1. Chapter 3 - Proteins

2. Test Your Knowledge About Basic Protein Structure
Name one polar and one nonpolar amino acid, then make a list of all the additional amino acids that you remember.
What are the four weak (noncovalent) interactions that determine the conformation of a protein?
(True/False) A protein is at a near entropy minimum (point of lowest disorder, or greatest order) when it is completely stretched out like a string and when it is properly folded up. Explain.
(True/False) Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules. Explain.
(True/False) For a family of related genes that do not match genes of known function in the sequence database, it should be possible to deduce their function using “evolutionary tracing” to see where conserved amino acids cluster on their surfaces. Explain.

7. Also Pro, Phe, Met, Trp, Gly, Cys

10. Reactions that promote protein folding

12. Adapted from L. Wu et al. , 1995, Nature Struc. Biol
Adapted from L. Wu et al., 1995, Nature Struc. Biol. 2:281; courtesy of J. Harris and P. S. Kim

13. Molecular chaperones Chaperones
Video – chaperone-aided protein folding

14. Average length ≈ 10 residues ≈ 15 Å.
Minimum length = 4 residues: how many H-bonds?
Maximum length = 40 residues.

15. Pleated - look edge-on
Strands ~ 5 Å apart
Note direction of H-bonds will differ in anti-parallel & mixed sheets

16. Loops & Turns
Connect secondary structural elements.
Loops often carry the functional groups.
Hairpin turns: Shortest possible loops (2 residues).
Gly often in tight turns.

17. Motifs (protein folds) Domains/Modules
Beta-Hairpins I
Beta-Hairpins II
Beta Corners
Beta Barrels
Helix Hairpins
Alpha-Alpha Corners
E-F Hand
Helix-Turn-Helix
Beta-Alpha-Beta Motifs
Greek Key Motifs
Most domains can be classified into a smaller number of "folds". Many domains are not unique to the proteins produced by one gene or one gene family but instead appear in a variety of proteins. The domains found most commonly are often called promiscuous. Structural domains vary in length from between about 25 amino acids up to 500 amino acids in length. The shortest domains such as zinc fingers are stabilised by metal ions or disulphide bridges. Domains often are named and singled out because they play an important role in the biological function of the protein they belong to; for example, the "calcium-binding" domain of calmodulin. Because they are self-stabilizing, domains can be "swapped" by genetic engineering between one protein and another to make chimera proteins. A domain may be composed of none, one, or many structural motifs.
Some simple combinations of secondary structure elements have been found to frequently occur in protein structure and are referred to as 'super-secondary structure' or motifs. For example, the β-hairpin motif consists of two adjacent antiparallel β-strands joined by a small loop.
Pyruvate kinase

18. B sheet core with protruding loops
Loops for binding interactions
N and C terminals at opposite poles or form “plug-ins”
Domain shuffling

19. Families/Clans Pyruvate kinase
This is a member of the Pyruvatekinase-likeTIM barrel superfamily
Other families
GP120
Family
Envelope glycoprotein GP120
RVT_1
Reverse transcriptase (RNA-dependent DNA polymerase)
COX1
Cytochrome C and Quinol oxidase polypeptide I
Oxidored_q1
NADH-Ubiquinone/plastoquinone (complex I), various chains
MFS_1
Major Facilitator Superfamily
HCV_NS1
Hepatitis C virus non-structural protein E2/NS1

20. Serine Protease family

21. Other Important Protein Structural Features
Subunits
Dimers, tetramers, large assemblies of monomers
Filamentous proteins
Globular proteins
Video – clathrin assembly

23. Test Your Knowledge Now
Amino Acid Side Chain
Proportion Buried
I = Ile
0.60
V=Val
0.54
C=Cys
0.50
F=Phe
L=Leu
0.45
M=Met
0.40
A=Ala
0.38
G=Gly
0.36
W=Trp
0.27
T=Thr
0.23
S=Ser
0.22
E=Glu
0.18
P=Pro
H=His
0.17
D=Asp
0.15
Y=Tyr
N=Asn
0.12
Q=Gln
0.07
K=Lys
0.03
R=Arg
0.01
Small proteins may have only one or two amino acid side chains that are totally inaccessible to solvent. Even in large proteins, only about 15% of the amino acids are fully buried. A list of buried side chains from a study of twelve proteins is shown in Table 1. The list is ordered by the proportion of amino acids of each type that are fully buried. What types of amino acids are most commonly buried? Least commonly buried? Are there any surprises? If so, why?
Table 1. Proportions of amino acids that are inaccessible to solvent in a study of twelve proteins.