PAIN: Program for Analysis of Internal motion
An Application to MD Simulated Motions of Major Urinary Protein-I


P. Novák1, P. Macek1, L.Žídek1, V.Sklenář1


1NCBR, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37


Trajectories from the molecular dynamics (MD) simulations of proteins contain wealth of information. From the MD trajectory not only coordinates of all atoms are available, but also their change in course of time as the molecule is varying its position and conformation. Therefore, motional parameters can be extracted from MD trajectories if the proper tools do exist. For this purpose the program PAIN (Program for Analysis of Internal motioN) was written.  Some key features implemented in PAIN up to date are calculation of the :

            * correlation function of the interatomic vectors

            * generalized order parameter

            * frequency dependent generalized order parameter

            * conformation-dependent generalized order parameter

            * spatial distribution of the interatomic vector orientations

            * histogram of the dihedral angle distribution

               (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[1]. The calculated order parameters S2 for a free- and ligand-bound protein supply evidence that mobility in various regions of MUP-I can be directly related to small conformational changes of the free- and complexed protein resulting from modifications of the hydrogen bonding network.


1.     P. Macek, P. Novák, H. Křížová, L. Žídek, V. Sklenář, FEBS Letters, in press.




This work was supported by the Grant MSM0021622413 of the Ministry of Education of the Czech Republic. We are indebted to Zdenek Kříž and Petr Kulhánek for helpful suggestions and computational assistance.