Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading.
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.
Tainer
John A
JA
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB4, La Jolla, California 92037, USA.
McCammon
J Andrew
JA
Ivanov
Ivaylo
I
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
D018809:Proliferating Cell Nuclear Antigen; D051818:Replication Protein C
Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6477-82
16611731
Crit Rev Biochem Mol Biol. 2008 May-Jun;43(3):163-87
18568846
J Mol Graph Model. 2001;19(1):13-25
11381523
Mol Cell. 2003 Jan;11(1):275-82
12535540
Nature. 2002 Sep 12;419(6903):135-41
12226657
Cell. 2004 Jan 9;116(1):39-50
14718165
J Chem Phys. 2005 Dec 22;123(24):244906
16396572
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13801-6
16169903
Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2546-51
16476998
Nat Rev Mol Cell Biol. 2006 Oct;7(10):751-61
16955075
J Cell Sci. 2003 Aug 1;116(Pt 15):3051-60
12829735
Annu Rev Biochem. 2005;74:283-315
15952889
FEBS Lett. 2005 Feb 7;579(4):863-7
15680964
Genes Cells. 1996 Jan;1(1):101-13
9078370
J Biol Chem. 2006 Apr 21;281(16):10653-6
16421093
EMBO J. 2006 May 17;25(10):2209-18
16628222
J Mol Biol. 1993 Dec 5;234(3):779-815
8254673
Nature. 2004 Jun 17;429(6993):724-30
15201901
J Comput Chem. 2005 Dec;26(16):1781-802
16222654
Cell. 1994 Dec 30;79(7):1233-43
8001157
Annu Rev Biochem. 2001;70:181-208
11395406
Chromosoma. 1998 Sep;107(4):218-27
9745046
Mol Microbiol. 2008 Apr;68(1):216-22
18312273
Curr Opin Struct Biol. 2006 Feb;16(1):35-41
16377178
Curr Biol. 2005 Dec 20;15(24):R989-92
16360676
Oncogene. 1997 Feb 13;14(6):629-40
9038370
J Comput Chem. 2003 Dec;24(16):1999-2012
14531054
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13795-800
16169902
J Biol Chem. 2006 Jun 23;281(25):17528-17539
16608854
Cell. 2007 May 18;129(4):665-79
17512402