1
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Marie Haynes R, Myers J, López CS, Evans J, Davulcu O, Yoshioka C. A strategic approach for efficient cryo-EM grid optimization using design of experiments. J Struct Biol 2024:108068. [PMID: 38364988 DOI: 10.1016/j.jsb.2024.108068] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has become a practical and effective method of determining structures at previously unattainable resolutions due to advances in detection, automation, and data processing. However, sample preparation remains a major bottleneck in the cryo-EM workflow. Even after the arduous process of biochemical sample optimization, it often takes several iterations of grid vitrification and screening to determine the optimal grid freezing parameters that yield suitable ice thickness and particle distribution for data collection. Since a high-quality sample is imperative for high-resolution structure determination, grid optimization is a vital step. For researchers who rely on cryo-EM facilities for grid screening, each iteration of this optimization process may delay research progress by a matter of months. Therefore, a more strategic and efficient approach should be taken to ensure that the grid optimization process can be completed in as few iterations as possible. Here, we present an implementation of Design of Experiments (DOE) to expedite and strategize the grid optimization process. A Fractional Factorial Design (FFD) guides the determination of a limited set of experimental conditions which can model the full parameter space of interest. Grids are frozen with these conditions and screened for particle distribution and ice thickness. Quantitative scores are assigned to each of these grid characteristics based on a qualitative rubric. Input conditions and response scores are used to generate a least-squares regression model of the parameter space in JMP, which is used to determine the conditions which should, in theory, yield optimal grids. Upon testing this approach on apoferritin and L-glutamate dehydrogenase on both the Vitrobot Mark IV and the Leica GP2 plunge freezers, the resulting grid conditions reliably yielded grids with high-quality ice and particle distribution that were suitable for collecting large overnight datasets on a Krios. We conclude that a DOE-based approach is a cost-effective and time-saving tool for cryo-EM grid preparation.
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Affiliation(s)
- Rose Marie Haynes
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA; Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Janette Myers
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA
| | - Claudia S López
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA
| | - James Evans
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Omar Davulcu
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA
| | - Craig Yoshioka
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA
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2
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Childers KC, Avery NG, Estrada Alamo KA, Davulcu O, Haynes RM, Lollar P, Doering CB, Coxon CH, Spiegel PC. Structure of coagulation factor VIII bound to a patient-derived anti-C1 domain antibody inhibitor. Blood 2023; 142:197-201. [PMID: 37192299 PMCID: PMC10352601 DOI: 10.1182/blood.2023020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/21/2023] [Revised: 04/07/2023] [Accepted: 04/25/2023] [Indexed: 05/18/2023] Open
Abstract
The development of pathogenic antibody inhibitors against coagulation factor VIII (FVIII) occurs in ∼30% of patients with congenital hemophilia A receiving FVIII replacement therapy, as well as in all cases of acquired hemophilia A. KM33 is an anti-C1 domain antibody inhibitor previously isolated from a patient with severe hemophilia A. In addition to potently blocking FVIII binding to von Willebrand factor and phospholipid surfaces, KM33 disrupts FVIII binding to lipoprotein receptor-related protein 1 (LRP1), which drives FVIII hepatic clearance and antigen presentation in dendritic cells. Here, we report on the structure of FVIII bound to NB33, a recombinant derivative of KM33, via single-particle cryo-electron microscopy. Structural analysis revealed that the NB33 epitope localizes to the FVIII residues R2090-S2094 and I2158-R2159, which constitute membrane-binding loops in the C1 domain. Further analysis revealed that multiple FVIII lysine and arginine residues, previously shown to mediate binding to LRP1, dock onto an acidic cleft at the NB33 variable domain interface, thus blocking a putative LRP1 binding site. Together, these results demonstrate a novel mechanism of FVIII inhibition by a patient-derived antibody inhibitor and provide structural evidence for engineering FVIII with reduced LRP1-mediated clearance.
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Affiliation(s)
| | - Nathan G. Avery
- Chemistry Department, Western Washington University, Bellingham, WA
| | | | - Omar Davulcu
- Pacific Northwest Center for Cryo-EM, Oregon Health & Science University, Portland, OR
- Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richland, WA
| | - Rose Marie Haynes
- Pacific Northwest Center for Cryo-EM, Oregon Health & Science University, Portland, OR
- Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richland, WA
| | - Pete Lollar
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University, Atlanta, GA
| | - Christopher B. Doering
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University, Atlanta, GA
- Expression Therapeutics Inc, Tucker, GA
| | - Carmen H. Coxon
- National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom
| | - P. Clint Spiegel
- Chemistry Department, Western Washington University, Bellingham, WA
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3
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Abstract
![]()
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 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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5
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Meyer NL, Hu G, Davulcu O, Xie Q, Noble AJ, Yoshioka C, Gingerich DS, Trzynka A, David L, Stagg SM, Chapman MS. Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR. eLife 2019; 8:e44707. [PMID: 31115336 PMCID: PMC6561701 DOI: 10.7554/elife.44707] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [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: 12/24/2018] [Accepted: 05/22/2019] [Indexed: 11/26/2022] Open
Abstract
Adeno-associated virus (AAV) vectors are preeminent in emerging clinical gene therapies. Generalizing beyond the most tractable genetic diseases will require modulation of cell specificity and immune neutralization. Interactions of AAV with its cellular receptor, AAVR, are key to understanding cell-entry and trafficking with the rigor needed to engineer tissue-specific vectors. Cryo-electron tomography shows ordered binding of part of the flexible receptor to the viral surface, with distal domains in multiple conformations. Regions of the virus and receptor in close physical proximity can be identified by cross-linking/mass spectrometry. Cryo-electron microscopy with a two-domain receptor fragment reveals the interactions at 2.4 Å resolution. AAVR binds between AAV's spikes on a plateau that is conserved, except in one clade whose structure is AAVR-incompatible. AAVR's footprint overlaps the epitopes of several neutralizing antibodies, prompting a re-evaluation of neutralization mechanisms. The structure provides a roadmap for experimental probing and manipulation of viral-receptor interactions.
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Affiliation(s)
- Nancy L Meyer
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Guiqing Hu
- Institute Molecular BiophysicsFlorida State UniversityTallahasseeUnited States
| | - Omar Davulcu
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Qing Xie
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Alex J Noble
- Institute Molecular BiophysicsFlorida State UniversityTallahasseeUnited States
| | - Craig Yoshioka
- OHSU Center for Spatial Systems BiomedicinePortlandUnited States
| | - Drew S Gingerich
- OHSU Center for Spatial Systems BiomedicinePortlandUnited States
| | - Andrew Trzynka
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Larry David
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Scott M Stagg
- Institute Molecular BiophysicsFlorida State UniversityTallahasseeUnited States
- Department of Chemistry and BiochemistryFlorida State UniversityTallahasseeUnited States
| | - Michael Stewart Chapman
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
- Department of BiochemistryUniversity of MissouriColumbiaUnited States
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6
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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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7
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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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8
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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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9
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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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10
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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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11
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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: 299] [Impact Index Per Article: 37.4] [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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12
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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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13
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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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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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15
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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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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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17
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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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18
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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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Hoffman GG, Davulcu O, Sona S, Ellington WR. Contributions to catalysis and potential interactions of the three catalytic domains in a contiguous trimeric creatine kinase. FEBS J 2008; 275:646-54. [PMID: 18190534 DOI: 10.1111/j.1742-4658.2007.06226.x] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three separate creatine kinase (CK) isoform families exist in animals. Two of these (cytoplasmic and mitochondrial) are obligate oligomers. A third, flagellar, is monomeric but contains the residues for three complete CK domains. It is not known whether the active sites in each of the contiguous flagellar domains are catalytically competent, and, if so, whether they are capable of acting independently. Here we have utilized site-directed mutagenesis to selectively disable individual active sites and all possible combinations thereof. Kinetic studies showed that these mutations had minimal impact on substrate binding and synergism. Interestingly, the active sites were not catalytically equivalent, and were in fact interdependent, a phenomenon that has previously been reported only in the oligomeric CK isoforms.
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Affiliation(s)
- Gregg G Hoffman
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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Davulcu O, Clark SA, Chapman MS, Skalicky JJ. Main chain 1H, 13C, and 15N resonance assignments of the 42-kDa enzyme arginine kinase. J Biomol NMR 2005; 32:178. [PMID: 16034675 DOI: 10.1007/s10858-005-6731-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 02/09/2005] [Indexed: 05/03/2023]
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