Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [1H,15N]-HSQC-NOESY-[1H,15N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73â??82Â*%) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95Â*% of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzymeÂ*I. The program including source code is available at https://github.com/thomasexner/4Dassign.
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules
Abstract
We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poissonâ??Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation...
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08-02-2015 07:10 AM
[NMR paper] Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Related Articles Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Adv Exp Med Biol. 2015;827:49-70
Authors: Zhu T, Zhang JZ, He X
Abstract
The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the...
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11-14-2014 08:33 AM
Structure-based prediction of methyl chemical shifts in proteins
Structure-based prediction of methyl chemical shifts in proteins
Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...
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07-15-2011 09:10 PM
Exclusively NOESY-based automated NMR assignment and structure determination of proteins
Exclusively NOESY-based automated NMR assignment and structure determination of proteins
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
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04-01-2011 09:31 PM
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] 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...
Automated assignment of NMR chemical shifts based on a known structure and 4D spectra
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