This course introduces physical aspects of the interactions of biological molecules and some cellular processes. It will also provide understanding how composition determines the structure and properties of proteins, DNA, and RNA and membranes. Practical classes will be focused on design of peptides and oligonucleotides with desirable properties, skills to use specialized software and web services, investigation of mechanisms of biological processes with special attention to the issues that arise in drug development.
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Course: 7 lectures, 4 seminars
Lectures: Volodymyr Shvadchak
Seminars: Volodymyr Shvadchak, Ivan Muzalov
Covalent, hydrogen, ionic bonds. Individual molecules and biopolymers. Diffusion and size of molecules. Primary, secondary, ternary structure of proteins. Disulfide bonds. Relationship between amino acid sequence and secondary structure. Structure prediction, MD.
Complementarity. Helix. Hairpins. tRNA. Annealing. UV absorbance to monitor dsDNS-ssDNA transition. Atypical conformations. Viral and non-coding RNA. RNAzymes.
Lipid bilayer. Model membranes. Membrane phase. Structure and composition of cell membrane. Proteins and membranes. Membrane permeability. Membrane asymmetry. Transmembrane potential. Channels.
ATP-synthase. Bacterial flagella.
Tubulin microtubules. Kinesin and dynein. Actin microfilamens and myosin.
Reversible and irreversible processes. Laws of Thermodynamics. Heat and reaction enthalpy. Entropy. ΔG. Nernst equation. Hess law. Equilibrium constants. Determining Kd and stoichiometry of protein interactions.
First-order reactions. Two-stage reactions. Reversible reaction rates and equilibrium constants. Second order reaction. Kinetics in complex systems. Basics of kinetic modelling. Modeling of epidemics development. Catalysis. Kinetics of fermentative reactions. Inhibition. Kinetics in studies of reaction mechanisms.
Protein structure. Construction of peptides. DNA/RNA structure. Online calculators of oligonucleotide and peptide properties Lipids and membranes.
Oligonucleotide properties calculator
Bioenergetics. Motor proteins.
Numerical modelling of reaction kinetics.
Download VMD https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
Download protein structrue files with atom coordinates https://www.rcsb.org/ (PDB format).