메뉴 건너뛰기




Volumn 1260, Issue , 2015, Pages 17-32

Protein structural information derived from nmr chemical shift with the neural network program talos-n

Author keywords

Artifcial neural network; Backbone torsion angle; Chemical shifts; NMR; Protein structure; Secondary structure; Side chain conformation

Indexed keywords

STRUCTURAL PROTEIN; CARBON; PROTEIN;

EID: 84958627859     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2239-0_2     Document Type: Article
Times cited : (185)

References (36)
  • 2
    • 0023662538 scopus 로고
    • Main-chain-directed strategy for the assignment of 1H NMR spectra of proteins
    • Englander SW, Wand AJ (1987) Main-chain-directed strategy for the assignment of 1H NMR spectra of proteins. Biochemistry 26: 5953–5958
    • (1987) Biochemistry , vol.26 , pp. 5953-5958
    • Englander, S.W.1    Wand, A.J.2
  • 3
    • 0024285541 scopus 로고
    • Protein 13C spin systems by a single two-dimensional nuclear magnetic resonance experiment
    • Oh BH, Westler WM, Darba P et al (1988) Protein 13C spin systems by a single two-dimensional nuclear magnetic resonance experiment. Science 240:908–911
    • (1988) Science , vol.240 , pp. 908-911
    • Oh, B.H.1    Westler, W.M.2    Darba, P.3
  • 4
    • 0025341339 scopus 로고
    • A novel approach for sequential assignment of 1H, 13C, and 15N spectra of larger proteins: Heteronu-clear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin
    • Ikura M, Kay LE, Bax A (1990) A novel approach for sequential assignment of 1H, 13C, and 15N spectra of larger proteins: heteronu-clear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry 29:4659–4667
    • (1990) Biochemistry , vol.29 , pp. 4659-4667
    • Ikura, M.1    Kay, L.E.2    Bax, A.3
  • 5
    • 0027633499 scopus 로고
    • Prospects for NMR of large proteins
    • Wagner G (1993) Prospects for NMR of large proteins. J Biomol NMR 3:375–385
    • (1993) J Biomol NMR , vol.3 , pp. 375-385
    • Wagner, G.1
  • 6
    • 84989629173 scopus 로고
    • Conformation-dependent C13 chemical shifts—a new means of conforma-tional characterization as obtained by high resolution solid state C13 NMR
    • Saito H (1986) Conformation-dependent C13 chemical shifts—a new means of conforma-tional characterization as obtained by high resolution solid state C13 NMR. Magn Reson Chem 24:835–852
    • (1986) Magn Reson Chem , vol.24 , pp. 835-852
    • Saito, H.1
  • 7
    • 0026410969 scopus 로고
    • Relationship between nuclear magnetic resonance chemical shift and protein secondary structure
    • Wishart DS, Sykes BD, Richards FM (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 222:311–333
    • (1991) J Mol Biol , vol.222 , pp. 311-333
    • Wishart, D.S.1    Sykes, B.D.2    Richards, F.M.3
  • 8
    • 0347610773 scopus 로고
    • Empirical correlation between protein backbone conformation and Ca and Cb 13C nuclear magnetic resonance chemical shifts
    • Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and Ca and Cb 13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113: 5490–5492
    • (1991) J am Chem Soc , vol.113 , pp. 5490-5492
    • Spera, S.1    Bax, A.2
  • 9
  • 10
    • 10644250720 scopus 로고    scopus 로고
    • Protein chemical shifts arising from alpha-helices and beta-sheets depend on solvent exposure
    • Avbelj F, Kocjan D, Baldwin RL (2004) Protein chemical shifts arising from alpha-helices and beta-sheets depend on solvent exposure. Proc Natl Acad Sci U S A 101: 17394–17397
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 17394-17397
    • Avbelj, F.1    Kocjan, D.2    Baldwin, R.L.3
  • 11
    • 0027308278 scopus 로고
    • Secondary and tertiary structural effects on protein NMR chemical shifts—an ab initio approach
    • de Dios AC, Pearson JG, Oldfeld E (1993) Secondary and tertiary structural effects on protein NMR chemical shifts—an ab initio approach. Science 260:1491–1496
    • (1993) Science , vol.260 , pp. 1491-1496
    • De Dios, A.C.1    Pearson, J.G.2    Oldfeld, E.3
  • 12
    • 0031765856 scopus 로고    scopus 로고
    • The use of chemical shifts and their anisotropies in biomolecular structure determination
    • Case DA (1998) The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol 8: 624–630
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 624-630
    • Case, D.A.1
  • 13
    • 55749100006 scopus 로고    scopus 로고
    • Quantum chemical C-13(alpha) chemical shift calculations for protein NMR structure determination, refnement, and validation
    • Vila JA, Aramini JM, Rossi P et al (2008) Quantum chemical C-13(alpha) chemical shift calculations for protein NMR structure determination, refnement, and validation. Proc Natl Acad Sci U S A 105:14389–14394
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 14389-14394
    • Vila, J.A.1    Aramini, J.M.2    Rossi, P.3
  • 14
    • 70349627256 scopus 로고    scopus 로고
    • Fast and accurate predictions of protein NMR chemical shifts from interatomic distances
    • Kohlhoff KJ, Robustelli P, Cavalli A et al (2009) Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J Am Chem Soc 131:13894–13895
    • (2009) J am Chem Soc , vol.131 , pp. 13894-13895
    • Kohlhoff, K.J.1    Robustelli, P.2    Cavalli, A.3
  • 15
    • 0000635348 scopus 로고
    • The relationship between amide proton chemical shifts and secondary structure in proteins
    • Asakura T, Taoka K, Demura M et al (1995) The relationship between amide proton chemical shifts and secondary structure in proteins. J Biomol NMR 6:227–236
    • (1995) J Biomol NMR , vol.6 , pp. 227-236
    • Asakura, T.1    Taoka, K.2    Demura, M.3
  • 16
    • 12044252858 scopus 로고
    • Methodological advances in protein NMR
    • Bax A, Grzesiek S (1993) Methodological advances in protein NMR. Acc Chem Res 26:131–138
    • (1993) Acc Chem Res , vol.26 , pp. 131-138
    • Bax, A.1    Grzesiek, S.2
  • 17
    • 0347722841 scopus 로고    scopus 로고
    • Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed feld gradients
    • Sattler M, Schleucher J, Griesinger C (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed feld gradients. Prog Nucl Magn Reson Spectrosc 34:93–158
    • (1999) Prog Nucl Magn Reson Spectrosc , vol.34 , pp. 93-158
    • Sattler, M.1    Schleucher, J.2    Griesinger, C.3
  • 18
    • 0033518575 scopus 로고    scopus 로고
    • TROSY-type triple-resonance experiments for sequential NMR assignments of large proteins
    • Salzmann M, Wider G, Pervushin K et al (1999) TROSY-type triple-resonance experiments for sequential NMR assignments of large proteins. J Am Chem Soc 121:844–848
    • (1999) J am Chem Soc , vol.121 , pp. 844-848
    • Salzmann, M.1    Wider, G.2    Pervushin, K.3
  • 19
    • 33845552240 scopus 로고
    • Hydrogen-bond length and H-1-NMR chemical- shifts in proteins
    • Wagner G, Pardi A, Wuthrich K (1983) Hydrogen-bond length and H-1-NMR chemical- shifts in proteins. J Am Chem Soc 105:5948–5949
    • (1983) J am Chem Soc , vol.105 , pp. 5948-5949
    • Wagner, G.1    Pardi, A.2    Wuthrich, K.3
  • 20
    • 0033003335 scopus 로고    scopus 로고
    • Protein backbone angle restraints from searching a database for chemical shift and sequence homology
    • Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302
    • (1999) J Biomol NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 21
    • 84857982668 scopus 로고    scopus 로고
    • The Protein Data Bank at 40: Refecting on the past to prepare for the future
    • Berman HM, Kleywegt GJ, Nakamura H et al (2012) The Protein Data Bank at 40: refecting on the past to prepare for the future. Structure 20:391–396
    • (2012) Structure , vol.20 , pp. 391-396
    • Berman, H.M.1    Kleywegt, G.J.2    Nakamura, H.3
  • 22
    • 41149116500 scopus 로고    scopus 로고
    • BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): New policies affecting biomolecular NMR depositions
    • Markley JL, Ulrich EL, Berman HM et al (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 40:153–155
    • (2008) J Biomol NMR , vol.40 , pp. 153-155
    • Markley, J.L.1    Ulrich, E.L.2    Berman, H.M.3
  • 23
    • 79451469120 scopus 로고    scopus 로고
    • Interpreting protein chemical shift data
    • Wishart DS (2011) Interpreting protein chemical shift data. Prog Nucl Magn Reson Spectrosc 58:62–87
    • (2011) Prog Nucl Magn Reson Spectrosc , vol.58 , pp. 62-87
    • Wishart, D.S.1
  • 24
    • 68349093958 scopus 로고    scopus 로고
    • TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
    • Shen Y, Delaglio F, Cornilescu G et al (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223
    • (2009) J Biomol NMR , vol.44 , pp. 213-223
    • Shen, Y.1    Delaglio, F.2    Cornilescu, G.3
  • 25
    • 84880132018 scopus 로고    scopus 로고
    • Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artifcial neural networks
    • Shen Y, Bax A (2013) Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artifcial neural networks. J Biomol NMR 56:227–241
    • (2013) J Biomol NMR , vol.56 , pp. 227-241
    • Shen, Y.1    Bax, A.2
  • 26
    • 77956478902 scopus 로고    scopus 로고
    • SPARTA plus: A modest improvement in empirical NMR chemical shift prediction by means of an artifcial neural network
    • Shen Y, Bax A (2010) SPARTA plus: a modest improvement in empirical NMR chemical shift prediction by means of an artifcial neural network. J Biomol NMR 48:13–22
    • (2010) J Biomol NMR , vol.48 , pp. 13-22
    • Shen, Y.1    Bax, A.2
  • 27
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specifc scoring matrices
    • Jones DT (1999) Protein secondary structure prediction based on position-specifc scoring matrices. J Mol Biol 292:195–202
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 28
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70 percent accuracy
    • Rost B, Sander C (1993) Prediction of protein secondary structure at better than 70 percent accuracy. J Mol Biol 232:584–599
    • (1993) J Mol Biol , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 29
    • 0034486021 scopus 로고    scopus 로고
    • Solution structure of DinI provides insight into its mode of RecA inactiva-tion
    • Ramirez BE, Voloshin ON, Camerini-Otero RD et al (2000) Solution structure of DinI provides insight into its mode of RecA inactiva-tion. Protein Sci 9:2161–2169
    • (2000) Protein Sci , vol.9 , pp. 2161-2169
    • Ramirez, B.E.1    Voloshin, O.N.2    Camerini-Otero, R.D.3
  • 30
    • 84868200793 scopus 로고    scopus 로고
    • Deuterium isotope shifts for backbone 1H, 15N and 13C nuclei in intrinsically disordered protein alpha-synuclein
    • Maltsev AS, Ying JF, Bax A (2012) Deuterium isotope shifts for backbone 1H, 15N and 13C nuclei in intrinsically disordered protein alpha-synuclein. J Biomol NMR 54:181–191
    • (2012) J Biomol NMR , vol.54 , pp. 181-191
    • Maltsev, A.S.1    Ying, J.F.2    Bax, A.3
  • 31
    • 27544456339 scopus 로고    scopus 로고
    • A simple method to predict protein fexibility using secondary chemical shifts
    • Berjanskii MV, Wishart DS (2005) A simple method to predict protein fexibility using secondary chemical shifts. J Am Chem Soc 127: 14970–14971
    • (2005) J am Chem Soc , vol.127 , pp. 14970-14971
    • Berjanskii, M.V.1    Wishart, D.S.2
  • 32
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 33
    • 0013293280 scopus 로고    scopus 로고
    • The Xplor-NIH NMR molecular structure determination package
    • Schwieters CD, Kuszewski JJ, Tjandra N et al (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65–73
    • (2003) J Magn Reson , vol.160 , pp. 65-73
    • Schwieters, C.D.1    Kuszewski, J.J.2    Tjandra, N.3
  • 34
    • 0036308102 scopus 로고    scopus 로고
    • Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
    • Herrmann T, Guntert P, Wuthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227
    • (2002) J Mol Biol , vol.319 , pp. 209-227
    • Herrmann, T.1    Guntert, P.2    Wuthrich, K.3
  • 35
    • 0032584781 scopus 로고    scopus 로고
    • Recommendations for the presentation of NMR structures of proteins and nucleic acids (Reprinted from Pure and Applied Chemistry, vol 70, pp. 117–142, 1998)
    • Markley JL, Bax A, Arata Y et al (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids (Reprinted from Pure and Applied Chemistry, vol 70, pp. 117–142, 1998). J Mol Biol 280: 933–952
    • (1998) J Mol Biol , vol.280 , pp. 933-952
    • Markley, J.L.1    Bax, A.2    Arata, Y.3
  • 36
    • 23144462958 scopus 로고    scopus 로고
    • Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifcations
    • Wang LY, Eghbalnia HR, Bahrami A et al (2005) Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifcations. J Biomol NMR 32:13–22
    • (2005) J Biomol NMR , vol.32 , pp. 13-22
    • Wang, L.Y.1    Eghbalnia, H.R.2    Bahrami, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.