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Giles AR, Sims JJ, Turner KB, Govindasamy L, Alvira MR, Lock M, Wilson JM. Deamidation of Amino Acids on the Surface of Adeno-Associated Virus Capsids Leads to Charge Heterogeneity and Altered Vector Function. Mol Ther 2018; 26:2848-2862. [PMID: 30343890 DOI: 10.1016/j.ymthe.2018.09.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [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: 03/10/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/19/2022] Open
Abstract
Post-translational modification of the adeno-associated virus capsids is a poorly understood factor in the development of these viral vectors into pharmaceutical products. Here we report the extensive capsid deamidation of adeno-associated virus serotype 8 and seven other diverse adeno-associated virus serotypes, with supporting evidence from structural, biochemical, and mass spectrometry approaches. The extent of deamidation at each site depended on the vector's age and multiple primary-sequence and three-dimensional structural factors. However, the extent of deamidation was largely independent of the vector recovery and purification conditions. We demonstrate the potential for deamidation to impact transduction activity and, moreover, correlate an early time point loss in vector activity to rapidly progressing spontaneous deamidation at several adeno-associated virus 8 asparagines. We explore mutational strategies that stabilize side-chain amides, improving vector transduction and reducing the lot-to-lot molecular variability that presents a key concern in biologics manufacturing. This study illuminates a previously unknown aspect of adeno-associated virus capsid heterogeneity and highlights its importance in the development of these vectors for gene therapy.
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Affiliation(s)
- April R Giles
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua J Sims
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin B Turner
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lakshmanan Govindasamy
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mauricio R Alvira
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martin Lock
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Giles AR, Govindasamy L, Somanathan S, Wilson JM. Mapping an Adeno-associated Virus 9-Specific Neutralizing Epitope To Develop Next-Generation Gene Delivery Vectors. J Virol 2018; 92:e01011-18. [PMID: 30089698 PMCID: PMC6158442 DOI: 10.1128/jvi.01011-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 06/11/2018] [Accepted: 07/31/2018] [Indexed: 01/11/2023] Open
Abstract
Recent clinical trials have demonstrated the potential of adeno-associated virus (AAV)-based vectors for treating rare diseases. However, significant barriers remain for the translation of these vectors into widely available therapies. In particular, exposure to the AAV capsid can generate an immune response of neutralizing antibodies. One approach to overcome this response is to map the AAV-specific neutralizing epitopes and rationally design an AAV capsid able to evade neutralization. To accomplish this, we isolated a monoclonal antibody against AAV9 following immunization of BALB/c mice and hybridoma screening. This antibody, PAV9.1, is specific for intact AAV9 capsids and has a high neutralizing titer of >1:160,000. We used cryo-electron microscopy to reconstruct PAV9.1 in complex with AAV9. We then mapped its epitope to the 3-fold axis of symmetry on the capsid, specifically to residues 496-NNN-498 and 588-QAQAQT-592. Capsid mutagenesis demonstrated that even a single amino acid substitution within this epitope markedly reduced binding and neutralization by PAV9.1. In addition, in vivo studies showed that mutations in the PAV9.1 epitope conferred a "liver-detargeting" phenotype to the mutant vectors, unlike AAV9, indicating that the residues involved in PAV9.1 interactions are also responsible for AAV9 tropism. However, we observed minimal changes in binding and neutralizing titer when we tested these mutant vectors for evasion of polyclonal sera from mice, macaques, or humans previously exposed to AAV. Taken together, these studies demonstrate the complexity of incorporating mapped neutralizing epitopes and previously identified functional motifs into the design of novel capsids able to evade immune response.IMPORTANCE Gene therapy utilizing viral vectors has experienced recent success, culminating in U.S. Food and Drug Administration approval of the first adeno-associated virus vector gene therapy product in the United States: Luxturna for inherited retinal dystrophy. However, application of this approach to other tissues faces significant barriers. One challenge is the immune response to viral infection or vector administration, precluding patients from receiving an initial or readministered dose of vector, respectively. Here, we mapped the epitope of a novel neutralizing antibody generated in response to this viral vector to design a next-generation capsid to evade immune responses. Epitope-based mutations in the capsid interfered with the binding and neutralizing ability of the antibody but not when tested against polyclonal samples from various sources. Our results suggest that targeted mutation of a greater breadth of neutralizing epitopes will be required to evade the repertoire of neutralizing antibodies responsible for blocking viral vector transduction.
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Affiliation(s)
- April R Giles
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lakshmanan Govindasamy
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Suryanarayan Somanathan
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Giles AR, Govindasamy L, Calcedo R, Tretiakova A, Boyd S, Qin Q, Schneider M, Wilson JM. 82. Mapping the Humoral Immune Response to AAV by Molecular Docking and Cryo-Electron Microscopy for the Design of Next-Generation AAV Vectors. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)32891-x] [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: 10/20/2022] Open
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Aslanidi GV, Rivers AE, Ortiz L, Song L, Ling C, Govindasamy L, Van Vliet K, Tan M, Agbandje-McKenna M, Srivastava A. Optimization of the capsid of recombinant adeno-associated virus 2 (AAV2) vectors: the final threshold? PLoS One 2013; 8:e59142. [PMID: 23527116 PMCID: PMC3602601 DOI: 10.1371/journal.pone.0059142] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [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: 09/16/2012] [Accepted: 02/12/2013] [Indexed: 12/31/2022] Open
Abstract
The ubiquitin-proteasome pathway plays a critical role in the intracellular trafficking of AAV2 vectors, and phosphorylation of certain surface-exposed amino acid residues on the capsid provides the primary signal for ubiquitination. Removal of several critical tyrosine (Y) and serine (S) residues on the AAV2 capsid has been shown to significantly increase transduction efficiency compared with the wild-type (WT) vectors. In the present study, site-directed mutagenesis of each of the 17 surface-exposed threonine (T) residues was conducted, and the transduction efficiency of four of these mutants, T455V, T491V, T550V, and T659V, was observed to increase up to 4-fold in human HEK293 cells in vitro. The most critical Y, S, and T mutations were subsequently combined, and the quadruple-mutant (Y444+500+730F+T491V) AAV2 vector was identified as the most efficient. This vector increased the transduction efficiency ∼24-fold over the WT AAV2 vector, and ∼2-3-fold over the previously described triple-mutant (Y444+500+730F) vector in a murine hepatocyte cell line, H2.35, in vitro. Similar results were obtained in murine hepatocytes in vivo following tail vein injection of the Y444+500+730F+T491V scAAV2 vector, and whole-body bioluminescence imaging of C57BL/6 mice. The increase in the transduction efficiency of the Y-T quadruple-mutant over that of the Y triple-mutant correlated with an improved nuclear translocation of the vectors, which exceeded 90%. These observations suggest that further optimization of the AAV2 capsid by targeting amino acid residues involved in phosphorylation may not be possible. This study has thus led to the generation of a novel Y444+500+730F+T491V quadruple-mutant AAV2 vector with potential for use in liver-directed human gene therapy.
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Affiliation(s)
- George V Aslanidi
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, United States of America.
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Halder S, Nam HJ, Govindasamy L, Vogel M, Dinsart C, Salomé N, McKenna R, Agbandje-McKenna M. Production, purification, crystallization and structure determination of H-1 Parvovirus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1571-6. [PMID: 23192051 PMCID: PMC3509992 DOI: 10.1107/s1744309112045563] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/04/2012] [Indexed: 11/10/2022]
Abstract
Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a=255.4, b=350.4, c=271.6 Å, β=90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined.
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Affiliation(s)
- Sujata Halder
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Hyun-Joo Nam
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Michèle Vogel
- Research Program Infection and Cancer, Division of Tumor Virology, DKFZ F010 – Inserm U701, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Christiane Dinsart
- Research Program Infection and Cancer, Division of Tumor Virology, DKFZ F010 – Inserm U701, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Nathalie Salomé
- Research Program Infection and Cancer, Division of Tumor Virology, DKFZ F010 – Inserm U701, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
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Sun Z, Do PM, Rhee MS, Govindasamy L, Wang Q, Ingram LO, Shanmugam KT. Amino acid substitutions at glutamate-354 in dihydrolipoamide dehydrogenase of Escherichia coli lower the sensitivity of pyruvate dehydrogenase to NADH. Microbiology (Reading) 2012; 158:1350-1358. [PMID: 22343352 DOI: 10.1099/mic.0.055590-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pyruvate dehydrogenase (PDH) of Escherichia coli is inhibited by NADH. This inhibition is partially reversed by mutational alteration of the dihydrolipoamide dehydrogenase (LPD) component of the PDH complex (E354K or H322Y). Such a mutation in lpd led to a PDH complex that was functional in an anaerobic culture as seen by restoration of anaerobic growth of a pflB, ldhA double mutant of E. coli utilizing a PDH- and alcohol dehydrogenase-dependent homoethanol fermentation pathway. The glutamate at position 354 in LPD was systematically changed to all of the other natural amino acids to evaluate the physiological consequences. These amino acid replacements did not affect the PDH-dependent aerobic growth. With the exception of E354M, all changes also restored PDH-dependent anaerobic growth of and fermentation by an ldhA, pflB double mutant. The PDH complex with an LPD alteration E354G, E354P or E354W had an approximately 20-fold increase in the apparent K(i) for NADH compared with the native complex. The apparent K(m) for pyruvate or NAD(+) for the mutated forms of PDH was not significantly different from that of the native enzyme. A structural model of LPD suggests that the amino acid at position 354 could influence movement of NADH from its binding site to the surface. These results indicate that glutamate at position 354 plays a structural role in establishing the NADH sensitivity of LPD and the PDH complex by restricting movement of the product/substrate NADH, although this amino acid is not directly associated with NAD(H) binding.
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Affiliation(s)
- Zhentao Sun
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- College of Resources and Environmental Sciences, China Agricultural University, PR China
| | - Phi Minh Do
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Mun Su Rhee
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA
| | - Qingzhao Wang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lonnie O Ingram
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - K T Shanmugam
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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Bowles DE, McPhee SWJ, Li C, Gray SJ, Samulski JJ, Camp AS, Li J, Wang B, Monahan PE, Rabinowitz JE, Grieger JC, Govindasamy L, Agbandje-McKenna M, Xiao X, Samulski RJ. Phase 1 gene therapy for Duchenne muscular dystrophy using a translational optimized AAV vector. Mol Ther 2012; 20:443-55. [PMID: 22068425 PMCID: PMC3277234 DOI: 10.1038/mt.2011.237] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [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: 06/17/2011] [Accepted: 10/06/2011] [Indexed: 12/12/2022] Open
Abstract
Efficient and widespread gene transfer is required for successful treatment of Duchenne muscular dystrophy (DMD). Here, we performed the first clinical trial using a chimeric adeno-associated virus (AAV) capsid variant (designated AAV2.5) derived from a rational design strategy. AAV2.5 was generated from the AAV2 capsid with five mutations from AAV1. The novel chimeric vector combines the improved muscle transduction capacity of AAV1 with reduced antigenic crossreactivity against both parental serotypes, while keeping the AAV2 receptor binding. In a randomized double-blind placebo-controlled phase I clinical study in DMD boys, AAV2.5 vector was injected into the bicep muscle in one arm, with saline control in the contralateral arm. A subset of patients received AAV empty capsid instead of saline in an effort to distinguish an immune response to vector versus minidystrophin transgene. Recombinant AAV genomes were detected in all patients with up to 2.56 vector copies per diploid genome. There was no cellular immune response to AAV2.5 capsid. This trial established that rationally designed AAV2.5 vector was safe and well tolerated, lays the foundation of customizing AAV vectors that best suit the clinical objective (e.g., limb infusion gene delivery) and should usher in the next generation of viral delivery systems for human gene transfer.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Capsid Proteins/chemistry
- Capsid Proteins/genetics
- Capsid Proteins/immunology
- Cell Line
- Child
- Child, Preschool
- Dependovirus/genetics
- Dependovirus/physiology
- Dystrophin/genetics
- Dystrophin/metabolism
- Genetic Therapy
- Genetic Vectors/administration & dosage
- Genetic Vectors/genetics
- Genetic Vectors/immunology
- Humans
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Models, Molecular
- Molecular Sequence Data
- Muscle, Skeletal/metabolism
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/immunology
- Muscular Dystrophy, Duchenne/therapy
- Protein Conformation
- Sequence Alignment
- T-Lymphocytes/immunology
- Transduction, Genetic
- Viral Tropism
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Affiliation(s)
- Dawn E Bowles
- Department of Surgery, Division of Surgical Sciences, Duke University Medical Center, Durham, North Carolina, USA
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8
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Aslanidi G, Rivers A, Ortiz L, Govindasamy L, Agbandje-McKenna M, Srivastava A. Abstract C240: Modification on the capsid of recombinant adeno-associated virus vectors (rAAV) leads to high-efficiency transduction of human monocyte-derived dendritic cells (moDCs). Mol Cancer Ther 2011. [DOI: 10.1158/1535-7163.targ-11-c240] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genetically modified dendritic cell (DC) has been extensively studied and numerous phase I and II clinical trials evaluating the efficacy of DC-based vaccine have been initiated. Among different methods for gene delivery, vectors based on a human parvovirus, the adeno-associated virus (AAV), have attracted much attention mainly because of the non-pathogenic nature of this replication deficient virus, and its ability to mediate long-term, sustained therapeutic gene expression. Successful transduction of different subsets of DC by different commonly used serotypes of AAV was demonstrated in recent studies and the potential advantage of an AAV-based antitumor vaccine was discussed. However, further improvement of gene transfer by rAAV to DC in terms of specificity and transduction efficiency should be made to have a significant impact in the choice of vector used as an antitumor vaccine.
Serine/threonine protein kinases, such as p-38 MAPK, are involved in a wide variety of cellular processes such as differentiation, transcription regulation and development of many cell types including immune cells. Such kinases can also negatively regulate efficiency of rAAV-mediated gene transfer by phosphorylating serine or threonine surface exposed residues on viral capsid and target virus for proteasome-mediated degradation. In present studies we show that pre-treatment of cells with selective p-38 MAPK inhibitors prior to AAV infection significantly increased the transduction by AAV2 vectors. We hypothesized that prevention of phosphorylation of the surface-exposed serine residues might allow the vectors to evade phosphorylation and subsequent ubiquitination and, thus, prevent proteasomal degradation. The AAV2 capsid contains 50 serine residues in the VP3 region, of which 15 residues (S261, S264, S267, S276, S384, S458, S468, S492, S498, S578, S658, S662, S668, S707, S721) are surface-exposed. Each of the fifteen serine (S) residues was substituted with valine (V), and each S-V mutant vector was evaluated for transduction efficiency in moDC. We identified that single serine residue (S662) substitution to valine leads to increased transduction efficiency of moDC up to 6 times. We next evaluated the possibility whether S662V-AAV vectors could be used for generating antigen-specific cytotoxic T-cells (CTLs). To this end, S662V-AAV2 vectors encoding a truncated human telomerase (hTERT) gene were generated, and used to stimulate CTLs against a human immortalised myelogenous leukaemia cell line, K562. Our data show that S662V-AAV2-hTERT-transduced DCs resulted in rapid (within one week), specific T-cell clone proliferation and generation of robust CTLs. A killing curve was generated and specific cell lysis was determined by fluorescence-activated cell sorting (FACS) analysis of live/dead cell ratios. These results suggest that high-efficiency transduction of moDCs by capsid-modified AAV vectors is feasible, which supports the potential utility of these vectors for future human DC-based vaccine studies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr C240.
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Kapoor A, Mehta N, Dubovi EJ, Simmonds P, Govindasamy L, Medina JL, Street C, Shields S, Lipkin WI. Characterization of novel canine bocaviruses and their association with respiratory disease. J Gen Virol 2011; 93:341-346. [PMID: 22031527 DOI: 10.1099/vir.0.036624-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We report the first identification, genetic characterization and disease association studies of several novel species of canine bocaviruses (CBoV). Evolutionary analysis confirmed that CBoV are genetically distinct from the only other known canine bocavirus, minute virus of canines, with which they share less than 63, 62 and 64 % protein identity in NS, NP and VP genes, respectively. Comparative genetic analysis of 37 VP gene variants found in diseased and healthy animals showed that these novel viruses are genetically highly diverse and are common in canine respiratory infections that have remained undetected until now. Interestingly, we observed that a CBoV genotype with a unique deletion in the VP2 gene was significantly more prevalent in animals with respiratory diseases compared with healthy animals.
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Affiliation(s)
- Amit Kapoor
- Center for Infection and Immunity, Columbia University, New York 10032, USA
| | - Natasha Mehta
- Center for Infection and Immunity, Columbia University, New York 10032, USA
| | - Edward J Dubovi
- College of Veterinary Medicine at Cornell, Ithaca, NY 14853, USA
| | - Peter Simmonds
- Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Jan L Medina
- Center for Infection and Immunity, Columbia University, New York 10032, USA
| | - Craig Street
- Center for Infection and Immunity, Columbia University, New York 10032, USA
| | - Shelly Shields
- Pfizer Veterinary Medicine Research and Development, New York 10017, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York 10032, USA
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Ling C, Lu Y, Kalsi JK, Jayandharan GR, Li B, Ma W, Cheng B, Gee SWY, McGoogan KE, Govindasamy L, Zhong L, Agbandje-McKenna M, Srivastava A. Human hepatocyte growth factor receptor is a cellular coreceptor for adeno-associated virus serotype 3. Hum Gene Ther 2011; 21:1741-7. [PMID: 20545554 DOI: 10.1089/hum.2010.075] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Adeno-associated viruses (AAVs) use a variety of cellular receptors/coreceptors to gain entry into cells. A number of AAV serotypes are now available, and the cognate receptors/coreceptors for only a handful of those have been identified thus far. Of the 10 commonly used AAV serotypes, AAV3 is by far the least efficient in transducing cells in general. However, in our more recent studies, we observed that AAV3 vectors transduced human liver cancer cells remarkably well, which led to the hypothesis that AAV3 uses hepatocyte growth factor receptor (HGFR) as a cellular coreceptor for viral entry. AAV3 infection of human liver cancer cell lines was strongly inhibited by hepatocyte growth factor, HGFR-specific small interfering RNA, and anti-HGFR antibody, which corroborated this hypothesis. However, AAV3 vectors failed to transduce murine hepatocytes, both in vitro and in vivo, suggesting that AAV3 specifically uses human HGFR, but not murine HGFR, as a cellular coreceptor for transduction. AAV3 may prove to be a useful vector for targeting human liver cancers for the potential gene therapy.
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Affiliation(s)
- Chen Ling
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, 32611, USA
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Petrs-Silva H, Dinculescu A, Li Q, Deng WT, Pang JJ, Min SH, Chiodo V, Neeley AW, Govindasamy L, Bennett A, Agbandje-McKenna M, Zhong L, Li B, Jayandharan GR, Srivastava A, Lewin AS, Hauswirth WW. Novel properties of tyrosine-mutant AAV2 vectors in the mouse retina. Mol Ther 2010; 19:293-301. [PMID: 21045809 DOI: 10.1038/mt.2010.234] [Citation(s) in RCA: 209] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Vectors based on adeno-associated virus serotype 2 (AAV2) have been used extensively in many gene-delivery applications, including several successful clinical trials for one type of Leber congenital amaurosis in the retina. Many studies have focused on improving AAV2 transduction efficiency and cellular specificity by genetically engineering its capsid. We have previously shown that vectors-containing single-point mutations of capsid surface tyrosines in serotypes AAV2, AAV8, and AAV9 displayed significantly increased transduction efficiency in the retina compared with their wild-type counterparts. In the present study, we evaluated the transduction characteristics of AAV2 vectors containing combinations of multiple tyrosine to phenylalanine mutations in seven highly conserved surface-exposed capsid tyrosine residues following subretinal or intravitreal delivery in adult mice. The multiply mutated vectors exhibited different in vivo transduction properties, with some having a unique ability of transgene expression in all retinal layers. Such novel vectors may be useful in developing valuable new therapeutic strategies for the treatment of many genetic diseases.
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Affiliation(s)
- Hilda Petrs-Silva
- Department of Ophthalmology, University of Florida, Gainesville, FL, USA
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12
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Sippel KH, Genis C, Govindasamy L, Agbandje-McKenna M, Kiddle JJ, Tripp BC, McKenna R. Synchrotron Radiation Provides a Plausible Explanation for the Generation of a Free Radical Adduct of Thioxolone in Mutant Carbonic Anhydrase II. J Phys Chem Lett 2010; 1:2898-2902. [PMID: 20976122 PMCID: PMC2957018 DOI: 10.1021/jz100954h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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] [Indexed: 05/30/2023]
Abstract
Thioxolone acts as a prodrug in the presence of carbonic anhydrase II (CA II), whereby the molecule is cleaved by thioester hydrolysis to the carbonic anhydrase inhibitor, 4-mercaptobenzene-1,3-diol (TH0). Thioxolone was soaked into the proton transfer mutant H64A of CA II in an effort to capture a reaction intermediate via X-ray crystallography. Structure determination of the 1.2 Å resolution data revealed the TH0 had been modified to a 4,4'-disulfanediyldibenzene-1,3-diol, a product of crystallization conditions, and a zinc ligated 2,4-dihydroxybenzenesulfenic acid, most likely induced by radiation damage. Neither ligand was likely a result of an enzymatic mechanism.
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Affiliation(s)
- Katherine H. Sippel
- Department of Biochemistry and Molecular Biology, P.O. Box 100245, College of Medicine, University of Florida, Gainesville, Florida 32610
| | - Caroli Genis
- Department of Biochemistry and Molecular Biology, P.O. Box 100245, College of Medicine, University of Florida, Gainesville, Florida 32610
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, P.O. Box 100245, College of Medicine, University of Florida, Gainesville, Florida 32610
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, P.O. Box 100245, College of Medicine, University of Florida, Gainesville, Florida 32610
| | - James J. Kiddle
- Department of Chemistry Western Michigan University, Kalamazoo, Michigan 49008
| | - Brian C. Tripp
- Department of Chemistry Western Michigan University, Kalamazoo, Michigan 49008
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, P.O. Box 100245, College of Medicine, University of Florida, Gainesville, Florida 32610
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13
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Majumder A, Govindasamy L, Magis A, Kiss R, Polgár T, Baskin R, Allan RW, Agbandje-McKenna M, Reuther GW, Keseru GM, Bisht KS, Sayeski PP. Structure-function correlation of G6, a novel small molecule inhibitor of Jak2: indispensability of the stilbenoid core. J Biol Chem 2010; 285:31399-407. [PMID: 20667821 DOI: 10.1074/jbc.m110.168211] [Citation(s) in RCA: 11] [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] [Indexed: 01/15/2023] Open
Abstract
Somatic mutations in the Jak2 protein, such as V617F, cause aberrant Jak/STAT signaling and can lead to the development of myeloproliferative neoplasms. This discovery has led to the search for small molecule inhibitors that target Jak2. Using structure-based virtual screening, our group recently identified a novel small molecule inhibitor of Jak2 named G6. Here, we identified a structure-function correlation of this compound. Specifically, five derivative compounds of G6 having structural similarity to the original lead compound were obtained and analyzed for their ability to (i) inhibit Jak2-V617F-mediated cell growth, (ii) inhibit the levels of phospho-Jak2, phospho-STAT3, and phospho-STAT5; (iii) induce apoptosis in human erythroleukemia cells; and (iv) suppress pathologic cell growth of Jak2-V617F-expressing human bone marrow cells ex vivo. Additionally, we computationally examined the interactions of these compounds with the ATP-binding pocket of the Jak2 kinase domain. We found that the stilbenoid core-containing derivatives of G6 significantly inhibited Jak2-V617F-mediated cell proliferation in a time- and dose-dependent manner. They also inhibited phosphorylation of Jak2, STAT3, and STAT5 proteins within cells, resulting in higher levels of apoptosis via the intrinsic apoptotic pathway. Finally, the stilbenoid derivatives inhibited the pathologic growth of Jak2-V617F-expressing human bone marrow cells ex vivo. Collectively, our data demonstrate that G6 has a stilbenoid core that is indispensable for maintaining its Jak2 inhibitory potential.
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Affiliation(s)
- Anurima Majumder
- Department of Physiology and Functional Genomics, Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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14
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Majumder A, Govindasamy L, Magis A, Kiss R, Polgar T, Allan RW, Agbandje‐McKenna M, Keseru GM, Bisht K, Sayeski PP. Structure‐Function Correlation of G6, a Novel Small Molecule Inhibitor of Jak2: Indispensability of the Stilbenoid Core. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.620.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Robert Kiss
- PhysiologyUniversity of FloridaGainesvilleFL
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15
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Genis C, Sippel KH, Case N, Cao W, Avvaru BS, Tartaglia LJ, Govindasamy L, Tu C, Agbandje-McKenna M, Silverman DN, Rosser CJ, McKenna R. Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties. Biochemistry 2009; 48:1322-31. [PMID: 19170619 PMCID: PMC2713499 DOI: 10.1021/bi802035f] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Recently, a convincing body of evidence has accumulated suggesting that the overexpression of carbonic anhydrase isozyme IX (CA IX) in some cancers contributes to the acidification of the extracellular matrix, which in turn promotes the growth and metastasis of the tumor. These observations have made CA IX an attractive drug target for the selective treatment of certain cancers. Currently, there is no available X-ray crystal structure of CA IX, and this lack of availability has hampered the rational design of selective CA IX inhibitors. In light of these observations and on the basis of structural alignment homology, using the crystal structure of carbonic anhydrase II (CA II) and the sequence of CA IX, a double mutant of CA II with Ala65 replaced by Ser and Asn67 replaced by Gln has been constructed to resemble the active site of CA IX. This CA IX mimic has been characterized kinetically using (18)O-exchange and structurally using X-ray crystallography, alone and in complex with five CA sulfonamide-based inhibitors (acetazolamide, benzolamide, chlorzolamide, ethoxzolamide, and methazolamide), and compared to CA II. This structural information has been evaluated by both inhibition studies and in vitro cytotoxicity assays and shows a correlated structure-activity relationship. Kinetic and structural studies of CA II and CA IX mimic reveal chlorzolamide to be a more potent inhibitor of CA IX, inducing an active-site conformational change upon binding. Additionally, chlorzolamide appears to be cytotoxic to prostate cancer cells. This preliminary study demonstrates that the CA IX mimic may provide a useful model to design more isozyme-specific CA IX inhibitors, which may lead to development of new therapeutic treatments of some cancers.
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Affiliation(s)
- Caroli Genis
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Katherine H. Sippel
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Nicolette Case
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Wengang Cao
- Department of Urology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Balendu Sankara Avvaru
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Lawrence J. Tartaglia
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Chingkuang Tu
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - David N. Silverman
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA,Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Charles J. Rosser
- Department of Urology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA,Corresponding Author: Phone: (352)-392-5696. Fax: (352) 392-3422. E-mail: (R.M.)
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16
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Levy HC, Bowman VD, Govindasamy L, McKenna R, Nash K, Warrington K, Chen W, Muzyczka N, Yan X, Baker TS, Agbandje-McKenna M. Heparin binding induces conformational changes in Adeno-associated virus serotype 2. J Struct Biol 2008; 165:146-56. [PMID: 19121398 DOI: 10.1016/j.jsb.2008.12.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 11/29/2008] [Accepted: 12/03/2008] [Indexed: 01/08/2023]
Abstract
Adeno-associated virus serotype 2 (AAV2) uses heparan sulfate proteoglycan as a cell surface-attachment receptor. In this study the structures of AAV2 alone and complexed with heparin were determined to approximately 18A resolution using cryo-electron microscopy and three-dimensional image reconstruction. A difference map showed positive density, modeled as heparin, close to the icosahedral twofold axes and between the protrusions that surround the threefold axes of the capsid. Regions of the model near the threefold place the receptor in close proximity to basic residues previously identified as part of the heparin binding site. The region of the model near the twofold axes identifies a second contact site, not previously characterized but which is also possibly configured by heparin binding. The difference map also revealed two significant conformational changes: (I) at the tops of the threefold protrusions, which have become flattened in the complex, and (II) at the fivefold axes where the top of the channel is widened possibly in response to movement of the HI loops in the capsid proteins. Ordered density in the interior of the capsid in the AAV2-heparin complex was interpreted as nucleic acid, consistent with the presence of non-viral DNA in the expressed capsids.
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Affiliation(s)
- Hazel C Levy
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, 1600 SW Archer Road, P.O. Box 100245, University of Florida, Gainesville, FL 32610, USA
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17
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Sippel KH, Robbins AH, Reutzel R, Domsic J, Boehlein SK, Govindasamy L, Agbandje-McKenna M, Rosser CJ, McKenna R. Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37. Acta Crystallogr D Biol Crystallogr 2008; 64:1172-8. [PMID: 19020356 DOI: 10.1107/s0907444908030175] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 09/18/2008] [Indexed: 11/10/2022]
Abstract
The crystal structure of the Mycoplasma hyorhinis protein Mh-p37 has been solved and refined to 1.9 A resolution. This is the first de novo structure to be determined using the recently described heavy-atom reagent [Beck et al. (2008), Acta Cryst. D64, 1179-1182] 5-amino-2,4,6-triiodoisophthalic acid (I3C), which contains three I atoms arranged in an equilateral triangle, by SIRAS methods. Data collection was performed in-house at room temperature. SHELXD and SHELXE were used to determine the I-atom positions and phase the native protein and PHENIX AutoBuild software was used to automatically fit the amino-acid sequence to the electron-density map. The structure was refined using SHELX97 to an R(cryst) of 18.6% and an R(free) of 24.0%. Mh-p37 is an alpha/beta protein with two well defined domains which are separated by a deep cleft. An unanticipated ligand bound in the center of the molecule at the base of the cleft has been modeled as thiamine pyrophosphate or vitamin B(1). Retrospective attempts to solve the crystal structure by Patterson search methods using either isomorphous or anomalous differences failed. Additionally, attempts to use proteins with the highest structural homology in the Protein Data Bank to phase the data by molecular replacement were unsuccessful, most likely in hindsight because of their poor structural agreement. Therefore, the I3C reagent offers an alternative, quick and inexpensive method for in-house phasing of de novo structures where other methods may not be successful.
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Affiliation(s)
- Katherine H Sippel
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
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18
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Barrese, AA, Genis C, Fisher SZ, Orwenyo JN, Kumara MT, Dutta SK, Phillips E, Kiddle JJ, Tu C, Silverman DN, Govindasamy L, Agbandje-McKenna M, McKenna R, Tripp BC. Inhibition of Carbonic Anhydrase II by Thioxolone: A Mechanistic and Structural Study. Biochemistry 2008; 47:3174-84. [DOI: 10.1021/bi702385k] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Albert A. Barrese,
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Caroli Genis
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - S. Zoe Fisher
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Jared N. Orwenyo
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Mudalige Thilak Kumara
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Subodh K. Dutta
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Eric Phillips
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - James J. Kiddle
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Chingkuang Tu
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - David N. Silverman
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Lakshmanan Govindasamy
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Mavis Agbandje-McKenna
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Robert McKenna
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
| | - Brian C. Tripp
- Department of Biological Sciences, Mailstop 5410, College of Arts and Sciences, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, Michigan 49008-5410, Department of Biochemistry and Molecular Biology, College of Medicine, P.O. Box 100245, University of Florida, Gainesville, Florida 32610-0267, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5410, and Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville,
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19
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Clemente JC, Robbins A, Graña P, Paleo MR, Correa JF, Villaverde MC, Sardina FJ, Govindasamy L, Agbandje-McKenna M, McKenna R, Dunn BM, Sussman F. Design, synthesis, evaluation, and crystallographic-based structural studies of HIV-1 protease inhibitors with reduced response to the V82A mutation. J Med Chem 2008; 51:852-60. [PMID: 18215016 DOI: 10.1021/jm701170f] [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: 11/29/2022]
Abstract
In our quest for HIV-1 protease inhibitors that are not affected by the V82A resistance mutation, we have synthesized and tested a second generation set of C2-symmetric HIV-1 protease inhibitors that contain a cyclohexane group at P1 and/or P1'. The binding affinity results indicate that these compounds have an improved response to the appearance of the V82A mutation than the parent compound. The X-ray structure of one of these compounds with the V82A HIV-1 PR variant provides the structural rationale for the better resistance profile of these compounds. Moreover, scrutiny of the X-ray structure suggests that the ring of the Cha side chain might be in a boat rather than in the chair conformation, a result supported by molecular dynamics simulations.
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Affiliation(s)
- José C Clemente
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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20
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Quesada O, Gurda B, Govindasamy L, McKenna R, Kohlbrenner E, Aslanidi G, Zolotukhin S, Muzyczka N, Agbandje-McKenna M. Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:1073-6. [PMID: 18084098 PMCID: PMC2344100 DOI: 10.1107/s1744309107060289] [Citation(s) in RCA: 16] [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: 10/19/2007] [Accepted: 11/17/2007] [Indexed: 11/10/2022]
Abstract
Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to approximately 3.0 A resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 A in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R(merge) of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of a capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.
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Affiliation(s)
- Odayme Quesada
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Brittney Gurda
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Erik Kohlbrenner
- Division of Cell and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - George Aslanidi
- Division of Cell and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - Sergei Zolotukhin
- Division of Cell and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - Nicholas Muzyczka
- Department of Molecular Genetics and Microbiology and Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
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21
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Zhong L, Zhao W, Wu J, Li B, Zolotukhin S, Govindasamy L, Agbandje-McKenna M, Srivastava A. A dual role of EGFR protein tyrosine kinase signaling in ubiquitination of AAV2 capsids and viral second-strand DNA synthesis. Mol Ther 2007; 15:1323-30. [PMID: 17440440 DOI: 10.1038/sj.mt.6300170] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A 52 kd cellular protein, FK506-binding protein (FKBP52), phosphorylated at tyrosine residues by epidermal growth factor receptor protein tyrosine kinase (EGFR-PTK), inhibits adeno-associated virus 2 (AAV2) second-strand DNA synthesis and transgene expression. FKBP52 is dephosphorylated at tyrosine residues by T-cell protein tyrosine phosphatase (TC-PTP), and TC-PTP over-expression leads to improved viral second-strand DNA synthesis and improved transgene expression. In these studies, we observed that perturbation of EGFR-PTK signaling by a specific inhibitor, Tyrphostin 23 (Tyr23), augmented the transduction efficiency of the single-stranded AAV (ssAAV) vector as well as the self-complementary AAV (scAAV) vector. Similarly, tyrosine-dephosphorylation of FKBP52 by TC-PTP resulted in increased transduction by both vectors. These data suggested that EGFR-PTK signaling also affects aspects of AAV transduction other than viral second-strand DNA synthesis. We document that inhibition of EGFR-PTK signaling leads to decreased ubiquitination of AAV2 capsids which, in turn, facilitates nuclear transport by limiting proteasome-mediated degradation of AAV vectors. We also document that Tyr23-mediated increase in AAV2 transduction efficiency is not further enhanced by a specific proteasome inhibitor, MG132. Thus, EGFR-PTK signaling modulates ubiquitin (Ub)/proteasome pathway-mediated intracellular trafficking as well as FKBP52-mediated second-strand DNA synthesis of AAV2 vectors. This has implications in the optimal use of AAV vectors in gene therapy.
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Affiliation(s)
- Li Zhong
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, USA
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22
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Zhong L, Zhao W, Wu J, Li B, Zolotukhin S, Govindasamy L, Agbandje-McKenna M, Srivastava A. A dual role of EGFR protein tyrosine kinase signaling in ubiquitination of AAV2 capsids and viral second-strand DNA synthesis. Mol Ther 2007. [PMID: 17440440 DOI: 10.1038/mt.sj.6300170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A 52 kd cellular protein, FK506-binding protein (FKBP52), phosphorylated at tyrosine residues by epidermal growth factor receptor protein tyrosine kinase (EGFR-PTK), inhibits adeno-associated virus 2 (AAV2) second-strand DNA synthesis and transgene expression. FKBP52 is dephosphorylated at tyrosine residues by T-cell protein tyrosine phosphatase (TC-PTP), and TC-PTP over-expression leads to improved viral second-strand DNA synthesis and improved transgene expression. In these studies, we observed that perturbation of EGFR-PTK signaling by a specific inhibitor, Tyrphostin 23 (Tyr23), augmented the transduction efficiency of the single-stranded AAV (ssAAV) vector as well as the self-complementary AAV (scAAV) vector. Similarly, tyrosine-dephosphorylation of FKBP52 by TC-PTP resulted in increased transduction by both vectors. These data suggested that EGFR-PTK signaling also affects aspects of AAV transduction other than viral second-strand DNA synthesis. We document that inhibition of EGFR-PTK signaling leads to decreased ubiquitination of AAV2 capsids which, in turn, facilitates nuclear transport by limiting proteasome-mediated degradation of AAV vectors. We also document that Tyr23-mediated increase in AAV2 transduction efficiency is not further enhanced by a specific proteasome inhibitor, MG132. Thus, EGFR-PTK signaling modulates ubiquitin (Ub)/proteasome pathway-mediated intracellular trafficking as well as FKBP52-mediated second-strand DNA synthesis of AAV2 vectors. This has implications in the optimal use of AAV vectors in gene therapy.
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Affiliation(s)
- Li Zhong
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, USA
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23
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Fisher SZ, Tu C, Bhatt D, Govindasamy L, Agbandje-McKenna M, McKenna R, Silverman DN. Speeding up proton transfer in a fast enzyme: kinetic and crystallographic studies on the effect of hydrophobic amino acid substitutions in the active site of human carbonic anhydrase II. Biochemistry 2007; 46:3803-13. [PMID: 17330962 DOI: 10.1021/bi602620k] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [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] [Indexed: 11/28/2022]
Abstract
Catalysis of the hydration of CO2 by human carbonic anhydrase isozyme II (HCA II) is sustained at a maximal catalytic turnover of 1 mus-1 by proton transfer between a zinc-bound solvent and bulk solution. This mechanism of proton transfer is facilitated via the side chain of His64, which is located 7.5 A from the zinc, and mediated via intervening water molecules in the active-site cavity. Three hydrophilic residues that have previously been shown to contribute to the stabilization of these intervening waters were replaced with hydrophobic residues (Y7F, N62L, and N67L) to determine their effects on proton transfer. The structures of all three mutants were determined by X-ray crystallography, with crystals equilibrated from pH 6.0 to 10.0. A range of changes were observed in the ordered solvent and the conformation of the side chain of His64. Correlating these structural variants with kinetic studies suggests that the very efficient proton transfer (approximately 7 micros-1) observed for Y7F HCA II in the dehydration direction, compared with the wild type and other mutants of this study, is due to a combination of three features. First, in this mutant, the side chain of His64 showed an appreciable inward orientation pointing toward the active-site zinc. Second, in the structure of Y7F HCA II, there is an unbranched chain of hydrogen-bonded waters linking the proton donor His64 and acceptor zinc-bound hydroxide. Finally, the difference in pKa of the donor and acceptor appears favorable for proton transfer. The data suggest roles for residues 7, 62, and 67 in fine-tuning the properties of His64 for optimal proton transfer in catalysis.
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Affiliation(s)
- S Zoë Fisher
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610-0267, USA
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Fisher SZ, Maupin CM, Budayova-Spano M, Govindasamy L, Tu C, Agbandje-McKenna M, Silverman DN, Voth GA, McKenna R. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism†,‡. Biochemistry 2007; 46:2930-7. [PMID: 17319692 DOI: 10.1021/bi062066y] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [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] [Indexed: 11/29/2022]
Abstract
Human carbonic anhydrase II (HCA II) is a zinc-metalloenzyme that catalyzes the reversible interconversion of CO2 and HCO3-. The rate-limiting step of this catalysis is the transfer of a proton between the Zn-bound solvent molecule and residue His64. In order to fully characterize the active site structural features implicated in the proton transfer mechanism, the refined X-ray crystal structure of uncomplexed wild type HCA II to 1.05 A resolution with an Rcryst value of 12.0% and an Rfree value of 15.1% has been elucidated. This structure provides strong clues as to the pathway of the intramolecular proton transfer between the Zn-bound solvent and His64. The structure emphasizes the role of the solvent network, the unique positioning of solvent molecule W2, and the significance of the dual conformation of His64 in the active site. The structure is compared with molecular dynamics (MD) simulation calculations of the Zn-bound hydroxyl/His64+ (charged) and the Zn-bound water/His64 (uncharged) HCA II states. A comparison of the crystallographic anisotropic atomic thermal parameters and MD simulation root-mean-square fluctuation values show excellent agreement in the atomic motion observed between the two methods. It is also interesting that the observed active site solvent positions in the crystal structure are also the most probable positions of the solvent during the MD simulations. On the basis of the comparative study of the MD simulation results, the HCA II crystal structure observed is most likely in the Zn-bound water/His64 state. This conclusion is based on the following observations: His64 is mainly (80%) orientated in an inward conformation; electron density omit maps infer that His64 is not charged in an either inward or outward conformation; and the Zn-bound solvent is most likely a water molecule.
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Affiliation(s)
- S Zoë Fisher
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
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Miller EB, Gurda-Whitaker B, Govindasamy L, McKenna R, Zolotukhin S, Muzyczka N, Agbandje-McKenna M. Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1271-4. [PMID: 17142915 PMCID: PMC2225374 DOI: 10.1107/s1744309106048184] [Citation(s) in RCA: 38] [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: 09/10/2006] [Accepted: 11/12/2006] [Indexed: 11/10/2022]
Abstract
Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 A, alpha = 62.3 degrees) and shown to diffract X-rays to at least 2.5 A resolution. The diffraction data were subsequently processed and reduced with an overall R(sym) of 12.3% and a completeness of 89.0%. Based on the unit-cell volume, rotation-function and translation-function results and packing considerations, there is one virus capsid (60 viral proteins) per unit cell and there are ten viral proteins per crystallographic asymmetric unit. The AAV1 capsid shares both the twofold and threefold crystallographic symmetry operators. The AAV1 data have been initially phased using a polyalanine model (based on the crystal structure of AAV4) to 4.0 A resolution and the structure determination and refinement is in progress using tenfold noncrystallographic symmetry electron-density averaging.
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Affiliation(s)
- Edward B. Miller
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Brittney Gurda-Whitaker
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Sergei Zolotukhin
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nicholas Muzyczka
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Correspondence e-mail:
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Asokan A, Hamra JB, Govindasamy L, Agbandje-McKenna M, Samulski RJ. Adeno-associated virus type 2 contains an integrin alpha5beta1 binding domain essential for viral cell entry. J Virol 2006; 80:8961-9. [PMID: 16940508 PMCID: PMC1563945 DOI: 10.1128/jvi.00843-06] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [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] [Indexed: 11/20/2022] Open
Abstract
Integrins have been implicated as coreceptors in the infectious pathways of several nonenveloped viruses. For example, adenoviruses are known to interact with alphaV integrins by virtue of a high-affinity arginine-glycine-aspartate (RGD) domain present in the penton bases of the capsids. In the case of adeno-associated virus type 2 (AAV2), which lacks this RGD motif, integrin alphaVbeta5 has been identified as a coreceptor for cellular entry. However, the molecular determinants of AAV2 capsid-integrin interactions and the potential exploitation of alternative integrins as coreceptors by AAV2 have not been established thus far. In this report, we demonstrate that integrin alpha5beta1 serves as an alternative coreceptor for AAV2 infection in human embryonic kidney 293 cells. Such interactions appear to be mediated by a highly conserved domain that contains an asparagine-glycine-arginine (NGR) motif known to bind alpha5beta1 integrin with moderate affinity. The mutation of this domain reduces transduction efficiency by an order of magnitude relative to that of wild-type AAV2 vectors in vitro and in vivo. Further characterization of mutant and wild-type AAV2 capsids through transduction assays in cell lines lacking specific integrins, cell adhesion studies, and cell surface/solid-phase binding assays confirmed the role of the NGR domain in promoting AAV2-integrin interactions. Molecular modeling studies suggest that NGR residues form a surface loop close to the threefold axis of symmetry adjacent to residues previously implicated in binding heparan sulfate, the primary receptor for AAV2. The aforementioned results suggest that the internalization of AAV2 in 293 cells might follow a "click-to-fit" mechanism that involves the cooperative binding of heparan sulfate and alpha5beta1 integrin by the AAV2 capsids.
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Affiliation(s)
- Aravind Asokan
- Gene Therapy Center, 7113 Thurston Building, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7352, USA
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Govindasamy L, Padron E, McKenna R, Muzyczka N, Kaludov N, Chiorini JA, Agbandje-McKenna M. Structurally mapping the diverse phenotype of adeno-associated virus serotype 4. J Virol 2006; 80:11556-70. [PMID: 16971437 PMCID: PMC1642620 DOI: 10.1128/jvi.01536-06] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.2] [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] [Indexed: 12/23/2022] Open
Abstract
The adeno-associated viruses (AAVs) can package and deliver foreign DNA into cells for corrective gene delivery applications. The AAV serotypes have distinct cell binding, transduction, and antigenic characteristics that have been shown to be dictated by the capsid viral protein (VP) sequence. To understand the contribution of capsid structure to these properties, we have determined the crystal structure of AAV serotype 4 (AAV4), one of the most diverse serotypes with respect to capsid protein sequence and antigenic reactivity. Structural comparison of AAV4 to AAV2 shows conservation of the core beta strands (betaB to betaI) and helical (alphaA) secondary structure elements, which also exist in all other known parvovirus structures. However, surface loop variations (I to IX), some containing compensating structural insertions and deletions in adjacent regions, result in local topological differences on the capsid surface. These include AAV4 having a deeper twofold depression, wider and rounder protrusions surrounding the threefold axes, and a different topology at the top of the fivefold channel from that of AAV2. Also, the previously observed "valleys" between the threefold protrusions, containing AAV2's heparin binding residues, are narrower in AAV4. The observed differences in loop topologies at subunit interfaces are consistent with the inability of AAV2 and AAV4 VPs to combine for mosaic capsid formation in efforts to engineer novel tropisms. Significantly, all of the surface loop variations are associated with amino acids reported to affect receptor recognition, transduction, and anticapsid antibody reactivity for AAV2. This observation suggests that these capsid regions may also play similar roles in the other AAV serotypes.
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Affiliation(s)
- Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Wu Z, Asokan A, Grieger JC, Govindasamy L, Agbandje-McKenna M, Samulski RJ. Single amino acid changes can influence titer, heparin binding, and tissue tropism in different adeno-associated virus serotypes. J Virol 2006; 80:11393-7. [PMID: 16943302 PMCID: PMC1642158 DOI: 10.1128/jvi.01288-06] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [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] [Indexed: 12/25/2022] Open
Abstract
Despite the high degree of sequence homology between adeno-associated virus (AAV) serotype 1 and 6 capsids (99.2%), these viruses have different liver transduction profiles when tested as vectors. Examination of the six amino acid residues that differ between AAV1 and AAV6 revealed that a lysine-to-glutamate change (K531E) suppresses the heparin binding ability of AAV6. In addition, the same mutation in AAV6 reduces transgene expression to levels similar to those achieved with AAV1 in HepG2 cells in vitro and in mouse liver following portal vein administration. In corollary, the converse E531K mutation in AAV1 imparts heparin binding ability and increases transduction efficiency. Extraction of vector genomes from liver tissue suggests that the lysine 531 residue assists in preferential transduction of parenchymal cells by AAV6 vectors in comparison with AAV1. Lysine 531 is unique to AAV6 among other known AAV serotypes and is located in a basic cluster near the spikes that surround the icosahedral threefold axes of the AAV capsid. Similar to studies with autonomous parvoviruses, this study describes the first example of single amino acid changes that can explain differential phenotypes such as viral titer, receptor binding, and tissue tropism exhibited by closely related AAV serotypes. In particular, a single lysine residue appears to provide the critical minimum charged surface required for interacting with heparin through electrostatic interaction and simultaneously plays an unrelated yet critical role in the liver tropism of AAV6 vectors.
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Affiliation(s)
- Zhijian Wu
- Gene Therapy Center, 7113 Thurston Building, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7352, USA
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29
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Fisher SZ, Govindasamy L, Boyle N, Agbandje-McKenna M, Silverman DN, Blackburn GM, McKenna R. X-ray crystallographic studies reveal that the incorporation of spacer groups in carbonic anhydrase inhibitors causes alternate binding modes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:618-22. [PMID: 16820676 PMCID: PMC2242956 DOI: 10.1107/s1744309106020446] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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: 03/24/2006] [Accepted: 05/30/2006] [Indexed: 11/10/2022]
Abstract
Human carbonic anhydrases (CAs) are well studied targets for the development of inhibitors for pharmaceutical applications. The crystal structure of human CA II has been determined in complex with two CA inhibitors (CAIs) containing conventional sulfonamide and thiadiazole moieties separated by a -CF2- or -CHNH2- spacer group. The structures presented here reveal that these spacer groups allow novel binding modes for the thiadiazole moiety compared with conventional CAIs.
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Affiliation(s)
- S. Zoë Fisher
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nicholas Boyle
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, England
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - David N. Silverman
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | | | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Correspondence e-mail:
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30
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Clemente JC, Coman RM, Thiaville MM, Janka LK, Jeung JA, Nukoolkarn S, Govindasamy L, Agbandje-McKenna M, McKenna R, Leelamanit W, Goodenow MM, Dunn BM. Analysis of HIV-1 CRF_01 A/E protease inhibitor resistance: structural determinants for maintaining sensitivity and developing resistance to atazanavir. Biochemistry 2006; 45:5468-77. [PMID: 16634628 PMCID: PMC2518317 DOI: 10.1021/bi051886s] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [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] [Indexed: 11/29/2022]
Abstract
A series of HIV-1 protease mutants has been designed in an effort to analyze the contribution to drug resistance provided by natural polymorphisms as well as therapy-selective (active and non-active site) mutations in the HIV-1 CRF_01 A/E (AE) protease when compared to that of the subtype B (B) protease. Kinetic analysis of these variants using chromogenic substrates showed differences in substrate specificity between pretherapy B and AE proteases. Inhibition analysis with ritonavir, indinavir, nelfinavir, amprenavir, saquinavir, lopinavir, and atazanavir revealed that the natural polymorphisms found in A/E can influence inhibitor resistance. It was also apparent that a high level of resistance in the A/E protease, as with B protease, is due to it aquiring a combination of active site and non-active site mutations. Structural analysis of atazanavir bound to a pretherapy B protease showed that the ability of atazanavir to maintain its binding affinity for variants containing some resistance mutations is due to its unique interactions with flap residues. This structure also explains why the I50L and I84V mutations are important in decreasing the binding affinity of atazanavir.
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Affiliation(s)
- José C. Clemente
- Johnson & Johnson Pharmaceutical Research & Development, LLC, 665 Stockton Dr. Exton, PA 19341, University of Florida College of Medicine
| | | | | | | | | | - Sarawut Nukoolkarn
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayuthaya Rd., Bangkok 10400, Thailand
| | | | | | | | - Wichet Leelamanit
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayuthaya Rd., Bangkok 10400, Thailand
| | - Maureen M. Goodenow
- Department of Pathology, Immunology, and Laboratory Medicine, Gainesville, Florida 32610
| | - Ben M. Dunn
- *To whom correspondence should be addressed. Phone: (352) 392-3362, Fax: (352) 846-0412,
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31
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Clemente JC, Govindasamy L, Madabushi A, Fisher SZ, Moose RE, Yowell CA, Hidaka K, Kimura T, Hayashi Y, Kiso Y, Agbandje-McKenna M, Dame JB, Dunn BM, McKenna R. Structure of the aspartic protease plasmepsin 4 from the malarial parasitePlasmodium malariaebound to an allophenylnorstatine-based inhibitor. Acta Crystallogr D Biol Crystallogr 2006; 62:246-52. [PMID: 16510971 DOI: 10.1107/s0907444905041260] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Accepted: 12/08/2005] [Indexed: 11/10/2022]
Abstract
The malarial parasite continues to be one of the leading causes of death in many developing countries. With the development of resistance to the currently available treatments, the discovery of new therapeutics is imperative. Currently, the plasmepsin enzymes found in the food vacuole of the parasite are a chief target for drug development. Allophenylnorstatine-based compounds originally designed to inhibit HIV-1 protease have shown efficacy against all four plasmepsin enzymes found in the food vacuole of Plasmodium falciparum. In this study, the first crystal structure of P. malariae plasmepsin 4 (PmPM4) bound to the allophenylnorstatine-based compound KNI-764 is described at 3.3 Angstroms resolution. The PmPM4-inhibitor complex crystallized in the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 95.9, b = 112.6, c = 90.4 Angstroms, with two molecules in the asymmetric unit related by a non-crystallographic symmetry operator. The structure was refined to a final R factor of 24.7%. The complex showed the inhibitor in an unexpected binding orientation with allophenylnorstatine occupying the S1' pocket. The P2 group was found outside the S2 pocket, wedged between the flap and a juxtaposed loop. Inhibition analysis of PmPM4 also suggests the potential for allophenylnorstatine-based compounds to be effective against all species of malaria infecting humans and for the future development of a broad-based inhibitor.
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Affiliation(s)
- José C Clemente
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, USA
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32
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Fisher SZ, Govindasamy L, Tu C, Agbandje-McKenna M, Silverman DN, Rajaniemi HJ, McKenna R. Structure of human salivary alpha-amylase crystallized in a C-centered monoclinic space group. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:88-93. [PMID: 16511271 PMCID: PMC2150953 DOI: 10.1107/s1744309105042491] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [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: 09/09/2005] [Accepted: 12/19/2005] [Indexed: 11/11/2022]
Abstract
Human salivary alpha-amylase (HSA) is a major secretory protein component of saliva and has important biological functions, including the initial digestion of starch. HSA acts as a monomer and mediates the hydrolysis of alpha-1,4-glucosidic linkages in oligosaccharides. To date, all published crystal structures of HSA have been crystallized as monomers in space group P2(1)2(1)2(1). Here, the serendipitous purification, crystallization and ultimate structure determination of a HSA non-crystallographic symmetry (NCS) dimer, while attempting to purify human carbonic anhydrase VI (HCA VI) from saliva using an affinity resin for alpha-class carbonic anhydrases, is presented. On further investigation, it was shown that HSA could only be copurified using the affinity resin in the presence of HCA VI which is glycosylated and not the non-glycosylated HCA II. The identification of the HSA crystals was carried out by peptide mapping and mass spectrometry. HSA was shown to have crystallized as an NCS dimer in space group C2, with unit-cell parameters a = 150.9, b = 72.3, c = 91.3 A, beta = 102.8 degrees. The NCS dimer crystal structure is reported to 3.0 A resolution, with a refined Rcryst of 0.228. The structure is compared with the previously reported P2(1)2(1)2(1) monomer structures and the crystal packing and dimer interface are discussed.
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Affiliation(s)
- S. Zoë Fisher
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32601, USA
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32601, USA
| | - Chingkuang Tu
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32601, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32601, USA
| | - David N. Silverman
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32601, USA
| | - Hannu J. Rajaniemi
- Department of Anatomy and Cell Biology, PO Box 5000, University of Oulu, Oulu, Finland
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32601, USA
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33
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DiMattia M, Govindasamy L, Levy HC, Gurda-Whitaker B, Kalina A, Kohlbrenner E, Chiorini JA, McKenna R, Muzyczka N, Zolotukhin S, Agbandje-McKenna M. Production, purification, crystallization and preliminary X-ray structural studies of adeno-associated virus serotype 5. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:917-21. [PMID: 16511195 PMCID: PMC1991325 DOI: 10.1107/s1744309105028514] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [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: 05/26/2005] [Accepted: 09/10/2005] [Indexed: 11/10/2022]
Abstract
Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 A resolution using synchrotron radiation and belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 264.7, b = 447.9, c = 629.7 A. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.
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Affiliation(s)
- Michael DiMattia
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Hazel C. Levy
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Brittney Gurda-Whitaker
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Amy Kalina
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Erik Kohlbrenner
- Division of Cell and Molecular Therapy, University of Florida, Gainesville, FL 32610, USA
| | - John A. Chiorini
- GTTB, NIDCR, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Nicholas Muzyczka
- Department of Molecular Genetics and Microbiology and Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Sergei Zolotukhin
- Division of Cell and Molecular Therapy, University of Florida, Gainesville, FL 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
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34
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Kontou M, Govindasamy L, Nam HJ, Bryant N, Llamas-Saiz AL, Foces-Foces C, Hernando E, Rubio MP, McKenna R, Almendral JM, Agbandje-McKenna M. Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice. J Virol 2005; 79:10931-43. [PMID: 16103145 PMCID: PMC1193591 DOI: 10.1128/jvi.79.17.10931-10943.2005] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two strains of the parvovirus minute virus of mice (MVM), the immunosuppressive (MVMi) and the prototype (MVMp) strains, display disparate in vitro tropism and in vivo pathogenicity. We report the crystal structures of MVMp virus-like particles (MVMp(b)) and native wild-type (wt) empty capsids (MVMp(e)), determined and refined to 3.25 and 3.75 A resolution, respectively, and their comparison to the structure of MVMi, also refined to 3.5 A resolution in this study. A comparison of the MVMp(b) and MVMp(e) capsids showed their structures to be the same, providing structural verification that some heterologously expressed parvovirus capsids are indistinguishable from wt capsids produced in host cells. The structures of MVMi and MVMp capsids were almost identical, but local surface conformational differences clustered from symmetry-related capsid proteins at three specific domains: (i) the icosahedral fivefold axis, (ii) the "shoulder" of the protrusion at the icosahedral threefold axis, and (iii) the area surrounding the depression at the icosahedral twofold axis. The latter two domains contain important determinants of MVM in vitro tropism (residues 317 and 321) and forward mutation residues (residues 399, 460, 553, and 558) conferring fibrotropism on MVMi. Furthermore, these structural differences between the MVM strains colocalize with tropism and pathogenicity determinants mapped for other autonomous parvovirus capsids, highlighting the importance of common parvovirus capsid regions in the control of virus-host interactions.
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Affiliation(s)
- Maria Kontou
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, 32610-0245, USA
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35
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Duda DM, Tu C, Fisher SZ, An H, Yoshioka C, Govindasamy L, Laipis PJ, Agbandje-McKenna M, Silverman DN, McKenna R. Human Carbonic Anhydrase III: Structural and Kinetic Study of Catalysis and Proton Transfer,. Biochemistry 2005; 44:10046-53. [PMID: 16042381 DOI: 10.1021/bi050610h] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [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] [Indexed: 11/29/2022]
Abstract
The residue phenylalanine 198 (Phe 198) is a prominent cause of the lower activity of human carbonic anhydrase III (HCA III) compared with HCA II and other isozymes which have leucine at this site. We report the crystal structures of HCA III and the site-directed mutant F198L HCA III, both at 2.1 A resolution, and the enhancement of catalytic activity by exogenous proton donors containing imidazole rings. Both enzymes had a hexahistidine extension at the carboxy-terminal end, used to aid in purification, that was ordered in the crystal structures bound in the active site cavity of an adjacent symmetry-related enzyme. This observation allowed us to comment on a number of possible binding sites for imidazole and derivatives as exogenous proton donors/acceptors in catalysis by HCA III. Kinetic and structural evidence indicates that the phenyl side chain of Phe 198 in HCA III, about 5 A from the zinc, is a steric constriction in the active site, may cause altered interactions at the zinc-bound solvent, and is a binding site for the activation of catalysis by histidylhistidine. This suggests that sites of activation of the proton-transfer pathway in carbonic anhydrase are closer to the zinc than considered in previous studies.
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Affiliation(s)
- David M Duda
- Departments of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
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36
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Padron E, Bowman V, Kaludov N, Govindasamy L, Levy H, Nick P, McKenna R, Muzyczka N, Chiorini JA, Baker TS, Agbandje-McKenna M. Structure of adeno-associated virus type 4. J Virol 2005; 79:5047-58. [PMID: 15795290 PMCID: PMC1069529 DOI: 10.1128/jvi.79.8.5047-5058.2005] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [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] [Indexed: 01/29/2023] Open
Abstract
Adeno-associated virus (AAV) is a member of the Parvoviridae, belonging to the Dependovirus genus. Currently, several distinct isolates of AAV are in development for use in human gene therapy applications due to their ability to transduce different target cells. The need to manipulate AAV capsids for specific tissue delivery has generated interest in understanding their capsid structures. The structure of AAV type 4 (AAV4), one of the most antigenically distinct serotypes, was determined to 13-A resolution by cryo-electron microscopy and image reconstruction. A pseudoatomic model was built for the AAV4 capsid by use of a structure-based sequence alignment of its major capsid protein, VP3, with that of AAV2, to which AAV4 is 58% identical and constrained by its reconstructed density envelope. The model showed variations in the surface loops that may account for the differences in receptor binding and antigenicity between AAV2 and AAV4. The AAV4 capsid surface topology also shows an unpredicted structural similarity to that of Aleutian mink disease virus and human parvovirus B19, autonomous members of the genus, despite limited sequence homology.
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Affiliation(s)
- Eric Padron
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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37
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Govindasamy L, Pedersen B, Lian W, Kukar T, Gu Y, Jin S, Agbandje-McKenna M, Wu D, McKenna R. Structural insights and functional implications of choline acetyltransferase. J Struct Biol 2005; 148:226-35. [PMID: 15477102 DOI: 10.1016/j.jsb.2004.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [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: 03/08/2004] [Revised: 06/01/2004] [Indexed: 11/21/2022]
Abstract
The biosynthetic enzyme for the neurotransmitter acetylcholine, choline acetyltransferase (ChAT) (E.C. 2.3.1.6), is essential for the development and neuronal activities of cholinergic systems involved in many fundamental brain functions. ChAT catalyzes the transfer of an acetyl group from acetyl-coenzyme A to choline to form the neurotransmitter acetylcholine. Since its discovery more than 60 years ago much research has been devoted to the kinetic studies of this enzyme. For the first time we report the crystal structure of rat ChAT (rChAT) to 1.55 A resolution. The structure of rChAT is a monomer and consists of two domains with an interfacial active site tunnel. This structure, with the modeled substrate binding, provides critical insights into the molecular basis for the production of acetylcholine and may further our understanding of disease causing mutations.
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Affiliation(s)
- Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute and University of Florida, Gainesville, FL 32610, USA
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38
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Fisher Z, Hernandez Prada JA, Tu C, Duda D, Yoshioka C, An H, Govindasamy L, Silverman DN, McKenna R. Structural and kinetic characterization of active-site histidine as a proton shuttle in catalysis by human carbonic anhydrase II. Biochemistry 2005; 44:1097-105. [PMID: 15667203 DOI: 10.1021/bi0480279] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [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] [Indexed: 11/29/2022]
Abstract
In the catalysis of the hydration of carbon dioxide and dehydration of bicarbonate by human carbonic anhydrase II (HCA II), a histidine residue (His64) shuttles protons between the zinc-bound solvent molecule and the bulk solution. To evaluate the effect of the position of the shuttle histidine and pH on proton shuttling, we have examined the catalysis and crystal structures of wild-type HCA II and two double mutants: H64A/N62H and H64A/N67H HCA II. His62 and His67 both have their side chains extending into the active-site cavity with distances from the zinc approximately equivalent to that of His64. Crystal structures were determined at pH 5.1-10.0, and the catalysis of the exchange of (18)O between CO(2) and water was assessed by mass spectrometry. Efficient proton shuttle exceeding a rate of 10(5) s(-)(1) was observed for histidine at positions 64 and 67; in contrast, relatively inefficient proton transfer at a rate near 10(3) s(-)(1) was observed for His62. The observation, in the crystal structures, of a completed hydrogen-bonded water chain between the histidine shuttle residue and the zinc-bound solvent does not appear to be required for efficient proton transfer. The data suggest that the number of intervening water molecules between the donor and acceptor supporting efficient proton transfer in HCA II is important, and furthermore suggest that a water bridge consisting of two intervening water molecules is consistent with efficient proton transfer.
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Affiliation(s)
- Zoë Fisher
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
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39
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Govindasamy L, Kukar T, Lian W, Pedersen B, Gu Y, Agbandje-McKenna M, Jin S, McKenna R, Wu D. Structural and mutational characterization of L-carnitine binding to human carnitine acetyltransferase. J Struct Biol 2005; 146:416-24. [PMID: 15099582 DOI: 10.1016/j.jsb.2004.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 12/09/2003] [Revised: 01/23/2004] [Indexed: 11/26/2022]
Abstract
We report the crystal structure of a binary complex of human peroxisomal carnitine acetyltransferase and the substrate l-carnitine, refined to a resolution of 1.8 Angstrom with an R(factor) value of 18.9% (R(free)=22.3%). L-carnitine binds to a preformed pocket in the active site tunnel of carnitine acetyltransferase aligned with His(322). The quaternary nitrogen of carnitine forms a pi-cation interaction with Phe(545), while Arg(497) forms an electrostatic interaction with the negatively charged carboxylate group. An extensive hydrogen bond network also occurs between the carboxylate group and Tyr(431), Thr(444), and a bound water molecule. Site-directed mutagenesis and kinetic characterization reveals that Tyr(431), Thr(444), Arg(497), and Phe(545) are essential for high affinity binding of L-carnitine.
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Affiliation(s)
- Lakshmanan Govindasamy
- Biochemistry and Molecular Biology, University of Florida and The McKnight Brain Institute, 1600 Archer Rd., Gainesville, FL 32610, USA
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40
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Clemente JC, Moose RE, Hemrajani R, Whitford LRS, Govindasamy L, Reutzel R, McKenna R, Agbandje-McKenna M, Goodenow MM, Dunn BM. Comparing the accumulation of active- and nonactive-site mutations in the HIV-1 protease. Biochemistry 2004; 43:12141-51. [PMID: 15379553 DOI: 10.1021/bi049459m] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [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] [Indexed: 11/28/2022]
Abstract
Protease inhibitor resistance still poses one of the greatest challenges in treating HIV. To better design inhibitors able to target resistant proteases, a deeper understanding is needed of the effects of accumulating mutations and the contributions of active- and nonactive-site mutations to the resistance. We have engineered a series of variants containing the nonactive-site mutations M46I and I54V and the active-site mutation I84V. These mutations were added to a protease clone (V6) isolated from a pediatric patient on ritonavir therapy. This variant possessed the ritonavir-resistance-associated mutations in the active-site (V32I and V82A) and nonactive-site mutations (K20R, L33F, M36I, L63P, A71V, and L90M). The I84V mutation had the greatest effect on decreasing catalytic efficiency, 10-fold when compared to the pretherapy clone LAI. The decrease in catalytic efficiency was partially recovered by the addition of mutations M46I and I54V. The M46I and I54V were just as effective at decreasing inhibitor binding as the I84V mutation when compared to V6 and LAI. The V6(54/84) variant showed over 1000-fold decrease in inhibitor-binding strength to ritonavir, indinavir, and nelfinavir when compared to LAI and V6. Crystal-structure analysis of the V6(54/84) variant bound to ritonavir and indinavir shows structural changes in the 80's loops and active site, which lead to an enlarged binding cavity when compared to pretherapy structures in the Protein Data Bank. Structural changes are also seen in the 10's and 30's loops, which suggest possible changes in the dynamics of flap opening and closing.
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Affiliation(s)
- José C Clemente
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610, USA.
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41
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Reutzel R, Yoshioka C, Govindasamy L, Yarmola EG, Agbandje-McKenna M, Bubb MR, McKenna R. Actin crystal dynamics: structural implications for F-actin nucleation, polymerization, and branching mediated by the anti-parallel dimer. J Struct Biol 2004; 146:291-301. [PMID: 15099571 DOI: 10.1016/j.jsb.2003.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2003] [Revised: 12/10/2003] [Indexed: 10/26/2022]
Abstract
Actin filament nucleation, polymerization, and branching are crucial steps in many forms of cell motility, cell shape, and intracellular organelle movements in a wide range of organisms. Previous biochemical data suggests that an anti-parallel actin dimer can incorporate itself into growing filamentous actin (F-actin) and has a role in branching. Furthermore, it is a widespread belief that nucleation is spawned from an actin trimer complex. Here we present the structures of actin dimers and trimers in two tetragonal crystal systems P4(3)2(1)2 and P4(3). Both crystal systems formed by an induced condensation transformation of a previously reported orthorhombic crystal system P2(1)2(1)2(1). Comparison between the three crystal systems demonstrates the dynamics and flexibility of actin-actin interactions. The dimer and trimer actin rearrangements observed between the three crystal systems may provide insight to in vivo actin-actin interactions that occur during the nucleation, polymerization, and branching of F-actin.
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Affiliation(s)
- Robbie Reutzel
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
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42
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Govindasamy L, Reutzel R, Agbandje-McKenna M, McKenna R. Structural determination of a partially hemihedrally twinned actin crystal. Acta Crystallogr D Biol Crystallogr 2004; 60:1040-7. [PMID: 15159563 DOI: 10.1107/s0907444904006948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Accepted: 03/23/2004] [Indexed: 11/10/2022]
Abstract
An orthorhombic actin crystal (space group P2(1)2(1)2(1), unit-cell parameters a = 101.6, b = 103.0, c = 127.0 angstroms) was converted into a partially hemihedrally twinned tetragonal crystal (space group P4(3), unit-cell parameters a = b = 101.5, c = 104.2 angstroms) by induced condensation. This condensation (decrease in the c axis) was caused by the flash-freezing of the crystal, with 30% PEG 400 as a cryoprotectant, prior to data collection. Diffraction data for the twinned tetragonal crystal were collected at 100 K to 3.0 angstroms resolution (99.8% completeness with an Rsym of 8.1%) using synchrotron radiation. The hemihedral twinning of the data was observed by self-rotation function analysis and was determined to have a partial twin fraction of 0.376 from intensity statistics. The structure, with two actin molecules in the crystallographic asymmetric unit, was determined by molecular-replacement methods and refined to an R factor of 0.193. As a consequence of the crystal lattice transformation from the orthorhombic P2(1)2(1)2(1) to the tetragonal P4(3) space group, actin-actin contacts were rearranged and an inter-actin dimer disulfide bond (Cys374) observed in the orthorhombic crystal form was broken in the tetragonal crystal form.
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Affiliation(s)
- Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, University of Florida College of Medicine, Gainesville, Florida 32601, USA
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43
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Lian W, Gu Y, Pedersen B, Kukar T, Govindasamy L, Agbandje-McKenna M, Jin S, McKenna R, Wu D. Crystallization and preliminary X-ray crystallographic studies on recombinant rat choline acetyltransferase. Acta Crystallogr D Biol Crystallogr 2004; 60:374-5. [PMID: 14747730 DOI: 10.1107/s090744490302818x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Accepted: 12/08/2003] [Indexed: 11/10/2022]
Abstract
Choline acetyltransferase (ChAT) catalyzes the biosynthesis of the neurotransmitter acetylcholine from acetyl-CoA and choline in cholinergic neurons. Rat ChAT (rChAT) was overexpressed in Escherichia coli, purified by affinity chromatography and crystallized. Diffraction data were collected from a single crystal under cryoconditions at the F1 beamline at the Cornell High Energy Synchrotron Source, with a maximal useful diffraction pattern to 1.55 A resolution. The crystals were shown to belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 138.97, b = 77.67, c = 59.67 A and a scaling R(sym) of 0.054 for 72 446 unique reflections. Packing considerations indicate there to be one molecule per asymmetric unit. It is expected that in the near future the structure of rChAT will be obtained using molecular-replacement methods. Elucidation of the structure of rChAT will aid in the development of therapeutic agents for Alzheimer's disease.
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Affiliation(s)
- Wei Lian
- Department of Medicinal Chemistry, McKnight Brain Institute and University of Florida, Gainesville, Florida 32610, USA
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44
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Govindasamy L, Hueffer K, Parrish CR, Agbandje-McKenna M. Structures of host range-controlling regions of the capsids of canine and feline parvoviruses and mutants. J Virol 2003; 77:12211-21. [PMID: 14581558 PMCID: PMC254256 DOI: 10.1128/jvi.77.22.12211-12221.2003] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [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] [Indexed: 11/20/2022] Open
Abstract
Canine parvovirus (CPV) and feline panleukopenia virus (FPV) differ in their ability to infect dogs and dog cells. Canine cell infection is a specific property of CPV and depends on the ability of the virus to bind the canine transferrin receptor (TfR), as well as other unidentified factors. Three regions in the capsid structure, located around VP2 residues 93, 300, and 323, can all influence canine TfR binding and canine cell infection. These regions were compared in the CPV and FPV capsid structures that have been determined, as well as in two new structures of CPV capsids that contain substitutions of the VP2 Asn-93 to Asp and Arg, respectively. The new structures, determined by X-ray crystallography to 3.2 and 3.3 A resolutions, respectively, clearly showed differences in the interactions of residue 93 with an adjacent loop on the capsid surface. Each of the three regions show small differences in structure, but each appears to be structurally independent of the others, and the changes likely act together to affect the ability of the capsid to bind the canine TfR and to infect canine cells. This emphasizes the complex nature of capsid alterations that change the virus-cell interaction to allow infection of cells from different hosts.
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Affiliation(s)
- Lakshmanan Govindasamy
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
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45
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Wu D, Govindasamy L, Lian W, Gu Y, Kukar T, Agbandje-McKenna M, McKenna R. Structure of human carnitine acetyltransferase. Molecular basis for fatty acyl transfer. J Biol Chem 2003; 278:13159-65. [PMID: 12562770 DOI: 10.1074/jbc.m212356200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [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] [Indexed: 11/06/2022] Open
Abstract
Carnitine acyltransferases are a family of ubiquitous enzymes that play a pivotal role in cellular energy metabolism. We report here the x-ray structure of human carnitine acetyltransferase to a 1.6-A resolution. This structure reveals a monomeric protein of two equally sized alpha/beta domains. Each domain is shown to have a partially similar fold to other known but oligomeric enzymes that are also involved in group-transfer reactions. The unique monomeric arrangement of the two domains constitutes a central narrow active site tunnel, indicating a likely universal feature for all members of the carnitine acyltransferase family. Superimposition of the substrate complex of a related protein, dihydrolipoyl trans-acetylase, reveals that both substrates localize to the active site tunnel of human carnitine acetyltransferase, suggesting the location of the ligand binding sites for carnitine and coenzyme A. Most significantly, this structure provides critical insights into the molecular basis for fatty acyl chain transfer and a possible common mechanism among a wide range of acyltransferases utilizing a catalytic dyad.
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Affiliation(s)
- Donghai Wu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, USA
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46
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Govindasamy L, Rajakannan V, Velmurugan D, Mohanakrishnan AK, Srinivasan PC. Crystal structure of 3-hydroxy methyl 4,6-dimethoxy-9-phenylsulfonyl-carbazole. Cryst Res Technol 2003. [DOI: 10.1002/crat.200310021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Kaludov N, Padron E, Govindasamy L, McKenna R, Chiorini JA, Agbandje-McKenna M. Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 4. Virology 2003; 306:1-6. [PMID: 12620791 DOI: 10.1016/s0042-6822(02)00037-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adeno-associated virus (AAV) serotypes 1 to 5 are currently under development as clinical gene delivery vectors for the treatment of human diseases. However, the ubiquitous nature of their cell surface receptors, heparin sulfate (AAV2 and 3) and sialic acids (AAV4 and 5), can preclude specific tissue targeting in vivo. Structural studies of AAV4 were initiated to characterize its capsid surface for re-targeting manipulations. Crystals obtained diffracted synchrotron radiation to 3.2 A resolution. The unit cell is body-centered orthorhombic, I222, with a = 339.6, b = 319.2 and c = 285.0 A. The virus particle orientation and position have been determined.
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Affiliation(s)
- Nikola Kaludov
- GTTB, NIDCR, National Institutes of Health, Bethesda, MD 20892, USA
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48
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Duda D, Govindasamy L, Agbandje-McKenna M, Tu C, Silverman DN, McKenna R. The refined atomic structure of carbonic anhydrase II at 1.05 A resolution: implications of chemical rescue of proton transfer. Acta Crystallogr D Biol Crystallogr 2003; 59:93-104. [PMID: 12499545 DOI: 10.1107/s0907444902019455] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2002] [Accepted: 10/22/2002] [Indexed: 11/10/2022]
Abstract
Using synchrotron radiation and a CCD detector, X-ray data have been collected at 100 K for the His64Ala mutant of human carbonic anhydrase II complexed with 4-methylimidazole (4-MI) to a maximal 1.05 A resolution, allowing full anisotropic least-squares refinement. The refined model has a conventional R factor of 15.7% for all reflections. The C(alpha) coordinates of the model presented here have an r.m.s. deviation of 0.10 A relative to the previously determined structure at 1.6 A resolution. Several amino-acid residues (six of the 255 observed) have been identified with multiple rotamer side-chain conformations. C, N and O atoms can be differentiated with selective electron-density map contouring. The estimated standard deviations for all main-chain non-H atom bond lengths and angles are 0.013 and 0.030 A, respectively, based on unrestrained full-matrix least-squares refinement. This structure gives detailed information about the tetrahedrally arranged zinc ion coordinated by three histidine N atoms (His94 N(epsilon 2), His96 N(epsilon2) and His119 N(delta1)) and a water/hydroxide, the multiple binding sites of the proton chemical rescue molecule 4-MI and the solvent networks linking the zinc-bound water/hydroxide and 4-MI molecules. This structure presents the highest resolution structure of a carbonic anhydrase isozyme so far determined and adds to the understanding of proton-transfer processes.
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Affiliation(s)
- David Duda
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
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49
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Reutzel R, Boehlein SK, Govindasamy L, Brenes RB, Agbandje-McKenna M, Schuster SM, McKenna R. Crystallization and preliminary X-ray analysis of the tumor metastasis factor p37. Acta Crystallogr D Biol Crystallogr 2002; 58:2141-4. [PMID: 12454480 DOI: 10.1107/s0907444902015536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2002] [Accepted: 08/27/2002] [Indexed: 11/10/2022]
Abstract
P37, an outer-membrane bacterial protein from Mycoplasma hyorhinis, is a molecule whose presence on the surface of many tumor cells correlates highly with increased neoplastic invasivity and metastasis. P37 was overexpressed in Escherichia coli, purified by affinity chromatography and crystallized. Useful single crystals for X-ray diffraction structural studies have been grown by oil-immersion methods from a solution of 40% PEG 4000, 0.1 M ammonium bromide in a 0.1 M citrate buffer at pH 4.0. X-ray diffraction data were collected at the F2 beamline at CHESS with a crystal-to-CCD detector distance of 150 mm, collecting 1 degrees oscillation slices with an exposure time of 30 s per frame. A 212 degrees sweep of data (99.8% completeness) were collected from a single crystal under cryoconditions, with a maximal useful diffraction pattern to 1.8 A resolution. The crystals are shown to be monoclinic and have been assigned to space group P2(1), with unit-cell parameters a = 50.02, b = 67.26, c = 59.89 A, beta = 108.29 degrees and a scaling R(sym) of 0.076 for 34,882 unique reflections. Packing considerations indicate that there is one molecule per asymmetric unit. It is expected that in the near future the structure of p37 will be obtained using phases from traditional heavy-atom isomorphous replacement and/or halide-soak methods. Elucidation of the structure of p37 may be paramount to producing new antibody-based anticancer therapeutic agents.
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Affiliation(s)
- Robbie Reutzel
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
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Govindasamy L, Rajakannan V, Velmurugan D, Shanmuga Sundara Raj S, Rajendran TM, Venkatesan R, Srinivasan R, Fun HK. Crystal Structure of Dimeric Cu(II) Complex {μ,μ'-acetato O,O bis [N-salicylidene-2-amino-pyridine-methanolato N,N,O]} : perchlorate. Cryst Res Technol 2002. [DOI: 10.1002/1521-4079(200209)37:9<1018::aid-crat1018>3.0.co;2-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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