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Volumn 58, Issue 4, 2005, Pages 880-892

Properties of polyproline II, a secondary structure element implicated in protein-protein interactions

Author keywords

Polyproline II; Protein protein interaction

Indexed keywords

AROMATIC AMINO ACID; GLYCINE; POLYPROLINE II; PROLINE; UNCLASSIFIED DRUG;

EID: 13944275600     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20327     Document Type: Article
Times cited : (96)

References (52)
  • 1
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 2
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 3
    • 0034636977 scopus 로고    scopus 로고
    • Is polyproline II helix the killer conformation?: A Raman optical activity study of teh amyloidogenic prefibrillar intermediate of human lysozyme
    • Blanch EW, Morozova-Roche LA, Cochran DA, Doig AJ, Hecht L, Barron LD. Is polyproline II helix the killer conformation?: a Raman optical activity study of teh amyloidogenic prefibrillar intermediate of human lysozyme. J Mol Biol 2000;301:553-563.
    • (2000) J Mol Biol , vol.301 , pp. 553-563
    • Blanch, E.W.1    Morozova-Roche, L.A.2    Cochran, D.A.3    Doig, A.J.4    Hecht, L.5    Barron, L.D.6
  • 4
    • 2642567722 scopus 로고    scopus 로고
    • Aβ1-28 fragment of the amyloid peptide predominantly adopts a polyproline II conformation in an acidic solution
    • Eker F, Griebenow K, Schweitzer-Stenner R. Aβ1-28 fragment of the amyloid peptide predominantly adopts a polyproline II conformation in an acidic solution. Biochemistry 2004;43:6893-6898.
    • (2004) Biochemistry , vol.43 , pp. 6893-6898
    • Eker, F.1    Griebenow, K.2    Schweitzer-Stenner, R.3
  • 5
    • 1842427563 scopus 로고    scopus 로고
    • The extended left-handed helix: A simple nucleic acid-binding motif
    • Hicks JM, Hsu VL. The extended left-handed helix: a simple nucleic acid-binding motif. Proteins 2004;55:330-338.
    • (2004) Proteins , vol.55 , pp. 330-338
    • Hicks, J.M.1    Hsu, V.L.2
  • 6
    • 0014227144 scopus 로고
    • New chain conformations of poly(glutamic acid) and polylysine
    • Tiffany ML, Krimm S. New chain conformations of poly(glutamic acid) and polylysine. Biopolymers 1968;6:1379-1382.
    • (1968) Biopolymers , vol.6 , pp. 1379-1382
    • Tiffany, M.L.1    Krimm, S.2
  • 8
    • 3142754280 scopus 로고    scopus 로고
    • UV Raman demonstrates that alpha-helical polyalanine peptides melt to polyproline II conformation
    • Asher SA, Mikhonin AV, Bykov S. UV Raman demonstrates that alpha-helical polyalanine peptides melt to polyproline II conformation. J Am Chem Soc 2004;126:8433-8400.
    • (2004) J Am Chem Soc , vol.126 , pp. 8433-18400
    • Asher, S.A.1    Mikhonin, A.V.2    Bykov, S.3
  • 9
    • 0037372297 scopus 로고    scopus 로고
    • The effect of the polyproline II (PPII) conformation on the denatured state entropy
    • Ferreon JC, Hilser VJ. The effect of the polyproline II (PPII) conformation on the denatured state entropy. Protein Sci 2003;12: 447-457.
    • (2003) Protein Sci , vol.12 , pp. 447-457
    • Ferreon, J.C.1    Hilser, V.J.2
  • 10
    • 1542366657 scopus 로고    scopus 로고
    • Role of solvent in determining conformational preferences of alanine dipeptide in water
    • Drozdov AN, Grossfield A, Pappu RV. Role of solvent in determining conformational preferences of alanine dipeptide in water. J Am Chem Soc 2004;126:2574-2581.
    • (2004) J Am Chem Soc , vol.126 , pp. 2574-2581
    • Drozdov, A.N.1    Grossfield, A.2    Pappu, R.V.3
  • 11
    • 1842500993 scopus 로고    scopus 로고
    • Unfolded state of polyalanine is a segmented polyproline II helix
    • Kentsis A, Mezei M, Gindin T, Osman R. Unfolded state of polyalanine is a segmented polyproline II helix. Proteins 2004;55: 493-501.
    • (2004) Proteins , vol.55 , pp. 493-501
    • Kentsis, A.1    Mezei, M.2    Gindin, T.3    Osman, R.4
  • 12
    • 1842500992 scopus 로고    scopus 로고
    • Polyproline II helix is teh preferred conformation for unfolded polyalanine in water
    • Mezei M, Fleming PJ, Srinivasan R, Rose GD. Polyproline II helix is teh preferred conformation for unfolded polyalanine in water. Proteins 2004;55:502-507.
    • (2004) Proteins , vol.55 , pp. 502-507
    • Mezei, M.1    Fleming, P.J.2    Srinivasan, R.3    Rose, G.D.4
  • 13
    • 0032811196 scopus 로고    scopus 로고
    • Molecular dynamics simulations of polypeptide conformations in water: A comparison of alpha, beta and poly(Pro)II conformations
    • Sreerama N, Woody RW. Molecular dynamics simulations of polypeptide conformations in water: a comparison of alpha, beta and poly(Pro)II conformations. Proteins 1999;36:400-406.
    • (1999) Proteins , vol.36 , pp. 400-406
    • Sreerama, N.1    Woody, R.W.2
  • 16
    • 2442522724 scopus 로고    scopus 로고
    • Short sequences of non-proline residues can adopt the polyproline II helical conformation
    • Chellgren BW, Creamer TP. Short sequences of non-proline residues can adopt the polyproline II helical conformation. Biochemistry 2004;43:5864-5869.
    • (2004) Biochemistry , vol.43 , pp. 5864-5869
    • Chellgren, B.W.1    Creamer, T.P.2
  • 17
    • 0027474991 scopus 로고
    • Left-handed polyproline II helices commonly occur in globular proteins
    • Adzhubei AA, Sternberg MJ. Left-handed polyproline II helices commonly occur in globular proteins. J Mol Biol 1993;229:472-493.
    • (1993) J Mol Biol , vol.229 , pp. 472-493
    • Adzhubei, A.A.1    Sternberg, M.J.2
  • 18
    • 0032980562 scopus 로고    scopus 로고
    • A survey of left-handed polyproline II helices
    • Stapley BJ, Creamer TP. A survey of left-handed polyproline II helices. Protein Sci 1999;8:587-595.
    • (1999) Protein Sci , vol.8 , pp. 587-595
    • Stapley, B.J.1    Creamer, T.P.2
  • 19
    • 0031766401 scopus 로고    scopus 로고
    • HOMSTRAD: A database of protein structure alignments for homologous families
    • Mizuguchi K, Deane CM, Blundell TL, Overington JP. HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci 1998;7:2469-2471.
    • (1998) Protein Sci , vol.7 , pp. 2469-2471
    • Mizuguchi, K.1    Deane, C.M.2    Blundell, T.L.3    Overington, J.P.4
  • 21
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi J, Blundell TL, Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001;310: 243-257.
    • (2001) J Mol Biol , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 23
    • 0027049243 scopus 로고
    • The kinemage: A tool for scientific illustration
    • Richardson DC, Richardson JS. The kinemage: a tool for scientific illustration. Protein Sci 1992;1:3-9.
    • (1992) Protein Sci , vol.1 , pp. 3-9
    • Richardson, D.C.1    Richardson, J.S.2
  • 24
    • 0013033189 scopus 로고    scopus 로고
    • MAGE, PROBE, and Kinemages
    • Rossmann MG, Arnold E, editors. Vol. F. Dordrecht: Kluwer
    • Richardson DC, Richardson JS. MAGE, PROBE, and Kinemages. In: Rossmann MG, Arnold E, editors. International tables for crystallography. Vol. F. Dordrecht: Kluwer; 2001. p 727-730.
    • (2001) International Tables for Crystallography , pp. 727-730
    • Richardson, D.C.1    Richardson, J.S.2
  • 25
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly ML. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983;221:709-713.
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 27
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 1999;285:1735-1747.
    • (1999) J Mol Biol , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 28
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 29
    • 0025398721 scopus 로고
    • WHATIF: A molecular modelling and drug design program
    • Vriend G. WHATIF: a molecular modelling and drug design program. J Mol Graphics 1990;8:52-56.
    • (1990) J Mol Graphics , vol.8 , pp. 52-56
    • Vriend, G.1
  • 30
    • 0027996196 scopus 로고
    • Crystal and molecular structure of a collagen-like peptide at 1.9 Å resolution
    • Bella J, Eaton M, Brodsky B, Berman HM. Crystal and molecular structure of a collagen-like peptide at 1.9 Å resolution. Science 1994;266:75-81.
    • (1994) Science , vol.266 , pp. 75-81
    • Bella, J.1    Eaton, M.2    Brodsky, B.3    Berman, H.M.4
  • 31
    • 0031692650 scopus 로고    scopus 로고
    • Left-handed polyproline II helix formation is (very) locally driven
    • Creamer TP. Left-handed polyproline II helix formation is (very) locally driven. Proteins 1998;33:218-226.
    • (1998) Proteins , vol.33 , pp. 218-226
    • Creamer, T.P.1
  • 32
    • 0033950079 scopus 로고    scopus 로고
    • The importance of being proline:the interaction of proline: The interaction of proline-rich motifs in signalling proteins with their cognate domains
    • Kay BK, Williamson MP, Sudol M. The importance of being proline:the interaction of proline: the interaction of proline-rich motifs in signalling proteins with their cognate domains. FASEB J 2000;14:231-241.
    • (2000) FASEB J , vol.14 , pp. 231-241
    • Kay, B.K.1    Williamson, M.P.2    Sudol, M.3
  • 33
    • 0035861991 scopus 로고    scopus 로고
    • Solution structures of the YAP65 WW domain and the variant L30 K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope
    • Pires JR, Taha-Nejad F, Toepert F, Ast T, Hoffmuller U, Schneider-Mergener J, Kuhne R, Macias MJ, Oschkinat H. Solution structures of the YAP65 WW domain and the variant L30 K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope. J Mol Biol 2001;314:1147-1156.
    • (2001) J Mol Biol , vol.314 , pp. 1147-1156
    • Pires, J.R.1    Taha-Nejad, F.2    Toepert, F.3    Ast, T.4    Hoffmuller, U.5    Schneider-Mergener, J.6    Kuhne, R.7    Macias, M.J.8    Oschkinat, H.9
  • 34
    • 0343081091 scopus 로고    scopus 로고
    • Structure of a WW domain containing fragment of dystrophin in complex with beta-dystroglycan
    • Huang X, Poy F, Zhang R, Joachimiak A, Sudol M, Eck MJ. Structure of a WW domain containing fragment of dystrophin in complex with beta-dystroglycan. Nat Struct Biol 2000;7:634-638.
    • (2000) Nat Struct Biol , vol.7 , pp. 634-638
    • Huang, X.1    Poy, F.2    Zhang, R.3    Joachimiak, A.4    Sudol, M.5    Eck, M.J.6
  • 35
    • 0033031122 scopus 로고    scopus 로고
    • Structure of EVH1, a novel proline-rich ligand-binding module involved in cytoskeletal dynamics and neural function
    • Fedorov AA, Fedorov E, Gertler F, Almo SC. Structure of EVH1, a novel proline-rich ligand-binding module involved in cytoskeletal dynamics and neural function. Nat Struct Biol 1999;6:661-665.
    • (1999) Nat Struct Biol , vol.6 , pp. 661-665
    • Fedorov, A.A.1    Fedorov, E.2    Gertler, F.3    Almo, S.C.4
  • 36
    • 0033679292 scopus 로고    scopus 로고
    • Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition
    • Beneken J, Tu JC, Xiao B, Nuriya M, Yuan JP, Worley PF, Leahy DJ. Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition. Neuron 2000;26:143-154.
    • (2000) Neuron , vol.26 , pp. 143-154
    • Beneken, J.1    Tu, J.C.2    Xiao, B.3    Nuriya, M.4    Yuan, J.P.5    Worley, P.F.6    Leahy, D.J.7
  • 37
    • 0035107308 scopus 로고    scopus 로고
    • CODA: A combined algorithm for predicting the structurally variable regions of protein models
    • Deane CM, Blundell TL. CODA: A combined algorithm for predicting the structurally variable regions of protein models. Protein Sci 2001;10:599-612.
    • (2001) Protein Sci , vol.10 , pp. 599-612
    • Deane, C.M.1    Blundell, T.L.2
  • 38
    • 0032516465 scopus 로고    scopus 로고
    • The crystal structure of benzoylformate decarboxylase at 1.6 Å resolution: Diversity of catalytic residues in thiamin diphosphate-dependent enzymes
    • Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D. The crystal structure of benzoylformate decarboxylase at 1.6 Å resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes. Biochemistry 1998;37:9918-9930.
    • (1998) Biochemistry , vol.37 , pp. 9918-9930
    • Hasson, M.S.1    Muscate, A.2    McLeish, M.J.3    Polovnikova, L.S.4    Gerlt, J.A.5    Kenyon, G.L.6    Petsko, G.A.7    Ringe, D.8
  • 39
    • 0019883211 scopus 로고
    • Carbon-13 nuclear magnetic resonance studies of mandelate metabolism in whole bacterial cells and in isolated, in vivo cross-linked enzyme complexes
    • Halpin RA, Hegeman GD, Kenyon GL. Carbon-13 nuclear magnetic resonance studies of mandelate metabolism in whole bacterial cells and in isolated, in vivo cross-linked enzyme complexes. Biochemistry 1981;20:1525-1533.
    • (1981) Biochemistry , vol.20 , pp. 1525-1533
    • Halpin, R.A.1    Hegeman, G.D.2    Kenyon, G.L.3
  • 41
    • 0034724569 scopus 로고    scopus 로고
    • SH3-SPOT: An algorithm to predict preferred ligands to different members of the SH3 gene family
    • Brannetti B, Via A, Cestra G, Cesareni G, Helmer-Citterich M. SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family. J Mol Biol 2000;298:313-328.
    • (2000) J Mol Biol , vol.298 , pp. 313-328
    • Brannetti, B.1    Via, A.2    Cestra, G.3    Cesareni, G.4    Helmer-Citterich, M.5
  • 42
    • 0037138411 scopus 로고    scopus 로고
    • WW and SH3 domains, two different scaffolds to recognize proline-rich ligands
    • Macias MJ, Wiesner S, Sudol M. WW and SH3 domains, two different scaffolds to recognize proline-rich ligands. FEBS Lett 2002;513:30-37.
    • (2002) FEBS Lett , vol.513 , pp. 30-37
    • Macias, M.J.1    Wiesner, S.2    Sudol, M.3
  • 43
    • 0037138362 scopus 로고    scopus 로고
    • EVH1 domains: Structure, function and interactions
    • Ball LJ, Jarchau T, Oschkinat H, Walter U. EVH1 domains: structure, function and interactions. FEBS Lett 2002;513:45-52.
    • (2002) FEBS Lett , vol.513 , pp. 45-52
    • Ball, L.J.1    Jarchau, T.2    Oschkinat, H.3    Walter, U.4
  • 44
    • 0032985562 scopus 로고    scopus 로고
    • The GYF domain is a novel structural fold that is involved in lymphoid signaling through proline-rich sequences
    • Freund C, Dotsch V, Nishizawa K, Reinherz EL, Wagner G. The GYF domain is a novel structural fold that is involved in lymphoid signaling through proline-rich sequences. Nat Struct Biol 1999;6: 656-660.
    • (1999) Nat Struct Biol , vol.6 , pp. 656-660
    • Freund, C.1    Dotsch, V.2    Nishizawa, K.3    Reinherz, E.L.4    Wagner, G.5
  • 46
    • 0037245913 scopus 로고    scopus 로고
    • BIND: The biomolecular interaction network database
    • Bader GD, Betel D, Hogue CW. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 2003;31:248-250.
    • (2003) Nucleic Acids Res , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.3
  • 48
    • 0028805516 scopus 로고
    • A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein
    • Lee CH, Leung B, Lemmon MA, Zheng J, Cowburn D, Kuriyan J, Saksela K. A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein. EMBO J 1995;14:5006-5015.
    • (1995) EMBO J , vol.14 , pp. 5006-5015
    • Lee, C.H.1    Leung, B.2    Lemmon, M.A.3    Zheng, J.4    Cowburn, D.5    Kuriyan, J.6    Saksela, K.7
  • 49
    • 0030475459 scopus 로고    scopus 로고
    • Structural requirements and thermodynamics of the interaction of proline peptides with profilin
    • Petrella EC, Machesky LM, Kaiser DA, Pollard TD. Structural requirements and thermodynamics of the interaction of proline peptides with profilin. Biochemistry 1996;35:16535-16543.
    • (1996) Biochemistry , vol.35 , pp. 16535-16543
    • Petrella, E.C.1    Machesky, L.M.2    Kaiser, D.A.3    Pollard, T.D.4
  • 51
    • 0028577684 scopus 로고
    • Conservation of polyproline II helices in homologous proteins: Implications for structure prediction by model building
    • Adzhubei AA, Sternberg MJ. Conservation of polyproline II helices in homologous proteins: implications for structure prediction by model building. Protein Sci 1994;3:239S-2410.
    • (1994) Protein Sci , vol.3
    • Adzhubei, A.A.1    Sternberg, M.J.2
  • 52
    • 0013033597 scopus 로고    scopus 로고
    • The structure and function of proline recognition domains
    • Zarrinpar A, Bhattacharyya RP, Lim WA. The structure and function of proline recognition domains. Sci STKE 2003;179: 1-10.
    • (2003) Sci STKE , vol.179 , pp. 1-10
    • Zarrinpar, A.1    Bhattacharyya, R.P.2    Lim, W.A.3


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