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ALTENS

Determines the alignment tensor of a molecule based on user-supplied residual dipolar couplings (RDC) and atom coordinates of a single or multiple conformers. The RDCs can be for multiple types of bond vectors and nuclear spin pairs.

Accessibility

The ALTENS module is accessible from the Beta section of the main menu.

Basic Usage

The purpose of the module is determine the molecular alignment tensor using experimental RDC data measured for one or more types of bond vectors (for example, N-H, Cα-Hα, N-C) and nuclear spins (e.g., 1H, 15N, 13C)[1,2]. This analysis can also be used to assess how well the molecular structure agrees with experimental RDC data.

Notes

Screen Shots and Description of Input Fields

This example calculates the alignment tensor and Euler angles of Ubiquitin monomer (1D3Z.pdb) and performs Monte Carlo analysis.

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Example Output

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Results are written to a new directory within the given "run name" as noted in the output. For example, in the figure it is noted that the RDCs, the alignment tensor, and the Euler angles were saved to files within the current project directory within the chosen "run name" directory:

run_0/altens/run_0_00001.txt               -- summary of the ALTENS run
run_0/altens/run_0_average.txt             -- average results over models 
run_0/altens/run_0_out_per_model.txt       -- results of each model  
run_0/altens/run_0_calc_rdc_00001.txt      -- experimental and back-calculated RDC data   
run_0/altens/run_0_calc_rdc_average.txt    -- averaged back-calculated RDC data over models 
run_0/altens/run_0_mc_trajectory_00001.txt -- trajectory of Monte Carlo sampling 
run_0/altens/run_0_mc_per_model.txt        -- Monte Carlo sampling results of each model  

run_0/altens/run_0_single_model_first.html -- html file for users to regenerate plots                                              
run_0/altens/run_0_mc_histogram.html       -- html file for users to regenerate plots 

run_0/altens/run_0_residue_list.txt        -- list of actual resiudes  
run_0/altens/run_0_exclusion_list.txt      -- template to define the exclusion list refinements      

Visualization

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Files Used and Created in Example

Example 1: Refinement using exclusion list file

This example refines the results of the previous run with Ubiquitin monomer (1D3Z.pdb) by excluding residues 75 and 76 located at the flexible C terminus.

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The exclusion list is defined in Ub_exclusion_list.txt as below.

# A N H
75
76

The resulting correlation coefficient = 0.991 and R-factor = 0.089 indicating an improvement in the overall agreement between the experiment and back-calculation.

Visualization

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Files Used and Created in Example

Example 2: Averaging over multiple models/conformers

This example calculates the alignment tensors for 10 conformations of a monomeric protein Ubiquitin (1D3Z_10frames.pdb).

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The figure below is the snapshot of the bottom set of plots provided in the case when the pdb/dcd file input contains multiple models/conformers, resulting in model-dependent outputs.

This figure appears only when the DCD file contains more than one model/conformer. Left panel: plot of the R-factors vs. Correlation coefficients for all the models/conformers analyzed (red circles), as well as their average results over the values of each model/conformer (blue cross).

Middle panel: Eigenvalues of the alignment tensor as a function of model/conformer number. Right panel: Euler angles for the alignment tensor orientation as a function of model/conformer number.

Visualization

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Files Used and Created in Example

Reference(s) and Citations

  1. Structural properties of polyubiquitin chains in solution R. Varadan, O. Walker, C. Pickart, D. Fushman, J. Mol. Biol. 324 637-647 (2002). BIBTex, Endnote, Plain Text
  2. Determining domain orientation in macromolecules by using spin-relaxation and residual dipolar coupling measurements D. Fushman, R. Varadan, M. Assfalg, O.Walker, Progress in NMR Spectroscopy, 44 189-214 (2004). BIBTex, Endnote, Plain Text
  3. R-factor, Free R, and Complete Cross-Validation for Dipolar Coupling Refinement of NMR Structures G. M. Clore, D. S. Garrett, J. Am. Chem. Soc. 121 9008-9012 (1999). BIBTex, Endnote

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