Computational analysis of molecular basis of 1:1 interactions of NRG-1β wild-type and variants with ErbB3 and ErbB4

Proteins: Structure, Function and Genetics

Volumn 59, Issue 4, 2005, Pages 742-756

  Luo, Cheng ^a   Xu, Lingfei ^b   Zheng, Suxin ^a   Luo, Xiaomin ^a   Shen, Jianhua ^a   Jiang, Hualiang ^a,c   Liu, Xifu ^b   Zhou, Mingdong ^a,b  

^a SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

^b Zensun (Shanghai) Sci and Tech Ltd   (China)

^c EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Binding free energy; EGFR; ErbB; Ligand protein interactions; MM PBSA; Molecular dynamics; NRG 1

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 3; EPIDERMAL GROWTH FACTOR RECEPTOR 4; NEU DIFFERENTIATION FACTOR; NEU DIFFERENTIATION FACTOR BETA; UNCLASSIFIED DRUG;

ADRENERGIC SYSTEM; ARTICLE; BINDING SITE; CALCULATION; HEART DEVELOPMENT; HEART FAILURE; HUMAN; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; WILD TYPE;

ALANINE; AMINO ACID SUBSTITUTION; BINDING SITES; CONSERVED SEQUENCE; EPIDERMAL GROWTH FACTOR; MODELS, BIOLOGICAL; MUTAGENESIS, SITE-DIRECTED; NEUREGULIN-1; PROTEIN ISOFORMS; RECEPTOR, EPIDERMAL GROWTH FACTOR; RECEPTOR, ERBB-3; RECOMBINANT PROTEINS; SOLVENTS; VARIATION (GENETICS);

EID: 18844371223     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20443     Document Type: Article

References (53)

1. Yarden Y, Sliwkowski MX. untangling the erbb signaling network. Nat Mol Cell Biol 2001;2:127-137.
2. Carpenter G. Receptors for epidermal growth factor and other polypeptide mitogens. Annu Rev Biochem 1987;56:881-914.
3. Barton J, Blackledge G, Wakeling A. Growth factors and their receptors: new targets for prostate cancer therapy. Urology 2001; 58(Suppl 1):114-122.
4. Peles E, Yarden Y. Neu and its ligands: from an oncogene to neural factors. Bioessays 1993;15:815-824.
5. Fischbach GD, Rosen KM. ARIA: a neuromuscular junction neuregulin. Annu Rev Neurosci 1997;20:429-458.
6. Sliwkowski MX, Schaefer G, Akita RW, Lofgren JA, Fitzpatrick VD, Nuijens A, Fendly BM, Cerione RA, Vandlen RL, Carraway KL III. Coexpression of erbB2 and erbB3 proteins reconstitutes a high affinity receptor for heregulin. J Biol Chem 1994;269:14661-14665.
7. Tzahar E, Levkowitz G, Karunagaran D, Yi L, Peles E, Lavi S, Chang D, Liu N, Yayon A, Wen D. ErbB-3 and ErbB-4 function as the respective low and high affinity receptors of all Neu differentiation factor/heregulin isoforms. J Biol Chem 1994;269:25226-25233.
8. Plowman GD, Green JM, Culouscou JM, Carlton GW, Rothwell VM, Buckley S. Heregulin induces tyrosine phosphorylation of HER4/p180erbB4. Nature 1993;366:473-475.
9. Negro A, Brar BK, Lee KF. Essential roles of Her2/erbB2 in cardiac development and function. Recent Prog Horm Res 2004;59: 1-12.
10. Fitzpatrick VD, Pisacane PI, Vandlen RL, Sliwkowski MX. Formation of a high affinity heregulin binding site using the soluble extracellular domains of ErbB2 with ErbB3 or ErbB4. FEBS Lett 1998;431:102-106.
11. Britsch S, Li L, Kirchhoff S, Theuring F, Brinkmann V, Birchmeier C, Riethmacher D. The ErbB2 and ErbB3 receptors and their ligand, neuregulin-1, are essential for development of the sympathetic nervous system. Genes Dev 1998;12:1825-1836.
12. Buonanno A, Fischbach GD. Neuregulin and ErbB receptor signaling pathways in the nervous system. Curr Opin Neurobiol 2001;11:287-296.
13. Lee KF, Simon H, Chen H, Bates B, Hung MC, Hauser C. Requirement for neuregulin receptor erbB2 in neural and cardiac development. Nature 1995;378:394-398.
14. Gassmann M, Casagranda F, Orioli D, Simon H, Lai C, Klein R, Lemke G. Aberrant neural and cardiac development in mice lacking the ErbB4 neuregulin receptor. Nature 1995;378:390-394.
15. Liu X, Hwang H, Cao L, Buckland M, Cunningham A, Chen J, Chien KR, Graham RM, Zhou M. Domain-specific gene disruption reveals critical regulation of neuregulin signaling by its cytoplasmic tail. Proc Natl Acad Sci USA 1998;95:13024-13029.
16. Liu X, Gu X, Li X, Li H, Chen P, Giu H, Yuan P, Jin J, Yao H, Xi B, Chen D, Lai D, Graham RM, Zhou M. Neuregulin-1/erbB-activation improves cardiac function and survival in models of ischemic, dilated and viral cardiomyopathy. Submitted to circulation.
17. You TJ, Maxwell DS, Kogan TP, Chen Q, Li J, Kassir J, Holland GW, Dixon RA. A 3D structure model of integrin alpha 4 beta 1 complex: I. Construction of a homology model of beta 1 and ligand binding analysis. Biophys J 2002;82:447-457.
18. Al-Lazikani B, Jung J, Xiang Z, Honig B. Protein structure prediction. Curr Opin Chem Biol 2001;5:51-56.
19. Wang W, Donini O, Reyes CM, Kollman PA. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct 2001;30:211-243.
20. Zeng J, Treutlein HR, Simonson T. Molecular dynamics simulations of the Ras:Raf and Rap:Raf complexes. Proteins 1999;35:89-100.
21. Srinivasan J, Miller J, Kollman PA, Case DA. Continuum solvent studies of the stability of RNA hairpin loops and helices. J Biomol Struct Dyn 1998;16:671-682.
22. Reyes CM, Kollman PA. Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. J Mol Biol 2000;297:1145-1158.
23. Wang W, Kollman PA. Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. J Mol Biol 2000;303:567-582.
24. Massova I, Kollman P. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J Am Chem Soc 1999;121:8133-8143.
25. Huo S, Massova I, Kollman PA. Computational alanine scanning of the 1:1 human growth hormone-receptor complex. J Comput Chem 2002;23:15-27.
26. Ogiso H, Ishitani R, Nureki O, Fukai S, Yamanaka M, Kim JH, Saito K, Sakamoto A, Inoue M, Shirouzu M, Yokoyama S. Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell 2002;110:775-787.
27. Jones JT, Ballinger MD, Pisacane PI, Lofgren JA, Fitzpatrick VD, Fairbrother WJ, Wells JA, Sliwkowski MX. Binding interaction of the heregulinbeta egf domain with ErbB3 and ErbB4 receptors assessed by alanine scanning mutagenesis. J Biol Chem 1998;273: 11667-11674.
28. Laskowski RA, MacArthur MW, Moss D, Thornton JM. PROCHECK: a program to check to the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
29. 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.
30. Huang XQ, Jiang HL, Luo XM, Chen KX, Ji RY, Cao Y, Pei G. Building three-dimensional structures of HIV-1 coreceptor CCR5 and its interaction with antagonist TAK779 by comparative molecular modeling. Acta Pharmacol Sin 2000;21:521-528.
31. Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
32. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, David M. Ferguson, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
33. Case DA, Pearlman DA, Caldwell JW, Cheatham TEI, Wang J, Ross WS, Simmerling C, Darden T, Merz KM, Stanton RV, Cheng A, Vincent JJ, Crowley M, Tsui V, Gohlke H, R. R, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner P, Kollman PA. AMBER 7. San Francisco: University of California; 2002.
34. Jorgensen WL, Chandrasekhar J, Madurs J, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
35. Darden T, York D, Pedersen L. Particle mesh Ewald: an NLog(N) method for Ewald sums in large systems. J Chem Phys 1993;98: 10089-10092.
36. Ryckaert JP, Ciccotti G, Berendsen JC. Numerical integration of the Cartesian equation of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
37. Berendsen H, C. J, Postma JPM, van Gunsteren WF, DiNole A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
38. Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8:127-134.
39. Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science 1995;268:1144-1149.
40. 40: Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 1994;98:1978-1988.
41. Sanner MF, Olson AJ, Spehner JC. Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 1996;38:305-320.
42. Chong LT, Duari Y, Wang L, Massova I, Kollman PA. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc Natl Acad Sci USA 1999;96:14330-14335.
43. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
44. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
45. Cho HS, Mason K, Ramyar KX, Stanley AM, Gabelli SB, Denney DW Jr, Leahy DJ. Structure of the extracellular region of HER2 alone and in complex with the herceptin Fab. Nature 2003;421: 756-760.
46. Ferguson KM, Berger MB, Mendrola JM, Cho HS, Leahy DJ, Lemmon MA. EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization. Mol Cell 2003;11:507-517.
47. Cho H-S, Leahy DJ. Structure of the extracellular region of HER3 reveals an interdomain tether. Science 2002;297:1330-1333.
48. Plowman GD, Culouscou JM, Whitney GS, Green JM, Carlton GW, Foy L, Neubauer MG, Shoyab M. Ligand-specific activation of HER4/p180erbB4, a fourth member of the epidermal growth factor receptor family. Proc Natl Acad Sci USA 1993;90:1746-1750.
49. Jacobsen NE, Abadi N, Sliwkowski MX, Reilly D, Skelton NJ, Fairbrother WJ. High-resolution solution structure of the EGF-like domain of heregulin-alpha. Biochemistry 1996;35:3402-3417.
50. Barbacci EG, Guarino BC, Stroh JG, Singleton DH, Rosnack KJ, Moyer JD, Andrews GC. The structural basis for the specificity of epidermal growth factor and heregulin binding. J Biol Chem 1995;270:9585-9589.
51. Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24: 946-950.
52. Singer E, Landgraf R, Horan T, Slamon D, Eisenberg D. Identification of a heregulin binding site in HER3 extracellular domain. J Biol Chem 2001;276:44266-44274.
53. Ballinger MD, Jones JT, Lofgren JA, Fairbrother WJ, Akita RW, Sliwkowski MX, Wells JA. Selection of heregulin variants having higher affinity for the ErbB3 receptor by monovalent phage display. J Biol Chem 1998;273:11675-11684.