cryo-EM, in favorable cases, to characterize mutant or ligand-bound complexes.
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Affiliation(s)
- Thomas F. Lerch
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jason K. O’Donnell
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Nancy L. Meyer
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Qing Xie
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kenneth A. Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Scott M. Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Michael S. Chapman
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
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30
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Lerch TF, Chapman MS. Identification of the heparin binding site on adeno-associated virus serotype 3B (AAV-3B). Virology 2011; 423:6-13. [PMID: 22169623 DOI: 10.1016/j.virol.2011.10.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/27/2011] [Accepted: 10/10/2011] [Indexed: 12/12/2022]
Abstract
Adeno-associated virus is a promising vector for gene therapy. In the current study, the binding site on AAV serotype 3B for the heparan sulfate proteoglycan (HSPG) receptor has been characterized. X-ray diffraction identified a disaccharide binding site at the most positively charged region on the virus surface. The contributions of basic amino acids at this and other sites were characterized using site-directed mutagenesis. Both heparin and cell binding are correlated to positive charge at the disaccharide binding site, and transduction is significantly decreased in AAV-3B vectors mutated at this site to reduce heparin binding. While the receptor attachment sites of AAV-3B and AAV-2 are both in the general vicinity of the viral spikes, the exact amino acids that participate in electrostatic interactions are distinct. Diversity in the mechanisms of cell attachment by AAV serotypes will be an important consideration for the rational design of improved gene therapy vectors.
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Affiliation(s)
- Thomas F Lerch
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA
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31
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Abstract
We have observed sub-Poissonian spin correlations generated by collisionally induced spin mixing in a spin-1 Bose-Einstein condensate. We measure a quantum noise reduction of -7 dB (-10 dB corrected for detection noise) below the standard quantum limit for the corresponding coherent spin states. The spin fluctuations are detected as atom number differences in the spin states using fluorescent imaging that achieves a detection noise floor of 8 atoms per spin component for a probe time of 100 μs.
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Affiliation(s)
- Eva M Bookjans
- School of Physics, Georgia Institute of Technology, Atlanta, 30332-0430, USA
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32
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Xie Q, Lerch TF, Meyer NL, Chapman MS. Structure-function analysis of receptor-binding in adeno-associated virus serotype 6 (AAV-6). Virology 2011; 420:10-9. [PMID: 21917284 PMCID: PMC3185213 DOI: 10.1016/j.virol.2011.08.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Revised: 07/04/2011] [Accepted: 08/18/2011] [Indexed: 01/22/2023]
Abstract
Crystal structures of the AAV-6 capsid at 3Å reveal a subunit fold homologous to other parvoviruses with greatest differences in two external loops. The electrostatic potential suggests that receptor-attachment is mediated by four residues: Arg(576), Lys(493), Lys(459) and Lys(531), defining a positively charged region curving up from the valley between adjacent spikes. It overlaps only partially with the receptor-binding site of AAV-2, and the residues endowing the electrostatic character are not homologous. Mutational substitution of each residue decreases heparin affinity, particularly Lys(531) and Lys(459). Neither is conserved among heparin-binding serotypes, indicating that diverse modes of receptor attachment have been selected in different serotypes. Surface topology and charge are also distinct at the shoulder of the spike, where linear epitopes for AAV-2's neutralizing monoclonal antibody A20 come together. Evolutionarily, selection of changed side-chain charge may have offered a conservative means to evade immune neutralization while preserving other essential functionality.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098
| | - Thomas F. Lerch
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098
| | - Nancy L. Meyer
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098
| | - Michael S. Chapman
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098
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Abstract
Arginine kinase catalyzes the reversible transfer of a phosphoryl group between ATP and arginine. It is the arthropod homologue of creatine kinase, buffering cellular ATP levels. Crystal structures of arginine kinase, in substrate-free and substrate-bound forms, have revealed large conformational changes associated with the catalytic cycle. Recent nuclear magnetic resonance identified movements of the N-terminal domain and a loop comprising residues I182--G209 with conformational exchange rates in the substrate-free enzyme similar to the turnover rate. Here, to understand whether these motions might be rate-limiting, we determined activation barriers for both the intrinsic dynamics and enzyme turnover using measurements over a temperature range of 15-30 °C. (15)N transverse relaxation dispersion yields activation barriers of 46 ± 8 and 34 ± 12 kJ/mol for the N-terminal domain and I182--G209 loop, respectively. An activation barrier of 34 ± 13 kJ/mol was obtained for enzyme turnover from steady-state kinetics. The similarity between the activation barriers is indeed consistent with turnover being limited by backbone conformational dynamics and pinpoints the locations of potentially rate-limiting motions.
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Affiliation(s)
- Omar Davulcu
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098, United States
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34
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Gibbons MJ, Hamley CD, Shih CY, Chapman MS. Nondestructive fluorescent state detection of single neutral atom qubits. Phys Rev Lett 2011; 106:133002. [PMID: 21517379 DOI: 10.1103/physrevlett.106.133002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Indexed: 05/30/2023]
Abstract
We demonstrate nondestructive (lossless) fluorescent state detection of individual neutral atom qubits trapped in an optical lattice. The hyperfine state of the atom is measured with a 95% accuracy and an atom loss rate of 1%. Individual atoms are initialized and detected over 100 times before being lost from the trap, representing a 100-fold improvement in data collection rates over previous experiments. Microwave Rabi oscillations are observed with repeated measurements of one and the same single atom.
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Affiliation(s)
- Michael J Gibbons
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332-0430, USA
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35
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Bush DJ, Kirillova O, Clark SA, Davulcu O, Fabiola F, Xie Q, Somasundaram T, Ellington WR, Chapman MS. The structure of lombricine kinase: implications for phosphagen kinase conformational changes. J Biol Chem 2011; 286:9338-50. [PMID: 21212263 DOI: 10.1074/jbc.m110.202796] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His(178). Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.
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Affiliation(s)
- D Jeffrey Bush
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
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36
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Wirz JA, Boudko SP, Lerch TF, Chapman MS, Bächinger HP. Crystal structure of the human collagen XV trimerization domain: a potent trimerizing unit common to multiplexin collagens. Matrix Biol 2011; 30:9-15. [PMID: 20932905 PMCID: PMC3048825 DOI: 10.1016/j.matbio.2010.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 09/25/2010] [Accepted: 09/29/2010] [Indexed: 12/01/2022]
Abstract
Correct folding of the collagen triple helix requires a self-association step which selects and binds α-chains into trimers. Here we report the crystal structure of the trimerization domain of human type XV collagen. The trimerization domain of type XV collagen contains three monomers each composed of four β-sheets and an α-helix. The hydrophobic core of the trimer is devoid of solvent molecules and is shaped by β-sheet planes from each monomer. The trimerization domain is extremely stable and forms at picomolar concentrations. It is found that the trimerization domain of type XV collagen is structurally similar to that of type XVIII, despite only 32% sequence identity. High structural conservation indicates that the multiplexin trimerization domain represents a three dimensional fold that allows for sequence variability while retaining structural integrity necessary for tight and efficient trimerization.
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Affiliation(s)
- Jacqueline A. Wirz
- Research Department of Shriners Hospital for Children, 3101 SW Sam Jackson Pk. Rd., Portland, OR 97239, USA
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3191 SW Sam Jackson Pk. Rd., Portland, OR 97239, USA
| | - Sergei P. Boudko
- Research Department of Shriners Hospital for Children, 3101 SW Sam Jackson Pk. Rd., Portland, OR 97239, USA
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3191 SW Sam Jackson Pk. Rd., Portland, OR 97239, USA
| | - Thomas F. Lerch
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3191 SW Sam Jackson Pk. Rd., Portland, OR 97239, USA
| | - Michael S. Chapman
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3191 SW Sam Jackson Pk. Rd., Portland, OR 97239, USA
| | - Hans Peter Bächinger
- Research Department of Shriners Hospital for Children, 3101 SW Sam Jackson Pk. Rd., Portland, OR 97239, USA
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3191 SW Sam Jackson Pk. Rd., Portland, OR 97239, USA
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37
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Niu X, Bruschweiler-Li L, Davulcu O, Skalicky JJ, Brüschweiler R, Chapman MS. Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility. J Mol Biol 2010; 405:479-96. [PMID: 21075117 DOI: 10.1016/j.jmb.2010.11.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 09/21/2010] [Accepted: 11/01/2010] [Indexed: 11/15/2022]
Abstract
The phosphagen kinase family, including creatine and arginine kinases (AKs), catalyzes the reversible transfer of a "high-energy" phosphate between ATP and a phosphoguanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of AK structures were interpreted as a plastic deformation. Here, the structure of Limulus substrate-free AK is refined against high-resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa) and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.7 Å transition-state analog complex shows large substrate-induced domain motions that can be broken down into movements of smaller quasi-rigid bodies. The solution-state structure of substrate-free AK is most consistent with an equilibrium of substrate-free and substrate-bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, "substrate-induced" motions are along modes that are intrinsically flexible in the substrate-free enzyme and likely involve some degree of conformational selection.
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Affiliation(s)
- Xiaogang Niu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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38
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Whittaker MM, Lerch TF, Kirillova O, Chapman MS, Whittaker JW. Subunit dissociation and metal binding by Escherichia coli apo-manganese superoxide dismutase. Arch Biochem Biophys 2010; 505:213-25. [PMID: 21044611 DOI: 10.1016/j.abb.2010.10.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 10/24/2010] [Accepted: 10/26/2010] [Indexed: 10/18/2022]
Abstract
Metal binding by apo-manganese superoxide dismutase (apo-MnSOD) is essential for functional maturation of the enzyme. Previous studies have demonstrated that metal binding by apo-MnSOD is conformationally gated, requiring protein reorganization for the metal to bind. We have now solved the X-ray crystal structure of apo-MnSOD at 1.9Å resolution. The organization of active site residues is independent of the presence of the metal cofactor, demonstrating that protein itself templates the unusual metal coordination geometry. Electrophoretic analysis of mixtures of apo- and (Mn₂)-MnSOD, dye-conjugated protein, or C-terminal Strep-tag II fusion protein reveals a dynamic subunit exchange process associated with cooperative metal binding by the two subunits of the dimeric protein. In contrast, (S126C) (SS) apo-MnSOD, which contains an inter-subunit covalent disulfide-crosslink, exhibits anti-cooperative metal binding. The protein concentration dependence of metal uptake kinetics implies that protein dissociation is involved in metal binding by the wild type apo-protein, although other processes may also contribute to gating metal uptake. Protein concentration dependent small-zone size exclusion chromatography is consistent with apo-MnSOD dimer dissociation at low protein concentration (K(D)=1×10⁻⁵ M). Studies on metal uptake by apo-MnSOD in Escherichia coli cells show that the protein exhibits similar behavior in vivo and in vitro.
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Affiliation(s)
- Mei M Whittaker
- Institute for Environmental Health, Oregon Health and Science University, Beaverton, 97006-8921, USA
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39
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Mitchell DAJ, Lerch TF, Hare JT, Chapman MS. A pseudo-plaque method for infectious particle assay and clonal isolation of adeno-associated virus. J Virol Methods 2010; 170:9-15. [PMID: 20708035 DOI: 10.1016/j.jviromet.2010.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Revised: 08/02/2010] [Accepted: 08/03/2010] [Indexed: 11/16/2022]
Abstract
A colorimetric method has been developed for the detection of adeno-associated virus (AAV) infectious centers in cell culture monolayers. Due to its non-cytopathic nature, AAV has not been amenable to the traditional plaque assay, involving an agar overlay and cellular stains. As a result, an alternate method was required. The pseudo-plaque assay is based on enzyme-catalyzed color development after a fixed cell monolayer is probed with anti-AAV monoclonal antibodies. In spite of chemical fixation, expected to damage the viral genomes and particles, infectious particles can be recovered and amplified for the propagation of viral clones.
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Affiliation(s)
- Daniel A J Mitchell
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA
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40
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Chapman MS, Somasundaram T. De-icing: recovery of diffraction intensities in the presence of ice rings. Acta Crystallogr D Biol Crystallogr 2010; 66:741-4. [PMID: 20516627 PMCID: PMC2879358 DOI: 10.1107/s0907444910012436] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 04/02/2010] [Indexed: 11/10/2022]
Abstract
Macromolecular structures are routinely determined at cryotemperatures using samples flash-cooled in the presence of cryoprotectants. However, sometimes the best diffraction is obtained under conditions where ice formation is not completely ablated, with the result that characteristic ice rings are superimposed on the macromolecular diffraction. In data processing, the reflections that are most affected by the ice rings are usually excluded. Here, an alternative approach of subtracting the ice diffraction is tested. High completeness can be retained with little adverse effect upon the quality of the integrated data. This offers an alternate strategy when high levels of cryoprotectant lead to loss of crystal quality.
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Affiliation(s)
- Michael S Chapman
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR 97239-3098, USA.
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41
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Lerch TF, Xie Q, Chapman MS. The structure of adeno-associated virus serotype 3B (AAV-3B): insights into receptor binding and immune evasion. Virology 2010; 403:26-36. [PMID: 20444480 DOI: 10.1016/j.virol.2010.03.027] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 03/03/2010] [Accepted: 03/17/2010] [Indexed: 12/19/2022]
Abstract
Adeno-associated viruses (AAVs) are leading candidate vectors for human gene therapy. AAV serotypes have broad cellular tropism and use a variety of cellular receptors. AAV serotype 3 binds to heparan sulfate proteoglycan prior to cell entry and is serologically distinct from other serotypes. The capsid features that distinguish AAV-3B from other serotypes are poorly understood. The structure of AAV-3B has been determined to 2.6A resolution from twinned crystals of an infectious virus. The most distinctive structural features are located in regions implicated in receptor and antibody binding, providing insights into the cell entry mechanisms and antigenic nature of AAVs. We show that AAV-3B has a lower affinity for heparin than AAV-2, which can be rationalized by the distinct features of the AAV-3B capsid. The structure of AAV-3B provides an additional foundation for the future engineering of improved gene therapy vectors with modified receptor binding or antigenic characteristics.
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Affiliation(s)
- Thomas F Lerch
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA
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42
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Boudko SP, Sasaki T, Engel J, Lerch TF, Nix J, Chapman MS, Bächinger HP. Crystal structure of human collagen XVIII trimerization domain: A novel collagen trimerization Fold. J Mol Biol 2009; 392:787-802. [PMID: 19631658 DOI: 10.1016/j.jmb.2009.07.057] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 07/17/2009] [Accepted: 07/18/2009] [Indexed: 11/15/2022]
Abstract
Collagens contain a unique triple-helical structure with a repeating sequence -G-X-Y-, where proline and hydroxyproline are major constituents in X and Y positions, respectively. Folding of the collagen triple helix requires trimerization domains. Once trimerized, collagen chains are correctly aligned and the folding of the triple helix proceeds in a zipper-like fashion. Here we report the isolation, characterization, and crystal structure of the trimerization domain of human type XVIII collagen, a member of the multiplexin family. This domain differs from all other known trimerization domains in other collagens and exhibits a high trimerization potential at picomolar concentrations. Strong chain association and high specificity of binding are needed for multiplexins, which are present at very low levels.
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Affiliation(s)
- Sergei P Boudko
- Research Department of Shriners Hospital for Children, Portland, OR 97239, USA
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43
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Campbell CJ, Steele AV, Churchill LR, Depalatis MV, Naylor DE, Matsukevich DN, Kuzmich A, Chapman MS. Multiply charged thorium crystals for nuclear laser spectroscopy. Phys Rev Lett 2009; 102:233004. [PMID: 19658933 DOI: 10.1103/physrevlett.102.233004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Indexed: 05/28/2023]
Abstract
We have produced laser-cooled crystals of 232Th3+ in a linear rf Paul trap. This is the first time that a multiply charged ion has been laser cooled. Our work opens an avenue for excitation of the nuclear transition in a trapped, cold 229Th3+ ion. Laser excitation of nuclear states would establish a new bridge between atomic and nuclear physics, with the promise of new levels of metrological precision.
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Affiliation(s)
- C J Campbell
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430, USA
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44
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Lerch TF, Xie Q, Ongley HM, Hare J, Chapman MS. Twinned crystals of adeno-associated virus serotype 3b prove suitable for structural studies. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:177-83. [PMID: 19194015 PMCID: PMC2635862 DOI: 10.1107/s1744309109000372] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 01/05/2009] [Indexed: 11/10/2022]
Abstract
Adeno-associated viruses (AAVs) are leading candidate vectors for gene-therapy applications. The AAV-3b capsid is closely related to the well characterized AAV-2 capsid (87% identity), but sequence and presumably structural differences lead to distinct cell-entry and immune-recognition properties. In an effort to understand these differences and to perhaps harness them, diffraction-quality crystals of purified infectious AAV-3b particles have been grown and several partial diffraction data sets have been recorded. The crystals displayed varying levels of merohedral twinning that in earlier times would have rendered them unsuitable for structure determination, but here is shown to be a tractable complication.
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Affiliation(s)
- Thomas F. Lerch
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Qing Xie
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Heather M. Ongley
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4381, USA
| | - Joan Hare
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4381, USA
| | - Michael S. Chapman
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR 97239-3098, USA
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Xie Q, Ongley HM, Hare J, Chapman MS. Crystallization and preliminary X-ray structural studies of adeno-associated virus serotype 6. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:1074-8. [PMID: 18997346 PMCID: PMC2581704 DOI: 10.1107/s1744309108033290] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 10/14/2008] [Indexed: 04/25/2023]
Abstract
Adeno-associated viruses are being developed as vectors for gene therapy and have been used in a number of clinical trials. Vectors to date have been based on the type species AAV-2, the structure of which was published in 2002. There is growing interest in modulating the cellular tropism and immune neutralization of AAV-2 with variants inspired by the properties of other serotypes. Towards the determination of a structure for AAV type 6, this paper reports the high-yield production, purification, crystallization and preliminary diffraction studies of infectious AAV-6 virions. The crystals diffracted to 3.2 A resolution using synchrotron radiation. The most promising crystal form belonged to space group R3 and appeared to be suitable for initial structure determination.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Heather M. Ongley
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4381, USA
| | - Joan Hare
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4381, USA
| | - Michael S. Chapman
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR 97239-3098, USA
- Correspondence e-mail:
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Ruben EA, Plumley JA, Chapman MS, Evanseck JD. Anomeric Effect in “High Energy” Phosphate Bonds. Selective Destabilization of the Scissile Bond and Modulation of the Exothermicity of Hydrolysis. J Am Chem Soc 2008; 130:3349-58. [DOI: 10.1021/ja073652x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eliza A. Ruben
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, Department of Biochemistry & Molecular Biology, School of MedicineMail Code L224, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, and Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282
| | - Joshua A. Plumley
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, Department of Biochemistry & Molecular Biology, School of MedicineMail Code L224, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, and Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282
| | - Michael S. Chapman
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, Department of Biochemistry & Molecular Biology, School of MedicineMail Code L224, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, and Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282
| | - Jeffrey D. Evanseck
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, Department of Biochemistry & Molecular Biology, School of MedicineMail Code L224, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, and Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282
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Ruben EA, Chapman MS, Evanseck JD. Hydrogen bonding mediated by key orbital interactions determines hydration enthalpy differences of phosphate water clusters. J Phys Chem A 2007; 111:10804-14. [PMID: 17915844 DOI: 10.1021/jp0748112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electronic structure calculations have been carried out to provide a molecular interpretation for dihydrogen phosphate stability in water relative to that of metaphosphate. Specifically, hydration enthalpies of biologically important metaphosphate and dihydrogen phosphate with one to three waters have been computed with second-order Møller-Plesset perturbation and density functional theory (B3LYP) with up to the aug-cc-pvtz basis set and compared to experiment. The inclusion of basis set superposition error corrections and supplemental diffuse functions are necessary to predict hydration enthalpies within experimental uncertainty. Natural bond orbital analysis is used to rationalize underlying hydrogen bond configurations and key orbital interactions responsible for the experimentally reported difference in hydration enthalpies between metaphosphate and dihydrogen phosphate. In general, dihydrogen phosphate forms stronger hydrogen bonds compared to metaphosphate due to a greater charge transfer or enhanced orbital overlap between the phosphoryl oxygen lone pairs, n(O), and the antibonding O-H bond of water. Intramolecular distal lone pair repulsion with the donor n(O) orbital of dihydrogen phosphate distorts symmetric conformations, which improves n(O) and sigma*(O-H) overlap and ultimately the hydrogen bond strength. Unlike metaphosphate, water complexed to dihydrogen phosphate can serve as both a hydrogen bond donor and a hydrogen bond acceptor, which results in cooperative charge transfer and a reduction of the energy gap between n(O) and sigma*(O-H), leading to stronger hydrogen bonds. This study offers insight into how orbital interactions mediate hydrogen bond strengths with potential implications on the understanding of the kinetics and mechanism in enzymatic phosphoryl transfer reactions.
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Affiliation(s)
- Eliza A Ruben
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
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Fortier KM, Kim SY, Gibbons MJ, Ahmadi P, Chapman MS. Deterministic loading of individual atoms to a high-finesse optical cavity. Phys Rev Lett 2007; 98:233601. [PMID: 17677905 DOI: 10.1103/physrevlett.98.233601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Indexed: 05/16/2023]
Abstract
Individual laser-cooled atoms are delivered on demand from a single atom magneto-optic trap to a high-finesse optical cavity using an atom conveyor. Strong coupling of the atom with the cavity field allows simultaneous cooling and detection of individual atoms for time scales exceeding 15 s. The single atom scatter rate is studied as a function of probe-cavity detuning and probe Rabi frequency, and the experimental results are in qualitative agreement with theoretical predictions. We demonstrate the ability to manipulate the position of a single atom relative to the cavity mode with excellent control and reproducibility.
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Affiliation(s)
- Kevin M Fortier
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332-0430, USA
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Chapman MS. Normalizing Normal Mode Analysis. Structure 2007; 15:135-6. [PMID: 17292830 DOI: 10.1016/j.str.2007.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Asbury T, Quine JR, Achuthan S, Hu J, Chapman MS, Cross TA, Bertram R. PIPATH: an optimized algorithm for generating alpha-helical structures from PISEMA data. J Magn Reson 2006; 183:87-95. [PMID: 16914335 DOI: 10.1016/j.jmr.2006.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 07/25/2006] [Accepted: 07/27/2006] [Indexed: 05/11/2023]
Abstract
An optimized algorithm for finding structures and assignments of solid-state NMR PISEMA data obtained from alpha-helical membrane proteins is presented. The description of this algorithm, PIPATH, is followed by an analysis of its performance on simulated PISEMA data derived from synthetic and experimental structures. pipath transforms the assignment problem into a path-finding problem for a directed graph, and then uses techniques of graph theory to efficiently find candidate assignments from a very large set of possibilities.
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Affiliation(s)
- T Asbury
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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