Dynamics of β3 integrin I-like and Hybrid domains: Insight from simulations on the mechanism of transition between open and closed forms

Proteins: Structure, Function and Bioinformatics

Volumn 76, Issue 4, 2009, Pages 977-994

  Gaillard, Thomas ^a   Dejaegere, Annick ^a   Stote, Roland H ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Allostery; Correlations; Fluctuations; Integrins; Low frequency motion; Normal mode analysis; Quasi harmonic analysis; Targeted molecular dynamics

Indexed keywords

BETA3 INTEGRIN;

ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; HUMAN; HYBRID; LIGAND BINDING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FUNCTION; SIGNAL TRANSDUCTION; SIMULATION; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; MOTION; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HUMANS; INTEGRIN BETA3; MODELS, MOLECULAR; MOTION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY;

EID: 68149158810     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22404     Document Type: Article

References (43)

1. Hynes RO. Integrins: bidirectional, allosteric signaling machines. Cell 2002;110:673-687.
2. Shimaoka M, Takagi J, Springer TA. Conformational regulation of integrin structure and function. Annu Rev Biophys Biomol Struct 2002;31:485-516. (Pubitemid 34666842)
3. Humphries MJ. Integrin structure. Biochem Soc Trans 2000;28:311-339.
4. Alonso JL, Essafi M, Xiong JP, Stehle T, Arnaout MA. Does the integrin alphaA domain act as a ligand for its betaA domain? Curr Biol 2002;12:R340-R342.
5. Xiong JP, Stehle T, Diefenbach B, Zhang R, Dunker R, Scott DL, Joachimiak A, Goodman SL, Arnaout MA. Crystal structure of the extracellular segment of integrin alphaVbeta3. Science 2001;294: 339-345. (Pubitemid 32963395)
6. Gottschalk KE, Kessler H. The structures of integrins and integrinligand complexes: implications for drug design and signal transduction. Angew Chem Int Ed Engl 2002;41:3767-3774. (Pubitemid 35277998)
7. Takagi J, Petre BM, Walz T, Springer TA. Global conformational rearrangements in integrin extracellular domains in outside-in and inside-out signaling. Cell 2002;110:599-1511 (Pubitemid 35247840)
8. Xiao T, Takagi J, Coller BS, Wang JH, Springer TA. Structural basis for allostery in integrins and binding to fibrinogen-mimetic therapeutics. Nature 2004;432:59-67. (Pubitemid 39490825)
9. Nishida N, Xie C, Shimaoka M, Cheng Y, Walz T, Springer TA. Activation of leukocyte beta2 integrins by conversion from bent to extended conformations. Immunity 2006;25:583-594. (Pubitemid 44529036)
10. Arnaout MA. Integrin structure: new twists and turns in dynamic cell adhesion. Immunol Rev 2002;186:125-140.
11. Arnaout MA, Goodman SL, Xiong JP. Coming to grips with integrin binding to ligands. Curr Opin Cell Biol 2002;14:641-651.
12. Liddington RC, Ginsberg MH. Integrin activation takes shape. J Cell Biol 2002;158:833-839.
13. Mould AP, Barton SJ, Askari JA, McEwan PA, Buckley PA, Craig SE, Humphries MJ. Conformational changes in the integrin beta A domain provide a mechanism for signal transduction via hybrid domain movement. J Biol Chem 2003;278:17028-17035.
14. Xiong JP, Stehle T, Zhang R, Joachimiak A, Frech M, Goodman SL, Arnaout MA. Crystal structure of the extracellular segment of integrin alphaVbeta3 in complex with an Arg-Gly-Asp ligand. Science 2002;296:151-155. (Pubitemid 34280076)
15. Xiong JP, Stehle T, Goodman SL, Arnaout MA. A novel adaptation of the integrin PSI domain revealed from its crystal structure. J Biol Chem 2004;279:40252-40254. (Pubitemid 39287606)
16. Luo BH, Carman CV, Springer TA. Structural basis of integrin regulation and signaling. Annu Rev Immunol 2007;25:619-647. (Pubitemid 46697919)
17. Craig D, Gao M, Schulten K, Vogel V. Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force. Structure 2004;12:2049-2058. (Pubitemid 39469402)
18. Puklin-Faucher E, Gao M, Schulten K, Vogel V. How the headpiece hinge angle is opened: new insights into the dynamics of integrin activation. J Cell Biol 2006;175:349-360. (Pubitemid 44631428)
19. Murcia M, Jirouskova M, Li J, Coller BS, Filizola M. Functional and computational studies of the ligand-associated metal binding site of beta3 integrins. Proteins 2008;71:1779-1791. (Pubitemid 351732934)
20. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
21. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4: 187-217.
22. MacKerell AD, Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WEI, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J,Watanabe M,Wiórkiewicz- Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616. (Pubitemid 128576688)
23. MacKerell AD, Jr, Feig M, Brooks CL, III. Extending the treatment of backbone energetics in protein force fields: limitations of gasphase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004;25:1400-1415.
24. Buck M, Bouguet-Bonnet S, Pastor RW, MacKerell AD, Jr. Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J 2006;90:L36-L38.
25. Brunger AT, Karplus M. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins 1988;4:148-156.
26. van Vlijmen HW, Schaefer M, Karplus M. Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure. Proteins 1998;33:145-158. (Pubitemid 28457969)
27. Davis ME, Madura JD, Luty BA, McCammon JA. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comput Phys Commun 1991;62:187-197.
28. Antosiewicz J, McCammon JA, Gilson MK. The determinants of pKas in proteins. Biochemistry 1996;35:7819-7833.
29. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781-1802.
30. Karplus M, Kushick JN. Method for estimating the configurational entropy of macromolecules. Macromolecules 1981;14:325-332.
31. Loncharich RJ, Brooks BR. The effects of truncating long-range forces on protein dynamics. Proteins 1989;6:32-45.
32. Brooks BR, Janezic D, Karplus M. Harmonic analysis of large systems. I. Methodology. J Comput Chem 1995;16:1522-1542.
33. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 2001;80:505-515. (Pubitemid 32108200)
34. Frauenfelder H, Petsko GA, Tsernoglou D. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 1979;280:558-563.
35. Petsko GA, Ringe D. Fluctuations in protein structure from X-ray diffraction. Annu Rev Biophys Bioeng 1984;13:331-371.
36. Kundu S, Melton JS, Sorensen DC, Phillips GN, Jr. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys J 2002;83:723-732.
37. Hinsen K. Structural flexibility in proteins: impact of the crystal environment. Bioinformatics 2008;24:521-528. (Pubitemid 351256296)
38. Hayward S, Kitao A, Hirata F, Go N. Effect of solvent on collective motions in globular protein. J Mol Biol 1993;234:1207-1217. (Pubitemid 24027248)
39. Gaillard T, Martin E, San Sebastian E, Cossio FP, Lopez X, Dejaegere A, Stote RH. Comparative normal mode analysis of LFA-1 integrin I-domains. J Mol Biol 2007;374:231-249. (Pubitemid 47610778)
40. Lee JO, Bankston LA, Arnaout MA, Liddington RC. Two conformations of the integrin A-domain (I-domain): a pathway for activation? Structure 1995;3:1333-1340.
41. Jin M, Andricioaei I, Springer TA. Conversion between three conformational states of integrin I domains with a C-terminal pull spring studied with molecular dynamics. Structure (Camb) 2004;12:2137-2147. (Pubitemid 39593193)
42. Nam K, Maiorov V, Feuston B, Kearsley S. Dynamic control of allosteric antagonism of leukocyte function antigen-1 and intercellular adhesion molecule-1 interaction. Proteins 2006;64:376-384. (Pubitemid 43993646)
43. Astrof NS, Salas A, Shimaoka M, Chen J, Springer TA. Importance of force linkage in mechanochemistry of adhesion receptors. Biochemistry 2006;45:15020-15028. (Pubitemid 44937014)