메뉴 건너뛰기




Volumn 2, Issue 1, 2017, Pages 15-21

Multi-scale simulations of membrane proteins: The case of bitter taste receptors

Author keywords

Bitter taste receptor; G protein coupled receptor; Molecular mechanics coarse grained simulations; TAS2R38; TAS2R46

Indexed keywords


EID: 85034112001     PISSN: 24682284     EISSN: 24682179     Source Type: Journal    
DOI: 10.1016/j.jsamd.2017.03.001     Document Type: Review
Times cited : (10)

References (106)
  • 1
    • 27944434112 scopus 로고    scopus 로고
    • Elucidation of mammalian bitter taste
    • Meyerhof, W., Elucidation of mammalian bitter taste. Rev. Physiol. Biochem. Pharmacol. 154 (2005), 37–72.
    • (2005) Rev. Physiol. Biochem. Pharmacol. , vol.154 , pp. 37-72
    • Meyerhof, W.1
  • 2
    • 84877287787 scopus 로고    scopus 로고
    • An evolutionary perspective on food and human taste
    • Breslin, P.A.S., An evolutionary perspective on food and human taste. Curr. Biol. 23:9 (2013), R409–R418.
    • (2013) Curr. Biol. , vol.23 , Issue.9 , pp. R409-R418
    • Breslin, P.A.S.1
  • 3
    • 80053459477 scopus 로고    scopus 로고
    • Gustatory and extragustatory functions of mammalian taste receptors
    • Behrens, M., Meyerhof, W., Gustatory and extragustatory functions of mammalian taste receptors. Physiol. Behav. 105:1 (2011), 4–13.
    • (2011) Physiol. Behav. , vol.105 , Issue.1 , pp. 4-13
    • Behrens, M.1    Meyerhof, W.2
  • 5
    • 85012918828 scopus 로고    scopus 로고
    • Extraoral bitter taste receptors in health and disease
    • Lu, P., Zhang, C.H., Lifshitz, L.M., ZhuGe, R., Extraoral bitter taste receptors in health and disease. J. Gen. Physiol. 149:2 (2017), 181–197.
    • (2017) J. Gen. Physiol. , vol.149 , Issue.2 , pp. 181-197
    • Lu, P.1    Zhang, C.H.2    Lifshitz, L.M.3    ZhuGe, R.4
  • 6
    • 0033582645 scopus 로고    scopus 로고
    • Putative mammalian taste receptors: a class of taste-specific GPCRs with distinct topographic selectivity
    • Hoon, M.A., Adler, E., Lindemeier, J., Battey, J.F., Ryba, N.J., Zuker, C.S., Putative mammalian taste receptors: a class of taste-specific GPCRs with distinct topographic selectivity. Cell 96:4 (1999), 541–551.
    • (1999) Cell , vol.96 , Issue.4 , pp. 541-551
    • Hoon, M.A.1    Adler, E.2    Lindemeier, J.3    Battey, J.F.4    Ryba, N.J.5    Zuker, C.S.6
  • 9
    • 84914153160 scopus 로고    scopus 로고
    • Bitter and sweet taste receptors in the respiratory epithelium in health and disease
    • Lee, R.J., Cohen, N.A., Bitter and sweet taste receptors in the respiratory epithelium in health and disease. J. Mol. Med. 92:12 (2014), 1235–1244.
    • (2014) J. Mol. Med. , vol.92 , Issue.12 , pp. 1235-1244
    • Lee, R.J.1    Cohen, N.A.2
  • 10
    • 84899050450 scopus 로고    scopus 로고
    • Cholinergic neurotransmission links solitary chemosensory cells to nasal inflammation
    • Saunders, C.J., Christensen, M., Finger, T.E., Tizzano, M., Cholinergic neurotransmission links solitary chemosensory cells to nasal inflammation. Proc. Natl. Acad. Sci. U. S. A. 111:16 (2014), 6075–6080.
    • (2014) Proc. Natl. Acad. Sci. U. S. A. , vol.111 , Issue.16 , pp. 6075-6080
    • Saunders, C.J.1    Christensen, M.2    Finger, T.E.3    Tizzano, M.4
  • 11
    • 78651282172 scopus 로고    scopus 로고
    • Expression of taste receptors in Solitary Chemosensory Cells of rodent airways
    • Tizzano, M., Cristofoletti, M., Sbarbati, A., Finger, T.E., Expression of taste receptors in Solitary Chemosensory Cells of rodent airways. BMC Pulm. Med., 11, 2011, 3.
    • (2011) BMC Pulm. Med. , vol.11 , pp. 3
    • Tizzano, M.1    Cristofoletti, M.2    Sbarbati, A.3    Finger, T.E.4
  • 12
    • 33847078811 scopus 로고    scopus 로고
    • Taste receptors in the gastrointestinal tract. IV. Functional implications of bitter taste receptors in gastrointestinal chemosensing
    • Sternini, C., Taste receptors in the gastrointestinal tract. IV. Functional implications of bitter taste receptors in gastrointestinal chemosensing. Am. J. Physiol-Gastrointest. Liver 292:2 (2007), G457–G461.
    • (2007) Am. J. Physiol-Gastrointest. Liver , vol.292 , Issue.2 , pp. G457-G461
    • Sternini, C.1
  • 13
    • 0037133261 scopus 로고    scopus 로고
    • Expression of bitter taste receptors of the T2R family in the gastrointestinal tract and enteroendocrine STC-1 cells
    • Wu, S.V., Rozengurt, N., Yang, M., Young, S.H., Sinnett-Smith, J., Rozengurt, E., Expression of bitter taste receptors of the T2R family in the gastrointestinal tract and enteroendocrine STC-1 cells. Proc. Natl. Acad. Sci. U. S. A. 99:4 (2002), 2392–2397.
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , Issue.4 , pp. 2392-2397
    • Wu, S.V.1    Rozengurt, N.2    Yang, M.3    Young, S.H.4    Sinnett-Smith, J.5    Rozengurt, E.6
  • 17
    • 79952138344 scopus 로고    scopus 로고
    • Bitter taste receptors and alpha-gustducin regulate the secretion of ghrelin with functional effects on food intake and gastric emptying
    • Janssen, S., Laermans, J., Verhulst, P.J., Thijs, T., Tack, J., Depoortere, I., Bitter taste receptors and alpha-gustducin regulate the secretion of ghrelin with functional effects on food intake and gastric emptying. Proc. Natl. Acad. Sci. U. S. A. 108:5 (2011), 2094–2099.
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , Issue.5 , pp. 2094-2099
    • Janssen, S.1    Laermans, J.2    Verhulst, P.J.3    Thijs, T.4    Tack, J.5    Depoortere, I.6
  • 18
    • 36248977649 scopus 로고    scopus 로고
    • Gustatory expression pattern of the human TAS2R bitter receptor gene family reveals a heterogenous population of bitter responsive taste receptor cells
    • Behrens, M., Foerster, S., Staehler, F., Raguse, J.D., Meyerhof, W., Gustatory expression pattern of the human TAS2R bitter receptor gene family reveals a heterogenous population of bitter responsive taste receptor cells. J. Neurosci. 27:46 (2007), 12630–12640.
    • (2007) J. Neurosci. , vol.27 , Issue.46 , pp. 12630-12640
    • Behrens, M.1    Foerster, S.2    Staehler, F.3    Raguse, J.D.4    Meyerhof, W.5
  • 19
    • 33746639193 scopus 로고    scopus 로고
    • Bitter taste receptors and human bitter taste perception
    • Behrens, M., Meyerhof, W., Bitter taste receptors and human bitter taste perception. Cell. Mol. Life Sci. 63:13 (2006), 1501–1509.
    • (2006) Cell. Mol. Life Sci. , vol.63 , Issue.13 , pp. 1501-1509
    • Behrens, M.1    Meyerhof, W.2
  • 21
    • 84973879531 scopus 로고    scopus 로고
    • Probing the binding pocket of the broadly tuned human bitter taste receptor TAS2R14 by chemical modification of cognate agonists
    • Karaman, R., Nowak, S., Di Pizio, A., Kitaneh, H., Abu-Jaish, A., Meyerhof, W., Niv, M.Y., Behrens, M., Probing the binding pocket of the broadly tuned human bitter taste receptor TAS2R14 by chemical modification of cognate agonists. Chem. Biol. Drug. Des. 88:1 (2016), 66–75.
    • (2016) Chem. Biol. Drug. Des. , vol.88 , Issue.1 , pp. 66-75
    • Karaman, R.1    Nowak, S.2    Di Pizio, A.3    Kitaneh, H.4    Abu-Jaish, A.5    Meyerhof, W.6    Niv, M.Y.7    Behrens, M.8
  • 22
    • 84856259611 scopus 로고    scopus 로고
    • Computer-assisted design for paracetamol masking bitter taste prodrugs
    • Hejaz, H., Karaman, R., Khamis, M., Computer-assisted design for paracetamol masking bitter taste prodrugs. J. Mol. Model 18:1 (2012), 103–114.
    • (2012) J. Mol. Model , vol.18 , Issue.1 , pp. 103-114
    • Hejaz, H.1    Karaman, R.2    Khamis, M.3
  • 23
    • 84878759581 scopus 로고    scopus 로고
    • Prodrugs for masking bitter taste of antibacterial drugs - a computational approach
    • Karaman, R., Prodrugs for masking bitter taste of antibacterial drugs - a computational approach. J. Mol. Model 19:6 (2013), 2399–2412.
    • (2013) J. Mol. Model , vol.19 , Issue.6 , pp. 2399-2412
    • Karaman, R.1
  • 24
    • 66249144426 scopus 로고    scopus 로고
    • The structure and function of G-protein-coupled receptors
    • Rosenbaum, D.M., Rasmussen, S.G.F., Kobilka, B.K., The structure and function of G-protein-coupled receptors. Nature 459:7245 (2009), 356–363.
    • (2009) Nature , vol.459 , Issue.7245 , pp. 356-363
    • Rosenbaum, D.M.1    Rasmussen, S.G.F.2    Kobilka, B.K.3
  • 25
    • 33751084573 scopus 로고    scopus 로고
    • The receptors and cells for mammalian taste
    • Chandrashekar, J., Hoon, M.A., Ryba, N.J.P., Zuker, C.S., The receptors and cells for mammalian taste. Nature 444:7117 (2006), 288–294.
    • (2006) Nature , vol.444 , Issue.7117 , pp. 288-294
    • Chandrashekar, J.1    Hoon, M.A.2    Ryba, N.J.P.3    Zuker, C.S.4
  • 27
    • 0038024615 scopus 로고    scopus 로고
    • The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
    • Fredriksson, R., Lagerstrom, M.C., Lundin, L.G., Schioth, H.B., The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol. Pharmacol. 63:6 (2003), 1256–1272.
    • (2003) Mol. Pharmacol. , vol.63 , Issue.6 , pp. 1256-1272
    • Fredriksson, R.1    Lagerstrom, M.C.2    Lundin, L.G.3    Schioth, H.B.4
  • 32
    • 80052158550 scopus 로고    scopus 로고
    • Independent HHsearch, Needleman-Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families
    • Nordstrom, K.J.V., Almen, M.S., Edstam, M.M., Fredriksson, R., Schioth, H.B., Independent HHsearch, Needleman-Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families. Mol. Biol. Evol. 28:9 (2011), 2471–2480.
    • (2011) Mol. Biol. Evol. , vol.28 , Issue.9 , pp. 2471-2480
    • Nordstrom, K.J.V.1    Almen, M.S.2    Edstam, M.M.3    Fredriksson, R.4    Schioth, H.B.5
  • 33
    • 84930867918 scopus 로고    scopus 로고
    • Computational studies of smell and taste receptors
    • Di Pizio, A., Niv, M.Y., Computational studies of smell and taste receptors. Isr. J. Chem. 54:8–9 (2014), 1205–1218.
    • (2014) Isr. J. Chem. , vol.54 , Issue.8-9 , pp. 1205-1218
    • Di Pizio, A.1    Niv, M.Y.2
  • 34
    • 84855402621 scopus 로고    scopus 로고
    • The origin of GPCRs: identification of mammalian like rhodopsin, adhesion, glutamate and frizzled GPCRs in fungi
    • Krishnan, A., Almen, M.S., Fredriksson, R., Schioth, H.B., The origin of GPCRs: identification of mammalian like rhodopsin, adhesion, glutamate and frizzled GPCRs in fungi. PLoS One, 7(1), 2012, e29817.
    • (2012) PLoS One , vol.7 , Issue.1 , pp. e29817
    • Krishnan, A.1    Almen, M.S.2    Fredriksson, R.3    Schioth, H.B.4
  • 38
    • 84892401045 scopus 로고    scopus 로고
    • Structure-based drug design for G protein-coupled receptors
    • Congreve, M., Dias, J.M., Marshall, F.H., Structure-based drug design for G protein-coupled receptors. Progr. Med. Chem. 53 (2014), 1–63.
    • (2014) Progr. Med. Chem. , vol.53 , pp. 1-63
    • Congreve, M.1    Dias, J.M.2    Marshall, F.H.3
  • 39
    • 84894152157 scopus 로고    scopus 로고
    • Current and emerging opportunities for molecular simulations in structure-based drug design
    • Michel, J., Current and emerging opportunities for molecular simulations in structure-based drug design. Phys. Chem. Chem. Phys. 16:10 (2014), 4465–4477.
    • (2014) Phys. Chem. Chem. Phys. , vol.16 , Issue.10 , pp. 4465-4477
    • Michel, J.1
  • 40
    • 84876469966 scopus 로고    scopus 로고
    • Emerging topics in structure-based virtual screening
    • Rastelli, G., Emerging topics in structure-based virtual screening. Pharm. Res-Dordr 30:5 (2013), 1458–1463.
    • (2013) Pharm. Res-Dordr , vol.30 , Issue.5 , pp. 1458-1463
    • Rastelli, G.1
  • 42
    • 80051521545 scopus 로고    scopus 로고
    • Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment
    • Kufareva, I., Rueda, M., Katritch, V., Stevens, R.C., Abagyan, R., GPCR Dock 2010 participants, Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 19:8 (2011), 1108–1126.
    • (2011) Structure , vol.19 , Issue.8 , pp. 1108-1126
    • Kufareva, I.1    Rueda, M.2    Katritch, V.3    Stevens, R.C.4    Abagyan, R.5    GPCR Dock 2010 participants6
  • 43
    • 84905732337 scopus 로고    scopus 로고
    • Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges
    • Kufareva, I., Katritch, V., GPCR Dock 2013 participants, Stevens, R.C., Abagyan, R., Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure 22:8 (2014), 1120–1139.
    • (2014) Structure , vol.22 , Issue.8 , pp. 1120-1139
    • Kufareva, I.1    Katritch, V.2    GPCR Dock 2013 participants3    Stevens, R.C.4    Abagyan, R.5
  • 44
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C., Lesk, A.M., The relation between the divergence of sequence and structure in proteins. EMBO J. 5:4 (1986), 823–826.
    • (1986) EMBO J. , vol.5 , Issue.4 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 46
    • 21644437700 scopus 로고    scopus 로고
    • Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets
    • Camacho, C.J., Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins 60:2 (2005), 245–251.
    • (2005) Proteins , vol.60 , Issue.2 , pp. 245-251
    • Camacho, C.J.1
  • 47
    • 84939813976 scopus 로고    scopus 로고
    • Open challenges in structure-based virtual screening: receptor modeling, target flexibility consideration and active site water molecules description
    • Spyrakis, F., Cavasotto, C.N., Open challenges in structure-based virtual screening: receptor modeling, target flexibility consideration and active site water molecules description. Arch. Biochem. Biophys. 583 (2015), 105–119.
    • (2015) Arch. Biochem. Biophys. , vol.583 , pp. 105-119
    • Spyrakis, F.1    Cavasotto, C.N.2
  • 49
    • 66649096395 scopus 로고    scopus 로고
    • Conserved waters mediate structural and functional activation of family A (rhodopsin-like) G protein-coupled receptors
    • Angel, T.E., Chance, M.R., Palczewski, K., Conserved waters mediate structural and functional activation of family A (rhodopsin-like) G protein-coupled receptors. Proc. Natl. Acad. Sci. U. S. A. 106:21 (2009), 8555–8560.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , Issue.21 , pp. 8555-8560
    • Angel, T.E.1    Chance, M.R.2    Palczewski, K.3
  • 50
    • 77953488648 scopus 로고    scopus 로고
    • Conserved water-mediated hydrogen bond network between TM-I, -II, -VI, and -VII in 7TM receptor activation
    • Nygaard, R., Valentin-Hansen, L., Mokrosinski, J., Frimurer, T.M., Schwartz, T.W., Conserved water-mediated hydrogen bond network between TM-I, -II, -VI, and -VII in 7TM receptor activation. J. Biol. Chem. 285:25 (2010), 19625–19636.
    • (2010) J. Biol. Chem. , vol.285 , Issue.25 , pp. 19625-19636
    • Nygaard, R.1    Valentin-Hansen, L.2    Mokrosinski, J.3    Frimurer, T.M.4    Schwartz, T.W.5
  • 51
    • 80054950510 scopus 로고    scopus 로고
    • Molecular dynamics simulations and drug discovery
    • Durrant, J.D., McCammon, J.A., Molecular dynamics simulations and drug discovery. BMC Biol., 9, 2011, 71.
    • (2011) BMC Biol. , vol.9 , pp. 71
    • Durrant, J.D.1    McCammon, J.A.2
  • 52
    • 84857446182 scopus 로고    scopus 로고
    • The future of molecular dynamics simulations in drug discovery
    • Borhani, D.W., Shaw, D.E., The future of molecular dynamics simulations in drug discovery. J. Comput. Aid. Mol. Des. 26:1 (2012), 15–26.
    • (2012) J. Comput. Aid. Mol. Des. , vol.26 , Issue.1 , pp. 15-26
    • Borhani, D.W.1    Shaw, D.E.2
  • 53
    • 84923166744 scopus 로고    scopus 로고
    • Enhanced sampling techniques in molecular dynamics simulations of biological systems
    • Bernardi, R.C., Melo, M.C.R., Schulten, K., Enhanced sampling techniques in molecular dynamics simulations of biological systems. BBA-Gen. Subjects 1850:5 (2015), 872–877.
    • (2015) BBA-Gen. Subjects , vol.1850 , Issue.5 , pp. 872-877
    • Bernardi, R.C.1    Melo, M.C.R.2    Schulten, K.3
  • 54
    • 84978531774 scopus 로고    scopus 로고
    • Guiding lead optimization with GPCR structure modeling and molecular dynamics
    • Heifetz, A., James, T., Morao, I., Bodkin, M.J., Biggin, P.C., Guiding lead optimization with GPCR structure modeling and molecular dynamics. Curr. Opin. Pharmacol. 30 (2016), 14–21.
    • (2016) Curr. Opin. Pharmacol. , vol.30 , pp. 14-21
    • Heifetz, A.1    James, T.2    Morao, I.3    Bodkin, M.J.4    Biggin, P.C.5
  • 55
    • 84938835133 scopus 로고    scopus 로고
    • The dynamic process of drug-GPCR binding at either orthosteric or allosteric sites evaluated by metadynamics
    • Schneider, S., Provasi, D., Filizola, M., The dynamic process of drug-GPCR binding at either orthosteric or allosteric sites evaluated by metadynamics. Methods Mol. Biol. 1335 (2015), 277–294.
    • (2015) Methods Mol. Biol. , vol.1335 , pp. 277-294
    • Schneider, S.1    Provasi, D.2    Filizola, M.3
  • 56
    • 0020488742 scopus 로고
    • Collective variable description of small-amplitude conformational fluctuations in a globular protein
    • Noguti, T., Go, N., Collective variable description of small-amplitude conformational fluctuations in a globular protein. Nature 296:5859 (1982), 776–778.
    • (1982) Nature , vol.296 , Issue.5859 , pp. 776-778
    • Noguti, T.1    Go, N.2
  • 57
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion, M.M., Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:9 (1996), 1905–1908.
    • (1996) Phys. Rev. Lett. , vol.77 , Issue.9 , pp. 1905-1908
    • Tirion, M.M.1
  • 58
    • 43949106243 scopus 로고    scopus 로고
    • Coarse-graining of Condensed Phase and Biomolecular Systems
    • CRC press Boca Raton
    • Voth, G.A., Coarse-graining of Condensed Phase and Biomolecular Systems. 2008, CRC press, Boca Raton.
    • (2008)
    • Voth, G.A.1
  • 59
    • 80053391759 scopus 로고    scopus 로고
    • Capturing the essence of folding and functions of biomolecules using coarse-grained models
    • Hyeon, C., Thirumalai, D., Capturing the essence of folding and functions of biomolecules using coarse-grained models. Nat. Commun., 2, 2011, 487.
    • (2011) Nat. Commun. , vol.2 , pp. 487
    • Hyeon, C.1    Thirumalai, D.2
  • 60
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems: in serial and in parallel
    • Ayton, G.S., Noid, W.G., Voth, G.A., Multiscale modeling of biomolecular systems: in serial and in parallel. Curr. Opin. Struc. Biol. 17:2 (2007), 192–198.
    • (2007) Curr. Opin. Struc. Biol. , vol.17 , Issue.2 , pp. 192-198
    • Ayton, G.S.1    Noid, W.G.2    Voth, G.A.3
  • 61
    • 33748266722 scopus 로고    scopus 로고
    • Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel
    • Shi, Q., Izvekov, S., Voth, G.A., Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel. J. Phys. Chem. B 110:31 (2006), 15045–15048.
    • (2006) J. Phys. Chem. B , vol.110 , Issue.31 , pp. 15045-15048
    • Shi, Q.1    Izvekov, S.2    Voth, G.A.3
  • 62
    • 18744391399 scopus 로고    scopus 로고
    • Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
    • Villa, E., Balaeff, A., Schulten, K., Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc. Natl. Acad. Sci. U. S. A. 102:19 (2005), 6783–6788.
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , Issue.19 , pp. 6783-6788
    • Villa, E.1    Balaeff, A.2    Schulten, K.3
  • 63
    • 37749005024 scopus 로고    scopus 로고
    • Microseconds dynamics simulations of the outer-membrane protease T
    • Neri, M., Baaden, M., Carnevale, V., Anselmi, C., Maritan, A., Carloni, P., Microseconds dynamics simulations of the outer-membrane protease T. Biophys. J. 94:1 (2008), 71–78.
    • (2008) Biophys. J. , vol.94 , Issue.1 , pp. 71-78
    • Neri, M.1    Baaden, M.2    Carnevale, V.3    Anselmi, C.4    Maritan, A.5    Carloni, P.6
  • 64
    • 79961038713 scopus 로고    scopus 로고
    • Multiscale simulations suggest a mechanism for integrin inside-out activation
    • Kalli, A.C., Campbell, I.D., Sansom, M.S.P., Multiscale simulations suggest a mechanism for integrin inside-out activation. Proc. Natl. Acad. Sci. U. S. A. 108:29 (2011), 11890–11895.
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108 , Issue.29 , pp. 11890-11895
    • Kalli, A.C.1    Campbell, I.D.2    Sansom, M.S.P.3
  • 65
    • 84875777145 scopus 로고    scopus 로고
    • Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations
    • Wassenaar, T.A., Ingolfsson, H.I., Priess, M., Marrink, S.J., Schafer, L.V., Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations. J. Phys. Chem. B 117:13 (2013), 3516–3530.
    • (2013) J. Phys. Chem. B , vol.117 , Issue.13 , pp. 3516-3530
    • Wassenaar, T.A.1    Ingolfsson, H.I.2    Priess, M.3    Marrink, S.J.4    Schafer, L.V.5
  • 66
    • 79959749835 scopus 로고    scopus 로고
    • Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites
    • Rzepiela, A.J., Louhivuori, M., Peter, C., Marrink, S.J., Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Phys. Chem. Chem. Phys. 13:22 (2011), 10437–10448.
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , Issue.22 , pp. 10437-10448
    • Rzepiela, A.J.1    Louhivuori, M.2    Peter, C.3    Marrink, S.J.4
  • 67
    • 84869023641 scopus 로고    scopus 로고
    • Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: improved backbone hydration and interactions between charged side chains
    • Han, W., Schulten, K., Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: improved backbone hydration and interactions between charged side chains. J. Chem. Theory Comput. 8:11 (2012), 4413–4424.
    • (2012) J. Chem. Theory Comput. , vol.8 , Issue.11 , pp. 4413-4424
    • Han, W.1    Schulten, K.2
  • 68
    • 84867684737 scopus 로고    scopus 로고
    • Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes
    • Leguebe, M., Nguyen, C., Capece, L., Hoang, Z., Giorgetti, A., Carloni, P., Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes. PLoS One, 7(10), 2012, e47332.
    • (2012) PLoS One , vol.7 , Issue.10 , pp. e47332
    • Leguebe, M.1    Nguyen, C.2    Capece, L.3    Hoang, Z.4    Giorgetti, A.5    Carloni, P.6
  • 69
    • 28844494903 scopus 로고    scopus 로고
    • Coarse-grained model of proteins incorporating atomistic detail of the active site
    • Neri, M., Anselmi, C., Cascella, M., Maritan, A., Carloni, P., Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys. Rev. Lett., 95(21), 2005, 218102.
    • (2005) Phys. Rev. Lett. , vol.95 , Issue.21 , pp. 218102
    • Neri, M.1    Anselmi, C.2    Cascella, M.3    Maritan, A.4    Carloni, P.5
  • 70
    • 85039772447 scopus 로고    scopus 로고
    • Molecular Mechanics/Coarse-grain simulations as a structural prediction tool for GPCRs/ligand complexes
    • C.N. Cavasotto CRC Press Boca Raton
    • Musiani, F., Giorgetti, A., Carloni, P., Molecular Mechanics/Coarse-grain simulations as a structural prediction tool for GPCRs/ligand complexes. Cavasotto, C.N., (eds.) In Silico Drug Discovery and Design: Theory, Methods, Challenges and Applications, 2015, CRC Press, Boca Raton, 337–352.
    • (2015) In Silico Drug Discovery and Design: Theory, Methods, Challenges and Applications , pp. 337-352
    • Musiani, F.1    Giorgetti, A.2    Carloni, P.3
  • 71
    • 84930245532 scopus 로고    scopus 로고
    • Molecular mechanics/coarse-grained models
    • A. Gamble Springer International Publishing Switzerland
    • Giorgetti, A., Carloni, P., Molecular mechanics/coarse-grained models. Gamble, A., (eds.) Protein Modelling, 2014, Springer International Publishing, Switzerland, 165–174.
    • (2014) Protein Modelling , pp. 165-174
    • Giorgetti, A.1    Carloni, P.2
  • 72
    • 84896915850 scopus 로고    scopus 로고
    • Chemosensorial G-proteins-coupled receptors: a perspective from computational methods
    • K. Han X. Zhang M. Yang
    • Musiani, F., Rossetti, G., Giorgetti, A., Carloni, P., Chemosensorial G-proteins-coupled receptors: a perspective from computational methods. Han, K., Zhang, X., Yang, M., (eds.) Protein Conformational Dynamics, 2014, 441–457.
    • (2014) Protein Conformational Dynamics , pp. 441-457
    • Musiani, F.1    Rossetti, G.2    Giorgetti, A.3    Carloni, P.4
  • 75
    • 84878530705 scopus 로고    scopus 로고
    • Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding
    • Marchiori, A., Capece, L., Giorgetti, A., Gasparini, P., Behrens, M., Carloni, P., Meyerhof, W., Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding. PLoS One, 8(5), 2013, e64675.
    • (2013) PLoS One , vol.8 , Issue.5 , pp. e64675
    • Marchiori, A.1    Capece, L.2    Giorgetti, A.3    Gasparini, P.4    Behrens, M.5    Carloni, P.6    Meyerhof, W.7
  • 77
    • 85040789290 scopus 로고    scopus 로고
    • Vertebrate bitter taste receptors: keys for survival in changing environments
    • Behrens, M., Meyerhof, W., Vertebrate bitter taste receptors: keys for survival in changing environments. J. Agric. Food. Chem., 2017, 10.1021/acs.jafc.6b04835.
    • (2017) J. Agric. Food. Chem.
    • Behrens, M.1    Meyerhof, W.2
  • 78
    • 84875615895 scopus 로고    scopus 로고
    • Bitter taste receptor research comes of age: from characterization to modulation of TAS2Rs
    • Behrens, M., Meyerhof, W., Bitter taste receptor research comes of age: from characterization to modulation of TAS2Rs. Semin. Cell Dev. Biol. 24:3 (2013), 215–221.
    • (2013) Semin. Cell Dev. Biol. , vol.24 , Issue.3 , pp. 215-221
    • Behrens, M.1    Meyerhof, W.2
  • 80
    • 84941107270 scopus 로고    scopus 로고
    • Protein structure modeling with MODELLER
    • Webb, B., Sali, A., Protein structure modeling with MODELLER. Methods Mol. Biol. 1137 (2014), 1–15.
    • (2014) Methods Mol. Biol. , vol.1137 , pp. 1-15
    • Webb, B.1    Sali, A.2
  • 81
    • 77955391393 scopus 로고    scopus 로고
    • The HADDOCK web server for data-driven biomolecular docking
    • De Vries, S.J., van Dijk, M., Bonvin, A.M.J.J., The HADDOCK web server for data-driven biomolecular docking. Nat. Protoc. 5:5 (2010), 883–897.
    • (2010) Nat. Protoc. , vol.5 , Issue.5 , pp. 883-897
    • De Vries, S.J.1    van Dijk, M.2    Bonvin, A.M.J.J.3
  • 82
    • 77954260902 scopus 로고    scopus 로고
    • Fpocket: online tools for protein ensemble pocket detection and tracking
    • Schmidtke, P., Le Guilloux, V., Maupetit, J., Tuffery, P., Fpocket: online tools for protein ensemble pocket detection and tracking. Nucleic Acids Res. 38 (2010), W582–W589.
    • (2010) Nucleic Acids Res. , vol.38 , pp. W582-W589
    • Schmidtke, P.1    Le Guilloux, V.2    Maupetit, J.3    Tuffery, P.4
  • 84
    • 0019569599 scopus 로고
    • Non-interacting local-structure model of folding and unfolding transition in globular-proteins.1. Formulation
    • Go, N., Abe, H., Non-interacting local-structure model of folding and unfolding transition in globular-proteins.1. Formulation. Biopolymers 20:5 (1981), 991–1011.
    • (1981) Biopolymers , vol.20 , Issue.5 , pp. 991-1011
    • Go, N.1    Abe, H.2
  • 85
    • 69549084858 scopus 로고    scopus 로고
    • Motile cilia of human airway epithelia are chemosensory
    • Shah, A.S., Ben-Shahar, Y., Moninger, T.O., Kline, J.N., Welsh, M.J., Motile cilia of human airway epithelia are chemosensory. Science 325:5944 (2009), 1131–1134.
    • (2009) Science , vol.325 , Issue.5944 , pp. 1131-1134
    • Shah, A.S.1    Ben-Shahar, Y.2    Moninger, T.O.3    Kline, J.N.4    Welsh, M.J.5
  • 87
    • 8544242989 scopus 로고    scopus 로고
    • Identification of ligands for two human bitter T2R receptors
    • Pronin, A.N., Tang, H., Connor, J., Keung, W., Identification of ligands for two human bitter T2R receptors. Chem. Senses 29:7 (2004), 583–593.
    • (2004) Chem. Senses , vol.29 , Issue.7 , pp. 583-593
    • Pronin, A.N.1    Tang, H.2    Connor, J.3    Keung, W.4
  • 88
    • 84864221004 scopus 로고    scopus 로고
    • A new era of GPCR structural and chemical biology
    • Granier, S., Kobilka, B., A new era of GPCR structural and chemical biology. Nat. Chem. Biol. 8:8 (2012), 670–673.
    • (2012) Nat. Chem. Biol. , vol.8 , Issue.8 , pp. 670-673
    • Granier, S.1    Kobilka, B.2
  • 92
    • 84895538768 scopus 로고    scopus 로고
    • Elastic network normal mode dynamics reveal the GPCR activation mechanism
    • Kolan, D., Fonar, G., Samson, A.O., Elastic network normal mode dynamics reveal the GPCR activation mechanism. Proteins 82:4 (2014), 579–586.
    • (2014) Proteins , vol.82 , Issue.4 , pp. 579-586
    • Kolan, D.1    Fonar, G.2    Samson, A.O.3
  • 94
    • 84960348606 scopus 로고    scopus 로고
    • The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor
    • Stanley, N., Pardo, L., De Fabritiis, G., The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor. Sci. Rep., 6, 2016, 22639.
    • (2016) Sci. Rep. , vol.6 , pp. 22639
    • Stanley, N.1    Pardo, L.2    De Fabritiis, G.3
  • 96
    • 18744411809 scopus 로고    scopus 로고
    • The second extracellular loop: a damper for G protein-coupled receptors?
    • Massotte, D., Kieffer, B.L., The second extracellular loop: a damper for G protein-coupled receptors?. Nat. Struct. Mol. Biol. 12:4 (2005), 287–288.
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , Issue.4 , pp. 287-288
    • Massotte, D.1    Kieffer, B.L.2
  • 97
    • 85008238656 scopus 로고    scopus 로고
    • Understanding the common themes and diverse roles of the second extracellular loop (ECL2) of the GPCR super-family
    • Woolley, M.J., Conner, A.C., Understanding the common themes and diverse roles of the second extracellular loop (ECL2) of the GPCR super-family. Mol. Cell. Endocrinol., 2016, 10.1016/j.mce.2016.11.023.
    • (2016) Mol. Cell. Endocrinol.
    • Woolley, M.J.1    Conner, A.C.2
  • 98
    • 77957055780 scopus 로고
    • [19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors
    • Ballesteros, J.A., Weinstein, H., [19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. Methods Neurosci. 25 (1995), 366–428.
    • (1995) Methods Neurosci. , vol.25 , pp. 366-428
    • Ballesteros, J.A.1    Weinstein, H.2
  • 99
    • 84856499826 scopus 로고    scopus 로고
    • BitterDB: a database of bitter compounds
    • Wiener, A., Shudler, M., Levit, A., Niv, M.Y., BitterDB: a database of bitter compounds. Nucleic Acids Res. 40:D1 (2012), D413–D419.
    • (2012) Nucleic Acids Res. , vol.40 , Issue.D1 , pp. D413-D419
    • Wiener, A.1    Shudler, M.2    Levit, A.3    Niv, M.Y.4
  • 100
    • 84962788258 scopus 로고    scopus 로고
    • Expression of the bitter receptor T2R38 in pancreatic cancer: localization in lipid droplets and activation by a bacteria-derived quorum-sensing molecule
    • Gaida, M.M., Mayer, C., Dapunt, U., Stegmaier, S., Schirmacher, P., Wabnitz, G.H., Hansch, G.M., Expression of the bitter receptor T2R38 in pancreatic cancer: localization in lipid droplets and activation by a bacteria-derived quorum-sensing molecule. Oncotarget 7:11 (2016), 12623–12632.
    • (2016) Oncotarget , vol.7 , Issue.11 , pp. 12623-12632
    • Gaida, M.M.1    Mayer, C.2    Dapunt, U.3    Stegmaier, S.4    Schirmacher, P.5    Wabnitz, G.H.6    Hansch, G.M.7
  • 104
  • 105
    • 74449087964 scopus 로고    scopus 로고
    • Variation in the gene TAS2R38 is associated with the eating behavior disinhibition in Old Order Amish women
    • Dotson, C.D., Shaw, H.L., Mitchell, B.D., Munger, S.D., Steinle, N.I., Variation in the gene TAS2R38 is associated with the eating behavior disinhibition in Old Order Amish women. Appetite 54:1 (2010), 93–99.
    • (2010) Appetite , vol.54 , Issue.1 , pp. 93-99
    • Dotson, C.D.1    Shaw, H.L.2    Mitchell, B.D.3    Munger, S.D.4    Steinle, N.I.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.