Studies of the macromolecular structure, dynamics and function in solution

Experimental and theoretical studies of biomolecular structure and function.

People involved
Jan Antosiewicz
Elżbieta Bojarska
Maciej Długosz

Collaboration with (in Department of Biophysics)
Agnieszka Bzowska
Edward Darżynkiewicz
Bogdan Lesyng
Ryszard Stolarski

Keywords
mechanism of receptor ligand recognition
relaxation methods
molecular dynamics, brownian dynamics
molecular electrostatics

Research interests

A. Electrostatic interactions in the mechanism of receptor-ligand recognition

It is generally recognized that electrostatic interactions constitute one of the most important determinants of binding affinity between ligands and their target receptors. Ionizable groups in biomolecules represent a dominant contribution to the electrostatic potential around these molecules. Their charge state depends on pH and as a result ligand-receptor interactions show some degree of pH-dependence. Moreover electrostatic interactions manifest themselves by dependence of kinetics and thermodynamics of binding on the ionic strength of the surrounding aqueous solvent.

We study significance of electrostatic interactions in receptor-ligand recognition by combined experimental and theoretical approach, involving spectroscopic (UV-VIS absorption and fluorescence) and transient kinetic methods (stopped-flow), on the one hand, and computer simulation methods (molecular electrostatics based on the Poisson-Boltzmann model of the solute-solvent system, brownian dynamics, molecular dynamics) on the other hand.

Currently we investigate two systems: eukaryotic initiation factor eIF4E and analogs of 5'-end of mRNA, and purine nucleoside phosphorylase with analogs of guanine nucleoside.

B. Protonation equilibria impact on biomolecular structure and function

One of the important determinants of protein structure and function is related to the ability of side groups of some of its constituting amino acids to exchange protons with the environment. There are numerous experimental evidences that protein's structure and dynamics are sensitive to protonation states of side groups of its titratable amino acids, mainly by observing pH dependence of experimental results. Yet, in molecular simulations, the effect of the pH on protein's structure is still treated in a simplified way: depending on the selected pH and on the approximate pKa of a given ionizable group, either the protonated or the unprotonated state is selected and used for the whole simulation. However, it seems that inclusion of explicit proton exchange in molecular simulation is necessary for obtaining physically sound picture of molecular mechanisms behind protein functioning, Ultimately, such algorithms for constant pH simulations should become a routine tool in molecular simulations, just as are constant temperature and constant pressure algorithms, and certainly they will find numerous useful applications to the study of biologically relevant problems. This project represents our contribution to development of algorithms for such simulations.

Currently we are working on an algorithm where explicit titration, based on the Poisson-Boltzmann model of solute-solvent system, is coupled to generation of protein structures by Molecular Dynamics simulations with implicit solvent. Our algorithm is applied to a short peptide derived from OMTKY3, acetyl-Ser-Asp-Asn-Lys-Thr-Tyr-Gly-amide which has interesting titration properties and is small enough to allow extensive testing of different variants of simulation protocols.

Selected publications

  1. J. Antosiewicz, E. Blachut-Okrasinska, T. Grycuk, J. M. Briggs, S. T. Wlodek, B. Lesyng, and J. A. McCammon, Prediction of pKas of titratable residues in proteins using a Poisson-Boltzmann model of the solute-solvent system, in "Algorithms for Molecular Modelling," P. Deuflhard, J. Hermans, B. Leimkuehler, A. Mark, R.D. Skeel, S. Reich, Eds., (Lecture Notes Comp. Sci. & Engn., 4:176-196 (1999))
  2. E. Blachut-Okrasinska, B. Lesyng, J. M. Briggs, J. A. McCammon and J. M. Antosiewicz, The Poisson-Boltzmann model studies of molecular electrostatic properties of protein kinases, Eur. Biophys. J., 28:457-467 (1999)
  3. J. Antosiewicz, E. Blachut-Okrasinska, T. Grycuk, and B. Lesyng, A correlation between protonation equilibria in biomolecular systems and their shapes: Studies using a Poisson-Boltzmann Model, in "Free Boundary Problems: Theory and Applications", N. Kenmochi, Editor, (GAKUTO International Series, Mathematical Sciences and Applications, 14:11-17 (2000))
  4. E. Blachut-Okrasinska, E. Bojarska, L. Chlebicka, A. Niedzwiecka-Kornas, E. Darzynkiewicz, R. Stolarski, J. Stepinski, and J. M. Antosiewicz, Stopped-flow and brownian dynamics studies of electrostatic effects in the kinetics of binding of 7-methyl-GpppG to the protein eIF4E, Eur. Biophys. J., 29:487-498 (2000)
  5. M. Dlugosz, E. Bojarska, and J. M. Antosiewicz, A procedure for analysis of stopped-flow transients for protein-ligand association, J. Biochem. Biophys. Methods, 51:179-193 (2002)
  6. A. M. Walczak and J. M. Antosiewicz, Langevin dynamics of proteins at constant pH, Phys. Rev. E, vol. 66 051911/1-8 (2002)
  7. M. Dlugosz, E. Blachut-Okrasinska, E. Bojarska, E. Darzynkiewicz, and J. M. Antosiewicz, Effects of pH in the kinetics of binding of mRNA-cap analogs by translation initiation factor eIF4E, Eur. Biophys. J., vol. 31, 608-616 (2003)