Description
Details
Lectures
References

Description

This course is directed to all students and researchers who perform - or plan to perform in the future - quantitative measurements of molecular interactions (the "binding" of molecules) in biochemistry or molecular biology. Given a postulated molecular mechanism, the goal of such experiments is to determine the overall strength of molecular binding (as measured by equilibrium constants), and also the rate of binding (the "kinetics") as measured by rate constants.

Current standard methods for the determination of equilibrium constants and rate constants have many drawbacks, because they are based on a large number of simplifying assumptions - imposed by the classical algebraic mathematical formalism. In this course, we will depart from the traditional algebraic methods of data analysis and avoid using complicated mathematical equations. Instead, we will let the computer handle all the mathematics for us, so we can focus entirely on the biology. This is made possible by using advanced numerical methods of data analysis.

Students will actively learn how to use the academic freeware software package DynaFit for symbolic modeling of arbitrary biochemical mechanisms.

Details

University	Masaryk University Brno, Czech Republic
College	Faculty of Science
Department	Institute of Experimental Biology
Term	Fall 2011
Dates	October 10 - October 14, 2011
Course code	IB023
Course title	Binding and Kinetics for Experimental Biologists
Language of instruction	English
Guarantor	doc. RNDr. Jiri Fajkus, CSc.
Contact	Mgr. Ctirad Hofr, Ph.D.
Instructor	Petr Kuzmic, Ph.D.
Co-instructor	Mgr. Ctirad Hofr, Ph.D.
Grading	Pass / Fail (zápočet)
Credits	2
Required courses	None
Maximum class size	30
Course format	Intensive lecture course with practical computer sessions
Evaluation criteria	Active participation during lecture and exercise sessions
Required literature	None
Formal discussion groups	None

Lectures

#	Topic	Slides	Handout
1	Numerical models Kinetic compiler
2	Initial estimates Differential evolution
3	Equilibrium binding Theory
4	Equilibrium binding Case study
5	Initial rate enzyme kinetics Substrate inhibition
6	Enzyme kinetics One day in the life of consultant
7	Confidence intervals Biological Oxygen Demand
8	Optimal design of experiments Kinetics of clathrin uncoating

References

• Original publication announcing DYNAFIT.
• Explains the rationale for numerical methods.

• New features in version 4 (2009).
• Literature references to Differential Evolution, Monte-Carlo confidence intervals, and other important algorithms.