메뉴 건너뛰기




Volumn 205, Issue 2, 2010, Pages 304-314

A Monte Carlo/simulated annealing algorithm for sequential resonance assignment in solid state NMR of uniformly labeled proteins with magic-angle spinning

Author keywords

Amyloid; Automated assignment; Chemical shifts; HET s; Prion; Stochastic recoupling

Indexed keywords

2D SPECTRA; 3D DATA; ANNEALING ALGORITHM; AUTOMATED ASSIGNMENT; COMPUTATIONAL APPROACH; HIGH QUALITY; LABELED PROTEINS; MAGIC ANGLE SPINNING; PROTEIN SEQUENCES; RECOUPLING; RESONANCE ASSIGNMENTS; SEQUENTIAL ASSIGNMENT; SIGNAL TO NOISE; SOLID STATE NMR;

EID: 77955304057     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2010.05.013     Document Type: Article
Times cited : (46)

References (47)
  • 2
    • 0035795429 scopus 로고    scopus 로고
    • 15N signal assignments of the alpha-spectrin SH3 domain by magic angle spinning solid state NMR at 17.6 tesla
    • 15N signal assignments of the alpha-spectrin SH3 domain by magic angle spinning solid state NMR at 17.6 tesla ChemBioChem 2 2001 272 281
    • (2001) ChemBioChem , vol.2 , pp. 272-281
    • Pauli, J.1    Baldus, M.2    Van Rossum, B.3    De Groot, H.4    Oschkinat, H.5
  • 3
    • 0038412551 scopus 로고    scopus 로고
    • Backbone and side chain assignment strategies for multiply labeled membrane peptides and proteins in the solid state
    • A.T. Petkova, M. Baldus, M. Belenky, M. Hong, R.G. Griffin, and J. Herzfeld Backbone and side chain assignment strategies for multiply labeled membrane peptides and proteins in the solid state J. Magn. Reson. 160 2003 1 12
    • (2003) J. Magn. Reson. , vol.160 , pp. 1-12
    • Petkova, A.T.1    Baldus, M.2    Belenky, M.3    Hong, M.4    Griffin, R.G.5    Herzfeld, J.6
  • 4
    • 1942489080 scopus 로고    scopus 로고
    • Assignment of the backbone resonances for microcrystalline ubiquitin
    • T.I. Igumenova, A.J. Wand, and A.E. McDermott Assignment of the backbone resonances for microcrystalline ubiquitin J. Am. Chem. Soc. 126 2004 5323 5331
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 5323-5331
    • Igumenova, T.I.1    Wand, A.J.2    McDermott, A.E.3
  • 6
    • 13444259506 scopus 로고    scopus 로고
    • 3D NMR spectroscopy for resonance assignment and structure elucidation of proteins under MAS: Novel pulse schemes and sensitivity considerations
    • H. Heise, K. Seidel, M. Etzkorn, S. Becker, and M. Baldus 3D NMR spectroscopy for resonance assignment and structure elucidation of proteins under MAS: novel pulse schemes and sensitivity considerations J. Magn. Reson. 173 2005 64 74
    • (2005) J. Magn. Reson. , vol.173 , pp. 64-74
    • Heise, H.1    Seidel, K.2    Etzkorn, M.3    Becker, S.4    Baldus, M.5
  • 7
    • 34848898190 scopus 로고    scopus 로고
    • Backbone assignments in solid state proteins using J-based 3D heteronuclear correlation spectroscopy
    • L. Chen, J.M. Kaiser, T. Polenova, J. Yang, C.M. Rienstra, and L.J. Mueller Backbone assignments in solid state proteins using J-based 3D heteronuclear correlation spectroscopy J. Am. Chem. Soc. 129 2007 10650 10651
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 10650-10651
    • Chen, L.1    Kaiser, J.M.2    Polenova, T.3    Yang, J.4    Rienstra, C.M.5    Mueller, L.J.6
  • 8
    • 34548504572 scopus 로고    scopus 로고
    • Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins
    • W.T. Franks, K.D. Kloepper, B.J. Wylie, and C.M. Rienstra Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins J. Biomol. NMR 39 2007 107 131
    • (2007) J. Biomol. NMR , vol.39 , pp. 107-131
    • Franks, W.T.1    Kloepper, K.D.2    Wylie, B.J.3    Rienstra, C.M.4
  • 9
    • 33847628307 scopus 로고    scopus 로고
    • Filamentous phage studied by magic-angle spinning NMR: Resonance assignment and secondary structure of the coat protein in Pf1
    • A. Goldbourt, B.J. Gross, L.A. Day, and A.E. McDermott Filamentous phage studied by magic-angle spinning NMR: resonance assignment and secondary structure of the coat protein in Pf1 J. Am. Chem. Soc. 129 2007 2338 2344
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 2338-2344
    • Goldbourt, A.1    Gross, B.J.2    Day, L.A.3    McDermott, A.E.4
  • 10
    • 34247848052 scopus 로고    scopus 로고
    • 15N chemical-shift assignments of the disulfide-bond-forming enzyme DSBb by 3D magic-angle spinning NMR spectroscopy
    • 15N chemical-shift assignments of the disulfide-bond-forming enzyme DSBb by 3D magic-angle spinning NMR spectroscopy ChemBioChem 8 2007 434 442
    • (2007) ChemBioChem , vol.8 , pp. 434-442
    • Li, Y.1    Berthold, D.A.2    Frericks, H.L.3    Gennis, R.B.4    Rienstra, C.M.5
  • 11
    • 34247208000 scopus 로고    scopus 로고
    • Solid state NMR spectroscopy of a paramagnetic protein: Assignment and study of human dimeric oxidized Cu(II)-Zn(II) superoxide dismutase (SOD)
    • G. Pintacuda, N. Giraud, R. Pierattelli, A. Bockmann, I. Bertini, and L. Emsley Solid state NMR spectroscopy of a paramagnetic protein: assignment and study of human dimeric oxidized Cu(II)-Zn(II) superoxide dismutase (SOD) Angew. Chem., Int. Ed. 46 2007 1079 1082
    • (2007) Angew. Chem., Int. Ed. , vol.46 , pp. 1079-1082
    • Pintacuda, G.1    Giraud, N.2    Pierattelli, R.3    Bockmann, A.4    Bertini, I.5    Emsley, L.6
  • 12
    • 49349116814 scopus 로고    scopus 로고
    • 15N enriched membrane protein, light-harvesting complex 1 (LH1), by solid state NMR
    • 15N enriched membrane protein, light-harvesting complex 1 (LH1), by solid state NMR Biochim. Biophys. Acta-Bioenerg. 1777 2008 1098 1108
    • (2008) Biochim. Biophys. Acta-Bioenerg. , vol.1777 , pp. 1098-1108
    • Huang, L.1    McDermott, A.E.2
  • 13
    • 38649130606 scopus 로고    scopus 로고
    • Chemical shift assignment of the transmembrane helices of DSBb, a 20-kDa integral membrane enzyme, by 3D magic-angle spinning NMR spectroscopy
    • Y. Li, D.A. Berthold, R.B. Gennis, and C.M. Rienstra Chemical shift assignment of the transmembrane helices of DSBb, a 20-kDa integral membrane enzyme, by 3D magic-angle spinning NMR spectroscopy Protein Sci. 17 2008 199 204
    • (2008) Protein Sci. , vol.17 , pp. 199-204
    • Li, Y.1    Berthold, D.A.2    Gennis, R.B.3    Rienstra, C.M.4
  • 16
    • 40849120669 scopus 로고    scopus 로고
    • Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core
    • C. Wasmer, A. Lange, H. Van Melckebeke, A.B. Siemer, R. Riek, and B.H. Meier Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core Science 319 2008 1523 1526
    • (2008) Science , vol.319 , pp. 1523-1526
    • Wasmer, C.1    Lange, A.2    Van Melckebeke, H.3    Siemer, A.B.4    Riek, R.5    Meier, B.H.6
  • 19
    • 18044391103 scopus 로고    scopus 로고
    • High-resolution solid state NMR spectroscopy of the prion protein HET-s in its amyloid conformation
    • A.B. Siemer, C. Ritter, M. Ernst, R. Riek, and B.H. Meier High-resolution solid state NMR spectroscopy of the prion protein HET-s in its amyloid conformation Angew. Chem., Int. Ed. 44 2005 2441 2444
    • (2005) Angew. Chem., Int. Ed. , vol.44 , pp. 2441-2444
    • Siemer, A.B.1    Ritter, C.2    Ernst, M.3    Riek, R.4    Meier, B.H.5
  • 23
    • 77749237271 scopus 로고    scopus 로고
    • Conformational flexibility of Y145Stop human prion protein amyloid fibrils probed by solid state nuclear magnetic resonance spectroscopy
    • J.J. Helmus, K. Surewicz, W.K. Surewicz, and C.P. Jaroniec Conformational flexibility of Y145Stop human prion protein amyloid fibrils probed by solid state nuclear magnetic resonance spectroscopy J. Am. Chem. Soc. 132 2010 2393 2403
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 2393-2403
    • Helmus, J.J.1    Surewicz, K.2    Surewicz, W.K.3    Jaroniec, C.P.4
  • 25
    • 0035872678 scopus 로고    scopus 로고
    • 13C dipolar recoupling under very fast magic angle spinning in solid state nuclear magnetic resonance. Applications to distance measurements, spectral assignments, and high-throughput secondary-structure determination
    • 13C dipolar recoupling under very fast magic angle spinning in solid state nuclear magnetic resonance. Applications to distance measurements, spectral assignments, and high-throughput secondary-structure determination J. Chem. Phys. 114 2001 8473 8483
    • (2001) J. Chem. Phys. , vol.114 , pp. 8473-8483
    • Ishii, Y.1
  • 27
    • 35948943896 scopus 로고    scopus 로고
    • Stochastic dipolar recoupling in nuclear magnetic resonance of solids
    • R. Tycko Stochastic dipolar recoupling in nuclear magnetic resonance of solids Phys. Rev. Lett. 99 2007 187601
    • (2007) Phys. Rev. Lett. , vol.99 , pp. 187601
    • Tycko, R.1
  • 28
    • 44949130685 scopus 로고    scopus 로고
    • Theory of stochastic dipolar recoupling in solid state nuclear magnetic resonance
    • R. Tycko Theory of stochastic dipolar recoupling in solid state nuclear magnetic resonance J. Phys. Chem. B 112 2008 6114 6121
    • (2008) J. Phys. Chem. B , vol.112 , pp. 6114-6121
    • Tycko, R.1
  • 31
    • 57449091884 scopus 로고    scopus 로고
    • Molecular structural basis for polymorphism in Alzheimer's β-amyloid fibrils
    • A.K. Paravastu, R.D. Leapman, W.M. Yau, and R. Tycko Molecular structural basis for polymorphism in Alzheimer's β-amyloid fibrils Proc. Natl. Acad. Sci. U. S. A. 105 2008 18349 18354
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 18349-18354
    • Paravastu, A.K.1    Leapman, R.D.2    Yau, W.M.3    Tycko, R.4
  • 32
    • 36749033116 scopus 로고    scopus 로고
    • Peptide conformation and supramolecular organization in amylin fibrils: Constraints from solid state NMR
    • S. Luca, W.M. Yau, R. Leapman, and R. Tycko Peptide conformation and supramolecular organization in amylin fibrils: constraints from solid state NMR Biochemistry 46 2007 13505 13522
    • (2007) Biochemistry , vol.46 , pp. 13505-13522
    • Luca, S.1    Yau, W.M.2    Leapman, R.3    Tycko, R.4
  • 33
    • 1842862922 scopus 로고    scopus 로고
    • Solid state NMR yields structural constraints on the V3 loop from HIV-1 gp120 bound to the 447-52d antibody Fv fragment
    • S. Sharpe, N. Kessler, J.A. Anglister, W.M. Yau, and R. Tycko Solid state NMR yields structural constraints on the V3 loop from HIV-1 gp120 bound to the 447-52d antibody Fv fragment J. Am. Chem. Soc. 126 2004 4979 4990
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 4979-4990
    • Sharpe, S.1    Kessler, N.2    Anglister, J.A.3    Yau, W.M.4    Tycko, R.5
  • 34
    • 0025906773 scopus 로고
    • Implementation of the main chain directed assignment strategy: Computer-assisted approach
    • S.J. Nelson, D.M. Schneider, and A.J. Wand Implementation of the main chain directed assignment strategy: computer-assisted approach Biophys. J. 59 1991 1113 1122
    • (1991) Biophys. J. , vol.59 , pp. 1113-1122
    • Nelson, S.J.1    Schneider, D.M.2    Wand, A.J.3
  • 35
    • 0000441606 scopus 로고    scopus 로고
    • GARANT: A general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra
    • C. Bartels, P. Guntert, M. Billeter, and K. Wuthrich GARANT: a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra J. Comput. Chem. 18 1997 139 149
    • (1997) J. Comput. Chem. , vol.18 , pp. 139-149
    • Bartels, C.1    Guntert, P.2    Billeter, M.3    Wuthrich, K.4
  • 36
    • 0031083526 scopus 로고    scopus 로고
    • Protein heteronuclear NMR assignments using mean-field simulated annealing
    • N.E.G. Buchler, E.R.P. Zuiderweg, H. Wang, and R.A. Goldstein Protein heteronuclear NMR assignments using mean-field simulated annealing J. Magn. Reson. 125 1997 34 42
    • (1997) J. Magn. Reson. , vol.125 , pp. 34-42
    • Buchler, N.E.G.1    Zuiderweg, E.R.P.2    Wang, H.3    Goldstein, R.A.4
  • 37
    • 0031133492 scopus 로고    scopus 로고
    • Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment
    • K.B. Li, and B.C. Sanctuary Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment J. Chem. Inf. Comput. Sci. 37 1997 467 477
    • (1997) J. Chem. Inf. Comput. Sci. , vol.37 , pp. 467-477
    • Li, K.B.1    Sanctuary, B.C.2
  • 40
    • 0033677333 scopus 로고    scopus 로고
    • The NOESY jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data
    • C. Bailey-Kellogg, A. Widge, J.J. Kelley, M.J. Berardi, J.H. Bushweller, and B.R. Donald The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data J. Comput. Biol. 7 2000 537 558
    • (2000) J. Comput. Biol. , vol.7 , pp. 537-558
    • Bailey-Kellogg, C.1    Widge, A.2    Kelley, J.J.3    Berardi, M.J.4    Bushweller, J.H.5    Donald, B.R.6
  • 41
    • 0034923123 scopus 로고    scopus 로고
    • Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data
    • H.N.B. Moseley, D. Monleon, and G.T. Montelione Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data Methods Enzymol. 339 2001 91 108
    • (2001) Methods Enzymol. , vol.339 , pp. 91-108
    • Moseley, H.N.B.1    Monleon, D.2    Montelione, G.T.3
  • 42
    • 0037266406 scopus 로고    scopus 로고
    • MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins
    • T.K. Hitchens, J.A. Lukin, Y.P. Zhan, S.A. McCallum, and G.S. Rule MONTE: an automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins J. Biomol. NMR 25 2003 1 9
    • (2003) J. Biomol. NMR , vol.25 , pp. 1-9
    • Hitchens, T.K.1    Lukin, J.A.2    Zhan, Y.P.3    McCallum, S.A.4    Rule, G.S.5
  • 43
    • 43649085607 scopus 로고    scopus 로고
    • Sequence specific resonance assignment via multicanonical Monte Carlo search using an ABACUS approach
    • A. Lemak, C.A. Steren, C.H. Arrowsmith, and M. Llinas Sequence specific resonance assignment via multicanonical Monte Carlo search using an ABACUS approach J. Biomol. NMR 41 2008 29 41
    • (2008) J. Biomol. NMR , vol.41 , pp. 29-41
    • Lemak, A.1    Steren, C.A.2    Arrowsmith, C.H.3    Llinas, M.4
  • 44
    • 0030253417 scopus 로고    scopus 로고
    • Prospects for resonance assignments in multidimensional solid state NMR spectra of uniformly labeled proteins
    • R. Tycko Prospects for resonance assignments in multidimensional solid state NMR spectra of uniformly labeled proteins J. Biomol. NMR 8 1996 239 251
    • (1996) J. Biomol. NMR , vol.8 , pp. 239-251
    • Tycko, R.1
  • 45
    • 0346103679 scopus 로고    scopus 로고
    • Rapid protein fold determination using unassigned NMR data
    • J. Meiler, and D. Baker Rapid protein fold determination using unassigned NMR data Proc. Natl. Acad. Sci. U. S. A. 100 2003 15404 15409
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 15404-15409
    • Meiler, J.1    Baker, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.