Secondary structure of ?-hydroxydecanoyl thiol ester dehydrase, a 39-kDa protein, derived from H?, C?, C? and CO signal assignments and the Chemical Shift Index: Comparison with the crystal structure

1996 ◽  
Vol 7 (4) ◽  
Author(s):  
Val�rie Copi� ◽  
JohnA. Battles ◽  
JohnM. Schwab ◽  
DennisA. Torchia
Keyword(s):  
Crystal Structure ◽  
Chemical Shift ◽  
Secondary Structure ◽  
Chemical Shift Index ◽  
Thiol Ester ◽  
Index Comparison

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.

scholarly journals A Bayesian approach to NMR crystal structure determination

2019 ◽  
Vol 21 (42) ◽  
pp. 23385-23400 ◽  
Author(s):  
Edgar A. Engel ◽  
Andrea Anelli ◽  
Albert Hofstetter ◽  
Federico Paruzzo ◽  
Lyndon Emsley ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Chemical Shift ◽  
Bayesian Approach ◽  
Structure Determination ◽  
Bayesian Framework ◽  
Crystal Structure Determination ◽  
Structure Determinations

We introduce a Bayesian framework for quantifying the reliability of structure determinations for powdered samples on the basis of NMR experiments and chemical shift predictions (with uncertainties) for a pool of candidate structures.

VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy

2011 ◽  
Vol 52 (1) ◽  
pp. 41-56 ◽  
Author(s):  
Michael C. Brothers ◽  
Anna E. Nesbitt ◽  
Michael J. Hallock ◽  
Sanjeewa G. Rupasinghe ◽  
Ming Tang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Chemical Shift ◽  
Secondary Structure ◽  
Homology Model ◽  
Secondary Structure Information ◽  
Model Accuracy ◽  
Structure Information
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