title: A novel dimer-tetramer transition captured by the crystal structure of the HIV-1 Nef.
abstract: HIV-1 Nef modulates disease progression through interactions with over 30 host proteins. Individual chains fold into membrane-interacting N-terminal and C-terminal core (Nef(core)) domains respectively. Nef exists as small oligomers near membranes and associates into higher oligomers such as tetramers or hexadecamers in the cytoplasm. Earlier structures of the Nef(core) in apo and complexed forms with the Fyn-kinase SH3 domain revealed dimeric association details and the role of the conserved PXXP recognition motif (residues 72-78) of Nef in SH3-domain interactions. The crystal structure of the tetrameric Nef reported here corresponds to the elusive cytoplasmic stage. Comparative analyses show that subunits of Nef(core) dimers (open conformation) swing out with a relative displacement of ~22 Å and rotation of ~174° to form the 'closed' tetrameric structure. The changes to the association are around Asp125, a conserved residue important for viral replication and the important XR motif (residues 107-108). The tetramer associates through C4 symmetry instead of the 222 symmetry expected when two dimers associate together. This novel dimer-tetramer transition agrees with earlier solution studies including small angle X-ray scattering, analytical ultracentrifugation, dynamic laser light scattering and our glutaraldehyde cross-linking experiments. Comparisons with the Nef(core)--Fyn-SH3 domain complexes reveal that the PXXP motif that interacts with the SH3-domain in the dimeric form is sterically occluded in the tetramer. However the 151-180 loop that is distal to the PXXP motif and contains several protein interaction motifs remains accessible. The results suggest how changes to the oligomeric state of Nef can help it distinguish between protein partners.
authors.affiliation: Toxicology Division, Central Drug Research Institute, Council of Scientific & Industrial Research, Chattar Manzil, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Singh
authors.forename: Gaya Prasad
authors.initials: GP
authors.lastname: Yadav
authors.forename: Sudeepti
authors.initials: S
authors.lastname: Gupta
authors.forename: Anil Kumar
authors.initials: AK
authors.lastname: Tripathi
authors.forename: Ravishankar
authors.initials: R
authors.lastname: Ramachandran
authors.forename: Raj Kamal
authors.initials: RK
authors.lastname: Tripathi
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001704:Biopolymers / Q000737:chemistry*; D018360:Crystallography, X-Ray; D017931:DNA Primers; D015693:Gene Products, nef / Q000737:chemistry*; D015497:HIV-1 / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012542:Scattering, Radiation; D017386:Sequence Homology, Amino Acid; D014461:Ultracentrifugation
chemical_list: D001704:Biopolymers; D017931:DNA Primers; D015693:Gene Products, nef
references.citation: Retrovirology. 2010 Sep 23;7:77
references.pmid: 20863404
references.citation: Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):72-82
references.pmid: 16369096
references.citation: Structure. 1997 Oct 15;5(10):1361-72
references.pmid: 9351809
references.citation: Annu Rev Biochem. 1970;39:25-62
references.pmid: 4920824
references.citation: J Virol. 1996 Dec;70(12):9051-4
references.pmid: 8971042
references.citation: FEBS Lett. 2001 May 11;496(2-3):91-5
references.pmid: 11356189
references.citation: Protein Sci. 2000 Jun;9(6):1137-48
references.pmid: 10892807
references.citation: Immunity. 2001 Jun;14(6):763-77
references.pmid: 11420046
references.citation: J Virol. 1993 Aug;67(8):4639-50
references.pmid: 8043040
references.citation: Cell. 1991 May 17;65(4):651-62
references.pmid: 2032289
references.citation: Cell. 1996 Jun 14;85(6):931-42
references.pmid: 8681387
references.citation: J Virol. 2000 Jun;74(11):5310-9
references.pmid: 10799608
references.citation: J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
references.pmid: 19461840
references.citation: Proteins. 2005 Sep 1;60(4):658-69
references.pmid: 16021629
references.citation: J Biol Chem. 1971 May 25;246(10):3092-102
references.pmid: 5574388
references.citation: J Virol. 1994 May;68(5):2906-14
references.pmid: 8151761
references.citation: J Infect Dis. 2000 Jan;181(1):132-40
references.pmid: 10608759
references.citation: PLoS One. 2010 Dec 13;5(12):e15312
references.pmid: 21179446
references.citation: Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55
references.pmid: 15299926
references.citation: Eur J Biochem. 1994 Apr 15;221(2):811-9
references.pmid: 8174561
references.citation: N Engl J Med. 1995 Jan 26;332(4):228-32
references.pmid: 7808489
references.citation: Biol Chem. 2007 Feb;388(2):181-3
references.pmid: 17261081
references.citation: Nature. 1998 Jan 22;391(6665):397-401
references.pmid: 9450757
references.citation: EMBO Rep. 2001 Jul;2(7):580-5
references.pmid: 11463741
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):163-75
references.pmid: 20124696
references.citation: Trends Biochem Sci. 2001 Jun;26(6):356-63
references.pmid: 11406408
references.citation: Cell Host Microbe. 2007 Apr 19;1(2):121-33
references.pmid: 18005690
references.citation: Traffic. 2011 Jul;12(7):867-77
references.pmid: 21477083
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
references.pmid: 20124702
references.citation: J Exp Med. 1994 Jan 1;179(1):101-13
references.pmid: 8270859
references.citation: J Mol Biol. 1999 May 28;289(1):123-38
references.pmid: 10339411
references.citation: J Mol Biol. 2009 Nov 27;394(2):329-42
references.pmid: 19781555
references.citation: Immunity. 2002 Apr;16(4):493-7
references.pmid: 11970873