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Volumn 171, Issue 3, 2010, Pages 345-352

Sulfate ion interaction with 'anion recognition' short peptide motif at the N-terminus of an isolated helix: A conformational landscape

Author keywords

Aib; Anion recognition; CD; FTIR; NMR; Peptide design; Sulfate ion

Indexed keywords

CHIMERIC PROTEIN; DNA GLYCOSYLTRANSFERASE; POLYPEPTIDE; SULFATE; PEPTIDE;

EID: 77955094958     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.06.003     Document Type: Article
Times cited : (10)

References (46)
  • 1
    • 0037086663 scopus 로고    scopus 로고
    • A cytochrome c mutant with high electron transfer and antioxidant activities but devoid of apoptogenic effect
    • Abdullaev Z.Kh., Bodrova M.E., Chernyak B.V., Dolgikh D.A., Kluck R.M., Pereverzev M.O., et al. A cytochrome c mutant with high electron transfer and antioxidant activities but devoid of apoptogenic effect. Biochem. J. 2002, 362:749-754.
    • (2002) Biochem. J. , vol.362 , pp. 749-754
    • Abdullaev, Z.1    Bodrova, M.E.2    Chernyak, B.V.3    Dolgikh, D.A.4    Kluck, R.M.5    Pereverzev, M.O.6
  • 2
    • 10644250720 scopus 로고    scopus 로고
    • Protein chemical shifts arising from α-helices and β-sheets depend on solvent exposure
    • Avbelj F., Kocjan D., Baldwin R.L. Protein chemical shifts arising from α-helices and β-sheets depend on solvent exposure. Proc. Natl. Acad. Sci. USA 2004, 101:17394-17397.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 17394-17397
    • Avbelj, F.1    Kocjan, D.2    Baldwin, R.L.3
  • 3
    • 0037011545 scopus 로고    scopus 로고
    • A short Aib/Ala-based peptide helix is as stable as an Ala-based peptide helix double its length
    • Banerjee R., Basu G. A short Aib/Ala-based peptide helix is as stable as an Ala-based peptide helix double its length. ChemBioChem 2002, 12:1263-1266.
    • (2002) ChemBioChem , vol.12 , pp. 1263-1266
    • Banerjee, R.1    Basu, G.2
  • 4
    • 66249139193 scopus 로고    scopus 로고
    • Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature
    • Banerjee R., Chattopadhyay S., Basu G. Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature. Proteins 2009, 76:184-200.
    • (2009) Proteins , vol.76 , pp. 184-200
    • Banerjee, R.1    Chattopadhyay, S.2    Basu, G.3
  • 5
    • 0032498302 scopus 로고    scopus 로고
    • Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions
    • Barrett T.E., Savva R., Panayotou G., Barlow T., Brown T., Jiricny J., Pearl L.H. Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. Cell (Cambridge Mass) 1998, 92:117-129.
    • (1998) Cell (Cambridge Mass) , vol.92 , pp. 117-129
    • Barrett, T.E.1    Savva, R.2    Panayotou, G.3    Barlow, T.4    Brown, T.5    Jiricny, J.6    Pearl, L.H.7
  • 6
    • 84985733652 scopus 로고
    • 1H NMR parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH
    • 1H NMR parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers 1979, 18:285-297.
    • (1979) Biopolymers , vol.18 , pp. 285-297
    • Bundi, A.1    Wuthrich, K.2
  • 7
    • 0027501461 scopus 로고
    • Anion binding sites in protein structures
    • Chakrabarti P. Anion binding sites in protein structures. J. Mol. Biol. 1993, 234:463-482.
    • (1993) J. Mol. Biol. , vol.234 , pp. 463-482
    • Chakrabarti, P.1
  • 8
    • 0033516517 scopus 로고    scopus 로고
    • Apo and holo crystal structures of an NADP-dependent aldehyde dehydrogenase from Streptococcus mutans
    • Cobessi D., Tete-Favier F., Marchal S., Azza S., Branlant G., Aubry A. Apo and holo crystal structures of an NADP-dependent aldehyde dehydrogenase from Streptococcus mutans. J. Mol. Biol. 1999, 290:161-173.
    • (1999) J. Mol. Biol. , vol.290 , pp. 161-173
    • Cobessi, D.1    Tete-Favier, F.2    Marchal, S.3    Azza, S.4    Branlant, G.5    Aubry, A.6
  • 9
    • 0027943884 scopus 로고
    • A structural analysis of phosphate and sulphate binding sites in proteins. Estimation of propensities for binding and conservation of phosphate binding sites
    • Copley R.R., Barton G.J. A structural analysis of phosphate and sulphate binding sites in proteins. Estimation of propensities for binding and conservation of phosphate binding sites. J. Mol. Biol. 1994, 242:321-329.
    • (1994) J. Mol. Biol. , vol.242 , pp. 321-329
    • Copley, R.R.1    Barton, G.J.2
  • 10
    • 0032499791 scopus 로고    scopus 로고
    • Crystal structure of chemically synthesized [N33A] stromal cell-derived factor-1α, a potent ligand for the HIV-1 'fusin' coreceptor
    • Dealwis C., Fernandez E.J., Thompson D.A., Simon R.J., Siani M.A., Lolis E. Crystal structure of chemically synthesized [N33A] stromal cell-derived factor-1α, a potent ligand for the HIV-1 'fusin' coreceptor. Proc. Natl. Acad. Sci. USA 1998, 95:6941-6946.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 6941-6946
    • Dealwis, C.1    Fernandez, E.J.2    Thompson, D.A.3    Simon, R.J.4    Siani, M.A.5    Lolis, E.6
  • 11
    • 0142154391 scopus 로고    scopus 로고
    • Acceptor-donor-acceptor motifs recognize the Watson-Crick, Hoogsteen and sugar " Acceptor-donor-acceptor" edges of adenine and adenosine-containing ligands
    • Denessiouk K.A., Johnson M.S. Acceptor-donor-acceptor motifs recognize the Watson-Crick, Hoogsteen and sugar " Acceptor-donor-acceptor" edges of adenine and adenosine-containing ligands. J. Mol. Biol. 2003, 333:1025-1043.
    • (2003) J. Mol. Biol. , vol.333 , pp. 1025-1043
    • Denessiouk, K.A.1    Johnson, M.S.2
  • 12
  • 14
    • 1242341176 scopus 로고    scopus 로고
    • Phosphate group binding " cup" of PLP-dependent and non-PLP-dependent enzymes: leitmotif and variations
    • Denesyuk A.I., Denessiouk K.A., Korpela T., Johnson M.S. Phosphate group binding " cup" of PLP-dependent and non-PLP-dependent enzymes: leitmotif and variations. Biochim. Biophys. Acta 2003, 1647:234-238.
    • (2003) Biochim. Biophys. Acta , vol.1647 , pp. 234-238
    • Denesyuk, A.I.1    Denessiouk, K.A.2    Korpela, T.3    Johnson, M.S.4
  • 15
    • 0642311564 scopus 로고
    • Infrared absorption spectra of water of crystallization in sodium sulfate decahydrate crystals
    • Gamo I. Infrared absorption spectra of water of crystallization in sodium sulfate decahydrate crystals. Bull. Chem. Soc. Jpn. 1962, 35:1058-1059.
    • (1962) Bull. Chem. Soc. Jpn. , vol.35 , pp. 1058-1059
    • Gamo, I.1
  • 17
    • 0026536746 scopus 로고
    • Crystal structure of the binary complex of pig muscle phosphoglycerate kinase and its substrate 3-phospho-d-glycerate
    • Harlos K., Vas M., Blake C.F. Crystal structure of the binary complex of pig muscle phosphoglycerate kinase and its substrate 3-phospho-d-glycerate. Proteins 1992, 12:133-144.
    • (1992) Proteins , vol.12 , pp. 133-144
    • Harlos, K.1    Vas, M.2    Blake, C.F.3
  • 18
    • 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
  • 19
    • 0028171471 scopus 로고
    • 10- and α-helix: structures of 8, 9 and 10 residue peptides containing the (Leu-Aib-Ala)2-Phe-Aib fragment
    • 10- and α-helix: structures of 8, 9 and 10 residue peptides containing the (Leu-Aib-Ala)2-Phe-Aib fragment. Protein Sci. 1994, 3:1547-1555.
    • (1994) Protein Sci. , vol.3 , pp. 1547-1555
    • Karle, I.L.1    Flippen-Anderson, J.L.2    Gurunath, R.3    Balaram, P.4
  • 20
    • 0025880710 scopus 로고
    • 10- and α-helices and β-bend ribbon structures in organic solution and in model biomembranes by Fourier transform infrared spectroscopy
    • 10- and α-helices and β-bend ribbon structures in organic solution and in model biomembranes by Fourier transform infrared spectroscopy. Biochemistry 1991, 30:6541-6548.
    • (1991) Biochemistry , vol.30 , pp. 6541-6548
    • Kennedy, D.F.1    Crisma, M.2    Toniolo, C.3    Chapman, D.4
  • 21
    • 0032972775 scopus 로고    scopus 로고
    • Structural motif of phosphate-binding site common to various protein superfamilies: all-against all structural comparison of protein-mononucleotide complexes
    • Kinoshita K., Sadanami K., Kidera A., Go N. Structural motif of phosphate-binding site common to various protein superfamilies: all-against all structural comparison of protein-mononucleotide complexes. Protein Eng. 1999, 12:11-14.
    • (1999) Protein Eng. , vol.12 , pp. 11-14
    • Kinoshita, K.1    Sadanami, K.2    Kidera, A.3    Go, N.4
  • 22
    • 0029900085 scopus 로고    scopus 로고
    • Negative electrostatic surface potential of protein sites specific for anionic ligands
    • Ledvina P.S., Yao N., Choudhary A., Quiocho F.A. Negative electrostatic surface potential of protein sites specific for anionic ligands. Proc. Natl. Acad. Sci. USA 1996, 93:6786-6791.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 6786-6791
    • Ledvina, P.S.1    Yao, N.2    Choudhary, A.3    Quiocho, F.A.4
  • 23
    • 0034695475 scopus 로고    scopus 로고
    • Crystal structure of the gephyrin-related molybdenum cofactor biosynthesis protein MogA from Escherichia coli
    • Liu M.T., Wuebbens M.M., Rajagopalan K.K.V., Schindelin H. Crystal structure of the gephyrin-related molybdenum cofactor biosynthesis protein MogA from Escherichia coli. J. Biol. Chem. 2000, 275:1814-1822.
    • (2000) J. Biol. Chem. , vol.275 , pp. 1814-1822
    • Liu, M.T.1    Wuebbens, M.M.2    Rajagopalan, K.K.V.3    Schindelin, H.4
  • 24
    • 0026143161 scopus 로고
    • Theoretical CD studies of polypeptide helices: examination of important electronic and geometric factors
    • Manning M., Woody R.W. Theoretical CD studies of polypeptide helices: examination of important electronic and geometric factors. Biopolymers 1991, 31:569-586.
    • (1991) Biopolymers , vol.31 , pp. 569-586
    • Manning, M.1    Woody, R.W.2
  • 25
    • 0027551639 scopus 로고
    • Characterization of β-turns in cyclic hexapeptides in solution by Fourier transform IR spectroscopy
    • Mantsch H.H., Peerczel A., Hollosi M., Fasman G.D. Characterization of β-turns in cyclic hexapeptides in solution by Fourier transform IR spectroscopy. Biopolymers 1993, 33:201-207.
    • (1993) Biopolymers , vol.33 , pp. 201-207
    • Mantsch, H.H.1    Peerczel, A.2    Hollosi, M.3    Fasman, G.D.4
  • 26
    • 0029064280 scopus 로고
    • FTIR spectroscopy of alanine-based peptides: assignment of the amide-I' modes for random coil and helix
    • Martinez G., Millhauser G. FTIR spectroscopy of alanine-based peptides: assignment of the amide-I' modes for random coil and helix. J. Struct. Biol. 1995, 114:23-27.
    • (1995) J. Struct. Biol. , vol.114 , pp. 23-27
    • Martinez, G.1    Millhauser, G.2
  • 27
    • 0026593991 scopus 로고
    • Inorganic phosphate binding and electrostatic effects in the active centre of aspartate aminotransferase apoenzyme
    • Martinez-Liarte J.H., Iriarte A., Martinez-Carrion M. Inorganic phosphate binding and electrostatic effects in the active centre of aspartate aminotransferase apoenzyme. Biochemistry 1992, 31:2712-2719.
    • (1992) Biochemistry , vol.31 , pp. 2712-2719
    • Martinez-Liarte, J.H.1    Iriarte, A.2    Martinez-Carrion, M.3
  • 28
    • 0026320781 scopus 로고
    • Characterization of phosphate binding in the active site of barnase by site-directed mutagenesis and NMR
    • Meiering E.M., Bycroft M., Fersht A.R. Characterization of phosphate binding in the active site of barnase by site-directed mutagenesis and NMR. Biochemistry 1991, 30:11348-11356.
    • (1991) Biochemistry , vol.30 , pp. 11348-11356
    • Meiering, E.M.1    Bycroft, M.2    Fersht, A.R.3
  • 29
    • 0029207339 scopus 로고
    • 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG
    • 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG. J. Biomol. NMR 1995, 5:14-24.
    • (1995) J. Biomol. NMR , vol.5 , pp. 14-24
    • Merutka, G.1    Dyson, H.J.2    Wright, P.E.3
  • 30
    • 18644380729 scopus 로고    scopus 로고
    • Sites for Phosphates and Iron-Sulfur Thiolates in the First Membranes: 3 to 6 Residue Anion-Binding Motifs (Nests)
    • Milner-White E.J., Russel M.J. Sites for Phosphates and Iron-Sulfur Thiolates in the First Membranes: 3 to 6 Residue Anion-Binding Motifs (Nests). Origins of Life and Evolution of Biospheres 2005, 35:19-27.
    • (2005) Origins of Life and Evolution of Biospheres , vol.35 , pp. 19-27
    • Milner-White, E.J.1    Russel, M.J.2
  • 31
    • 0037412181 scopus 로고    scopus 로고
    • A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins
    • Ramakrishnan C., Dani S., Ramasarma T.R. A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins. Protein Eng. 2002, 15:783-798.
    • (2002) Protein Eng. , vol.15 , pp. 783-798
    • Ramakrishnan, C.1    Dani, S.2    Ramasarma, T.R.3
  • 32
    • 0020483375 scopus 로고
    • Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7A resolution
    • Remington S., Wiegand G., Huber R. Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7A resolution. J. Mol. Biol. 1982, 158:111-152.
    • (1982) J. Mol. Biol. , vol.158 , pp. 111-152
    • Remington, S.1    Wiegand, G.2    Huber, R.3
  • 33
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of alpha helices
    • Richardson J.S., Richardson D.C. Amino acid preferences for specific locations at the ends of alpha helices. Science 1988, 240:1648-1652.
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 36
    • 35848970565 scopus 로고    scopus 로고
    • Conformational manifold of α-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations
    • Schweitzer-Stenner R., Gonzales W., Bourne G.T., Feng J.A., Marshall G.R. Conformational manifold of α-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations. J. Am. Chem. Soc. 2007, 129:13095-13109.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 13095-13109
    • Schweitzer-Stenner, R.1    Gonzales, W.2    Bourne, G.T.3    Feng, J.A.4    Marshall, G.R.5
  • 37
    • 0024375778 scopus 로고
    • Crystal versus solution structures of enzymes: NMR spectroscopy of a crystalline serine protease
    • Smith S.O., Farr-Jones S., Griffin R.G., Bachovchin W.W. Crystal versus solution structures of enzymes: NMR spectroscopy of a crystalline serine protease. Science 1989, 244:961-964.
    • (1989) Science , vol.244 , pp. 961-964
    • Smith, S.O.1    Farr-Jones, S.2    Griffin, R.G.3    Bachovchin, W.W.4
  • 38
    • 0027492164 scopus 로고
    • Determination of protein secondary structure by Fourier transform infrared spectroscopy: a critical assessment
    • Surewicz W.K., Mantsch H.H., Chapman D. Determination of protein secondary structure by Fourier transform infrared spectroscopy: a critical assessment. Biochemistry 1993, 32:389-394.
    • (1993) Biochemistry , vol.32 , pp. 389-394
    • Surewicz, W.K.1    Mantsch, H.H.2    Chapman, D.3
  • 39
    • 0034435974 scopus 로고    scopus 로고
    • A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation and regulation
    • Symmons M.F., Jones G.H., Luisi B.F. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation and regulation. Struct. Fold Des. 2000, 8:1215-1226.
    • (2000) Struct. Fold Des. , vol.8 , pp. 1215-1226
    • Symmons, M.F.1    Jones, G.H.2    Luisi, B.F.3
  • 40
    • 0015822129 scopus 로고
    • Variability in the tertiary structure of α-chymotrypsin at 2.8-Å resolution
    • Tulinsky A., Vandlen R.L., Morimoto C.N., Mani N.V., Wright L.H. Variability in the tertiary structure of α-chymotrypsin at 2.8-Å resolution. Biochemistry 1973, 12:4185-4192.
    • (1973) Biochemistry , vol.12 , pp. 4185-4192
    • Tulinsky, A.1    Vandlen, R.L.2    Morimoto, C.N.3    Mani, N.V.4    Wright, L.H.5
  • 41
    • 0025859914 scopus 로고
    • Anion binding at the active site of trypanosomal triosephosphate isomerase. Monohydrogen phosphate does not mimic sulphate
    • Verlinde C.L., Noble M.E., Kalk K.H., Groendijk H., Wierenga R.K., Hol W.G. Anion binding at the active site of trypanosomal triosephosphate isomerase. Monohydrogen phosphate does not mimic sulphate. Eur. J. Biochem. 1991, 198:53-57.
    • (1991) Eur. J. Biochem. , vol.198 , pp. 53-57
    • Verlinde, C.L.1    Noble, M.E.2    Kalk, K.H.3    Groendijk, H.4    Wierenga, R.K.5    Hol, W.G.6
  • 42
    • 0036293842 scopus 로고    scopus 로고
    • A novel main-chain anion-binding site in proteins: the nest. A particular combination of , ψ values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions
    • Watson J.D., Milner-White E.J. A novel main-chain anion-binding site in proteins: the nest. A particular combination of , ψ values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions. J. Mol. Biol. 2002, 315:171-182.
    • (2002) J. Mol. Biol. , vol.315 , pp. 171-182
    • Watson, J.D.1    Milner-White, E.J.2
  • 43
    • 0021764252 scopus 로고
    • Preliminary crystallographic studies of triosephosphate isomerase from the blood parasite Trypanosoma brucei brucei
    • Wierenga R.K., Hol W.G., Misset O., Opperdoes F.R. Preliminary crystallographic studies of triosephosphate isomerase from the blood parasite Trypanosoma brucei brucei. J. Mol. Biol. 1984, 178:487-490.
    • (1984) J. Mol. Biol. , vol.178 , pp. 487-490
    • Wierenga, R.K.1    Hol, W.G.2    Misset, O.3    Opperdoes, F.R.4
  • 44
    • 0028673594 scopus 로고
    • Chemical shifts as a tool for structure determination
    • Wishart D.S., Sykes B.D. Chemical shifts as a tool for structure determination. Methods Enzymol. 1994, 239:363-392.
    • (1994) Methods Enzymol. , vol.239 , pp. 363-392
    • Wishart, D.S.1    Sykes, B.D.2
  • 46
    • 0022503457 scopus 로고
    • Calculation of protein conformation from circular dichroism
    • Yang J.T., Wu C.S.C., Martinez H.M. Calculation of protein conformation from circular dichroism. Methods Enzymol. 1986, 130:208-269.
    • (1986) Methods Enzymol. , vol.130 , pp. 208-269
    • Yang, J.T.1    Wu, C.S.C.2    Martinez, H.M.3


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