Related ArticlesAn AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.
J Biomol NMR. 2005 Sep;33(1):15-24
Authors: Craft JW, Legge GB
Protein structure determination using Nuclear Magnetic Resonance (NMR) requires the use of molecular dynamics programs that incorporate both NMR experimental and implicit atomic data. Atomic parameters for each amino acid type are encoded in libraries used by structure calculation programs such as DYANA and AMBER. However, only a few non-standard amino acid library sets are included in these programs or the molecular visualization program MOLMOL. Our laboratory is calculating the phosphorylated and non-phosphorylated states of peptides and proteins using NMR methods. To calculate chemically correct structures, we have extended the available molecular libraries for these programs to include the modified amino acids phosphoserine, phosphothreonine, and phosphotyrosine.
An efficient protocol for incorporation of an unnatural amino acid in perdeuterated recombinant proteins using glucose-based media
An efficient protocol for incorporation of an unnatural amino acid in perdeuterated recombinant proteins using glucose-based media
Abstract The in vivo incorporation of unnatural amino acids into proteins is a well-established technique requiring an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is incorporated at a position encoded by a TAG amber codon. Although this technology provides unique opportunities to engineer protein structures, poor protein yields are usually obtained in deuterated media, hampering its application in the protein NMR...
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02-21-2012 03:40 AM
Hydrogen exchange during cell-free incorporation of deuterated amino acids and an approach to its inhibition
Hydrogen exchange during cell-free incorporation of deuterated amino acids and an approach to its inhibition
Abstract Perdeuteration, selective deuteration, and stereo array isotope labeling (SAIL) are valuable strategies for NMR studies of larger proteins and membrane proteins. To minimize scrambling of the label, it is best to use cell-free methods to prepare selectively labeled proteins. However, when proteins are prepared from deuterated amino acids by cell-free translation in H2O, exchange reactions can lead to contamination of 2H sites by 1H from the solvent. Examination of a...
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10-10-2011 06:27 AM
Elucidating metabolic pathways for amino acid incorporation into dragline spider silk using 13C enrichment and solid state NMR.
Elucidating metabolic pathways for amino acid incorporation into dragline spider silk using 13C enrichment and solid state NMR.
Elucidating metabolic pathways for amino acid incorporation into dragline spider silk using 13C enrichment and solid state NMR.
Comp Biochem Physiol A Mol Integr Physiol. 2011 Jul;159(3):219-24
Authors: Creager MS, Izdebski T, Brooks AE, Lewis RV
Abstract
Spider silk has been evolutionarily optimized for contextual mechanical performance over the last 400 Ma. Despite precisely balanced mechanical properties,...
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09-02-2011 05:40 PM
A Grid-enabled web portal for NMR structure refinement with AMBER.
A Grid-enabled web portal for NMR structure refinement with AMBER.
A Grid-enabled web portal for NMR structure refinement with AMBER.
Bioinformatics. 2011 Jul 14;
Authors: Bertini I, Case DA, Ferella L, Giachetti A, Rosato A
MOTIVATION: The typical workflow for NMR structure determination involves collecting thousands of conformational restraints, calculating a bundle of 20-40 conformers in agreement with them and refining the energetics of these conformers. The structure calculation step employs simulated annealing based on molecular dynamics...
[NMR paper] Phosphorylated amino acids: model compounds for solid-state 31P NMR spectroscopic stu
Phosphorylated amino acids: model compounds for solid-state 31P NMR spectroscopic studies of proteins.
Related Articles Phosphorylated amino acids: model compounds for solid-state 31P NMR spectroscopic studies of proteins.
Magn Reson Chem. 2004 Apr;42(4):369-72
Authors: Iuga A, Brunner E
Solid-state 31P NMR spectroscopy was applied to measure the isotropic chemical shifts, chemical shift anisotropies and asymmetry parameters of three phosphorylated amino acids, O-phospho-L-serine, O-phospho-L-threonine and O-phospho-L-tyrosine. The...
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11-24-2010 09:51 PM
[NMR paper] Torsion angle dynamics for NMR structure calculation with the new program DYANA.
Torsion angle dynamics for NMR structure calculation with the new program DYANA.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Torsion angle dynamics for NMR structure calculation with the new program DYANA.
J Mol Biol. 1997 Oct 17;273(1):283-98
Authors: Güntert P, Mumenthaler C, Wüthrich K
The new program DYANA (DYnamics Algorithm for Nmr Applications) for efficient calculation of three-dimensional protein and nucleic acid structures from distance constraints and...
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08-22-2010 05:08 PM
[NMR paper] Determinants of protein hyperthermostability: purification and amino acid sequence of
Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR.
Related Articles Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR.
Biochemistry. 1991 Nov 12;30(45):10885-95
Authors: Blake PR, Park JB, Bryant FO, Aono S, Magnuson JK, Eccleston E, Howard...
An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.
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