Abstract A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information. Applied to two small proteins, the approach yielded structures that coincided closely with conventionally determined structures.
Content Type Journal Article
Pages 1-10
DOI 10.1007/s10858-011-9502-8
Authors
Teppei Ikeya, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
Jun-Goo Jee, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
Yoshiki Shigemitsu, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
Junpei Hamatsu, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
Masaki Mishima, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
Yutaka Ito, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
Masatsune Kainosho, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan
Peter Güntert, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
J Biomol NMR. 2011 Mar 30;
Authors: Ikeya T, Jee JG, Shigemitsu Y, Hamatsu J, Mishima M, Ito Y, Kainosho M, Güntert P
A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information....
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03-31-2011 06:24 PM
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
J Comput Biol. 2011 Mar;18(3):347-63
Authors: Jang R, Gao X, Li M
Abstract In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow...
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03-10-2011 03:51 PM
[NMR paper] Protein NMR structure determination with automated NOE-identification in the NOESY sp
Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.
Related Articles Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.
J Biomol NMR. 2002 Nov;24(3):171-89
Authors: Herrmann T, Güntert P, Wüthrich K
Novel algorithms are presented for automated NOESY peak picking and NOE signal identification in homonuclear 2D and heteronuclear-resolved 3D -NOESY spectra during de novo protein structure determination by NMR,...
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11-24-2010 08:58 PM
[NMR paper] Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
Related Articles Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
J Biomol NMR. 2002 Aug;23(4):271-87
Authors: Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR
Automated assignment of NOESY spectra is a prerequisite for automated structure determination of biological macromolecules. With the program KNOWNOE we present a novel, knowledge based approach to this problem. KNOWNOE...
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11-24-2010 08:58 PM
[NMR paper] Protein NMR structure determination with automated NOE assignment using the new softw
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.
Related Articles Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.
J Mol Biol. 2002 May 24;319(1):209-27
Authors: Herrmann T, Güntert P, Wüthrich K
Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated...
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11-24-2010 08:49 PM
[NMR paper] The NOESY jigsaw: automated protein secondary structure and main-chain assignment fro
The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data.
Related Articles The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data.
J Comput Biol. 2000;7(3-4):537-58
Authors: Bailey-Kellogg C, Widge A, Kelley JJ, Berardi MJ, Bushweller JH, Donald BR
High-throughput, data-directed computational protocols for Structural Genomics (or Proteomics) are required in order to evaluate the protein products of genes for structure and...
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11-18-2010 09:15 PM
[NMR paper] Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain
Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment.
Related Articles Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment.
J Chem Inf Comput Sci. 1997 May-Jun;37(3):467-77
Authors: Li KB, Sanctuary BC
A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures...
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08-22-2010 03:31 PM
Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D [1H,1H]-NOESY
Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D -NOESY
Francesco Fiorito, Torsten Herrmann, Fred F. Damberger and Kurt Wüthrich
Journal of Biomolecular NMR; 2008; 42(1); pp 23-33
Abstract
ASCAN is a new algorithm for automatic sequence-specific NMR assignment of amino acid side-chains in proteins, which uses as input the primary structure of the protein, chemical shift lists of 1HN, 15N, 13Cα, 13Cβ and possibly 1Hα from the previous polypeptide backbone assignment, and one or several 3D 13C- or 15N-resolved -NOESY spectra. ASCAN has also been...
Exclusively NOESY-based automated NMR assignment and structure determination of proteins
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