Introduction to Structural Biology
These notes are from the Spring 1995 Structural Biology class
given at Berkeley.
Note: These are incomplete and I have no intention of completing them.
Introduction Table of Contents
Rules and Patterns for Protein Folding
- Levels of Protein Structure
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Rules and Patterns for Protein Folding
- Sequence similarity often leads to structural similarity
- Space is filled (proteins aren't hollow)
- Little strain -- atoms shouldn't overlap and bond angles should be fairly normal.
- Right-handed connections
- Inside=nonpolar, outside=charged
- Weak statistical preferences
These rules lead to rotamers: Preferred positions of side chains
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Levels of Structure
Primary
Sequence.
Secondary
Alpha Helix
- 3.6 amino acids per turn
- Carbonyl oxygen from residue i hydrogen bonds with Amino group on residue i+4
Beta Sheet
- Parallel
- H-bonds not parallel to each other
- Often buried, with all nonpolar residues
- Antiparallel
- H-bonds parallel to each other
- Often polar on outside, nonpolar on inside
Beta Barrel
Eight-stranded parallel beta sheet in center, 8 alpha helices around outside
Greek Key
Up-and-down beta sheets connected by alpha helices in this pattern:
Irregularities
In a beta sheet, this can mean that the sheet turns ninety degrees or even makes a hairpin turn.
Beta Turn
Reverses direction in four residues
Loops/Straps
Reverses direction with more than four residues
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Last revised: 1995 May 13 by
sev@byzantium.mckusick.com