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Volumn 20, Issue 2, 2014, Pages

C-H...pi interactions in proteins: Prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability

Author keywords

Adjacency; C H...pi interaction; PDB data mining; Secondary structure elements; Solvent accessible surface area (SASA); Stability

Indexed keywords

AMINO ACID; CARBON; HYDROGEN; PROTEIN; PROTON; SOLVENT;

EID: 84893668622     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-014-2136-5     Document Type: Article
Times cited : (41)

References (57)
  • 3
    • 84986435971 scopus 로고
    • The Nature of the N-H... O=C hydrogen bond: An intermolecular perturbation theory study of the formamide/formaldehyde complex
    • Mitchell JBO, Price SL (1990) The Nature of the N-H... O=C hydrogen bond: an intermolecular perturbation theory study of the formamide/formaldehyde complex. J Comput Chem 11:1217-1233
    • (1990) J Comput Chem , vol.11 , pp. 1217-1233
    • Mitchell, J.B.O.1    Price, S.L.2
  • 4
    • 0034718590 scopus 로고    scopus 로고
    • Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities
    • Avbelj F, Luo P, Baldwin RL (2000) Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities. Proc Natl Acad Sci U S A 97:10786-10791
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 10786-10791
    • Avbelj, F.1    Luo, P.2    Baldwin, R.L.3
  • 6
    • 0000648204 scopus 로고
    • On the structure of native, denatured, and coagulated proteins
    • Mirsky AE, Pauling L (1936) On the structure of native, denatured, and coagulated proteins. Proc Natl Acad Sci U S A 22:439-447
    • (1936) Proc Natl Acad Sci U S A , vol.22 , pp. 439-447
    • Mirsky, A.E.1    Pauling, L.2
  • 7
    • 0027485091 scopus 로고
    • Solvent water and protein behavior: View through a retroscope
    • Klotz IM (1993) Solvent water and protein behavior: view through a retroscope. Protein Sci Publ Protein Soc 2:1992-1999
    • (1993) Protein Sci Publ Protein Soc , vol.2 , pp. 1992-1999
    • Klotz, I.M.1
  • 9
    • 0021828928 scopus 로고
    • Hydrogen bonding and biological specificity analysed by protein engineering
    • DOI 10.1038/314235a0
    • Fersht AR, Shi JP, Knill-Jones J, Lowe DM, Wilkinson AJ, Blow DM, Brick P, Carter P, Waye MM, Winter G (1985) Hydrogen bonding and biological specificity analysed by protein engineering. Nature 314:235-238 (Pubitemid 15076511)
    • (1985) Nature , vol.314 , Issue.6008 , pp. 235-238
    • Fersht, A.R.1    Shi, J.P.2    Knill-Jones, J.3
  • 10
    • 3042848873 scopus 로고    scopus 로고
    • Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics
    • DOI 10.1038/nature02611
    • Deechongkit S, Nguyen H, Powers ET, Dawson PE, Gruebele M, Kelly JW (2004) Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics.Nature 430:101-105 (Pubitemid 38915233)
    • (2004) Nature , vol.430 , Issue.6995 , pp. 101-105
    • Deechongkit, S.1    Nguyen, H.2    Powers, E.T.3    Dawson, P.E.4    Gruebele, M.5    Kelly, J.W.6
  • 11
    • 67650340734 scopus 로고    scopus 로고
    • Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins
    • Gao J, Bosco DA, Powers ET, Kelly JW (2009) Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins. Nat Struct Mol Biol 16:684-690
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 684-690
    • Gao, J.1    Bosco, D.A.2    Powers, E.T.3    Kelly, J.W.4
  • 12
    • 33750255413 scopus 로고    scopus 로고
    • Electrostatic couplings in OmpA ion-channel gating suggest a mechanism for pore opening
    • DOI 10.1038/nchembio827, PII NCHEMBIO827
    • Hong H, Szabo G, Tamm LK (2006) Electrostatic couplilngs in OmpA ion-channel gating suggest a mechanism for pore opening. Nat Chem Biol 2:627-635 (Pubitemid 44610347)
    • (2006) Nature Chemical Biology , vol.2 , Issue.11 , pp. 627-635
    • Hong, H.1    Szabo, G.2    Tamm, L.K.3
  • 13
    • 46249089993 scopus 로고    scopus 로고
    • Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins
    • DOI 10.1038/nature06977, PII NATURE06977
    • Joh NH, Min A, Faham S, Whitelegge JP, Yang D, Woods VL Jr, Bowie JU (2008) Modest stabilization by most hydrogen-bonded side-chain interactions inmembrane proteins. Nature 453:1266-1270 (Pubitemid 351913594)
    • (2008) Nature , vol.453 , Issue.7199 , pp. 1266-1270
    • Joh, N.H.1    Min, A.2    Faham, S.3    Whitelegge, J.P.4    Yang, D.5    Woods Jr., V.L.6    Bowie, J.U.7
  • 14
    • 77953631827 scopus 로고    scopus 로고
    • A medicinal chemist's guide to molecular interactions
    • Bissantz C, Kuhn B, Stahl M (2010) A medicinal chemist's guide to molecular interactions. J Med Chem 53:5061-5084
    • (2010) J Med Chem , vol.53 , pp. 5061-5084
    • Bissantz, C.1    Kuhn, B.2    Stahl, M.3
  • 15
    • 34848842845 scopus 로고    scopus 로고
    • Geometry of nonbonded interactions involving planar groups in proteins
    • DOI 10.1016/j.pbiomolbio.2007.03.016, PII S0079610707000442
    • Chakrabarti P, Bhattacharyya R (2007) Geometry of nonbonded interactions involving planar groups in proteins. Prog Biophys Mol Biol 95:83-137 (Pubitemid 47513187)
    • (2007) Progress in Biophysics and Molecular Biology , vol.95 , Issue.1-3 , pp. 83-137
    • Chakrabarti, P.1    Bhattacharyya, R.2
  • 16
    • 84862847617 scopus 로고    scopus 로고
    • PROLIX: Rapid mining of protein-ligand interactions in large crystal structure databases
    • Weisel M, Bitter HM, Diederich F, So WV, Kondru R (2012) PROLIX: rapid mining of protein-ligand interactions in large crystal structure databases. J Chem Inf Model 52:1450-1461
    • (2012) J Chem Inf Model , vol.52 , pp. 1450-1461
    • Weisel, M.1    Bitter, H.M.2    Diederich, F.3    So, W.V.4    Kondru, R.5
  • 17
    • 84861653205 scopus 로고    scopus 로고
    • The CH/pi hydrogen bond: Implication in chemistry
    • Nishio M (2012) The CH/pi hydrogen bond: implication in chemistry. J Molec Struct 1018:2-7
    • (2012) J Molec Struct , vol.1018 , pp. 2-7
    • Nishio, M.1
  • 21
    • 0035910278 scopus 로고    scopus 로고
    • Hydrogen bonds with π-acceptors in proteins: Frequencies and role in stabilizing local 3D structures
    • DOI 10.1006/jmbi.2000.4301
    • Steiner T, Koellner G (2001) Hydrogen bonds with π-acceptors in proteins: frequencies and role in stabilizing local 3D structures. JMol Biol 305:535-557 (Pubitemid 33032860)
    • (2001) Journal of Molecular Biology , vol.305 , Issue.3 , pp. 535-557
    • Steiner, T.1    Koellner, G.2
  • 22
    • 4444261821 scopus 로고    scopus 로고
    • Role of CH/π interactions in substrate binding by Escherichia coli beta-galactosidase
    • DOI 10.1016/j.carres.2004.06.016, PII S0008621504002848
    • Spiwok V, Lipovova P, Skalova T, Buchtelova E, Hasek J, Kralova B (2004) Role of CH/pi interactions in substrate binding by Escherichia coli beta-galactosidase. Carbohydr Res 399:2275-2280 (Pubitemid 39165118)
    • (2004) Carbohydrate Research , vol.339 , Issue.13 , pp. 2275-2280
    • Spiwok, V.1    Lipovova, P.2    Skalova, T.3    Buchtelova, E.4    Hasek, J.5    Kralova, B.6
  • 23
    • 30544431762 scopus 로고    scopus 로고
    • CH/π hydrogen bonds as evidenced in the substrate specificity of acetylcholine esterase
    • DOI 10.1002/bip.20352
    • Umezawa Y, Nishio M (2005) CH/pi hydrogen bonds as evidenced in the substrate specificity of acetylcholine esterase. Biopolymers 79:248-258 (Pubitemid 43078513)
    • (2005) Biopolymers , vol.79 , Issue.5 , pp. 248-258
    • Umezawa, Y.1    Nishio, M.2
  • 24
    • 33747767210 scopus 로고    scopus 로고
    • A single CH/π weak hydrogen bond governs stability and the photocycle of the photoactive yellow protein
    • DOI 10.1021/ja062125v
    • Harigai M, Kataoka M, Imamoto Y (2006) A single CH/pi weak hydrogen bond governs stability and the photocycle of the photoactive yellow protein. J Am Chem Soc 128:10646-10647 (Pubitemid 44277731)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.33 , pp. 10646-10647
    • Harigai, M.1    Kataoka, M.2    Imamoto, Y.3
  • 26
    • 77949303325 scopus 로고    scopus 로고
    • Exploring the role of C-H...pi interactions on the structural stability of single chain "allalpha" proteins
    • Shanthi V, Ramanathan K, Rao S (2010) Exploring the role of C-H....pi interactions on the structural stability of single chain "allalpha" proteins. Appl Biochem Biotechnol 160:1473-1483
    • (2010) Appl Biochem Biotechnol , vol.160 , pp. 1473-1483
    • Shanthi, V.1    Ramanathan, K.2    Rao, S.3
  • 27
    • 79959975895 scopus 로고    scopus 로고
    • Contribution of C-H...pi interactions to the affinity and specificity of carbohydrate binding sites
    • Balaji PV (2011) Contribution of C-H...pi interactions to the affinity and specificity of carbohydrate binding sites.Mini Rev Org Chem 8:222-228
    • (2011) Mini Rev Org Chem , vol.8 , pp. 222-228
    • Balaji, P.V.1
  • 28
    • 0032054015 scopus 로고    scopus 로고
    • Ch/π interactions as demonstrated in the crystal structure of guanine- nucleotide binding proteins, src homology-2 domains and human growth hormone in complex with their specific ligands
    • DOI 10.1016/S0968-0896(98)00002-9, PII S0968089698000029
    • Umezawa Y, Nishio M (1998) CH/pi interactions as demonstrated in the crystal structure of guanine-nucleotide binding proteins, Src homology-2 domains and human growth hormone in complex with their specific ligands. Bioorg Med Chem 6:493-504 (Pubitemid 28179589)
    • (1998) Bioorganic and Medicinal Chemistry , vol.6 , Issue.4 , pp. 493-504
    • Umezawa, Y.1    Nishio, M.2
  • 29
    • 0032436501 scopus 로고    scopus 로고
    • CH/π interactions in the crystal structure of Class I MHC antigens and their complexes with peptides
    • DOI 10.1016/S0968-0896(98)80024-2, PII S0968089698001965
    • Umezawa Y, Nishio M (1998) CH/pi Interactions in the crystal structure of class IMHC antigens and their complexes with peptides. Bioorg Med Chem 6(12):2507-2515 (Pubitemid 29002937)
    • (1998) Bioorganic and Medicinal Chemistry , vol.6 , Issue.12 , pp. 2507-2515
    • Umezawa, Y.1    Nishio, M.2
  • 30
    • 0032836467 scopus 로고    scopus 로고
    • CH/π interaction in the conformation of peptides. A database study
    • DOI 10.1016/S0968-0896(99)00123-6, PII S0968089699001236
    • Umezawa Y, Tsuboyama S, Takahashi H, Uzawa J, Nishio M (1999) CH/pi interaction in the conformation of peptides. A database study. Bioorg Med Chem 7(9):2021-2026 (Pubitemid 29457700)
    • (1999) Bioorganic and Medicinal Chemistry , vol.7 , Issue.9 , pp. 2021-2026
    • Umezawa, Y.1    Tsuboyama, S.2    Takahashi, H.3    Uzawa, J.4    Nishio, M.5
  • 31
    • 0017411710 scopus 로고
    • The protein data bank: A computer based archival file for macromolecular structures
    • Bernstein FC, Koetzle TF, Williams GJ, Meyer Jr. EE, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535-542. www.rcsb.org (Pubitemid 8109216)
    • (1977) Journal of Molecular Biology , vol.112 , Issue.3 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3
  • 32
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang G, Dunbrack Jr RL (2003) PISCES: a protein sequence culling server. Bioinformatics 19:1589- 1591. http://dunbrack.fccc.edu/PISCES.php
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 34
    • 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, 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
  • 36
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • DOI 10.1007/S008940100045
    • Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. Mol Mod Annu 7:306-317 (Pubitemid 36153547)
    • (2001) Journal of Molecular Modeling , vol.7 , Issue.8 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 38
    • 0029117927 scopus 로고
    • The CH/π interaction. Significance in molecular recognition
    • Nishio M, Umezawa Y, Hirota M, Takeuchi Y (1995) The CH/π interaction. Significance in molecular recognition. Tetrahedron 51:8665-8671
    • (1995) Tetrahedron , vol.51 , pp. 8665-8671
    • Nishio, M.1    Umezawa, Y.2    Hirota, M.3    Takeuchi, Y.4
  • 39
    • 3242887525 scopus 로고    scopus 로고
    • STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins
    • DOI 10.1093/nar/gkh429
    • Heinig M and Frishman D (2004) STRIDE: a Web server for secondary structure assignment from known atomic coordinates of proteins. Nucl Acids Res 32:W500-W502. http://webclu.bio.wzw.tum.de/stride/ (Pubitemid 38997383)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Heinig, M.1    Frishman, D.2
  • 42
    • 0037468544 scopus 로고    scopus 로고
    • Amino acid substitutions in the human genome: Evolutionary implications of single nucleotide polymorphisms
    • DOI 10.1016/S0378-1119(03)00379-2
    • Majewski J, Ott J (2003) Amino acid substitutions in the human genome: evolutionary implications of single nucleotide polymorphisms. Gene 305:167-173 (Pubitemid 36259767)
    • (2003) Gene , vol.305 , Issue.2 , pp. 167-173
    • Majewski, J.1    Ott, J.2
  • 43
    • 33750165508 scopus 로고    scopus 로고
    • Atom-wise statistics and prediction of solvent accessibility in proteins
    • DOI 10.1016/j.bpc.2006.06.013, PII S030146220600216X
    • Singh YH, Gromiha MM, Sarai A, Ahmad S (2006) Atom-wise statistics and prediction of solvent accessibility in proteins. Biophys Chem 124:145-154 (Pubitemid 44602329)
    • (2006) Biophysical Chemistry , vol.124 , Issue.2 , pp. 145-154
    • Singh, Y.H.1    Gromiha, M.M.2    Sarai, A.3    Ahmad, S.4
  • 44
    • 8444244797 scopus 로고    scopus 로고
    • Role of weak interactions in thermal stability of proteins
    • DOI 10.1016/j.bbrc.2004.10.128, PII S0006291X04024696
    • Ibrahim BS, Pattabhi V (2004) Role of weak interactions in thermal stability of proteins. Biochem Biophys Res Comm 325:1082-1089 (Pubitemid 39487981)
    • (2004) Biochemical and Biophysical Research Communications , vol.325 , Issue.3 , pp. 1082-1089
    • Ibrahim, B.S.1    Pattabhi, V.2
  • 45
    • 34548009855 scopus 로고    scopus 로고
    • CH/π interactions in DNA and proteins. A theoretical study
    • DOI 10.1021/jp0717847
    • Gil A, Branchadell V, Bertran J, Oliva A (2007) CH/pi interactions in DNA and proteins. A theoretical study. J Phys Chem B 111:9372-9379 (Pubitemid 47280538)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.31 , pp. 9372-9379
    • Gil, A.1    Branchadell, V.2    Bertran, J.3    Oliva, A.4
  • 47
    • 28644449596 scopus 로고    scopus 로고
    • Functional restraints on the patterns of amino acid substitutions: Application to sequence-structure homology recognition
    • DOI 10.1002/prot.20617
    • Chelliah V, Blundell T, Mizuguchi K (2005) Functional restraints on the patterns of amino acid substitutions: application to sequence-structure homology recognition. Proteins 61:722-731 (Pubitemid 41753143)
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.4 , pp. 722-731
    • Chelliah, V.1    Blundell, T.2    Mizuguchi, K.3
  • 48
    • 67549086082 scopus 로고    scopus 로고
    • Understanding the functional roles of amino acid residues in enzyme catalysis
    • Holliday GL, Mitchell JBO, Thornton JM (2009) Understanding the functional roles of amino acid residues in enzyme catalysis. J Mol Biol 30:560-577
    • (2009) J Mol Biol , vol.30 , pp. 560-577
    • Holliday, G.L.1    Mitchell, J.B.O.2    Thornton, J.M.3
  • 49
    • 4644355809 scopus 로고    scopus 로고
    • The architecture of metal coordination groups in proteins
    • Harding MM (2004) The architecture of metal coordination groups in proteins. Acta Crystallogr D60:849-859
    • (2004) Acta Crystallogr , vol.D60 , pp. 849-859
    • Harding, M.M.1
  • 50
    • 33749634632 scopus 로고    scopus 로고
    • Aliphatic C-H/π interactions: Methane-benzene, methane-phenol, and methane-indole complexes
    • DOI 10.1021/jp062740l
    • Ringer AL, Figgs MS, Sinnokrot MO, Sherrill CD (2006) Aliphatic C-H/pi interactions: methane-benzene, methane-phenol, and methane-indole complexes. J Phys Chem A 110:10822-10828 (Pubitemid 44547227)
    • (2006) Journal of Physical Chemistry A , vol.110 , Issue.37 , pp. 10822-10828
    • Ringer, A.L.1    Figgs, M.S.2    Sinnokrot, M.O.3    Sherrill, C.D.4
  • 51
    • 43449091888 scopus 로고    scopus 로고
    • Nature and physical origin of CH/pi interaction: Significant difference from conventional hydrogen bonds
    • Tsuzuki S, Fujii A (2008) Nature and physical origin of CH/pi interaction: significant difference from conventional hydrogen bonds. Phys Chem Chem Phys 10:2584-2594
    • (2008) Phys Chem Chem Phys , vol.10 , pp. 2584-2594
    • Tsuzuki, S.1    Fujii, A.2
  • 52
    • 79960935413 scopus 로고    scopus 로고
    • The CH/pi hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates
    • Nishio M (2011) The CH/pi hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates. Phys Chem Chem Phys 13:13873-13900
    • (2011) Phys Chem Chem Phys , vol.13 , pp. 13873-13900
    • Nishio, M.1
  • 53
    • 33748282998 scopus 로고    scopus 로고
    • Saturated hydrocarbon-benzene complexes: Theoretical study of cooperative CH/π interactions
    • DOI 10.1021/jp0555403
    • Ran J, Wong MW (2006) Saturated hydrocarbon-benzene complexes: theoretical study of cooperative CH/pi interactions. J Phys Chem A 110:9702-9709 (Pubitemid 44318457)
    • (2006) Journal of Physical Chemistry A , vol.110 , Issue.31 , pp. 9702-9709
    • Ran, J.1    Wong, M.W.2
  • 55
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Porter TC, Bartlett GJ, Thornton JM (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucl Acids Res 32:D129-D133 (Pubitemid 38081621)
    • (2004) Nucleic Acids Research , vol.32 , Issue.DATABASE ISS.
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 56
    • 0033537899 scopus 로고    scopus 로고
    • Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts
    • DOI 10.1006/jmbi.1999.2643
    • Kopp J, Kopriva S, Suess KH, Schulz GE (1999) Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts. J Mol Biol 287:761-771 (Pubitemid 29176511)
    • (1999) Journal of Molecular Biology , vol.287 , Issue.4 , pp. 761-771
    • Kopp, J.1    Kopriva, S.2    Suss, K.-H.3    Schulz, G.E.4


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