西尼罗河病毒非结构蛋白结构与功能的Flavitrack分析
Flavitrack analysis of the structure and function of West Nile non-structural proteins.
作者信息
Danecek Petr, Schein Catherine H
机构信息
Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX 77555-0857, USA.
出版信息
Int J Bioinform Res Appl. 2010;6(2):134-46. doi: 10.1504/IJBRA.2010.032117.
Abstract
The Flavitrack database groups Flaviviruses (FV), evolutionarily related organisms with high subtype variability, according to their phenotypes. Here, PCPMer tools were used to calculate consensus sequences based on conservation of Physicochemical Properties (PCP) for 919 sequences of NS2a, a non-structural protein involved in preventing host interferon response to infection. Conserved PCP-motifs were detected, primarily in the N-terminal half of NS2a. One model structure, based on a nuclear receptor, groups residues essential for West Nile (WN) infectivity (I59, V61, and M103) in a pocket on the protein surface. These methods will aid in the design of vaccines and specific therapies against FV.
摘要
Flavitrack数据库根据黄病毒（FV）的表型对其进行分组，黄病毒是进化相关且具有高亚型变异性的生物体。在此，使用PCPMer工具基于物理化学性质（PCP）的保守性计算了919条NS2a序列的共有序列，NS2a是一种参与阻止宿主对感染产生干扰素反应的非结构蛋白。检测到保守的PCP基序，主要位于NS2a的N端一半区域。一种基于核受体的模型结构将西尼罗河病毒（WN）感染性所必需的残基（I59、V61和M103）聚集在蛋白质表面的一个口袋中。这些方法将有助于设计针对黄病毒的疫苗和特异性疗法。
相似文献
1
Flavitrack analysis of the structure and function of West Nile non-structural proteins.
Int J Bioinform Res Appl. 2010;6(2):134-46. doi: 10.1504/IJBRA.2010.032117.
2
Flavitrack: an annotated database of flavivirus sequences.
Bioinformatics. 2007 Oct 1;23(19):2645-7. doi: 10.1093/bioinformatics/btm383. Epub 2007 Jul 28.
3
PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.
J Mol Biol. 2010 Feb 26;396(3):550-63. doi: 10.1016/j.jmb.2009.11.070. Epub 2009 Dec 4.
4
A single amino acid substitution in the West Nile virus nonstructural protein NS2A disables its ability to inhibit alpha/beta interferon induction and attenuates virus virulence in mice.
J Virol. 2006 Mar;80(5):2396-404. doi: 10.1128/JVI.80.5.2396-2404.2006.
5
Noncoding Subgenomic Flavivirus RNA Is Processed by the Mosquito RNA Interference Machinery and Determines West Nile Virus Transmission by Culex pipiens Mosquitoes.
J Virol. 2016 Oct 28;90(22):10145-10159. doi: 10.1128/JVI.00930-16. Print 2016 Nov 15.
6
Molecular and functional analyses of Kunjin virus infectious cDNA clones demonstrate the essential roles for NS2A in virus assembly and for a nonconservative residue in NS3 in RNA replication.
J Virol. 2003 Jul;77(14):7804-13. doi: 10.1128/jvi.77.14.7804-7813.2003.
7
Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains.
Biochem Biophys Res Commun. 2017 Oct 28;492(4):565-571. doi: 10.1016/j.bbrc.2017.01.041. Epub 2017 Jan 11.
8
Nucleotide and complete amino acid sequences of Kunjin virus: definitive gene order and characteristics of the virus-specified proteins.
J Gen Virol. 1988 Jan;69 ( Pt 1):1-21. doi: 10.1099/0022-1317-69-1-1.
9
West Nile virus, Anopheles flavivirus, a novel flavivirus as well as Merida-like rhabdovirus Turkey in field-collected mosquitoes from Thrace and Anatolia.
Infect Genet Evol. 2018 Jan;57:36-45. doi: 10.1016/j.meegid.2017.11.003. Epub 2017 Nov 8.
10
Co-circulation of West Nile virus and distinct insect-specific flaviviruses in Turkey.
Parasit Vectors. 2017 Mar 20;10(1):149. doi: 10.1186/s13071-017-2087-7.
引用本文的文献
1
DGraph Clusters Flaviviruses and β-Coronaviruses According to Their Hosts, Disease Type, and Human Cell Receptors.
Bioinform Biol Insights. 2021 Jun 7;15:11779322211020316. doi: 10.1177/11779322211020316. eCollection 2021.
2
Designing multivalent immunogens for alphavirus vaccine optimization.
Virology. 2021 Sep;561:117-124. doi: 10.1016/j.virol.2020.11.010. Epub 2021 Feb 5.
3
D-graph clusters flaviviruses and β-coronaviruses according to their hosts, disease type and human cell receptors.
bioRxiv. 2020 Aug 14:2020.08.13.249649. doi: 10.1101/2020.08.13.249649.
4
NS2A comprises a putative viroporin of Dengue virus 2.
Virulence. 2017 Oct 3;8(7):1450-1456. doi: 10.1080/21505594.2017.1356540. Epub 2017 Jul 19.
5
Allosteric inhibitors of Coxsackie virus A24 RNA polymerase.
Bioorg Med Chem. 2016 Feb 15;24(4):570-7. doi: 10.1016/j.bmc.2015.12.023. Epub 2015 Dec 15.
6
Sequence specificity for uridylylation of the viral peptide linked to the genome (VPg) of enteroviruses.
Virology. 2015 Oct;484:80-85. doi: 10.1016/j.virol.2015.05.016. Epub 2015 Jun 11.
7
Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals.
BMC Bioinformatics. 2012;13 Suppl 13(Suppl 13):S9. doi: 10.1186/1471-2105-13-S13-S9. Epub 2012 Aug 24.
8
Simplifying complex sequence information: a PCP-consensus protein binds antibodies against all four Dengue serotypes.
Vaccine. 2012 Sep 14;30(42):6081-7. doi: 10.1016/j.vaccine.2012.07.042. Epub 2012 Jul 31.
9
NMR solution structure of poliovirus uridylyated peptide linked to the genome (VPgpU).
Peptides. 2010 Aug;31(8):1441-8. doi: 10.1016/j.peptides.2010.04.021. Epub 2010 May 2.
10
PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.
J Mol Biol. 2010 Feb 26;396(3):550-63. doi: 10.1016/j.jmb.2009.11.070. Epub 2009 Dec 4.
本文引用的文献
1
Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes.
Mol Immunol. 2008 Aug;45(14):3740-7. doi: 10.1016/j.molimm.2008.05.026. Epub 2008 Jul 14.
2
Role of nonstructural protein NS2A in flavivirus assembly.
J Virol. 2008 May;82(10):4731-41. doi: 10.1128/JVI.00002-08. Epub 2008 Mar 12.
3
Pathogenic flaviviruses.
Lancet. 2008 Feb 9;371(9611):500-9. doi: 10.1016/S0140-6736(08)60238-X.
4
Aplysia temptin - the 'glue' in the water-borne attractin pheromone complex.
FEBS J. 2007 Oct;274(20):5425-37. doi: 10.1111/j.1742-4658.2007.06070.x. Epub 2007 Sep 26.
5
Towards a dengue vaccine: progress to date and remaining challenges.
Comp Immunol Microbiol Infect Dis. 2008 Mar;31(2-3):239-52. doi: 10.1016/j.cimid.2007.07.011. Epub 2007 Sep 21.
6
The continuing spread of West Nile virus in the western hemisphere.
Clin Infect Dis. 2007 Oct 15;45(8):1039-46. doi: 10.1086/521911. Epub 2007 Sep 14.
7
Clustal W and Clustal X version 2.0.
Bioinformatics. 2007 Nov 1;23(21):2947-8. doi: 10.1093/bioinformatics/btm404. Epub 2007 Sep 10.
8
Flavitrack: an annotated database of flavivirus sequences.
Bioinformatics. 2007 Oct 1;23(19):2645-7. doi: 10.1093/bioinformatics/btm383. Epub 2007 Jul 28.
9
Characterization of a small plaque variant of West Nile virus isolated in New York in 2000.
Virology. 2007 Oct 25;367(2):339-47. doi: 10.1016/j.virol.2007.06.008. Epub 2007 Jul 6.
10
Mutations in West Nile virus nonstructural proteins that facilitate replicon persistence in vitro attenuate virus replication in vitro and in vivo.
Virology. 2007 Jul 20;364(1):184-95. doi: 10.1016/j.virol.2007.02.009. Epub 2007 Mar 23.
Zotero 插件