Foundation Course “Physical Chemistry of Proteins II: thermodynamics and kinetics of folding"

SEMESTER 2002-II

Persons in charge

Dr. Miguel Costas Basín (School of Chemistry). (costasmi@servidor.unam.mx)

Dr. Daniel Alejandro Fernández Velasco (School of Medicine) (fdaniel@servidor.unam.mx)

Dr. Enrique García Hernández (Chemistry Institute). (egarciah@servidor.unam.mx)

Dr. José de Jesús García Trejo (Cardiology Institute) (jjgarcia_trejo@yahoo.com)

Dr. Georgina Garza Ramos (School of Medicine) (ggarza@laguna.fmedic.unam.mx)

Dr. Edgar Vázquez-Contreras (Chemistry Institute) (evazquez@bq.unam.mx)

To participate in the discussion forum of this course click here

Course Justification

Due to their great conformational ability, proteins participate in practically all cell functions. The main objective of this course is to analyze, from the physico-chemical perspective, the conformational changes in proteins in folding to the native state.

In this course, the spectroscopic techniques discussed in the "Physical chemistry of proteins I" course are applied to the study of protein unfolding. Calorimetric techniques are also introduced as a further tool for the characterization of stability of the biologically active state.

The different topics covered by the program are approached through the critical, detailed analysis of the most influential, up to date theories on the subject. The objective is to give the student not only a coherent, up to date view, but a critical position on the main research lines in the field.

Place and Length of Sessions

Theoretical sessions 2 hours long, once or twice a week depending on the topic, giving a total of 24 sessions (48 hours in total).

Schedule: Tuesdays and Fridays, from 9:00 to 11:00 . BEGINS: 29 January

To be held in the Biochemistry Department, Chemistry Institute

Method of Assessment

Written assessments (75%); participation in class discussions (25%).

Topics

Presentation: 29 January

I. Bases of thermodynamics

Internal energy, calorie capacity, enthalpy, entropy, Gibbs free energy, chemical potential.

3 sessions (1, 8 and 12 February). Person in charge: MC

II. Principal forces involved in protein stability

Van der Waals interactions, electrostatic interactions, conformational entropy, hydration and hydrophobic effect. ,

2 sessions (15 and 19 February). Person in charge: EV

EXAMINATION 220202

III. Energetic characterization of unfolding through spectroscopic techniques

Denaturing agents: urea, guanidine, pH, temperature and pressure.

Calculation of DG, DH, DS, DCp and Tm, assuming the two states model: goodness and limitations.

Stable folding intermediaries

Protein complexes

4 sessions (22 and 26 February, 1 and 5 March). Persons in charge: GG(3) and EV(1)

EXAMINATION 120302

IV. Calorimetry

Theoretical bases and experimental developments of high resolution calorimetry.

Differential Sweep Calorimetry, Isothermal Titration Calorimetry

Analysis of thermograms and titration curves

3 sessions (8, 12 and 15 March). Person in charge: EG.

EXAMINATION 150402

V. Molecular origins of folding energetics: Estimation of cohesion forces

Study with model compounds

Thermodynamic-structural empirical relations

Mutations .

4 sessions (9,12,16 and 19 April). Person in charge: JG

EXAMINATION 230402

VI. Foundations of kinetics

Reaction mechanisms and laws of velocity, parallel and serial reactions, Arrhenius equation, theory of the transition state, rapid reactions, diffusion controlled reactions

1 session (26 April). Person in charge: EV

VII. Folding cooperativity and its kinetic implications

Two state transitions

Proline isomerization

Intermediaries

Transition state

Folding models: Nucleation-condensation

5 sessions (30 April, 3, 7, 10, and 14 May). Persons in charge: AF(4) y GG(1)

EXAMINATION 170502

VIII. Modern view of protein folding: thermodynamic control versus kinetic control

Levinthal's paradox

Folding routes and funnels

The transition state from the perspective of energy landscapes

2 sessions (21 and 24 May). Persons in charge: Everyone

GENERAL Bibliography

Alberty, R. A., Silbey, R. J. (1997) Physical Chemistry. Wiley, USA.

Branden C. and Tooze J. (1999) Introduction to Protein Structure. Ed. Garland Publishing, Inc,. New York, USA.

Bergethon, P.R. (1998) The physical basis of biochemistry. Springer-Verlag, USA.

Bogan, A. A. & Thorn, K.S. (1998) An analysis of hot spots in protein interfaces. J. Mol. Biol. 280, 1-9.

Chotia, C. & Janin, J. (1975) Principles of protein-protein recognition. Nature, 256: 705-708.

Creigthon, T.E. Ed. (1992). Protein Folding. Freeman. USA.

Dill, KA, Chan, HS (1997) >From Levinthal to pathways to funnels. Nature Struct Biol. 4:10-19.

Eisenberg, D. and Crothers, (1979). Physical Chemistry. The Benjamin/Cummings Publishing Company. USA.

Fersht, A.R. (1999). Structure and mechanism in protein science. Freeman. USA.

Hilser, VJ, Dowdy, D, Oas, TG, Freire, E (1998) The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble. Proc Natl Acad Sci USA 95:9903-9908.

Jacob, M. and F. X. Schmid, (1999). Protein Folding as a Diffusional Process. Biochem 38, 13773-13779.

Karplus, M. and D. L. Weaver, (1994). Protein Folding Dynamics: The Diffusion-collision Model and Experimental Data. Protein Sci 3, 650-668.

Lazaridis, T, Archontis, G, Karplus, M (1995) Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. Adv Protein Chem 47:231-306.

Luque, I, Gómez, J, Semo, N, Freire, E (1998) Structure-based thermodynamic design of peptide ligands: application to peptide inhibitors of the aspartic protease endothiapepsis. Proteins: Struct Funct Genet 30:74-85.

Makhatadze, GI, Privalov, PL (1995) Energetics of protein structure. Adv Protein Chem 47: 307-425.

Matthews, CR Ed. (2000) Protein folding mechanisms. Adv Protein Chem 53.

Nozaki, Y., Tanford, C. (1971) The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. J. Biol. Chem. 246, 2211-2217.

Plaxco, K. W. and D. Baker, (1998). Limited Internal Friction in the Rate-limiting Step of a Two-state Protein Folding Reaction. Proc Natl Acad Sci USA 95, 13591-13596.

Plticelli, F, Ascenzi, P, Bolognesi, M, Honig, B (1999) Structural determinants of trypsin affinity and specificity for cationic inhibitors. Protein Sci 8:2621-2629.

Steinfeld, J. F., Francisco J. S. and Hase, W. L. (1989). Chemical Kinetics and Dynamics. Prentice Hall. USA.

Tinoco, I., K. Sauer and J. C. Wang, (1995). Physical Chemistry. 3rd Edition, Prentice Hall. USA.

Weber, G. (1992) Protein Interactions. Chapman & Hall. USA.

Zhou, Y, Hall, CK, Karplus, M (1999) The calorimetric criterion for a two-state process revisited. Protein Sci 8:1064-1074.

suggestions or comments on this page:

Edgar Vázquez-Contreras (evazquez@bq.unam.mx)