Homology modeling and molecular dynamics simulations of the glycine receptor ligand binding domain

Proteins: Structure, Function and Genetics

Volumn 67, Issue 4, 2007, Pages 950-960

  Speranskiy, Kirill ^a   Cascio, Michael ^b   Kurnikova, Maria ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

Alpha1 subunit; Cys loop receptor; Glycine receptor; Ligand binding domain; Ligand docking; Ligand gated ion channel; Nicotinicoid receptor; Protein structure modeling; Protein structure prediction

Indexed keywords

ACETYLCHOLINE; DOCKING PROTEIN; FRESH WATER; GLYCINE RECEPTOR; ION CHANNEL; STRYCHNINE;

ALPHA CHAIN; AMINO ACID SEQUENCE; APLYSIA; ARTICLE; BINDING SITE; CONTROLLED STUDY; LIGAND BINDING; LYMNAEA STAGNALIS; MOLECULAR DYNAMICS; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN TARGETING; SEQUENCE HOMOLOGY; SIMULATION; SNAIL;

AMINO ACID SEQUENCE; BINDING SITES; COMPUTER SIMULATION; CONSERVED SEQUENCE; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; RECEPTORS, GLYCINE; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

APLYSIA CALIFORNICA; GASTROPODA; LYMNAEA STAGNALIS; STRYCHNOS TOXIFERA;

EID: 34248574413     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21251     Document Type: Article

References (51)

1. Betz H. Ligand-gated ion channels in the brain: the amino acid receptor superfamily. Neuron 1990;5:383-392.
2. Yamakura T, Bertaccini E, Trudell JR, Harris RA. Anesthetics and ion channels: molecular models and sites of action. Annu Rev Pharmacol Toxicol 2001;41:23-51.
3. Hemmings HC, Akabas MH, Goldstein PA, Trudell JR, Orser BA, Harrison NL. Emerging molecular mechanisms of general anesthetic action. Trends Pharmacol Sci 2005;26:503-510.
4. Beckstead MJ, Phelan R, Trudell JR, Bianchini MJ, Mihic SJ. Anesthetic and ethanol effects on spontaneously opening glycine receptor channels. J Neurochem 2002;82:1343-1351.
5. Eser D, Romeo E, Baghai T, di Michele F, Schule C, Pasini A, Zwanzger P, Padberg F, Rupprecht R. Neuroactive steroids as modulators of depression and anxiety. Neuroscience 2006;138: 1041-1048.
6. Belelli D, Herd M, Mitchell E, Peden D, Vardy A, Gentet L, Lambert J. Neuroactive steroids and inhibitory neurotransmission: mechanisms of action and physiological relevance. Neuroscience 2006;138:821-829.
7. Li M, Lester HA. Ion channel diseases of the central nervous system. CNS Drug Rev 2001;7:214-240.
8. Gundlach AL. Disorder of the inhibitory glycine receptor-inherited myoclonus in Poll Hereford calves. FASEB J 1990;4: 2761-2766.
9. Becker CM, Schmieden V, Tarroni P, Strasser U, Betz H. Isoform-selective deficit of glycine receptors in the mouse mutant spastic. Neuron 1992;8:283-289.
10. Shiang R, Ryan SG, Zhu YZ, Hahn AF, Oconnell P, Wasmuth JJ. Mutations in the α-1 subunit of the inhibitory glycine receptor cause the dominant neurologic disorder, hyperekplexia. Nat Genet 1993;5:351-358.
11. Jones-Davis DM, Macdonald RL. GABA(A) receptor function and pharmacology in epilepsy and status epilepticus. Curr Opin Pharmacol 2003;3:12-18.
12. Wong CGT, Bottiglieri T, Snead OC. GABA, γ-hydroxybutyric acid, and neurological disease. Ann Neurol 2003;54:S3-S12.
13. Legendre P. The glycinergic inhibitory synapse. Cell Mol Life Sci 2001;58(5/6):760-793.
14. Grenningloh G, Schmieden V, Schofield PR, Seeburg PH, Siddique T, Mohandas TK, Becker CM, Betz H. α-Subunit variants of the human glycine receptor - primary structures, functional expression and chromosomal localization of the corresponding genes. EMBO J 1990;9:771-776.
15. Cascio M, Schoppa NE, Grodzicki RL, Sigworth FJ, Fox RO. Functional expression and purification of a homomeric human-α-1 glycine receptor in baculovirus-infected insect cells. J Biol Chem 1993;268:22135-22142.
16. Eisele JL, Bertrand S, Galzi JL, Devillersthiery A, Changeux JP, Bertrand D. Chimeric nicotinic serotonergic receptor combines distinct ligand-binding and channel specificities. Nature 1993;366:479-483.
17. Grutter T, de Carvalho LP, Dufresne V, Taly A, Edelstein SJ, Changeux JP. Molecular tuning of fast gating in pentameric ligand-gated ion channels. Proc Natl Acad Sci USA 2005;102: 18207-18212.
18. Unwin N. Nicotinic acetylcholine-receptor at 9-Angstrom resolution. J Mol Biol 1993;229:1101-1124.
19. Unwin N. Acetylcholine-receptor channel imaged in the open state. Nature 1995;373:37-13.
20. Miyazawa A, Fujiyoshi Y, Unwin N. Structure and gating mechanism of the acetylcholine receptor pore. Nature 2003;423:949-955.
21. Unwin N. Refined structure of the nicotinic acetylcholine receptor at 4 Å resolution. J Mol Biol 2005;346:967-989.
22. Brejc K, van Dijk WJ, Klaassen RV, Schuurmans M, van der Oost J, Smit AB, Sixma TK. Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors. Nature 2001;411:269-276.
23. Celie PHN, Rossum-Fikkert SE, van Dijk WJ, Brejc K, Smit AB, Sixma TK. Nicotine and carbamylcholine binding to nicotinic acetylcholine receptors as studied in AChBP crystal structures. Neuron 2004;41:907-914.
24. Bourne Y, Talley TT, Hansen SB, Taylor P, Marchot P. Crystal structure of a Cbtx-AChBP complex reveals essential interactions between snake a-neurotoxins and nicotinic receptors. EMBO J 2005:1512-1522.
25. Le Novere N, Grutter T, Changeux JP. Models of the extracellular domain of the nicotinic receptors and of agonist- and Ca2+-binding sites. Proc Natl Acad Sci USA 2002;99:3210-3215.
26. Russell RB, Saqi MAS, Sayle RA, Bates PA, Sternberg MJE. Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J Mol Biol 1997;269:423-439.
27. Sine SM, Wang HL, Bren N. Lysine scanning mutagenesis delineates structural model of the nicotinic receptor ligand binding domain. J Biol Chem 2002;277:29210-29223.
28. Menziani MC, De Rienzo F, Cappelli A, Anzini M, De Benedetti PG. A computational model of the 5-HT3 receptor extracellular domain: search for ligand binding sites. Thermochim Acta 2001; 106(1/2):98-104.
29. Leite JF, Cascio M. Structure of ligand-gated ion channels: critical assessment of biochemical data supports novel topology. Mol Cell Neurosci 2001;17:777-792.
30. Absalom NL, Lewis TM, Kaplan W, Pierce KD, Schofield PR. Role of charged residues in coupling ligand binding and channel activation in the extracellular domain of the glycine receptor. J Biol Chem 2003;278:50151-50157.
31. Nevin ST, Cromer BA, Haddrill JL, Morton CJ, Parker MW, Lynch JW. Insights into the structural basis for zinc inhibition of the glycine receptor. J Biol Chem 2003;278:28985-28992.
32. Reeves DC, Lummis SCR. The molecular basis of the structure and function of the 5-HT3 receptor: a model ligand-gated ion channel. Mol Membr Biol 2002;19:11-26.
33. Henchman RH, Wang HL, Sine SM, Taylor P, McCammon JA. Asymmetric structural motions of the homomeric α7 nicotinic receptor ligand binding domain revealed by molecular dynamics simulation. Biophys J 2003;85:3007-3018.
34. Cromer BA, Morton CJ, Parker MW. Anxiety over GABA(A) receptor structure relieved by AChBP. Trends Biochem Sci 2002; 27:280-287.
35. Amiri S, Tai K, Beckstein O, Biggin PC, Sansom MSP. The α7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics. Mol Membr Biol 2005;22:151-162.
36. Hansen SB, Talley TT, Radic Z, Taylor P. Structural and ligand recognition characteristics of an acetylcholine-binding protein from Aplysia californica. J Biol Chem 2004;279:24197-24202.
37. Kirkpatrick S, Gelatt CD, Vecchi MP. Optimization by simulated annealing. Science 1983;220:671-680.
38. Mendieta J, Ramirez G, Gago F. Molecular dynamics simulations of the conformational changes of the glutamate receptor ligand-binding core in the presence of glutamate and kainate. Proteins: Struct Funct Genet 2001;44:460-469.
39. 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.
40. Thompson JD, Higgins DG, Gibson TJ. Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
41. Sali A, Blundell TL. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
42. Vriend G. What If - a molecular modeling and drug design program. J Mol Graphics 1990;8:52-56.
43. Case DA, Pearlman DA, Caldwell JW, Cheatham Iii TE, Wang J, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Gohlke H, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA. AMBER 7. San Francisco: University of California; 2002.
44. Darden T, York D, Pedersen L. Particle Mesh Ewald - An N log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
45. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977; 23:327-341.
46. Duke ER, Pedersen LG. PMEMD 3. Chapel Hill: University of North Carolina; 2003.
47. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, 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.
48. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998;19:1639-1662.
49. Henchman R, Hai-Long W, Sin SM, Taylor P, McCammon JA. Ligand-induced conformational change in the α7 nicotinic receptor. Biophys J 2005;88:2564-2576.
50. Grudzinska J, Schemm R, Haeger S, Nicke A, Schmalzing G, Betz H, Laube B. The β subunit determines the ligand binding properties of synaptic glycine receptors. Neuron 2005;45:727-739.
51. Unwin N, Miyazawa A, Li J, Fujiyoshi Y. Activation of the nicotinic acetylcholine receptor involves a switch in conformation of the a subunits. J Mol Biol 2002;319:1165-1176.