Abstract
We have constructed a molecular model of the ligand-binding domain of the GABAC receptor, which is a member of the Cys-loop ligand-gated ion channel family. The extracellular domains of these receptors share similar sequence homology (20%) with Limnaea acetylcholine-binding protein for which an X-ray crystal structure is available. We used this structure as a template for homology modeling of the GABAC receptor extracellular domain using FUGUE and MODELLER software. FlexX was then used to dock GABA into the receptor ligand-binding site, resulting in three alternative energetically favorable orientations. Residues located no more than 5 Å from the docked GABA were identified for each model; of these, three were found to be common to all models with 14 others present only in certain models. Using data from experimental studies, we propose that the most likely orientation of GABA is with its amine close to Y198, and its carboxylate close to R104. These studies have therefore provided a model of the ligand-binding domain, which will be useful for both GABAC and GABAA receptor studies, and have also yielded an experimentally testable hypothesis of the location of GABA in the binding pocket.
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Abbreviations
- LGIC:
-
Ligand-gated ion channel
- ACh:
-
Acetylcholine
- AChBP:
-
Acetylcholine-binding protein
- nAChR:
-
Nicotinic acetylcholine receptor
- SCAM:
-
Substituted cysteine accessibility method
References
Corringer PJ, Le Novere N, Changeux JP (2000) Annu Rev Pharmacol Toxicol 40:431–458
Celie PH, van Rossum-Fikkert SE, van Dijk WJ, Brejc K, Smit AB, Sixma TK (2004) Neuron 41:907–914
Cromer BA, Morton CJ, Parker MW (2002) Trends Biochem Sci 27:280–287
Le Novere N, Grutter T, Changeux JP (2002) Proc Natl Acad Sci USA 99:3210–3215
Maksay G, Bikadi Z, Simonyi M (2003) J Recept Signal Transduct Res 23:255–270
Schapira M, Abagyan R, Totrov M (2002) BMC Struct Biol 2:1
Reeves DC, Sayed MF, Chau PL, Price KL, Lummis SC (2003) Biophys J 84:2338–2344
Bouzat C, Gumilar F, Spitzmaul G, Wang HL, Rayes D, Hansen SB, Taylor P, Sine SM (2004) Nature 430:896–900
Cutting GR, Lu L, O’Hara BF, Kasch LM, Montrose-Rafizadeh C, Donovan DM, Shimada S, Antonarakis SE, Guggino WB, Uhl GR, Kazazian HH Jr (1991) Proc Natl Acad Sci USA 88:2673–2677
Johnston GA (1996) Trends Pharmacol Sci 17:319–323
Chiara DC, Trinidad JC, Wang D, Ziebell MR, Sullivan D, Cohen JB (2003) Biochemistry 42:271–283
Chang Y, Weiss DS (1999) Nat Neurosci 2:219–225
Brejc K, van Dijk WJ, Klaassen RV, Schuurmans M, van Der Oost J, Smit AB, Sixma TK (2001) Nature 411:269–276
Shi J, Blundell TL, Mizuguchi K (2001) J Mol Biol 310:243–257
Sali A, Blundell TL (1993) J Mol Biol 234:779–815
Deane CM, Blundell TL (2001) Protein Sci 10:599–612
Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P (1984) J Am Chem Soc 106:765–784
Thompson JD, Higgins DG, Gibson TJ (1994) Nucleic Acids Res 22:4673–4680
Nunez Miguel R, Shi J, Mizuguchi K (2001) Protein structure prediction: bioinformatic approach. International University Line Publishers, La Jolla, pp 143–169
Amin J, Weiss DS (1994) Receptors Channels 2:227–236
Rost B, Sander C (1993) J Mol Biol 232:584–599
Sedelnikova A, Smith CD, Zakharkin SO, Davis D, Weiss DS, Chang Y (2005) J Biol Chem 280:1535–1542
Zhong WG, Gallivan JP, Zhang YO, Li LT, Lester HA, Dougherty DA (1998) Proc Natl Acad Sci USA 95:12088–12093
Beene DL, Brandt GS, Zhong W, Zacharias NM, Lester HA, Dougherty DA (2002) Biochemistry 41:10262–10269
Beene DL, Price KL, Lester HA, Dougherty DA, Lummis SC (2004) J Neurosci 24:9097–9104
Wagner DA, Czajkowski C (2001) J Neurosci 21:67–74
Price KL, Lummis SCR (2004) J Biol Chem 279:23294–23301
Sullivan D, Chiara DC, Cohen JB (2002) Mol Pharmacol 61:463–472
Mu TW, Lester HA, Dougherty DA (2003) J Am Chem Soc 125:6850–6851
Steward LJ, Boess FG, Steele JA, Liu D, Wong N, Martin IL (2000) Mol Pharmacol 57:1249–1255
Boileau AJ, Newell JG, Czajkowski C (2002) J Biol Chem 277:2931–2937
Galzi JL, Bertrand D, Devillers-Thiery A, Revah F, Bertrand S, Changeux JP (1991) FEBS Lett 294:198–202
Jin P, Walther D, Zhang J, Rowe-Teeter C, Fu GK (2004) J Biol Chem 279:14179–14183
Sine SM, Quiram P, Papanikolaou F, Kreienkamp HJ, Taylor P (1994) J Biol Chem 269:8808–8816
Wagner DA, Czajkowski C, Jones MV (2004) J Neurosci 24:2733–2741
Torres VI, Weiss DS (2002) J Biol Chem 277:43741–43748
Holden JH, Czajkowski C (2002) J Biol Chem 277:18785–18792
Hartvig L, Lukensmejer B, Liljefors T, Dekermendjian K (2000) J Neurochem 75:1746–1753
Grutter T, Changeux JP (2001) Trends Biochem Sci 26:459–463
Acknowledgments
We thank the Wellcome Trust (SCRL), and the MRC (NLH) for funding. SCRL is a Wellcome Trust Senior Research Fellow in Basic Biomedical Studies. We also thank Dr. David Burke for his contributions in running MODELLER and Dr. Andy Thompson for his assistance in creation of the figures.
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Harrison, N.J., Lummis, S.C. Molecular modeling of the GABAC receptor ligand-binding domain. J Mol Model 12, 317–324 (2006). https://doi.org/10.1007/s00894-005-0034-6
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DOI: https://doi.org/10.1007/s00894-005-0034-6