Publication date: June–August 2018 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volumes 106–107
Author(s): Santrupti Nerli, Andrew C. McShan, Nikolaos G. Sgourakis
Chemical shifts are highly sensitive probes harnessed by NMR spectroscopists and structural biologists as conformational parameters to characterize a range of biological molecules. Traditionally, assignment of chemical shifts has been a labor-intensive process requiring numerous samples and a suite of multidimensional experiments. Over the past two decades, the development of complementary computational approaches has bolstered the analysis, interpretation and utilization of chemical shifts for elucidation of high resolution protein and nucleic acid structures. Here, we review the development and application of chemical shift-based methods for structure determination with a focus on ab initio fragment assembly, comparative modeling, oligomeric systems, and automated assignment methods. Throughout our discussion, we point out practical uses, as well as advantages and caveats, of using chemical shifts in structure modeling. We additionally highlight (i) hybrid methods that employ chemical shifts with other types of NMR restraints (residual dipolar couplings, paramagnetic relaxation enhancements and pseudocontact shifts) that allow for improved accuracy and resolution of generated 3D structures, (ii) the utilization of chemical shifts to model the structures of sparsely populated excited states, and (iii) modeling of sidechain conformations. Finally, we briefly discuss the advantages of contemporary methods that employ sparse NMR data recorded using site-specific isotope labeling schemes for chemical shift-driven structure determination of larger molecules. With this review, we aim to emphasize the accessibility and versatility of chemical shifts for structure determination of challenging biological systems, and to point out emerging areas of development that lead us towards the next generation of tools. Graphical abstract
Rapid and reliable protein structure determination via chemical shift threading
Rapid and reliable protein structure determination via chemical shift threading
Abstract
Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to...
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12-01-2017 08:23 AM
PPM_One: a static protein structure based chemical shift predictor
PPM_One: a static protein structure based chemical shift predictor
Abstract
We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM_One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to...
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06-21-2015 07:25 AM
[NMR paper] Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction.
Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction.
J Magn Reson. 2015 Mar 7;254:93-97
Authors: Li DW, Meng D, Brüschweiler R
Abstract
A robust NMR resonance assignment method...
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04-13-2015 09:11 PM
[NMR paper] Reliable Resonance Assignments of Selected Residues of Proteins with Known Structure Based on Empirical NMR Chemical Shift Prediction
Reliable Resonance Assignments of Selected Residues of Proteins with Known Structure Based on Empirical NMR Chemical Shift Prediction
Publication date: Available online 7 March 2015
Source:Journal of Magnetic Resonance</br>
Author(s): Da-Wei Li , Dan Meng , Rafael Brüschweiler</br>
A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins....
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03-08-2015 01:07 AM
[NMR paper] Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Phys Chem Chem Phys. 2014 Jul 23;
Authors: Zhu T, Zhang JZ, He X
Abstract
In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated...
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07-24-2014 11:56 AM
[NMR paper] An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
Related Articles An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
J Biomol NMR. 2014 Jun 19;
Authors: Wiedemann C, Bellstedt P, Herbst C, Görlach M, Ramachandran R
Abstract
A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential data acquisition for moderately sized...
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06-20-2014 08:14 PM
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction
Abstract
A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential \(^{1}\hbox {H}\) data acquisition for moderately sized proteins is presented. The suitability of the approach for obtaining sequential resonance assignments, including complete ...
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06-19-2014 10:21 PM
[NMR paper] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
J Biomol NMR. 2013 Apr 28;
Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M
Abstract
We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
Chemical shift-based methods in NMR structure determination
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