Learning objectives
Provide basic and advanced knowledge on spectroscopic and computational techniques in use today in macromolecular biophysics
Prerequisites
# <br />
biophysics laboratory exams 1 and 2
Course unit content
<br />Lab. for Bioph. III <br />
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A) Optical activity <br />
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Theoretical lectures: <br />
<br />
Asymmetry and dissymmetry <br />
<br />
Principles of circular dichroism (CD) <br />
<br />
CD of proteins <br />
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Practical activities: <br />
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Calibration of a dichrograph <br />
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CD spectra of polypeptides <br />
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CD spectra of globular proteins <br />
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Methods of analysing the secondary structure from CD spectra in far UV. <br />
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<br />
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B) Kinetics <br />
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Theoretical lectures: <br />
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Chemical kinetics <br />
<br />
Enzyme kinetics <br />
<br />
Protein folding kinetics <br />
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Exercises: < /B> <br />
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Dead time of a stopped-flow spectrophotometer <br />
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Enzyme activity of alcohol dehydrogenase <br />
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Kinetics of protein denaturation/renaturation <br />
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C) Computational biophysics <br />
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The PDB database and biomolecular structures. Structural analysis of proteins through software. Structural overlap and Root Mean Square Deviation. Introduction to the use of the two most widely used programs: RasMol and SwissPdbViewer. <br />
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Exercise 1: structural and comparative analysis of proteins. <br />
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Introduction to computational biophysics. Potential energy of a molecule and its minimization. Anfinsen’s principle and strategies for searching for the global minimum of energy. Fundamental principles of molecular dynamics and its applications. Solvent simulation. Analysis of the results. <br />
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Exercise 2: search for the structure in solution of an opiod peptide through simulated annealing and molecular dynamics
Bibliography
A) Optical activity <br />
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- D.G.Morris: Stereochemistry, RSC 2001 <br />
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- G.Fasman: CD and the conformational analysis of biomolecules, Plenum 1996 <br />
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- C.R.Cantor, P.R.Schimmel: Biophysical Chemistry, Vol. 2, W.H.Freeman 1980 <br />
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<br />
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B) Cinetica <br />
< /SPAN>- A.Fersht: Structure and mechanism in protein science, Freeman 1999 <br />
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- B.Noelting: Protein folding kinetics, Springer-Verlag 1999 <br />
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- I.Tinoco et al: Physical Chemistry, Prentice Hall 2002 <br />
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<br />
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C) Computational biophysics <br />
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- A. R. Leach: Molecular modelling (II ed.), Prentice Hall 2001.
Teaching methods
Oral exam on the theory topics and on the reports regarding the laboratory exercises <br />
