title: Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading.
abstract: Proliferating cell nuclear antigen (PCNA, sliding clamp) is a toroidal-shaped protein that encircles DNA and plays a pivotal role in DNA replication, modification and repair. To perform its vital functions, the clamp has to be opened and resealed at primer-template junctions by a clamp loader molecular machine, replication factor C (RFC). The mechanism of this process constitutes a significant piece in the puzzle of processive DNA replication. We show that upon clamp opening the RFC/PCNA complex undergoes a large conformational rearrangement, leading to the formation of an extended interface between the clamp and RFC. Binding of ring-open PCNA to all five RFC subunits transforms the free-energy landscape underlying the closed- to open state transition, trapping PCNA in an open conformation. Careful comparison of free-energy profiles for clamp opening in the presence and absence of RFC allowed us to substantiate the role of RFC in the initial stage of the clamp-loading cycle. RFC does not appreciably destabilize the closed state of PCNA. Instead, the function of the clamp loader is dependent on the selective stabilization of the open conformation of the clamp.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB4, La Jolla, California 92037, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Tainer
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
authors.forename: Ivaylo
authors.initials: I
authors.lastname: Ivanov
mesh_terms: D018360:Crystallography, X-Ray; D004261:DNA Replication; D056004:Molecular Dynamics Simulation; D018809:Proliferating Cell Nuclear Antigen / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D051818:Replication Protein C / Q000737:chemistry* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000378:metabolism
chemical_list: D018809:Proliferating Cell Nuclear Antigen; D051818:Replication Protein C
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6477-82
references.pmid: 16611731
references.citation: Crit Rev Biochem Mol Biol. 2008 May-Jun;43(3):163-87
references.pmid: 18568846
references.citation: J Mol Graph Model. 2001;19(1):13-25
references.pmid: 11381523
references.citation: Mol Cell. 2003 Jan;11(1):275-82
references.pmid: 12535540
references.citation: Nature. 2002 Sep 12;419(6903):135-41
references.pmid: 12226657
references.citation: Cell. 2004 Jan 9;116(1):39-50
references.pmid: 14718165
references.citation: J Chem Phys. 2005 Dec 22;123(24):244906
references.pmid: 16396572
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13801-6
references.pmid: 16169903
references.citation: Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2546-51
references.pmid: 16476998
references.citation: Nat Rev Mol Cell Biol. 2006 Oct;7(10):751-61
references.pmid: 16955075
references.citation: J Cell Sci. 2003 Aug 1;116(Pt 15):3051-60
references.pmid: 12829735
references.citation: Annu Rev Biochem. 2005;74:283-315
references.pmid: 15952889
references.citation: FEBS Lett. 2005 Feb 7;579(4):863-7
references.pmid: 15680964
references.citation: Genes Cells. 1996 Jan;1(1):101-13
references.pmid: 9078370
references.citation: J Biol Chem. 2006 Apr 21;281(16):10653-6
references.pmid: 16421093
references.citation: EMBO J. 2006 May 17;25(10):2209-18
references.pmid: 16628222
references.citation: J Mol Biol. 1993 Dec 5;234(3):779-815
references.pmid: 8254673
references.citation: Nature. 2004 Jun 17;429(6993):724-30
references.pmid: 15201901
references.citation: J Comput Chem. 2005 Dec;26(16):1781-802
references.pmid: 16222654
references.citation: Cell. 1994 Dec 30;79(7):1233-43
references.pmid: 8001157
references.citation: Annu Rev Biochem. 2001;70:181-208
references.pmid: 11395406
references.citation: Chromosoma. 1998 Sep;107(4):218-27
references.pmid: 9745046
references.citation: Mol Microbiol. 2008 Apr;68(1):216-22
references.pmid: 18312273
references.citation: Curr Opin Struct Biol. 2006 Feb;16(1):35-41
references.pmid: 16377178
references.citation: Curr Biol. 2005 Dec 20;15(24):R989-92
references.pmid: 16360676
references.citation: Oncogene. 1997 Feb 13;14(6):629-40
references.pmid: 9038370
references.citation: J Comput Chem. 2003 Dec;24(16):1999-2012
references.pmid: 14531054
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13795-800
references.pmid: 16169902
references.citation: J Biol Chem. 2006 Jun 23;281(25):17528-17539
references.pmid: 16608854
references.citation: Cell. 2007 May 18;129(4):665-79
references.pmid: 17512402