C5845 Advanced Biophysical Chemistry - theoretical methods

Faculty of Science
Autumn 2018
Extent and Intensity
2/1/0. 3 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
doc. RNDr. Mgr. Jozef Hritz, Ph.D. (lecturer)
RNDr. Mgr. et Mgr. Arnošt Mládek, Ph.D. (lecturer)
Mgr. Petr Louša, Ph.D. (lecturer)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Department of Chemistry – Chemistry Section – Faculty of Science
Supplier department: Department of Chemistry – Chemistry Section – Faculty of Science
Timetable
Mon 17. 9. to Fri 14. 12. Tue 13:00–15:50 C12/311
Prerequisites
Successful passing the courses: C5850 - Principles of Biophysical Chemistry (lecture) C5855 - Methods of Biophysical Chemistry (lecture) C5856 - Methods of Biophysical Chemistry (seminar)
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The aim of this subject is to gain deeper knowledge in biophysical chemistry applicable in biomolecular research. The emphasis is put to the theoretical description of biomolecular systems in solutions by means of physical-statistical and computational methods.
Learning outcomes
Students will be able: - to characterize general properties of proteins and nucleic acids in solutions and to describe the fundamental factors that help to stabilize the biomolecules - to apply physico-chemical approaches to study interactions of biomolecular systems from thermodynamic as well as kinetic perspective - to utilize appropriate computational methods to characterize biomolecular systems at atomic level.
Syllabus
  • 1.Probability theory (How do molecules “know” they should reach equilibrium?) 2.Equilibrium statistical mechanics (ergodic theory, fluctuations) 3.Biomolecular force-fields parameters and molecular dynamics 4.Enhanced sampling computational simulations (replica exchange molecular dynamics - REMD) 5.Free energy calculations 6.Calculations of potential of mean force (PMF) 7.Solubility and hydrophobicity 8.Binding affinity 9.Conformational and allosteric changes 10.Kinetics of conformational changes 11.Protein folding 12.Phase transitions of proteins (molten-globule state) Literature: [1] Peter R. Bergethon: The Physical Basis of Biochemistry [2] Finkelstein and Pittsyn: Protein Physics [3] Cantor & Schimmel: Biophysical Chemistry, Part I [4] Zuckerman D.M.: Statistical Physics of Biomolecules
Literature
    recommended literature
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. New York: W.H. Freeman and Company, 1980, s. i-xxix. ISBN 0716711907. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. New York: W.H. Freeman and Company, 1980, xxvii, 341. ISBN 0716711885. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. New York: W.H. Freeman and Company, 1980, s. i-xxix. ISBN 0716711923. info
Teaching methods
lecture (2 hours) including computational examples
Assessment methods
an exam consisting of written and oral part
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2016, autumn 2017, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Autumn 2018, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2018/C5845