13 January 2003

Biol 6312

Introduction to the course and the topics

Interplay of protein structure, function and design

The protein folding problem

The language of protein folding

Why are proteins so robust to site mutations?
J Mol Biol 2002 Jan 18;315(3):479-84
Taverna DM, Goldstein RA.

Properties of amino acids:

1. Polarity
2. Stereochemistry

Conformational flexibility of the peptide chain

1. Peptide bond (References below)

Deviations from Planarity of the Peptide Bond in Peptides and Proteins
Malcolm W. MacArthur, Janet M. Thornton
J. Mol. Biol. (1996) 264 pp. 1180-1195

The partial charge of the nitrogen atom in peptide bonds
EJ Milner-White
Protein Sci (1997) 6: 2477-2482.

Cis Peptide Bonds in Proteins: Residues Involved, their Conformations, Interactions and Locations
Journal of Molecular Biology, Volume 294, Issue 1, 19 November 1999, Pages 271-288
Debnath Pal and Pinak Chakrabarti

2. fy angles

Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures
K. Gunasekaran, C. Ramakrishnan, P. Balaram
J. Mol. Biol. (1996) 264 pp. 191-198

3. Secondary structure: pattens of fy values

4. Hydrogen bonding

Hydrogen bonding in globular proteins (Medline)

Stickle DF, Presta LG, Dill KA, Rose GD

J. Mol. Biol (1992) 226:1143-59

C-H···-Interactions in Protein
Journal of Molecular Biology, Volume 307, Issue 1, 16 March 2001, Pages 357-377
Maria Brandl, Manfred S. Weiss, Andreas Jabs, Jürgen Sühnel and Rolf Hilgenfeld
Abstract |

Strength of the Calpha H..O hydrogen bond of amino acid residues.
J Biol Chem 2001 Mar 30;276(13):9832-7 Scheiner S, Kar T, Gu Y.

Hydrogen Bonds with p-Acceptors in Proteins: Frequencies and Role in Stabilizing Local 3D Structures

Thomas Steiner, Gertraud Koellner

J. Mol. Biol (2001) 305: pp. 535-557

5. Ionic Interactions

Cation-p interactions in structural biology
Justin P. Gallivan and Dennis A. Dougherty
P.N.A.S. (1999) 96: 9459-9464

Complex Salt Bridges in Proteins: Statistical Analysis of Structure and Function
Boaz Musafia, Virginia Buchner, Dorit Arad
J. Mol. Biol. (1995) 254: pp. 761-770

Secondary Structure

1. a-helix
2. 3₁₀ helix
3. Polyproline II helix

   Left-handed Polyproline II Helices Commonly Occur in Globular Proteins

   Alexei A. Adzhubei, Michael J.E. Sternberg

   J. Mol. Biol. (1993) 229: pp. 472-493

4. b-sheet
5. Turns, loops, connections