Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins
Synopsis
An analytical relationship is presented for the estimation of NMR S2 order parameters of N-H vectors of the protein backbone from high-resolution protein structures. The relationship solely depends on close contacts of the peptide plane to the rest of the protein. Application of the relationship to a number of proteins with high-resolution x-ray and NMR structures yields S2 values that are in good agreement with the ones determined from experimental relaxation data.
Equation
where constants a = 0.8 and b = -0.1 and rOi-1,k and rHi,k are the inter-nuclear distances shortened by 1.2 Å.
Paper
F. Zhang and R. Brüschweiler (2002) "Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins" J. Am. Chem. Soc. 124(43), 12654-12655.
Click here to download the PDF file and supporting information.
Software
Download s2predict.py
The following implementation of the above equation uses the programming language Python together with the Molecular Modeling Toolkit (MMTK) by Hinsen [1]. To run the program, you need Python, MMTK, ScientificPython, and Numpy installed on your computer. The program was tested using Python-2.2, MMTK-2.2, ScientificPython-2.4.1, and Numpy-21.3.
To run the program type "./s2predict.py pdbfile s2file outfile" or "python2 s2predict.py pdbfile s2file outfile". It takes a PDB file and a S2-order parameter file as input and writes the result to outfile. If S2-order parameters are not available, one can create (e.g. by hand) a dummy file with non-zero S2 values with the same format as the file ubq.s2.dummy . For PDB files that contain proton coordinates, it is useful to remove all protons first and have them subsequently added in standard positions by the program using MMTK. Note: For multiple chain proteins (for example HIV protease described in the paper), the program needs to be modified (create additional chains and loop over them to add their heavy atoms to the atom list).
Examples for Ubiquitin
Click the links for NMR structure (1st structure in 1D3Z [2]), x-ray structure (1UBQ [3]), experimental 1-S2 data [4], and a dummy 1-S2 input file.
Here is an output from "./s2predict.py ubq.xray.pdb ubq.s2 ubq.out".
Acknowledgement
This material is based upon work supported by the National Science Foundation under Grant No. MCB-0211512.
References
[1] K. Hinsen, J. Comp. Chem. 21, 79-85 (2000).
[2] G. Cornilescu, J. L. Marquardt, M. Ottiger, and A. Bax, J. Am. Chem. Soc. 120, 6836-6837 (1998).
[3] S. Vijay-Kumar, C. E. Bugg, and W. J. Cook, J. Mol. Biol. 194, 531-544 (1987).
[4] S. F. Lienin, T. Bremi, B. Brutscher, R. Brüschweiler, and R. R. Ernst, J. Am. Chem. Soc. 120, 9870-9879 (1998).
Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins
Synopsis
An analytical relationship is presented for the estimation of NMR S2 order parameters of N-H vectors of the protein backbone from high-resolution protein structures. The relationship solely depends on close contacts of the peptide plane to the rest of the protein. Application of the relationship to a number of proteins with high-resolution x-ray and NMR structures yields S2 values that are in good agreement with the ones determined from experimental relaxation data.Equation
Paper
-
F. Zhang and R. Brüschweiler (2002) "Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins" J. Am. Chem. Soc. 124(43), 12654-12655.
Click here to download the PDF file and supporting information.
Software
-
Download s2predict.py
The following implementation of the above equation uses the programming language Python together with the Molecular Modeling Toolkit (MMTK) by Hinsen [1]. To run the program, you need Python, MMTK, ScientificPython, and Numpy installed on your computer. The program was tested using Python-2.2, MMTK-2.2, ScientificPython-2.4.1, and Numpy-21.3.
To run the program type "./s2predict.py pdbfile s2file outfile" or "python2 s2predict.py pdbfile s2file outfile". It takes a PDB file and a S2-order parameter file as input and writes the result to outfile. If S2-order parameters are not available, one can create (e.g. by hand) a dummy file with non-zero S2 values with the same format as the file ubq.s2.dummy . For PDB files that contain proton coordinates, it is useful to remove all protons first and have them subsequently added in standard positions by the program using MMTK. Note: For multiple chain proteins (for example HIV protease described in the paper), the program needs to be modified (create additional chains and loop over them to add their heavy atoms to the atom list).
Examples for Ubiquitin
-
Click the links for NMR structure (1st structure in 1D3Z [2]), x-ray structure (1UBQ [3]), experimental 1-S2 data [4], and a dummy 1-S2 input file.
Here is an output from "./s2predict.py ubq.xray.pdb ubq.s2 ubq.out".
Acknowledgement
This material is based upon work supported by the National Science Foundation under Grant No. MCB-0211512.References
[1] K. Hinsen, J. Comp. Chem. 21, 79-85 (2000).[2] G. Cornilescu, J. L. Marquardt, M. Ottiger, and A. Bax, J. Am. Chem. Soc. 120, 6836-6837 (1998).
[3] S. Vijay-Kumar, C. E. Bugg, and W. J. Cook, J. Mol. Biol. 194, 531-544 (1987).
[4] S. F. Lienin, T. Bremi, B. Brutscher, R. Brüschweiler, and R. R. Ernst, J. Am. Chem. Soc. 120, 9870-9879 (1998).