title: On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases.
abstract: Regulation of signaling pathways in the cell often involves multidomain allosteric enzymes that are able to adopt alternate active or inactive conformations in response to specific stimuli. It is therefore of great interest to elucidate the energetic and structural determinants that govern the conformational plasticity of these proteins. In this study, free-energy computations have been used to address this fundamental question, focusing on one important family of signaling enzymes, the Src tyrosine kinases. Inactivation of these enzymes depends on the formation of an assembly comprising a tandem of SH3 and SH2 modules alongside a catalytic domain. Activation results from the release of the SH3 and SH2 domains, which are then believed to be structurally uncoupled by virtue of a flexible peptide link. In contrast to this view, this analysis shows that inactivation depends critically on the intrinsic propensity of the SH3-SH2 tandem to adopt conformations that are conducive to the assembled inactive state, even when no interactions with the rest of the kinase are possible. This funneling of the available conformational space is encoded within the SH3-SH2 connector, which appears to have evolved to modulate the flexibility of the tandem in solution. To further substantiate this notion, we show how constitutively activating mutations in the SH3-SH2 connector shift the assembly equilibrium toward the disassembled, active state. Based on a similar analysis of several constructs of the kinase complex, we propose that assembly is characterized by the progressive optimization of the protein's conformational energy, with little or no energetic frustration.
authors: Center for Integrative Science, University of Chicago, Chicago, IL 60637, USA.
authors: José D
authors: JD
authors: Faraldo-Gómez
authors: Benoît
authors: B
authors: Roux
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D013499:Surface Properties; D019061:src-Family Kinases / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D019061:src-Family Kinases
references: Mol Cell. 1999 May;3(5):639-48
references: 10360180
references: J Biol Chem. 2000 Jan 28;275(4):2721-6
references: 10644735
references: J Biol Chem. 2001 May 18;276(20):17199-205
references: 11278857
references: Cell. 2001 Apr 6;105(1):115-26
references: 11301007
references: Nat Struct Biol. 2002 May;9(5):365-9
references: 11976726
references: Biochim Biophys Acta. 2002 Jun 21;1602(2):114-30
references: 12020799
references: Structure. 2002 Jul;10(7):901-11
references: 12121645
references: J Biol Chem. 2002 Oct 25;277(43):40428-33
references: 12181320
references: Cell. 2003 Mar 21;112(6):737-40
references: 12654240
references: Science. 2003 Apr 18;300(5618):445-52
references: 12702867
references: Curr Opin Struct Biol. 2004 Feb;14(1):70-5
references: 15102452
references: Proc Natl Acad Sci U S A. 2005 May 10;102(19):6825-30
references: 15867154
references: J Mol Biol. 2005 Oct 21;353(2):222-31
references: 16168436
references: Biochemistry. 2005 Oct 4;44(39):13043-50
references: 16185072
references: J Biol Chem. 2005 Dec 9;280(49):40832-7
references: 16210316
references: Protein Sci. 2006 Jan;15(1):65-73
references: 16322569
references: Acc Chem Res. 2006 Feb;39(2):135-42
references: 16489733
references: Mol Cell. 2006 Mar 17;21(6):787-98
references: 16543148
references: J Biol Chem. 2006 Aug 18;281(33):23776-84
references: 16790421
references: Biophys J. 2006 Oct 15;91(8):2798-814
references: 16844742
references: J Phys Chem B. 1998 Apr 30;102(18):3586-616
references: 24889800
references: Nature. 1994 Apr 21;368(6473):764-9
references: 7512222
references: Nature. 1997 Feb 13;385(6617):595-602
references: 9024657
references: Nature. 1997 Feb 13;385(6617):602-9
references: 9024658
references: Nature. 1997 Feb 13;385(6617):650-3
references: 9024665
references: Annu Rev Phys Chem. 1997;48:545-600
references: 9348663