Related ArticlesNMR assignments of sparsely labeled proteins using a genetic algorithm.
J Biomol NMR. 2017 Mar 13;:
Authors: Gao Q, Chalmers GR, Moremen KW, Prestegard JH
Abstract
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid ((15)N or (13)C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in heteronuclear single quantum coherence (HSQC) spectra is challenging. We present an alternative strategy which combines readily accessible NMR data with known protein domain structures. Based on the structures, chemical shifts are predicted, NOE cross-peak lists are generated, and residual dipolar couplings (RDCs) are calculated for each labeled site. Simulated data are then compared to measured values for a trial set of assignments and scored. A genetic algorithm uses the scores to search for an optimal pairing of HSQC crosspeaks with labeled sites. While none of the individual data types can give a definitive assignment for a particular site, their combination can in most cases. Four test proteins previously assigned using triple resonance methods and a sparsely labeled glycosylated protein, Robo1, previously assigned by manual analysis, are used to validate the method and develop a criterion for identifying sites assigned with high confidence.
PMID: 28289927 [PubMed - as supplied by publisher]
NMR assignments of sparsely labeled proteins using a genetic algorithm
NMR assignments of sparsely labeled proteins using a genetic algorithm
Abstract
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid (15N or 13C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in...
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03-14-2017 10:36 PM
Genetic Algorithm Optimized Triply Compensated Pulses in NMR Spectroscopy
Genetic Algorithm Optimized Triply Compensated Pulses in NMR Spectroscopy
Publication date: Available online 28 September 2015
Source:Journal of Magnetic Resonance</br>
Author(s): V.S. Manu, Gianluigi Veglia</br>
Sensitivity and resolution in NMR experiments are affected by magnetic field inhomogeneities (of both external and RF), errors in pulse calibration, and offset effects due to finite length of RF pulses. To remedy these problems, built-in compensation mechanisms for these experimental imperfections are often necessary. Here, we propose a new family of...
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09-29-2015 07:59 AM
[NMR paper] On the problem of resonance assignments in solid state NMR of uniformly (15)N,(13)C-labeled proteins.
On the problem of resonance assignments in solid state NMR of uniformly (15)N,(13)C-labeled proteins.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif On the problem of resonance assignments in solid state NMR of uniformly (15)N,(13)C-labeled proteins.
J Magn Reson. 2015 Apr;253:166-72
Authors: Tycko R
Abstract
Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in...
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03-24-2015 09:58 PM
On the problem of resonance assignments in solid state NMR of uniformly 15N,13C-labeled proteins
On the problem of resonance assignments in solid state NMR of uniformly 15N,13C-labeled proteins
Publication date: April 2015
Source:Journal of Magnetic Resonance, Volume 253</br>
Author(s): Robert Tycko</br>
Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated...
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03-20-2015 01:48 AM
[NMR paper] Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.
Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.
Related Articles Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.
J Biomol NMR. 2013 Oct 17;
Authors: Yang Y, Fritzsching KJ, Hong M
Abstract
A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths,...
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10-18-2013 06:23 PM
A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers
A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers
Abstract We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly 15N,13C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes...
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06-30-2011 05:01 AM
[NMR paper] GANA--a genetic algorithm for NMR backbone resonance assignment.
GANA--a genetic algorithm for NMR backbone resonance assignment.
Related Articles GANA--a genetic algorithm for NMR backbone resonance assignment.
Nucleic Acids Res. 2005;33(14):4593-601
Authors: Lin HN, Wu KP, Chang JM, Sung TY, Hsu WL
NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic algorithm to automatically perform backbone resonance assignment with a high degree of precision and recall....
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11-24-2010 11:14 PM
[NMR paper] GENFOLD: a genetic algorithm for folding protein structures using NMR restraints.
GENFOLD: a genetic algorithm for folding protein structures using NMR restraints.
Related Articles GENFOLD: a genetic algorithm for folding protein structures using NMR restraints.
Protein Sci. 1998 Feb;7(2):491-9
Authors: Bayley MJ, Jones G, Willett P, Williamson MP
We report the development and validation of the program GENFOLD, a genetic algorithm that calculates protein structures using restraints obtained from NMR, such as distances derived from nuclear Overhauser effects, and dihedral angles derived from coupling constants. The program...
NMR assignments of sparsely labeled proteins using a genetic algorithm.
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