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Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. Some of the most interesting CASP11 targets through the eyes of their authors. Proteins 2015; 84 Suppl 1:34-50. [PMID: 26473983 PMCID: PMC4834066 DOI: 10.1002/prot.24942] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/17/2015] [Accepted: 10/11/2015] [Indexed: 11/17/2022]
Abstract
The Critical Assessment of protein Structure Prediction (CASP) experiment would not have been possible without the prediction targets provided by the experimental structural biology community. In this article, selected crystallographers providing targets for the CASP11 experiment discuss the functional and biological significance of the target proteins, highlight their most interesting structural features, and assess whether these features were correctly reproduced in the predictions submitted to CASP11. Proteins 2016; 84(Suppl 1):34–50. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Alex Burgin
- Broad Institute, Cambridge, Massachusetts, 02142
| | | | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, California, 92182.,Department of Computer Science, San Diego State University, San Diego, California, 92182
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Mateusz Korycinski
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | | | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Janet Newman
- Biomedical Manufacturing Program, CSIRO, Parkville, VIC, Australia
| | - Thomas S Peat
- Biomedical Manufacturing Program, CSIRO, Parkville, VIC, Australia
| | - Kurt H Piepenbrink
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Janani Prahlad
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
| | - Mark J van Raaij
- Centro Nactional De Biotecnologia (CNB-CSIC), Madrid, E-28049, Spain
| | - Forest Rohwer
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, California, 92182
| | - Anca M Segall
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, California, 92182
| | | | - Eric J Sundberg
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, 21201.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, 21201.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Abhimanyu K Singh
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, 4056, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland.
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Crystal structure of the fibre head domain of the Atadenovirus Snake Adenovirus 1. PLoS One 2014; 9:e114373. [PMID: 25486282 PMCID: PMC4259310 DOI: 10.1371/journal.pone.0114373] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/06/2014] [Indexed: 02/05/2023] Open
Abstract
Adenoviruses are non-enveloped icosahedral viruses with trimeric fibre proteins protruding from their vertices. There are five known genera, from which only Mastadenoviruses have been widely studied. Apart from studying adenovirus as a biological model system and with a view to prevent or combat viral infection, there is a major interest in using adenovirus for vaccination, cancer therapy and gene therapy purposes. Adenoviruses from the Atadenovirus genus have been isolated from squamate reptile hosts, ruminants and birds and have a characteristic gene organization and capsid morphology. The carboxy-terminal virus-distal fibre head domains are likely responsible for primary receptor recognition. We determined the high-resolution crystal structure of the Snake Adenovirus 1 (SnAdV-1) fibre head using the multi-wavelength anomalous dispersion (MAD) method. Despite the absence of significant sequence homology, this Atadenovirus fibre head has the same beta-sandwich propeller topology as other adenovirus fibre heads. However, it is about half the size, mainly due to much shorter loops connecting the beta-strands. The detailed structure of the SnAdV-1 fibre head and other animal adenovirus fibre heads, together with the future identification of their natural receptors, may lead to the development of new strategies to target adenovirus vectors to cells of interest.
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Neutralization of Virus Infectivity by Antibodies: Old Problems in New Perspectives. ACTA ACUST UNITED AC 2014; 2014. [PMID: 27099867 DOI: 10.1155/2014/157895] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Neutralizing antibodies (NAbs) can be both sufficient and necessary for protection against viral infections, although they sometimes act in concert with cellular immunity. Successful vaccines against viruses induce NAbs but vaccine candidates against some major viral pathogens, including HIV-1, have failed to induce potent and effective such responses. Theories of how antibodies neutralize virus infectivity have been formulated and experimentally tested since the 1930s; and controversies about the mechanistic and quantitative bases for neutralization have continually arisen. Soluble versions of native oligomeric viral proteins that mimic the functional targets of neutralizing antibodies now allow the measurement of the relevant affinities of NAbs. Thereby the neutralizing occupancies on virions can be estimated and related to the potency of the NAbs. Furthermore, the kinetics and stoichiometry of NAb binding can be compared with neutralizing efficacy. Recently, the fundamental discovery that the intracellular factor TRIM21 determines the degree of neutralization of adenovirus has provided new mechanistic and quantitative insights. Since TRIM21 resides in the cytoplasm, it would not affect the neutralization of enveloped viruses, but its range of activity against naked viruses will be important to uncover. These developments bring together the old problems of virus neutralization-mechanism, stoichiometry, kinetics, and efficacy-from surprising new angles.
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Singh AK, Menéndez-Conejero R, San Martín C, van Raaij MJ. Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1374-9. [PMID: 24316834 PMCID: PMC3855724 DOI: 10.1107/s1744309113029308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/23/2013] [Indexed: 11/10/2022]
Abstract
Adenovirus fibre proteins play an important role in determining viral tropism. The C-terminal domain of the fibre protein from snake adenovirus type 1, a member of the Atadenovirus genus, has been expressed, purified and crystallized. Crystals were obtained belonging to space groups P2(1)2(1)2(1) (two different forms), I2(1)3 and F23. The best of these diffracted synchrotron radiation to a resolution of 1.4 Å. As the protein lacks methionines or cysteines, site-directed mutagenesis was performed to change two leucine residues to methionines. Crystals of selenomethionine-derivatized crystals of the I2(1)3 form were also obtained and a multi-wavelength anomalous dispersion data set was collected.
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Affiliation(s)
- Abhimanyu K. Singh
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB–CSIC), Calle Darwin 3, 28049 Madrid, Spain
| | - Rosa Menéndez-Conejero
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB–CSIC), Calle Darwin 3, 28049 Madrid, Spain
| | - Carmen San Martín
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB–CSIC), Calle Darwin 3, 28049 Madrid, Spain
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB–CSIC), Calle Darwin 3, 28049 Madrid, Spain
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Graziano V, McGrath WJ, Suomalainen M, Greber UF, Freimuth P, Blainey PC, Luo G, Xie XS, Mangel WF. Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: I. binding to DNA AND to hexon of the precursor to protein VI, pVI, of human adenovirus. J Biol Chem 2013; 288:2059-67. [PMID: 23043136 PMCID: PMC3548512 DOI: 10.1074/jbc.m112.377150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 08/02/2012] [Indexed: 11/06/2022] Open
Abstract
The precursor to adenovirus protein VI, pVI, is a multifunctional protein with different roles early and late in virus infection. Here, we focus on two roles late in infection, binding of pVI to DNA and to the major capsid protein hexon. pVI bound to DNA as a monomer independent of DNA sequence with an apparent equilibrium dissociation constant, K(d)((app)), of 46 nm. Bound to double-stranded DNA, one molecule of pVI occluded 8 bp. Upon the binding of pVI to DNA, three sodium ions were displaced from the DNA. A ΔG(0)(0) of -4.54 kcal/mol for the nonelectrostatic free energy of binding indicated that a substantial component of the binding free energy resulted from nonspecific interactions between pVI and DNA. The proteolytically processed, mature form of pVI, protein VI, also bound to DNA; its K(d)((app)) was much higher, 307 nm. The binding assays were performed in 1 mm MgCl(2) because in the absence of magnesium, the binding to pVI or protein VI to DNA was too tight to determine a K(d)((app)). Three molecules of pVI bound to one molecule of the hexon trimer with an equilibrium dissociation constant K(d)((app)) of 1.1 nm.
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Affiliation(s)
- Vito Graziano
- From the Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - William J. McGrath
- From the Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Maarit Suomalainen
- the Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, and
| | - Urs F. Greber
- the Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, and
| | - Paul Freimuth
- From the Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Paul C. Blainey
- the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Guobin Luo
- the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - X. Sunney Xie
- the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Walter F. Mangel
- From the Biology Department, Brookhaven National Laboratory, Upton, New York 11973
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Boyd JM, Loewenstein PM, Tang Qq QQ, Yu L, Green M. Adenovirus E1A N-terminal amino acid sequence requirements for repression of transcription in vitro and in vivo correlate with those required for E1A interference with TBP-TATA complex formation. J Virol 2002; 76:1461-74. [PMID: 11773419 PMCID: PMC135854 DOI: 10.1128/jvi.76.3.1461-1474.2002] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2001] [Accepted: 10/17/2001] [Indexed: 11/20/2022] Open
Abstract
The adenovirus (Ad) E1A 243R oncoprotein encodes an N-terminal transcription repression domain that is essential for early viral functions, cell immortalization, and cell transformation. The transcription repression function requires sequences within amino acids 1 to 30 and 48 to 60. To elucidate the roles of the TATA-binding protein (TBP), p300, and the CREB-binding protein (CBP) in the mechanism(s) of E1A repression, we have constructed 29 amino acid substitution mutants and 5 deletion mutants spanning the first 30 amino acids within the E1A 1-80 polypeptide backbone. These mutant E1A polypeptides were characterized with regard to six parameters: the ability to repress transcription in vitro and in vivo, to disrupt TBP-TATA box interaction, and to bind TBP, p300, and CBP. Two regions within E1A residues 1 to 30, amino acids 2 to 6 and amino acid 20, are critical for E1A transcription repression in vitro and in vivo and for the ability to interfere with TBP-TATA interaction. Replacement of 6Cys with Ala in the first region yields the most defective mutant. Replacement of 20Leu with Ala, but not substitutions in flanking residues, yields a substantially defective phenotype. Protein binding assays demonstrate that replacement of 6Cys with Ala yields a mutant completely defective in interaction with TBP, p300, and CBP. Our findings are consistent with a model in which the E1A repression function involves interaction of E1A with p300/CBP and interference with the formation of a TBP-TATA box complex.
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Affiliation(s)
- Janice M Boyd
- Institute for Molecular Virology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, USA
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Pring-Akerblom P, Trijssenaar FE, Adrian T. Hexon sequence of adenovirus type 7 and comparison with other serotypes of subgenus B. RESEARCH IN VIROLOGY 1995; 146:383-388. [PMID: 8834754 DOI: 10.1016/0923-2516(96)80897-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The hexon gene of human adenovirus (AV) type 7 (subgenus B) was sequenced. The determined nucleotide and the predicted amino acid sequences were compared to the corresponding sequences of AV3 and AV16. The hexons of AV7 and AV3 revealed an overall homology of 94.3% at the protein level, whereas the AV7 and AV16 hexons only showed an overall homology of 85.7%. Utilizing the three-dimensional model of the AV2 hexon, the structure of the AV7 hexon was predicted. The major differences between the three subgenus B hexon polypeptides were confined to the I1 and I2 surface loops. The AV7 I4 hexon loop was 100% identical to the other subgenus B I4 loops, but differed from the corresponding regions of other subgenera. This supports the idea that this loop carries a subgenus-specific determinant.
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Affiliation(s)
- P Pring-Akerblom
- Institut für Virologie und Seuchenhygiene, Medizinische Hochschule Hannover, Germany
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