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Title: Humidity control as a strategy for lattice optimization applied to crystals of HLA-A*1101 complexed with variant peptides from dengue virus

Abstract

Crystals of an MHC class I molecule bound to naturally occurring peptide variants from the dengue virus NS3 protein contained high levels of solvent and required optimization of cryoprotectant and dehydration protocols for each complex to yield well ordered diffraction, a process facilitated by the use of a free-mounting system. T-cell recognition of the antigenic peptides presented by MHC class I molecules normally triggers protective immune responses, but can result in immune enhancement of disease. Cross-reactive T-cell responses may underlie immunopathology in dengue haemorrhagic fever. To analyze these effects at the molecular level, the functional MHC class I molecule HLA-A*1101 was crystallized bound to six naturally occurring peptide variants from the dengue virus NS3 protein. The crystals contained high levels of solvent and required optimization of the cryoprotectant and dehydration protocols for each complex to yield well ordered diffraction, a process that was facilitated by the use of a free-mounting system.

Authors:
 [1];  [2]; ;  [3];  [1];  [2]; ; ; ;  [3];  [4];  [5];  [1];  [1];  [2];  [3];  [6]
  1. Department of Immunology, Division of Medicine, Hammersmith Hospital, Imperial College, London (United Kingdom)
  2. (Thailand)
  3. Division of Structural Biology and Oxford Protein Production Facility (OPPF), The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Headington, Oxford OX3 7BN (United Kingdom)
  4. Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University (Thailand)
  5. (BIOTEC), National Science and Technology Development Agency, Pathumthani, Bangkok (Thailand)
  6. (United Kingdom)
Publication Date:
OSTI Identifier:
22360322
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section F; Journal Volume: 63; Journal Issue: Pt 5; Other Information: PMCID: PMC2334998; PMID: 17565177; PUBLISHER-ID: en5229; OAI: oai:pubmedcentral.nih.gov:2334998; Copyright (c) International Union of Crystallography 2007; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United Kingdom
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; CRYSTALS; DEHYDRATION; DIFFRACTION; MOLECULES; OPTIMIZATION; SOLVENTS; YIELDS

Citation Formats

Chotiyarnwong, Pojchong, Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University, Stewart-Jones, Guillaume B., Tarry, Michael J., Dejnirattisai, Wanwisa, Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University, Siebold, Christian, Koch, Michael, Stuart, David I., Harlos, Karl, Malasit, Prida, Medical Biotechnology Unit, National Center for Genetic Engineering and Biotechnology, Screaton, Gavin, Mongkolsapaya, Juthathip, E-mail: j.mongkolsapaya@imperial.ac.uk, Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University, Jones, E. Yvonne, E-mail: j.mongkolsapaya@imperial.ac.uk, and Department of Immunology, Division of Medicine, Hammersmith Hospital, Imperial College, London. Humidity control as a strategy for lattice optimization applied to crystals of HLA-A*1101 complexed with variant peptides from dengue virus. United Kingdom: N. p., 2007. Web. doi:10.1107/S1744309107013693.
Chotiyarnwong, Pojchong, Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University, Stewart-Jones, Guillaume B., Tarry, Michael J., Dejnirattisai, Wanwisa, Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University, Siebold, Christian, Koch, Michael, Stuart, David I., Harlos, Karl, Malasit, Prida, Medical Biotechnology Unit, National Center for Genetic Engineering and Biotechnology, Screaton, Gavin, Mongkolsapaya, Juthathip, E-mail: j.mongkolsapaya@imperial.ac.uk, Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University, Jones, E. Yvonne, E-mail: j.mongkolsapaya@imperial.ac.uk, & Department of Immunology, Division of Medicine, Hammersmith Hospital, Imperial College, London. Humidity control as a strategy for lattice optimization applied to crystals of HLA-A*1101 complexed with variant peptides from dengue virus. United Kingdom. doi:10.1107/S1744309107013693.
Chotiyarnwong, Pojchong, Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University, Stewart-Jones, Guillaume B., Tarry, Michael J., Dejnirattisai, Wanwisa, Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University, Siebold, Christian, Koch, Michael, Stuart, David I., Harlos, Karl, Malasit, Prida, Medical Biotechnology Unit, National Center for Genetic Engineering and Biotechnology, Screaton, Gavin, Mongkolsapaya, Juthathip, E-mail: j.mongkolsapaya@imperial.ac.uk, Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University, Jones, E. Yvonne, E-mail: j.mongkolsapaya@imperial.ac.uk, and Department of Immunology, Division of Medicine, Hammersmith Hospital, Imperial College, London. Tue . "Humidity control as a strategy for lattice optimization applied to crystals of HLA-A*1101 complexed with variant peptides from dengue virus". United Kingdom. doi:10.1107/S1744309107013693.
@article{osti_22360322,
title = {Humidity control as a strategy for lattice optimization applied to crystals of HLA-A*1101 complexed with variant peptides from dengue virus},
author = {Chotiyarnwong, Pojchong and Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University and Stewart-Jones, Guillaume B. and Tarry, Michael J. and Dejnirattisai, Wanwisa and Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University and Siebold, Christian and Koch, Michael and Stuart, David I. and Harlos, Karl and Malasit, Prida and Medical Biotechnology Unit, National Center for Genetic Engineering and Biotechnology and Screaton, Gavin and Mongkolsapaya, Juthathip, E-mail: j.mongkolsapaya@imperial.ac.uk and Medical Molecular Biology Unit, Faculty of Medicine, Siriraj Hospital, Mahidol University and Jones, E. Yvonne, E-mail: j.mongkolsapaya@imperial.ac.uk and Department of Immunology, Division of Medicine, Hammersmith Hospital, Imperial College, London},
abstractNote = {Crystals of an MHC class I molecule bound to naturally occurring peptide variants from the dengue virus NS3 protein contained high levels of solvent and required optimization of cryoprotectant and dehydration protocols for each complex to yield well ordered diffraction, a process facilitated by the use of a free-mounting system. T-cell recognition of the antigenic peptides presented by MHC class I molecules normally triggers protective immune responses, but can result in immune enhancement of disease. Cross-reactive T-cell responses may underlie immunopathology in dengue haemorrhagic fever. To analyze these effects at the molecular level, the functional MHC class I molecule HLA-A*1101 was crystallized bound to six naturally occurring peptide variants from the dengue virus NS3 protein. The crystals contained high levels of solvent and required optimization of the cryoprotectant and dehydration protocols for each complex to yield well ordered diffraction, a process that was facilitated by the use of a free-mounting system.},
doi = {10.1107/S1744309107013693},
journal = {Acta Crystallographica. Section F},
number = Pt 5,
volume = 63,
place = {United Kingdom},
year = {Tue May 01 00:00:00 EDT 2007},
month = {Tue May 01 00:00:00 EDT 2007}
}
  • Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents anmore » interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration.« less
  • The production and crystallization of human leukocyte antigen class II molecules HLA-DQ2 and HLA-DQ8 in complex with deamidated gliadin peptides is reported. Crystals of HLA-DQ2{sup PQPELPYPQ} diffracted to 3.9 Å, while the HLA-DQ8{sup EGSFQPSQE} crystals diffracted to 2.1 Å, allowing structure determination by molecular replacement. The major histocompatibility complex (MHC) class II molecules HLA-DQ2 and HLA-DQ8 are key risk factors in coeliac disease, as they bind deamidated gluten peptides that are subsequently recognized by CD4{sup +} T cells. Here, the production and crystallization of both HLA-DQ2 and HLA-DQ8 in complex with the deamidated gliadin peptides DQ2 α-I (PQPELPYPQ) and DQ8more » α-I (EGSFQPSQE), respectively, are reported.« less
  • Flavivirus assembles into an inert particle that requires proteolytic activation by furin to enable transmission to other hosts. We previously showed that immature virus undergoes a conformational change at low pH that renders it accessible to furin (I. M. Yu, W. Zhang, H. A. Holdaway, L. Li, V. A. Kostyuchenko, P. R. Chipman, R. J. Kuhn, M. G. Rossmann, and J. Chen, Science 319:1834-1837, 2008). Here we show, using cryoelectron microscopy, that the structure of immature dengue virus at pH 6.0 is essentially the same before and after the cleavage of prM. The structure shows that after cleavage, the proteolyticmore » product pr remains associated with the virion at acidic pH, and that furin cleavage by itself does not induce any major conformational changes. We also show by liposome cofloatation experiments that pr retention prevents membrane insertion, suggesting that pr is present on the virion in the trans-Golgi network to protect the progeny virus from fusion within the host cell.« less
  • Studies of icosahedral virus capsids provide insights into the function of supramolecular machines. Virus capsid crystals have exceptionally large unit cells; as a result, they diffract weakly compared with protein crystals. HK97 is a dsDNA lambda-like bacteriophage whose 13 MDa capsid expands from 550 {angstrom} to 650 {angstrom} with large subunit conformational changes during virus maturation. The HK97 penultimate maturation intermediate was crystallized in a tetragonal unit cell that has lattice constants of 1010 {angstrom} x 1010 {angstrom} x 730 {angstrom}. The crystals could be cryoprotected, but diffracted to a modest resolution of 5 {angstrom} at a bending-magnet beamline. Whenmore » these crystals were optimally exposed with two orders-of-magnitude more photons from a new insertion-device beamline, data extending to better than 3.8 {angstrom} resolution were obtained. Here, the strategies to collect and process such data are described. These strategies can be adapted for other crystals with large unit cells and for microcrystals.« less