NEW TOOLS FOR AN ANALYSIS OF EXPERIMENTAL (NMR) AND THEORETICAL (MD) DATA
| Authors | |
|---|---|
| Year of publication | 2005 |
| Type | Article in Proceedings |
| Conference | Konference mladých vědeckých pracovníků "Strukturní biofyzika makromolekul" |
| MU Faculty or unit | |
| Citation | |
| Field | Biochemistry |
| Keywords | S3EPY; MD; RDC; PAIN; |
| Description | Once experiments or simulations are started one obtains a large amount of data which should be analyzed to get the desirable results. This is a fairly good reason for everlasting development of the new tools for the data analysis. Two major topics are covered by this work. Residual dipolar couplings (RDC) are measured as the difference of the scalar couplings in an isotropic and weakly aligned sample. In order to determine even the small scalar couplings (in the range of units or tens of Hertz), it is necessary to measure very sophisticated spin-state-selective E.COSY type experiments (1). The disadvantage of this approach is a tedious, error prone and complicated manipulation with the lots of spectra and with the large amount of data. To make this process as fast and fool-proof as possible, an S3E.py program was written. This is a Python extension of the program Sparky (2) commonly used for the graphical assignment and integration of the NMR spectra. Program has graphical users interface and is able to: * convert and process the spectra, * assign series of the spectra, * fit peaks and read precisely peak positions, * plot the graphs of the measured and theoretical peaks' displacements * fit dependencies and calculate real values of the small couplings Program was tested on and used for extract values of the small scalar couplings from the S3E type experiments measured on the molecule of ISL U6 RNA from Trypanosoma. Trajectories from the molecular dynamics (MD) simulations of the proteins contain wealth of data. From the MD trajectory not only coordinates of all atoms are known, but also their change in course of time as the molecule is position and conformation. That means possibility of extracting motional parameters if the proper tools do exist. For this purpose the program PAIN (Program for Analysis of Internal motioN) was written. It is written in C language so the analysis compared to the amount of data is fairly fast and it should be rather easily portable on the majority of the current platforms. Some key features implemented in PAIN up to date are calculation of the : * correlation function of the vector * generalized order parameter * frequency dependent generalized order parameter * conformation dependent generalized order parameter * spatial distribution of the internuclear vector orientations * histogram of the dihedral angle (including number of modes and distribution parameters estimation) * conformation transitions analysis Program was tested on and used for an analysis of the MD simulation of the mouse Major Urinary Protein-I in an explicit solvent. |
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