was developed in 1995. Please, take in attention that this program is adapted for
"pure" chemists (final-year students of chemical faculty) with strong
background in chemistry and is not appointed specially for drug designers,
rather for basic education in the field of physico-chemical principles of
biological processes (it is differ from the thing that can be called
"classic biochemistry", you see)..
Below is contents of this program:
1. Introductory part, 4 lectures (in our area 1 lecture is equal to 90 min.)
1.1. Common thermodynamics: phase space, configuration points and trajectories
in a phase space, conservative and dissipative systems, attractors.
1.2. Perturbations, bifurcation points, Gibbs ensembles, distributions of
Maxwell-Boltzmann, Fermi-Dirac and Boze-Einstein.
1.3. Strange and fractal attractors. Properties of mathematical and physical
fractals.
1.4. Building methods of linear and non-linear fractals: IFS-systems,
L(Lindenmayer)-grammatics, Mandelbroth and Julia sets. Applications of fractals
in bioinformatics.
2. Main part, 11 lectures.
2.1. Structure of water in biological systems. Non-frozed water. Structure of
water clusters. Percolation and fractal models.
Biomacromolecule assemblation onto water clusters. Phase transitions of the
second order in water structures. Proton transport.
2.2. Structure of DNA and RNA. Primary, secondary and tertiary structures.
Introduction in bioinformatics. Knots and catenanes in nucleic acid structures.
mRNA, tRNA, hnRNA. Ribozymes. Electron transport along DNA threads. Electron and
proton exitones. Fractal representation of genetic texts.
Computational practice: iterated function systems (writing a computer program
for fractal representation of genetic texts (VisualBasic)). Building morphs of
plants using L-grammars. Building of Mandelbroth, Julia and Lyapunov sets.
Vitten-Sander model of fractal growing.
2.3. Protein structure (2 lectures).
Primary structure. Biochemical pecularities of aminoacid residues.
Selenocysteine. Secondary and supersecondary structure. Davydov's solitones.
Example of tubuline assemblation. Semiconductor properties of proteins. Tertiary
structure. Fractal properies of proteins. Impact of environmental constituents
on fractal dimensionality of protein globules. Quaternary structure. Iso- and
heterologous oligomeres. Role of hydrophobic interactions and metal ions in
stabilisation of quaternary structure.
Subunit interactions. Influence of quaternary structure on protein properties
(using example of glutamine synthetases from diverse sources). Structural and
energetical domains in proteins. Protein folding and Levintal's paradox.
Conformational mobility of a protein globule. Denaturation and renaturation.
Difference between proteins and peptides.
2.4. Enzymes structure and functioning (2 lectures).
Pecularities of enzyme globules. Active center and regulatory sites. Passive
centers. Mechanisms of enzyme catalysis. Potential energy surface of an
enzymatic reaction and symmetry conditions. Influence of white and color noise
on velocity of an enzymatic reaction. Tunneling of reaction's coordinate through
stationary and fluctuating barriers. Two-well potentials. Mechanisms of binding
of substrates and prodicts to enzyme globules.
2.5. Biocoordination chemistry (2 lectures, in this section the term
"ligand" is used as in classic inorganic chemistry, not as in
biochemistry). Essential and xenobiotic elements. Lanthanides. Oxocationes
(vanadyl (IV, V), uranyl (VI)). Pecularities of complex formation of s-, p-, d-
and f-elements in biological systems. Processes of ligand substitution in
biological environment. The Jahn-Teller effect of the first and second order.
Pseudo Jahn-Teller effect. Enzymatic catalysis onto
binuclear and low-symmetric metal complexes. Complexes of metal ions with
macrocycles. Low-molecular enzyme models.
2.6. Biologically active compounds (further denoted here as BAC, 2 lectures).
Definitions. Quantitative structure-function relationships (well-known as QSAR).
Thermodynamic and biochemical approaches for description of BAC action. Common
methods of drug design. Distribution coefficients. Electronic and steric
effects. Role of formation of complexes with metals.
Computational practice: working with Cambridge DataBase System and Protein Data
Bank (PDB). Automated docking study (using the program Autodock, v. 2.4,
authors: Drs GM Morris, DS Goodsell, R Huey, AJ Olson from the Scripps Res.
Inst.) Introduction and little practice in MOPAC, Hyperchem and GAMESS programs.
Essentials of VisualBasic scripting in Hyperchem. Format of PDB files.
2.7. Biomembranes.
Membranes components. Thermodynamic phase transitions in membranes. Integral and
adsoption protein complexes. Signal transduction. Informatics of ion transfer.