title: Determining interdomain structure and dynamics of a retroviral capsid protein in the presence of oligomerization: implication for structural transition in capsid assembly.
abstract: Capsid (CA) proteins from all retroviruses, including HIV-1, are structurally homologous dual-domain helical proteins. They form a capsid lattice composed of unitary symmetric CA hexamers. X-ray crystallography has shown that within each hexamer a monomeric CA adopts a single conformation, where most helices are parallel to the symmetry axis. In solution, large differences in averaged NMR spin relaxation rates for the two domains were observed, suggesting they are dynamically independent. One relevant question for the capsid assembly remains: whether the interdomain conformer within a hexamer unit needs to be induced or pre-exists within the conformational space of a monomeric CA. The latter seems more consistent with the relaxation data. However, possible CA protein oligomerization and the structure of each domain will affect relaxation measurements and data interpretation. This study, using CA proteins from equine infectious anemia virus (EIAV) as an example, demonstrates a linear extrapolation approach to obtain backbone (15)N spin relaxation time ratios T1/T2 for a monomeric EIAV-CA in the presence of oligomerization equilibrium. The interdomain motion turns out to be limited. The large difference in the domain averaged <T1/T2> for a CA monomer is a consequence of the orthogonal distributions of helices in the two domains. The new monomeric interdomain conformation in solution is significantly different from that in CA hexamer. Therefore, if capsid assembly follows a nucleation-propagation process, the interdomain conformational change might be a key step during the nucleation, as the configuration in hexagonal assembly is never formed by diffusion of its two domains in solution.
authors.affiliation: Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Kang
authors.initials: K
authors.lastname: Chen
authors.forename: Nico
authors.initials: N
authors.lastname: Tjandra
mesh_terms: D002213:Capsid / Q000378:metabolism; D036022:Capsid Proteins / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D004860:Infectious Anemia Virus, Equine / Q000235:genetics* / Q000378:metabolism; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D012190:Retroviridae / Q000235:genetics / Q000378:metabolism
chemical_list: D036022:Capsid Proteins
references.citation: Structure. 2002 Jul;10(7):901-11
references.pmid: 12121645
references.citation: Science. 1996 Jul 12;273(5272):231-5
references.pmid: 8662505
references.citation: Biochemistry. 1999 Aug 10;38(32):10225-30
references.pmid: 10441115
references.citation: Science. 1999 Jan 1;283(5398):80-3
references.pmid: 9872746
references.citation: J Am Chem Soc. 2007 Jun 27;129(25):7894-902
references.pmid: 17550252
references.citation: Cell. 2007 Oct 5;131(1):70-9
references.pmid: 17923088
references.citation: Cell. 2009 Nov 13;139(4):780-90
references.pmid: 19914170
references.citation: J Chem Phys. 2012 Jan 21;136(3):034108
references.pmid: 22280745
references.citation: Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11016-21
references.pmid: 19541602
references.citation: Biochem Biophys Res Commun. 1989 Apr 28;160(2):486-94
references.pmid: 2541703
references.citation: Nature. 2004 Sep 23;431(7007):481-5
references.pmid: 15386017
references.citation: J Am Chem Soc. 2009 Jul 15;131(27):9522-31
references.pmid: 19537713
references.citation: J Mol Biol. 2000 Feb 18;296(2):633-49
references.pmid: 10669613
references.citation: EMBO J. 2003 Apr 1;22(7):1707-15
references.pmid: 12660176
references.citation: J Biomol NMR. 2011 Sep;51(1-2):131-50
references.pmid: 21947922
references.citation: Chem Rev. 2004 Aug;104(8):3623-40
references.pmid: 15303831
references.citation: Nature. 2009 Feb 5;457(7230):694-8
references.pmid: 19194444
references.citation: J Am Chem Soc. 2003 Sep 17;125(37):11379-84
references.pmid: 16220961
references.citation: J Am Chem Soc. 2010 May 5;132(17):5987-9
references.pmid: 20392103
references.citation: J Virol. 1992 Aug;66(8):4874-83
references.pmid: 1629958
references.citation: J Am Chem Soc. 2001 May 2;123(17):3953-9
references.pmid: 11457145
references.citation: Magn Reson Chem. 2006 Jul;44 Spec No:S143-51
references.pmid: 16823894
references.citation: J Am Chem Soc. 2006 Dec 6;128(48):15432-44
references.pmid: 17132010
references.citation: J Mol Biol. 1999 Feb 12;286(1):83-93
references.pmid: 9931251
references.citation: J Biol Chem. 2013 Jan 18;288(3):1511-20
references.pmid: 23184932
references.citation: J Am Chem Soc. 2008 Sep 24;130(38):12745-51
references.pmid: 18761455
references.citation: J Biomol NMR. 2001 Jul;20(3):223-31
references.pmid: 11519746
references.citation: J Magn Reson. 2011 Dec;213(1):151-7
references.pmid: 22015249
references.citation: J Biomol NMR. 1995 Nov;6(3):277-93
references.pmid: 8520220
references.citation: Q Rev Biophys. 2000 Nov;33(4):371-424
references.pmid: 11233409
references.citation: Adv Exp Med Biol. 2012;726:441-65
references.pmid: 22297526
references.citation: Nat Struct Mol Biol. 2004 Jul;11(7):676-7
references.pmid: 15208693
references.citation: Science. 1991 Dec 13;254(5038):1598-603
references.pmid: 1749933
references.citation: Science. 1995 May 12;268(5212):886-9
references.pmid: 7754375
references.citation: Protein Sci. 2003 May;12(5):973-81
references.pmid: 12717020
references.citation: Proteins. 2008 Oct;73(1):161-72
references.pmid: 18409193
references.citation: Nat Struct Mol Biol. 2004 Jul;11(7):672-5
references.pmid: 15208690
references.citation: J Mol Biol. 1999 Jan 8;285(1):1-32
references.pmid: 9878383
references.citation: J Am Chem Soc. 2007 Mar 21;129(11):3315-27
references.pmid: 17319663
references.citation: Nature. 2012 Jul 19;487(7407):385-9
references.pmid: 22722831
references.citation: Biochemistry. 1989 Nov 14;28(23):8972-9
references.pmid: 2690953
references.citation: Nat Struct Biol. 1997 Jun;4(6):443-9
references.pmid: 9187651
references.citation: Proteins. 2006 Jun 1;63(4):787-96
references.pmid: 16609980
references.citation: J Biol Chem. 2009 Nov 20;284(47):32932-41
references.pmid: 19759015
references.citation: Cell. 2009 Jun 26;137(7):1282-92
references.pmid: 19523676
references.citation: J Mol Biol. 2011 Jul 22;410(4):491-500
references.pmid: 21762795
references.citation: J Magn Reson. 2003 Jan;160(1):65-73
references.pmid: 12565051
references.citation: J Mol Biol. 2009 Sep 11;392(1):100-14
references.pmid: 19527730
references.citation: J Mol Biol. 2009 Mar 27;387(2):376-89
references.pmid: 19356593