PROTEIN AND PEPTIDE STRUCTURE
What the PDB Files Teach Us about Protein Structure
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8/27/98 (updated 2017)
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Table of Contents

{1} PROTEIN AND PEPTIDE STRUCTURE*

{2} What PDB teaches...

{3} What PDB teaches...

{4} water soluble proteins are "globular,"

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

{6} bond lengths and bond angles don't vary much

{7} Serine bond lengths...

{8} structures are stable and relatively rigid

{9} folding possibilities are limited,

{10} Along the backbone...

{11} Conformations are also limited in positions of sidechains.

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

{13} Consider the CB-CG dihedral angle:

{14} folding motifs are used repetitively.

{15} Some simple motifs

{16} Some simple motifs...

{17} Some simple motifs...

{18} The TIM barrel motif

{19} Other common motifs

{20} The SCOP* classification of proteins:

{21} proteins with similar function typically have similar structure.

{22} with similar proteins

{23} Other examples….

{24} Polar groups tend to be on surface

{25} Mutations and Natural Variations tend to be exterior

 Author: John E. Wampler

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References:

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

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

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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.

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