Structure of amino acids

Introduction to protein structure

250.326 Biological Macromolecules

Spring 2006 Woodson

Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)

Properties of amino acids:

(one way to sort them)

hydrophobic hydrophilic
gly, pro

aliphatic aromatic polar charged

ala phe asn acidic basic
val tyr gln asp lys
leu trp ser glu arg
ile thr his
met cys
from G. D. Rose
 Serine Threonine
(Ser, S) (Thr, T) Proline
(Gly, G)

Cysteine
(Cys, C)

Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)

Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)

Abbreviations for amino acids Polypeptide backbone is semi-flexible

Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)

Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)

 Sterics limit number of accessible
polypeptides conformations

beta sheet

alpha helix

Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)

Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)

Anti-parallel beta sheet Parallel beta sheet

Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)

Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)
Turns + loops: essential connectors,
A few protein domain motifs
often on protein exterior

4 helix bundle jelly roll (antiparallel beta)

Cyt b256, 1M6T Cu-Zn SOD, 1CBJ
Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)

How solid are proteins?

More protein domain motifs

Interior is well packed: volume of atoms = 75% total volume

alpha/beta barrel Interior is flexible: tolerance for mutations
Parallel beta helix
Triose phosphate isomerase
Pectate lyase, 1BN8
1M6J
Berg, Tymoczko, Stryer, Biochemistry, 5th ed, W.H. Freeman (2002)