GDP release preferentially occurs on the phosphate side in heterotrimeric G-proteins

PLoS Computational Biology

Volumn 8, Issue 7, 2012, Pages

  Louet, Maxime ^a   Martinez, Jean ^a   Floquet, Nicolas ^a  

^a UNIVERSITÉ DE MONTPELLIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; PROTEINS;

ACTIVATION CYCLES; CELLULAR STIMULATION; CONSTRAINED MOLECULAR DYNAMICS; DYNAMICS SIMULATION; G PROTEIN COUPLED RECEPTORS; GDP/GTP EXCHANGE; HETEROTRIMERIC G PROTEINS; MOLECULAR LEVELS; RATE-LIMITING STEPS; X-RAY STRUCTURE;

FREE ENERGY;

G PROTEIN COUPLED RECEPTOR; GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATE; HETEROTRIMERIC GUANINE NUCLEOTIDE BINDING PROTEIN;

ALPHA HELIX; ARTICLE; CRYSTAL STRUCTURE; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PROTEIN DOMAIN; PROTEIN NUCLEIC ACID INTERACTION; PROTEIN SECRETION; SIMULATION; STRUCTURE ANALYSIS; X RAY ANALYSIS;

EID: 84864622261     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002595     Document Type: Article

References (32)

1. Neves SR, Ram PT, Iyengar R, (2002) G Protein Pathways. Science 296: 1636-1639.
2. Higashijima T, Ferguson KM, Smigel MD, Gilman AG, (1987) The effect of GTP and Mg2+ on the GTPase activity and the fluorescent properties of Go. J Biol Chem 262: 757-761.
3. Heydorn A, Ward RJ, Jorgensen R, Rosenkilde MM, Frimurer TM, et al. (2004) Identification of a Novel Site within G Protein α Subunits Important for Specificity of Receptor-G Protein Interaction. Mol Pharmacol 66: 250-259.
4. Scheerer P, Park JH, Hildebrand PW, Kim YJ, Krauß N, et al. (2008) Crystal structure of opsin in its G-protein-interacting conformation. Nature 455: 497-502.
5. Wall MA, Coleman DE, Lee E, Iñiguez-Lluhi JA, Posner BA, et al. (1995) The structure of the G protein heterotrimer Gi alpha 1 beta 1 gamma 2. Cell 83: 1047-1058.
6. Lambright DG, Sondek J, Bohm A, Skiba NP, Hamm HE, et al. (1996) The 2.0 Å crystal structure of a heterotrimeric G protein. Nature 379: 311-319.
7. Wacker D, Fenalti G, Brown MA, Katritch V, Abagyan R, et al. (2010) Conserved Binding Mode of Human β2 Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography. J Am Chem Soc 132: 11443-11445.
8. Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS, et al. (2007) High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 318: 1258-1265.
9. Rasmussen SGF, DeVree BT, Zou Y, Kruse AC, Chung KY, et al. (2011) Crystal structure of the β2 adrenergic receptor-Gs protein complex. Nature 477: 549-555.
10. Westfield GH, Rasmussen SGF, Su M, Dutta S, DeVree BT, et al. (2011) Structural flexibility of the G alpha s alpha-helical domain in the beta2-adrenoceptor Gs complex. Proc Natl Acad Sci U S A 108: 16086-16091.
11. Schlitter J, Engels M, Krüger P, (1994) Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J Mol Graph 12: 84-89.
12. Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA, (1992) THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem 13: 1011-1021.
13. Louet M, Perahia D, Martinez J, Floquet N, (2011) A concerted mechanism for opening the GDP binding pocket and release of the nucleotide in hetero-trimeric G-proteins. J Mol Biol 411: 298-312.
14. Remmers AE, Engel C, Liu M, Neubig RR, (1999) Interdomain interactions regulate GDP release from heterotrimeric G proteins. Biochemistry 38: 13795-13800.
15. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802.
16. Zielinski T, Kimple AJ, Hutsell SQ, Koeff MD, Siderovski DP, et al. (2009) Two G i1 Rate-Modifying Mutations Act in Concert to Allow Receptor-Independent, Steady-State Measurements of RGS Protein Activity. J Biomol Screen 14: 1195-1206.
17. Ramachandran S, Cerione RA, (2011) A dominant-negative Galpha mutant that traps a stable rhodopsin-Galpha-GTP-betagamma complex. J Biol Chem 286: 12702-12711.
18. Amadei A, Linssen AB, Berendsen HJ, (1993) Essential dynamics of proteins. Proteins 17: 412-425.
19. Floquet N, M'Kadmi C, Perahia D, Gagne D, Bergé G, et al. (2010) Activation of the Ghrelin Receptor is Described by a Privileged Collective Motion: A Model for Constitutive and Agonist-induced Activation of a Sub-class A G-Protein Coupled Receptor (GPCR). J Mol Biol 395: 769-784.
20. Floquet N, Durand P, Maigret B, Badet B, Badet-Denisot M-A, et al. (2009) Collective motions in Glucosamine-6-phosphate Synthase: Influence of Ligand Binding and role in Ammonia Channelling and Opening of the Fructose-6-Phosphate Binding Site. J Mol Biol 385: 653-664.
21. Van Eps N, Preininger AM, Alexander N, Kaya AI, Meier S, et al. (2011) Interaction of a G protein with an activated receptor opens the interdomain interface in the alpha subunit. Proc Natl Acad Sci U S A 108: 9420-9424.
22. Kimple RJ, Kimple ME, Betts L, Sondek J, Siderovski DP, (2002) Structural determinants for GoLoco-induced inhibition of nucleotide release by G[alpha] subunits. Nature 416: 878-881.
23. Oldham WM, Hamm HE, (2007) How do Receptors Activate G Proteins? Advances in Protein Chemistry. Elsevier, Vol. 74 pp. 67-93 Available: http://linkinghub.elsevier.com/retrieve/pii/S0065323307740020. Accessed 4 April 2011.
24. Wang J, Wang W, Kollman P, Case D, (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model 25: 247-260.
25. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA, (2004) Development and testing of a general amber force field. J Comput Chem 25: 1157-1174.
26. Mackerell AD, Feig M, Brooks CL, (2004) Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25: 1400-1415.
27. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML, (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79: 926.
28. Darden T, Perera L, Li L, Pedersen L, (1999) New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure 7: R55-R60.
29. Humphrey W, Dalke A, Schulten K, (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33-38, 27-28.
30. Huang X, Pan Y, Zheng F, Zhan C-G, (2010) Reaction Pathway and Free Energy Profile for Pre-Chemical Reaction Step of Human Butyrylcholinesterase-Catalyzed Hydrolysis of (-)-Cocaine by Combined Targeted Molecular Dynamics and Potential of Mean Force Simulations. J Phys Chem B 114: 13545-13554.
31. Schulz R, Vargiu AV, Collu F, Kleinekathöfer U, Ruggerone P, (2010) Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations. PLoS Comput Biol 6: e1000806.
32. Mantel N, (1967) The Detection of Disease Clustering and a Generalized Regression Approach. Cancer Res 27: 209-220.