WHAT THE PDB TEACHES US ABOUT PROTEIN ARCHITECTURE?

Table of Contents

WHAT THE PDB TEACHES US ABOUT PROTEIN ARCHITECTURE?

What PDB teaches...

What PDB teaches...

water soluble proteins are "globular," tight packed, water excluded from interior, folded up.

?-TRYPSIN from PDB file 1BTY with waters of crytallization.

bond lengths and bond angles don't vary much from equilibrium positions. Bond lengths are consistent and nominal:

Serine bond lengths...

Bond angles are also near nominal values: Consider the CA, CB, CG bond angle. two general groups: Do the R’s make any difference?

While the nominal tetrahedral bond angle is 109.8o, substituents on the beta and gamma carbons make a difference.

When the NDI is low, the population of values is more complex than a single Gaussian distribution.

structures are stable and relatively rigid Salmonella typhimurium oligopeptide binding protein

folding possibilities are limited, both along the backbone chain and within the side chain groups.

Along the backbone...

Conformations are also limited in positions of sidechains.

Another example from a selection of cis Tyr-Pro fragments.

Consider the C?-C? dihedral angle:

folding motifs are used repetitively.

Some simple motifs

Some simple motifs...

Some simple motifs...

The ?/? (TIM) barrel motif:

The Open ?/?-sheet structure with ?-saddle

The SCOP* classification of proteins:

proteins with similar function typically have similar structure.

with similar proteins (say from different organisms) structure tends to be more conserved than the exact sequence of amino acids.

Other examples….

Polar groups tend to be on surface 

Mutations and Natural Variations tend to be exterior 

Email: wampler@bchiris.bmb.uga.edu

Home Page: http://bmbiris.bmb.uga.edu/wampler

References:

R. L. Almassy, C. A. Janson and D. Eisenberg, Nature 323, 304-309 (1986)

Carl Branden & John Tooze, Introduction to Protein Structure, Garland Publishing, Inc. New York (1991).

T. E. Creighton, Proteins, Structures and Molecular Properties, W. H. Freeman and Co., N.Y. (1993).

A. L. Lehninger, Biochemistry, Worth Publishers, Inc., N.Y. (1975)

A. L. Lehninger, D. L. Nelson, M.M. Cox, Principles of Biochemistry, Worth Publishers, Inc., N. Y. (1993).

D. L. Oxender and C. F. Fox, Protein Engineering, Alan R. Liss, Inc., N. Y. (1987)

J. S. Richardson & D. C. Richardson, in Prediction of Protein Structure and the Principles of Protein Conformation (G. D. Fasman, ed.), Plenum Press, N.Y. (1989) pp. 1-98.

D. E. Stewart, A. Sarkar and J. E. Wampler, J. Mol. Biol 214, 253-260 (1990)

E. Tronrud, M. Schmid and B. Matthews, J. Med. Biol. 188, 443 (1986)

K. S. Wilson, C. E. Vorgias, I. Tanaka, S. W. White and M. Kimura, Protein Engineering 4, 11-22 (1990).