메뉴 건너뛰기




Volumn 3, Issue MAY, 2012, Pages

Beyond modeling: All-atom olfactory receptor model simulations

Author keywords

GPCR; Ligand binding; Lipid bilayer; Molecular dynamics; Olfactory receptor; Protein modeling

Indexed keywords


EID: 84876016110     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00061     Document Type: Article
Times cited : (22)

References (45)
  • 1
    • 65549083717 scopus 로고    scopus 로고
    • Gridmat-md: a grid-based membrane analysis tool for use with molecular dynamics
    • Allen, W. J., Lemkul, J. A., and Bevan, D. R. (2009). Gridmat-md: a grid-based membrane analysis tool for use with molecular dynamics. J. Comput. Chem. 30, 1952-1958.
    • (2009) J. Comput. Chem. , vol.30 , pp. 1952-1958
    • Allen, W.J.1    Lemkul, J.A.2    Bevan, D.R.3
  • 2
    • 0000550720 scopus 로고    scopus 로고
    • Strength of hydrogen bonds in α helices
    • Arora, N., and Jayaram, B. (1996). Strength of hydrogen bonds in α helices. J. Comput. Chem. 18, 1245-1252.
    • (1996) J. Comput. Chem. , vol.18 , pp. 1245-1252
    • Arora, N.1    Jayaram, B.2
  • 3
    • 0025825726 scopus 로고
    • A novel multigene family may encode odorant receptors: a molecular basis for odor recognition
    • Buck, L., and Axel, R. (1991). A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65, 175-187.
    • (1991) Cell , vol.65 , pp. 175-187
    • Buck, L.1    Axel, R.2
  • 4
    • 84888005594 scopus 로고    scopus 로고
    • Hydrophobicity proles in G protein-coupled receptor transmembrane helical domains
    • Crasto, C. (2010). Hydrophobicity proles in G protein-coupled receptor transmembrane helical domains. J. Receptor Ligand Channel Res. 3, 123-133.
    • (2010) J. Receptor Ligand Channel Res. , vol.3 , pp. 123-133
    • Crasto, C.1
  • 5
    • 0035822998 scopus 로고    scopus 로고
    • A diverse family of GPCRs expressed in specic subsets of noci-ceptive sensory neurons
    • Dong, X., Han, S. K., Zylka, M. J., Simon, M. I., and Anderson, D. J.(2001). A diverse family of GPCRs expressed in specic subsets of noci-ceptive sensory neurons. Cell 106, 619-632.
    • (2001) Cell , vol.106 , pp. 619-632
    • Dong, X.1    Han, S.K.2    Zylka, M.J.3    Simon, M.I.4    Anderson, D.J.5
  • 6
    • 0025952856 scopus 로고
    • Olfactory impairment in motor neuron disease: a pilot study
    • Elian, M. (1991). Olfactory impairment in motor neuron disease: a pilot study. J. Neurol. Neurosurg. Psychiatr. 54, 927-928.
    • (1991) J. Neurol. Neurosurg. Psychiatr. , vol.54 , pp. 927-928
    • Elian, M.1
  • 8
    • 0038024615 scopus 로고    scopus 로고
    • The G-protein-coupled receptors in the human genome form ve main families.Phylogenetic analysis, paralogon groups, and ngerprints
    • Fredriksson, R., Lagerström, M. C., Lundin, L.-G., and Schiöth, H. B. (2003). The G-protein-coupled receptors in the human genome form ve main families.Phylogenetic analysis, paralogon groups, and ngerprints. Mol. Pharmacol. 63, 1256-1272.
    • (2003) Mol. Pharmacol. , vol.63 , pp. 1256-1272
    • Fredriksson, R.1    Lagerström, M.C.2    Lundin, L.-G.3    Schiöth, H.B.4
  • 9
    • 0037357440 scopus 로고    scopus 로고
    • Population differences in the human functional olfactory repertoire
    • Gilad,Y., and Lancet,D. (2003). Population differences in the human functional olfactory repertoire.Mol. Biol. Evol. 20, 307-314.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 307-314
    • Gilad, Y.1    Lancet, D.2
  • 10
    • 0035001936 scopus 로고    scopus 로고
    • The complete human olfactory subgenome
    • Glusman, G., Yanai, I., Rubin, I., and Lancet, D. (2001). The complete human olfactory subgenome. Genome Res. 11, 685-702.
    • (2001) Genome Res , vol.11 , pp. 685-702
    • Glusman, G.1    Yanai, I.2    Rubin, I.3    Lancet, D.4
  • 11
    • 0031984517 scopus 로고    scopus 로고
    • The many faces of G protein signaling
    • Hamm, H. E. (1998). The many faces of G protein signaling. J. Biol. Chem. 273, 669-672.
    • (1998) J. Biol. Chem. , vol.273 , pp. 669-672
    • Hamm, H.E.1
  • 12
    • 33645783040 scopus 로고    scopus 로고
    • Probing a model of a gpcr/ligand complex in an explicit membrane environment: the human cholecystokinin-1 receptor
    • Hénin, J., Maigret, B., Tarek, M., Escrieut,C., Fourmy,D., and Chipot, C. (2006). Probing a model of a gpcr/ligand complex in an explicit membrane environment: the human cholecystokinin-1 receptor. Biophys. J. 90, 1232-1240.
    • (2006) Biophys. J. , vol.90 , pp. 1232-1240
    • Hénin, J.1    Maigret, B.2    Tarek, M.3    Escrieut, C.4    Fourmy, D.5    Chipot, C.6
  • 13
    • 46249092554 scopus 로고    scopus 로고
    • Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. (2008). Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435-447.
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 14
    • 54449098286 scopus 로고    scopus 로고
    • Structural basis for ligand binding and specificity in adrenergic receptors: implications for GPCR-targeted drug discovery
    • Huber, T., Menon, S., and Sakmar, T. P. (2008). Structural basis for ligand binding and specicity in adrenergic receptors: implications for GPCR-targeted drug discovery. Biochemistry 47, 11013-11023.
    • (2008) Biochemistry , vol.47 , pp. 11013-11023
    • Huber, T.1    Menon, S.2    Sakmar, T.P.3
  • 18
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
    • Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. L. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580.
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.L.4
  • 19
    • 27944475233 scopus 로고    scopus 로고
    • Structural activation pathways from dynamic olfactory receptor-odorant interactions
    • Lai, P. C., Singer, M. S., and Crasto, C. J. (2005). Structural activation pathways from dynamic olfactory receptor-odorant interactions. Chem. Senses 30, 781-792.
    • (2005) Chem. Senses , vol.30 , pp. 781-792
    • Lai, P.C.1    Singer, M.S.2    Crasto, C.J.3
  • 20
    • 25444478851 scopus 로고    scopus 로고
    • Molecular dynamics simulations of retinal in rhodopsin: fromthe dark-adapted state towards lumirhodopsin
    • Lemaître, V., Yeagle, P., and Watts, A. (2005). Molecular dynamics simulations of retinal in rhodopsin: fromthe dark-adapted state towards lumirhodopsin. Biochemistry 44, 12667-12680.
    • (2005) Biochemistry , vol.44 , pp. 12667-12680
    • Lemaître, V.1    Yeagle, P.2    Watts, A.3
  • 22
    • 0033525727 scopus 로고    scopus 로고
    • Combinatorial receptor codes for odors
    • Malnic,B.,Hirono, J., Sato,T., and Buck, L. B. (1999). Combinatorial receptor codes for odors. Cell 96, 712-723.
    • (1999) Cell , vol.96 , pp. 712-723
    • Malnic, B.1    Hirono, J.2    Sato, T.3    Buck, L.B.4
  • 25
    • 0031886320 scopus 로고    scopus 로고
    • Olfaction in neurodegenerative disease: a meta-analysis of olfactory functioning in Alzheimer's and Parkinson's diseases
    • Mesholam, R. I.,Moberg, P. J.,Mahr, R. N., and Doty, R. L. (1998). Olfaction in neurodegenerative disease: a meta-analysis of olfactory functioning in Alzheimer's and Parkinson's diseases. Arch. Neurol. 55, 85-90.
    • (1998) Arch. Neurol. , vol.55 , pp. 85-90
    • Mesholam, R.I.1    Moberg, P.J.2    Mahr, R.N.3    Doty, R.L.4
  • 26
    • 0034899781 scopus 로고    scopus 로고
    • Evaluation of methods for the prediction of membrane spanning regions
    • Möller, S., Croning, M. D. R., and Apweiler, R. (2001). Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17, 646-653.
    • (2001) Bioinformatics , vol.17 , pp. 646-653
    • Möller, S.1    Croning, M.D.R.2    Apweiler, R.3
  • 27
    • 46149089973 scopus 로고    scopus 로고
    • Simulations of proteins with inhomogeneous degrees of freedom: the effect of thermostats
    • Mor, A., Ziv, G., and Levy, Y. (2008). Simulations of proteins with inhomogeneous degrees of freedom: the effect of thermostats. J. Comput. Chem. 29, 1992-1998.
    • (2008) J. Comput. Chem. , vol.29 , pp. 1992-1998
    • Mor, A.1    Ziv, G.2    Levy, Y.3
  • 29
    • 80051769266 scopus 로고    scopus 로고
    • The role of conformational ensembles in ligand recognition in G-protein coupled receptors
    • Niesen, M. J. M., Bhattacharya, S., and Vaidehi, N. (2011). The role of conformational ensembles in ligand recognition in G-protein coupled receptors. J.Am.Chem. Soc. 133, 13197-13204.
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 13197-13204
    • Niesen, M.J.M.1    Bhattacharya, S.2    Vaidehi, N.3
  • 30
    • 0142091376 scopus 로고    scopus 로고
    • Evolution of olfactory receptor genes in the human genome
    • Niimura, Y., and Nei, M. (2003). Evolution of olfactory receptor genes in the human genome. Proc.Natl.Acad. Sci. U.S.A. 100, 12235-12240.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 12235-12240
    • Niimura, Y.1    Nei, M.2
  • 31
    • 0035928480 scopus 로고    scopus 로고
    • Length analyses of mammalian G-protein coupled receptors
    • Otaki, J. M., and Firestein, S. (2001). Length analyses of mammalian G-protein coupled receptors. J. Theor. Biol. 211, 315-327.
    • (2001) J. Theor. Biol. , vol.211 , pp. 315-327
    • Otaki, J.M.1    Firestein, S.2
  • 32
    • 33947381686 scopus 로고    scopus 로고
    • The highly conserved dry motif of class a G protein-coupled receptors: beyond the ground state
    • Rovati, G. E., Capra, V., and Neubig, R. R. (2007). The highly conserved dry motif of class a G protein-coupled receptors: beyond the ground state. Mol. Pharmacol. 71, 959-964.
    • (2007) Mol. Pharmacol. , vol.71 , pp. 959-964
    • Rovati, G.E.1    Capra, V.2    Neubig, R.R.3
  • 33
    • 29244479584 scopus 로고    scopus 로고
    • Molecular dynamics simulations of bovine rhodopsin: infiuence of protonation states and differentmembrane-mimicking environments
    • Schlegel, B., Sippl, W., and Holtje, H. D. (2005). Molecular dynamics simulations of bovine rhodopsin: infiuence of protonation states and differentmembrane-mimicking environments. J. Mol. Model. 12, 49-64.
    • (2005) J. Mol. Model. , vol.12 , pp. 49-64
    • Schlegel, B.1    Sippl, W.2    Holtje, H.D.3
  • 34
    • 0034042247 scopus 로고    scopus 로고
    • Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor
    • Singer, M. S. (2000). Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor. Chem. Senses 25, 155-165.
    • (2000) Chem. Senses , vol.25 , pp. 155-165
    • Singer, M.S.1
  • 35
    • 79952116502 scopus 로고    scopus 로고
    • Beyond rhodopsin: G protein-coupled receptor structure and modeling incorporating the beta2-adrenergic and adenosine a(2a) crystal structures
    • Tebben, A. J., and Schnur, D.M. (2010). Beyond rhodopsin: G protein-coupled receptor structure and modeling incorporating the beta2-adrenergic and adenosine a(2a) crystal structures. Methods Mol. Biol. 672, 359-386.
    • (2010) Methods Mol. Biol. , vol.672 , pp. 359-386
    • Tebben, A.J.1    Schnur, D.M.2
  • 36
    • 0034786532 scopus 로고    scopus 로고
    • The HMMTOP transmembrane topology prediction server
    • Tusnady, G. E., and Simon, I. (2001). The HMMTOP transmembrane topology prediction server. Bioinformatics 17, 849-850.
    • (2001) Bioinformatics , vol.17 , pp. 849-850
    • Tusnady, G.E.1    Simon, I.2
  • 37
    • 33646138957 scopus 로고    scopus 로고
    • Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques
    • Ulmschneider, M. B., Sansom, M. S. P., and Di Nola, A. (2006). Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques. Biophys. J. 90, 1650-1660.
    • (2006) Biophys. J. , vol.90 , pp. 1650-1660
    • Ulmschneider, M.B.1    Sansom, M.S.P.2    Di Nola, A.3
  • 38
    • 0030248996 scopus 로고    scopus 로고
    • Low-resolution docking: prediction of complexes for underdetermined structures
    • Vakser, I. A. (1996). Low-resolution docking: prediction of complexes for underdetermined structures. Biopolymers 39, 455-464.
    • (1996) Biopolymers , vol.39 , pp. 455-464
    • Vakser, I.A.1
  • 39
    • 79551571786 scopus 로고    scopus 로고
    • Predicting novel bindingmodes of agonists to β adrenergic receptors using allatom molecular dynamics simulations
    • doi:10.1371/journal.pcbi.1001053
    • Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U. (2011). Predicting novel bindingmodes of agonists to β adrenergic receptors using allatom molecular dynamics simulations. PLoS Comput. Biol. 7, e1001053. doi:10.1371/journal.pcbi.1001053
    • (2011) PLoS Comput. Biol. , vol.7
    • Vanni, S.1    Neri, M.2    Tavernelli, I.3    Rothlisberger, U.4
  • 43
    • 77954256616 scopus 로고    scopus 로고
    • g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation
    • Wolf, M. G., Hoefiing, M., Aponte-Santamaria, C., Grubmüller,H., and Groenhof, G. (2010). g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J. Comput. Chem. 31, 2169-2174.
    • (2010) J. Comput. Chem. , vol.31 , pp. 2169-2174
    • Wolf, M.G.1    Hoeing, M.2    Aponte-Santamaria, C.3    Grubmüller, H.4    Groenhof, G.5
  • 44
    • 21044437346 scopus 로고    scopus 로고
    • Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane-aqueous system
    • Zhang, Y., Sham, Y. Y., Rajamani, R., Gao, J., and Portoghese, P. S. (2005). Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane-aqueous system. Chembiochem 6, 853-859.
    • (2005) Chembiochem , vol.6 , pp. 853-859
    • Zhang, Y.1    Sham, Y.Y.2    Rajamani, R.3    Gao, J.4    Portoghese, P.S.5
  • 45
    • 0035237870 scopus 로고    scopus 로고
    • The human olfactory receptor repertoire
    • research0018.1-research0018.12
    • Zozulya, S., Echeverri, F., and Nguyen, T. (2001). The human olfactory receptor repertoire. Genome Biol. 2, research0018.1-research0018.12
    • (2001) Genome Biol. , vol.2
    • Zozulya, S.1    Echeverri, F.2    Nguyen, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.