scholarly journals How to Lift Chemical Shift Degeneracy for Sequential Resonance Assignments of Intrinsically Disordered Proteins in 3D NMR Spectra

2016 ◽  
Vol 56 (1) ◽  
pp. 040-043
Author(s):  
Yuichi YOSHIMURA
Keyword(s):  
Chemical Shift ◽  
Nmr Spectra ◽  
Intrinsically Disordered Proteins ◽  
Resonance Assignments ◽  
Disordered Proteins ◽  
3D Nmr ◽  
Intrinsically Disordered ◽  
Chemical Shift Degeneracy

Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins

2013 ◽  
Vol 55 (3) ◽  
pp. 231-237 ◽  
Author(s):  
Wolfgang Bermel ◽  
Marta Bruix ◽  
Isabella C. Felli ◽  
Vasantha Kumar M. V. ◽  
Roberta Pierattelli ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Nmr Spectra ◽  
Intrinsically Disordered Proteins ◽  
Multidimensional Nmr ◽  
Disordered Proteins ◽  
Intrinsically Disordered

scholarly journals Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range

2019 ◽  
Vol 73 (12) ◽  
pp. 713-725 ◽  
Author(s):  
Ruth Hendus-Altenburger ◽  
Catarina B. Fernandes ◽  
Katrine Bugge ◽  
Micha B. A. Kunze ◽  
Wouter Boomsma ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Random Coil ◽  
Disordered Proteins ◽  
Phosphoryl Group ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Secondary Chemical

Abstract Phosphorylation is one of the main regulators of cellular signaling typically occurring in flexible parts of folded proteins and in intrinsically disordered regions. It can have distinct effects on the chemical environment as well as on the structural properties near the modification site. Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins (IDPs) and the reliability of the analysis depends on an appropriate choice of random coil model. Random coil chemical shifts and sequence correction factors were previously determined for an Ac-QQXQQ-NH2-peptide series with X being any of the 20 common amino acids. However, a matching dataset on the phosphorylated states has so far only been incompletely determined or determined only at a single pH value. Here we extend the database by the addition of the random coil chemical shifts of the phosphorylated states of serine, threonine and tyrosine measured over a range of pH values covering the pKas of the phosphates and at several temperatures (www.bio.ku.dk/sbinlab/randomcoil). The combined results allow for accurate random coil chemical shift determination of phosphorylated regions at any pH and temperature, minimizing systematic biases of the secondary chemical shifts. Comparison of chemical shifts using random coil sets with and without inclusion of the phosphoryl group, revealed under/over estimations of helicity of up to 33%. The expanded set of random coil values will improve the reliability in detection and quantification of transient secondary structure in phosphorylation-modified IDPs.

Incorporating 1H chemical shift determination into 13C-direct detected spectroscopy of intrinsically disordered proteins in solution

2009 ◽  
Vol 200 (2) ◽  
pp. 354-358 ◽  
Author(s):  
Bernie O’Hare ◽  
Alan J. Benesi ◽  
Scott A. Showalter
Keyword(s):  
Chemical Shift ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered

Rapid NMR assignments of intrinsically disordered proteins using two-dimensional13C-detection based experiments

2019 ◽  
Vol 55 (54) ◽  
pp. 7820-7823
Author(s):  
Sujeesh Sukumaran ◽  
Shahid A. Malik ◽  
Shankararama Sharma R. ◽  
Kousik Chandra ◽  
Hanudatta S. Atreya
Keyword(s):  
Amino Acid ◽  
Intrinsically Disordered Proteins ◽  
Nmr Assignments ◽  
Resonance Assignments ◽  
Disordered Proteins ◽  
Intrinsically Disordered

An approach for rapid resonance assignments in proteins based on 2D13C-detected NMR experiments combined with amino acid selective unlabeling.

scholarly journals DEEP picker is a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Da-Wei Li ◽  
Alexandar L. Hansen ◽  
Chunhua Yuan ◽  
Lei Bruschweiler-Li ◽  
Rafael Brüschweiler
Keyword(s):  
Neural Network ◽  
Nmr Spectra ◽  
Deep Neural Network ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Two Dimensional ◽  
Molecular Systems ◽  
Intrinsically Disordered ◽  
Identification And Characterization

AbstractThe analysis of nuclear magnetic resonance (NMR) spectra for the comprehensive and unambiguous identification and characterization of peaks is a difficult, but critically important step in all NMR analyses of complex biological molecular systems. Here, we introduce DEEP Picker, a deep neural network (DNN)-based approach for peak picking and spectral deconvolution which semi-automates the analysis of two-dimensional NMR spectra. DEEP Picker includes 8 hidden convolutional layers and was trained on a large number of synthetic spectra of known composition with variable degrees of crowdedness. We show that our method is able to correctly identify overlapping peaks, including ones that are challenging for expert spectroscopists and existing computational methods alike. We demonstrate the utility of DEEP Picker on NMR spectra of folded and intrinsically disordered proteins as well as a complex metabolomics mixture, and show how it provides access to valuable NMR information. DEEP Picker should facilitate the semi-automation and standardization of protocols for better consistency and sharing of results within the scientific community.

scholarly journals MD Simulations of Intrinsically Disordered Proteins with Replica-Averaged Chemical Shift Restraints

2014 ◽  
Vol 106 (2) ◽  
pp. 481a ◽  
Author(s):  
Biao Fu ◽  
Predrag Kukic ◽  
Carlo Camilloni ◽  
Michele Vendruscolo
Keyword(s):  
Chemical Shift ◽  
Intrinsically Disordered Proteins ◽  
Md Simulations ◽  
Disordered Proteins ◽  
Intrinsically Disordered

scholarly journals Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data

2016 ◽  
Vol 23 (5) ◽  
pp. 300-310 ◽  
Author(s):  
Huichao Gong ◽  
Sai Zhang ◽  
Jiangdian Wang ◽  
Haipeng Gong ◽  
Jianyang Zeng
Keyword(s):  
Chemical Shift ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Chemical Shift Data ◽  
Shift Data
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