Dual role of protein phosphorylation in DNA activator/coactivator binding.
Binding free energies are calculated for the phosphorylated and unphosphorylated complexes between the kinase inducible domain (KID) of the DNA transcriptional activator cAMP response element binding (CREB) protein and the KIX domain of its coactivator, CREB-binding protein (CBP). To our knowledge, this is the first application of a method based on a potential of mean force (PMF) with restraining potentials to compute the binding free energy of protein-protein complexes. The KID:KIX complexes are chosen here because of their biological relevance to the DNA transcription process and their relatively small size (81 residues for the KIX domain of CBP, and 28 residues for KID). The results for pKID:KIX and KID:KIX are -9.55 and -4.96 kcal/mol, respectively, in good agreement with experimental estimates (-8.8 and -5.8 kcal/mol, respectively). A comparison between specific contributions to protein-protein binding for the phosphorylated and unphosphorylated complexes reveals a dual role for the phosphorylation of KID at Ser-133 in effecting a more favorable free energy of the bound system: 1), stabilization of the unbound conformation of phosphorylated KID due to favorable intramolecular interactions of the phosphate group of Ser-133 with the charged groups of an arginine-rich region spanning both α-helices, which lowers the configurational entropy; and 2), more favorable intermolecular electrostatic interactions between pSer-133 and Arg-131 of KID, and Lys-662, Tyr-658, and Glu-666 of KIX. Charge reduction through ligand phosphorylation emerges as a possible mechanism for controlling the unbound state conformation of KID and, ultimately, gene expression. This work also demonstrates that the PMF-based method with restraining potentials provides an added benefit in that important elements of the binding pathway are evidenced. Furthermore, the practicality of the PMF-based method for larger systems is validated by agreement with experiment. In addition, we provide a somewhat differently structured exposition of the PMF-based method with restraining potentials and outline its generalization to systems in which both protein and ligand may adopt unbound conformations that are different from those of the bound state.
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA.
Voichita M
VM
Dadarlat
Robert D
RD
Skeel
D001665:Binding Sites / Q000502:physiology; D050882:CREB-Binding Protein / Q000737:chemistry*; D003198:Computer Simulation; D017362:Cyclic AMP Response Element-Binding Protein / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009687:Nuclear Proteins / Q000737:chemistry; D010766:Phosphorylation / Q000502:physiology*; D011485:Protein Binding / Q000502:physiology; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D015534:Trans-Activators / Q000737:chemistry
D017362:Cyclic AMP Response Element-Binding Protein; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D015534:Trans-Activators; D050882:CREB-Binding Protein
Nature. 2007 Jun 21;447(7147):1021-5
17522630
Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2061-6
9482838
Cell. 1996 May 3;85(3):403-14
8616895
J Mol Biol. 1999 Oct 22;293(2):321-31
10550212
J Phys Chem B. 2009 Feb 26;113(8):2234-46
19146384
J Am Chem Soc. 2009 Apr 15;131(14):5214-23
19278259
Curr Opin Struct Biol. 1996 Dec;6(6):762-9
8994876
Eur Biophys J. 2001;30(1):75-81
11372536
Mol Cell Biol. 1999 Aug;19(8):5601-7
10409749
Proc Natl Acad Sci U S A. 1986 Sep;83(18):6682-6
2875459
Cell. 1997 Dec 12;91(6):741-52
9413984
Proc Natl Acad Sci U S A. 2007 May 15;104(20):8311-5
17494761
Chemistry. 2004 Nov 19;10(23):6172-8
15515068
J Am Chem Soc. 2007 Jan 31;129(4):820-7
17243818
Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14609-14
20639465
Biophys J. 2006 Oct 15;91(8):2798-814
16844742
Proteins. 2006 Aug 15;64(3):749-57
16761278
Nature. 1997 Jun 19;387(6635):819-23
9194564
PLoS Comput Biol. 2008 Apr 11;4(4):e1000060
18404207
Nat Struct Biol. 1999 Jul;6(7):613-4
10404213
Annu Rev Biochem. 1999;68:821-61
10872467
Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2627-32
10077561
Methods Mol Biol. 2008;443:109-20
18446284
Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10412-7
10973497
Mol Cell Biol. 2000 Dec;20(24):9409-22
11094091
Proc Natl Acad Sci U S A. 2005 May 10;102(19):6825-30
15867154
J Biol Chem. 2002 Nov 1;277(44):42241-8
12196545
Biophys J. 2005 Sep;89(3):1433-45
15994888
J Mol Graph Model. 2001;19(1):26-59
11381529
J Am Chem Soc. 2004 Jun 23;126(24):7683-9
15198616