Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online

CHAPTER 2 - PROTEIN STRUCTURE

C: UNDERSTANDING PROTEIN CONFORMATION

BIOCHEMISTRY - DR. JAKUBOWSKI

3/4/16

Learning Goals/Objectives for Chapter 2C:  After class and this reading, students will be able to

  • describe the differences between primary, secondary, supersecondary, tertiary, quaternary and domain protein structure
  • explain the basis of CD measurements for secondary structure
  • describe the similarities between torsion angles and an energy vs torsion angle plot for the rotation of the C2-C3 torison angle with phi/psi angles of peptide bonds and the 2D plots off allowed conformations around a given amino acid in a protein (Ramachandran plot).
  • (from reading give explanation for observed propensities of amino acids for different secondary structure)

In contrast to micelles and bilayers, which are composed of aggregates of single and double chain amphiphiles, proteins are covalent polymers of 20 different amino acids, which fold, to a first approximation,  in a thermodynamically spontaneous process into a single unique conformation, theoretically at a global energy minimum. This chapter section will investigate the possible conformations available to proteins, just as we studied the conformations of free fatty acids and acyl chains in lipid aggregates. The next chapter section will discuss the actual processes of folding and of unfolding (denaturation), both in vitro and in vivo. Then we will discuss the thermodynamics and intermolecular forces which stabilize the folded (or native) shape and the unfolded (or denatured state) of proteins, in a fashion similar to how we discussed micelle and bilayer stability.

C7.  Recent References

  1. Pace, C. et al. Protein Ionizable Groups:  pK values and Their Contribution to Protein Stability and Solubility.  J. Biol Chem.  284, 13285 (2009)
  2. Chothia, C. et al. Evolution of Protein Repertoire. Science, 300, pg1701 (2003)
  3. Stebbins & Galan. Structural Mimicry in Bacterial Virulence . Nature. 416. pg 701 (2001)
  4. Taylor.  A deeply knotted protein structure and how it might fold. Nature. 406. pg 916 (2000)
  5. Innate immunity:  ancient system gets new respect (about antimicrobial peptides).  Science. 291 pg 2068 (2001)
  6. Graether et al. b-helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect.  Nature. 406, pg 249, 325 (2000); Liou et al. Mimicry of ice structure of surface hydroxyls and water of a b-helix antifreeze protein.   Nature. 406, pg 322,(2000)
  7. Kanamaru. S et al. Structure of the cell-puncturing device of Bacteriophage T4.  Nature. 415. pg 553 (2002)

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