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Jak lepiej zrozumieć strukturę i funkcje złożonych układów biomolekularnych ? Bogdan Lesyng ICM and Wydział Fizyki, Uniwersytet Warszawski (

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Presentation on theme: "Jak lepiej zrozumieć strukturę i funkcje złożonych układów biomolekularnych ? Bogdan Lesyng ICM and Wydział Fizyki, Uniwersytet Warszawski ("— Presentation transcript:

1 Jak lepiej zrozumieć strukturę i funkcje złożonych układów biomolekularnych ? Bogdan Lesyng ICM and Wydział Fizyki, Uniwersytet Warszawski ( oraz European Centre of Excellence for Multiscale Biomolecular Modelling, Bioinformatics and Applications ( Warsztaty z bioinformatyki-SGGW 3/06/2005

2 Dynamics, classical and/or quantum one in the real molecular environment Sequences at the protein & nucleic acids levels 3D & electronic structure Function Metabolic pathways & signalling Sub-cellular structures & processes Cell(s), structure(s) & functions 1 RPDFCLEPPY TGPCKARIIR YFYNAKAGLC QTFVYGGCRA KRNNFKSAED CMRTCGGA 58


4 Active site (quantum subsystem) Classical molecular scaffold (real molecular environment) Solvent (real thermal bath) Interacting quantum and classical subsytsems. Enzymes, special case of much more general problem.

5 Quantum-classical dynamics in simulations of enzymatic processes (phospholipase A 2 – a case study)

6 Multi-scale modeling. Classes of models Microscopic models Mesoscopic models

7 Fields are equally important as structures !

8 Microscopic (quantum) description of intermolecular interactions : Mesoscopic description of intermolecular interactions (free energies) Electrostatic Poisson-Boltzmann energy Interaction potentials See eg. E.Gallicchio and R.M.Levy, J.Comput. Chem.,25, (2004)

9 Microscopic generators of the potential energy function AVB – (quantum) AVB/GROMOS - (quantum-classical) SCC-DFTB - (quantum) SCC-DFTB/GROMOS - (quantum-classical) SCC-DFTB/CHARMM - (quantum -classical).... Dynamics MD (classical) QD (quantum) QCMD (quantum-classical).... Mesoscopic potential energy functions Poisson-Boltzmann (PB) Generalized Born (GB)....



12 R : H, R : H, OH X : H, OH, NH 2 Y : H, OH, NH 2 W.R.Rudnicki et al., Acta Biochim. Polon., 47, 1-9(2000)


14 Determination of biomolecular structures X-ray and neutron diffraction data NMR Molecular quantum mechanics. Minimization of the B.-O. energy Homology analysis and structure prediction Ab intio methods Minimization of the MM-energy or free energy Experimental and data-mining approaches

15 Chapter 4.5, page 72

16 W.Saenger & K.H.Sheit, J.Mol.Biol., 50, (1970) B.Lesyng & W.Saenger, Z.Naturforsch. C, 36, (1981) Crystallized from water Crystallized from butyric acid !

17 Formy DNA B AZ

18 B AZ Widok wzdłuż osi helis BAZ Formy DNA - widok z góry

19 (Prp C ) Normalne białko prionowe (Prp Sc ) Forma powodująca chorobę

20 Towards global minimum of the free energy (Gibbs & Boltzmann – equilibrium properties, Kramers & Eyring - kinetics)

21 Symplektyczne algorytmy dynamiki molekularnej




25 Optimal sequence alignment, followed by a 3D structure alignment, results in prediction of a correct, 3D-hierarchical biomolecular structure. Optimal – consistent with current evolutionary concepts. Wrong sequence alignment typically results in a wrong structure.

26 Homology analysis and structure prediction. Making use of molecular evolution concepts and Darwinian-type approach.


28 P.Setny, J.Leluk,..

29 29 Protonation equilibria in proteins

30 Protonation equilibria - microstates


32 The model group – a reference state This difference assumed to be purely electrostatic

33 Ensamble -role of a reference state (model group)

34 Phosphotyrosine in phospholipase C- SH2 domain of phospholipase C- 1 (pdb: 2PLE) S.M.Pascal,A.U.Singer,G.Gish,T.Yamazki S.E.Shoelson, T.Pawson, L.E.Kay, J.D.Forman-Kay, Nuclear Magnetic Resonance Structure Of An Sh2 2ple Domain Of Phospholipase C-Gamma1 Complexed With A High Affinity Binding Peptide, Cell, 77, (1994) phosphotyrosine

35 phosphoglucomutase (pdb: 3PMG) W.J.Ray, Junior, Y.Liu, S.Baranidharan, Structure of Rabbit Muscle Phosphoglucomutase at 2.4 Angstroms Resolution. Use of Freezing Point Depressant and Reduced Temperature to Enhance Diffractivity, to be published phosphoserine Phosphoserine in phosphoglucomutase

36 Typical results for phosphorylated proteins moleculepredictionexperimental phopsphotyrosine tetrapeptide dodecapeptide phospholipase C phosphoserine tetrapeptide phosphoglucomutase <4 phosphothreonine tetrapeptide 36.1

37 Open and close forms of PKA

38 . Multiscale modelling methods, the approach to refine structures and to understend functioning of complex biomolecular systems and processes Virtual titration -J. Antosiewicz, E. Błachut-Okrasińska, T. Grycuk, J. Briggs, S. Włodek, B. Lesyng, J.A. McCammon, Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzman Model of the Solute-Solvent System, in Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering, vol. 4, Eds. P.Deuflhard et al, Springer-Verlag, Berlin, Heidelberg, pp ,1999 –J.Antosiewicz, E. Błachut-Okrasińska, T. Grycuk and B. Lesyng, A Correlation Between Protonation Equilibria in Biomolecular Systems and their Shapes: Studies using a Poisson-Boltzmann model., in GAKUTO International Series, Mathematical Science and Applications. Kenmochi, N., editor, vol. 14, , Tokyo, GAKKOTOSHO CO, pp.11-17, M. Wojciechowski, T. Grycuk, J. Antosiewicz, B.Lesyng, Prediction of Secondary Ionization of the Phosphate Group in Phosphotyrosine Peptides, Biophys.J, 84, (2003) Quantum forces and dynamics in complex biomolecular systems. –P. Bala, P. Grochowski, B. Lesyng, J.A. McCammon, Quantum Mechanical Simulation Methods for Studying Biological System, in: Quantum-Classical Molecular Dynamics. Models and Applications, Springer-Verlag, (1995) –Grochowski, B. Lesyng, Extended Hellmann-Feynman Forces, Canonical Representations, and Exponential Propagators in the Mixed Quantum-Classical Molecular Dynamics, J.Chem.Phys, 119, (2003)



41 GB – Generalized Born A k - van der Waals surface area of atom k k - surface tension parameter assigned to atom k First papers on Born models: M.Born, Z.Phys., 1,45(1920) R.Constanciel and R.Contreas, Theor.Chim.Acta, 65,111(1984) W.C.Still, A.Tempczyk,R.C.Hawlely,T.Hendrikson, J.Am.Chem.Soc.,112,6127(1990) D.Bashford, D.Case, Annu.Rev.Phys.Chem., 51,129(2000)

42 M.Feig, W.Im, C.L.Brooks, J.Chem.Phys.,120, (2004) (I) (II) (III) (IV) Coulomb Field appr. Kirkwood Model

43 Ratio of the GB solvation enery to the Kirkwood solvation energy

44 Acknowledgements PhD students: Marta Hallay Jarek Kalinowski Piotr Kmieć Magda Gruziel Michał Wojciechowski Łukasz Walewski Franek Rakowski Janek Iwaszkiewicz Coworkers: Dr hab. J.Antosiewicz Dr hab. P.Bała Dr hab. M.Geller Dr P.Grochowski Dr J.Trylska Collaboration: Prof. J.A.McCammon Prof. W.Saenger Studies are supported by European CoE for Multiscale Biomolecular Modelling, Bioinformatics and Applications and Polish State Committee for Scientific Research.


46 Structures in the crystalline state can be interpreted in terms of packing forces, properties of hydrogen bonds, a kind of consensus between the intramolecular energy and the intermolecular interaction energy, etc. B.Lesyng, G.A.Jeffrey, H.A.Maluszynska, A Model for the Hydrogen-bond-length Probability Distributions in the Crystal Structures of Small-molecule Components of the Nucleic Acids, Acta Crystallog., B44, 193-8(1988) However, this problem can also be seen in a different, more abstract way, namely as minimization of the free energy of a selected molecular system in its real molecular environment – in this particular case this is the environment formed by surrounding molecules with imposed constraints resulting from the symmetry. Towards generalization of experimentally observed structural changes

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