Dipolar Couplings, Chemical Shifts, and Protein Structure
NMRPipe: a Comprehensive Software System for Biomolecular NMR
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Dipolar Couplings, Chemical Shifts, and Protein Structure
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  Frank Delaglio, Ph.D.

   Software Science Consultant
  13840 Grey Colt Drive
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  Tel: 301 806-0867
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  E-mail: delaglio@nmrscience.com

Dipolar Couplings, Chemical Shifts, and Protein Structure

Conventional NMR Structure Data Ubiquitin: Protein Fold Ubiquitin: H-atoms Ubiquitin: Network of H-H Distances 5 Angstroms or Less
C-alpha Vs C-Beta Chemical Shift by Residue Type (TALOS Database) C-alpha Vs C-Beta Secondary Shift by Residue Type (TALOS Database) Ubiquitin: C-Alpha Vs C-Beta Colorized by Secondary Structure C-Alpha and C-Beta Secondary Shift Distributions for Sheet and Helix
TALOS Protein Backbone Residue Triplet TALOS Backbone Angle Prediction: Consensus (good) Result TALOS TALOS Secondary Shift Phi/Psi Surfaces and Backbone Chemical Shift Predictions
Cartoon of Molecule in Bicelle Liquid Crystal Dipolar Coupling: Mathematical Expression and Alignment Tensor Dipolar Coupling: Linear Coefficient Expression, Observed vs SVD Fit Dipolar Coupling: Use of Two Tensors to Reduce Ambiguity
Dipolar Coupling: Sidechain Orientation by Relation to Backbone Dipolar Coupling Stereochemical Analysis: Observed vs Fit for Wrong Model Dipolar Coupling Stereochemical Analysis: Observed vs Fit for Correct Model Dipolar Couplings Can Reveal Structural Details that are Difficult to Characterize from Distances
Refinement of Fold Against HN-N DC: DC Agreement Changes Drastically, Structure Does Not X-Ray Backbone Angles Superimposed on Ideal Geometry Yields Bad Fold Ubiquitin: Backbone Fold Ubiquitin: HN-N Bond Vector Orientations are Not Random or Uniform Ubiquitin: HN-N Bond Vector Orientations are Not Random or Uniform HN-N Bond Vector Orientation Surfaces for Two Proteins are Distinct and Not Uniform
Structure Determination by NMR Homology: Molecular Fragment Replacement (MFR) Ramachandran Trajectory of 7-Residue Fragments from NMR Homology Search MFR Phi/Psi Estimates for Ubiquitin are Mostly Unambiguous Refinement of Crude MFR Starting Structure from Average Phi/Psi MFR Can Estimate Tensor Parameters before Structure is Known MFR Tensor Magnitude Estimates Reveal Dynamics
Three Stage MFR Protocol: Search with Free Tensor, Search with Fixed Tensor, Refine Fragments Protocol for MFR Torsion Forces During Simulated Annealing DYNAMO Simulated Annealing Script DYNAMO Annealing Display for a Gamma-S Refinement with MFR Torsions and Sparse NOEs Results for MFR Structure Determination of Gamma-S Crystallin

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last updated: July 2008 / big frank

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