Cα-H⋯O = C hydrogen bonds contribute to the specificity of RGD cell-adhesion interactions

BMC Structural Biology

Volumn 5, Issue , 2005, Pages

  Bella, Jordi ^a   Humphries, Martin J ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARGINYLGLYCYLASPARTIC ACID; CARBONYL DERIVATIVE; COLLAGEN; INTEGRIN; PEPTIDE; ARGININE; ARGINYL-GLYCYL-ASPARTIC ACID; ASPARTIC ACID; HYDROGEN; LIGAND; OLIGOPEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CELL ADHESION; CRYSTAL STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PROTEIN BINDING; PROTEIN STRUCTURE; SIMULATION; CELL COMMUNICATION; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; EXTRACELLULAR MATRIX; METABOLISM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; STEREOISOMERISM;

ARGININE; ASPARTIC ACID; CELL ADHESION; CELL COMMUNICATION; EXTRACELLULAR MATRIX; HYDROGEN; HYDROGEN BONDING; INTEGRINS; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MODELS, MOLECULAR; OLIGOPEPTIDES; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; STEREOISOMERISM;

EID: 15444374992     PISSN: 14726807     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-5-4     Document Type: Article

References (45)

1. Ruoslahti E: The RGD story: a personal account. Matrix Biol 2003, 22:459-465.
2. Pierschbacher MD, Ruoslahti E: Cell attachment activity of fibronectin can be duplicated by small synthetic fragments of the molecule. Nature 1984, 309:30-33.
3. D'Souza SE, Ginsberg MH, Burke TA, Lam SC, Plow EF: Localization of an Arg-Gly-Asp recognition site within an integrin adhesion receptor. Science 1988, 242:91-93.
4. Ruoslahti E: RGD and other recognition sites for integrins. Annu Rev Cell Dev Biol 1996, 12:697-715.
5. Hynes RO: Integrins: bidirectional, allosteric signaling machines. Cell 2002, 110:673-687.
6. Emsley J, Knight CG, Farndale RW, Barnes MJ, Liddington RC: Structural basis of collagen recognition by integrin α2β1. Cell 2000, 101:47-56.
7. 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 α Vβ3. Science 2001, 294:339-345.
8. Xiong JP, Stehle T, Zhang R, Joachimiak A, Frech M, Goodman SL, Arnaout MA: Crystal structure of the extracellular segment of integrin α Vβ3 in complex with an Arg-Gly-Asp ligand. Science 2002, 296:151-155.
9. Takagi J, Petre BM, Walz T, Springer TA: Global conformational rearrangements in integrin extracellular domains in outside-in and inside-out signalling. Cell 2002, 110:599-611.
10. Mould AP, Symonds EJ, Buckley PA, Grossmann JG, McEwan PA, Barton SJ, Askari JA, Craig SE, Bella J, Humphries MJ: Structure of an integrin-ligand complex deduced from solution X-ray scattering and site-directed mutagenesis. J Biol Chem 2003, 278:39993-39999.
11. Humphries MJ, McEwan PA, Barton SJ, Buckley PA, Bella J, Mould AP: Integrin structure: heady advances in ligand binding, but activation still makes the knees wobble. Trends Biochem Sci 2003, 28:313-320.
12. 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.
13. Mould AP, Humphries MJ: Cell biology: adhesion articulated. Nature 2004, 432:27-28.
14. Gottschalk KE, Kessler H: The structures of integrins and integrin-ligand complexes: implications for drug design and signal transduction. Angew Chem Int Ed Engl 2002, 41:3767-3774.
15. Bella J, Berman HM: Crystallographic evidence for Cα-H⋯O = C hydrogen bonds in a collagen triple helix. J Mol Biol 1996, 264:734-742.
16. Derewenda ZS, Lee L, Derewenda U: The occurrence of C-H⋯O hydrogen bonds in proteins. J Mol Biol 1995, 252:248-262.
17. Ho BK, Curmi PMG: Twist and shear in β-sheets and β-ribbons. J Mol Biol 2002, 317:291-308.
18. Desiraju GR, Steiner T: The weak hydrogen bond in structural chemistry and biology Oxford: Oxford University Press; 1999.
19. Steiner T: The hydrogen bond in the solid state. Angew Chem Int Ed 2002, 41:48-76.
20. Gu Y, Kar T, Scheiner S: Fundamental properties of the CH⋯O interaction: is it a true hydrogen bond? J Am Chem Soc 1999, 121:9411-9422.
21. Vargas R, Garza J, Dixon DA, Hay BP: How strong is the Cα-H⋯O = C hydrogen bond? J Am Chem Soc 2000, 122:4750-4755.
22. Scheiner S, Kar T, Gu Y: Strength of the Calpha;H⋯O hydrogen bond of amino acid residues. J Biol Chem 2001, 276:9832-9837.
23. +-C-H⋯O = C hydrogen bonding. J Am Chem Soc 2002, 124:7163-7169.
24. Senes A, Ubarretxena-Belandia I, Engelman DM: The Cα-H⋯O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Proc Natl Acad Sci U S A 2001, 98:9056-9061.
25. Kleiger G, Grothe R, Mallick P, Eisenberg D: GXXXG and AXXXA: common α-helical interaction motifs in proteins, particularly in extremophiles. Biochemistry 2002, 41:5990-5997.
26. Mandel-Gutfreund Y, Margalit H, Jernigan RL, Zhurkin VB: A role for CH⋯O interactions in protein-DNA recognition. J Mol Biol 1998, 277:1129-1140.
27. Jiang L, Lai L: CH⋯O hydrogen bonds at protein-protein interfaces. J Biol Chem 2002, 277:37732-37740.
28. ε-H...O = C< hydrogen bond in the active sites of serine hydrolases. J Mol Biol 1994, 241:83-93.
29. Kleiger G, Eisenberg D: GXXXG and GXXXA motifs stabilize FAD and NAD(P)-binding Rossmann folds through Cα-H⋯O hydrogen bonds and van der Waals interactions. J Mol Biol 2002, 323:69-76.
30. Pierce AC, Sandretto KL, Bemis GW: Kinase inhibitors and the case for CH⋯O hydrogen bonds in protein-ligand binding. Proteins 2002, 49:567-576.
31. Klaholz BP, Moras D: C-H⋯O hydrogen bonds in the nuclear receptor RARγ - a potential tool for drug selectivity. Structure (Camb) 2002, 10:1197-1204.
32. Sarkhel S, Desiraju GR: N-H...O, O-H...O, and C-H...O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition. Proteins 2004, 54:247-259.
33. Babu MM: NCI: a server to identify non-canonical interactions in protein structures. Nucleic Acids Res 2003, 31:3345-3348.
34. Copie V, Tomita Y, Akiyama S, Aota S, Yamada K, Venable R, Pastor R, Krueger S, Torchia D: Solution structure and dynamics of linked cell attachment modules of mouse fibronectin containing the RGD and synergy regions: comparison with the human fibronectin crystal structure. J Mol Biol 1998, 277:663-682.
35. Marinelli L, Lavecchia A, Gottschalk KE, Novellino E, Kessler H: Docking studies on αvβ3 integrin ligands: pharmacophore refinement and implications for drug design. J Med Chem 2003, 46:4393-4404.
36. Marinelli L, Gottschalk KE, Meyer A, Novellino E, Kessler H: Human integrin αvβ5: homology modeling and ligand binding. J Med Chem 2004, 47:4166-4177.
37. Gibson C, Goodman SL, Hahn D, Hölzemann G, Kessler H: Novel solid-phase synthesis of azapeptides and azapeptoides via Fmoc-strategy and its application in the synthesis of RGD-mimetics. J Org Chem 1999, 64:7388-7394.
38. Sulyok GAG, Gibson C, Goodman SL, Holzemann G, Wiesner M, Kessler H: Solid-phase synthesis of a nonpeptide RGD mimetic library: New selective α vβ 3 integrin antagonists. J Med Chem 2001, 44:1938-1950.
39. Goodman SL, Hölzemann G, Sulyok GAG, Kessler H: Nanomolar small molecule inhibitors for αvβ 6, αvβ 5, and αvβ3 integrins J Med Chem 2002, 45:1045-1051.
40. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucl Acids Res 2000, 28:235-242.
41. Word JM, Lovell SC, Richardson JS, Richardson DC: Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 1999, 285:1735-1747.
42. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kuntsleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL: Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 1998, 54:905-921.
43. Sack JS: CHAIN - A crystallographic modeling program. J Mol Graph 1988, 6:224-225.
44. Allen FH: The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr 2002, B58:380-388.
45. Evans SV: SETOR: hardware lighted three-dimensional solid model representation of macromolecules. J Mol Graphics 1993, 11:134-138.