Protein Structure
Lecture 2/26/2003
beta sheets are twisted
• Parallel sheets are less twisted than antiparallel and are always buried.
• In contrast, antiparallel sheets can withstand greater distortions (twisting and betabulges) and greater exposure to solvent.
The twist is due to chiral (l)- amino acids in the
extended plane.
This chirality gives the twist and distorts Hbonding.
A tug of war exists between conformational
energies of the side chain and maximal Hbonding.
Two proteins exhibiting a twisting b
sheet
Bovine carboxypeptidase
Triose phosphate isomerase
Connections between adjacent b sheets
Sheet facts
•Repeat distance is 7.0 Å
•R group on the Amino acids alternate up-down-up
above and below the plane of the sheet
•2 - 15 amino acids residues long
•2 - 15 strands per sheet
•Ave of 6 strands with a width of 25 Å
•parallel less stable than anti-parallel
•Anti-parallel needs a hairpin turn
•Tandem parallel needs crossover connection which
has a right handed sense
Non-repetitive regions
Turns - coils or loops link regions of secondary structure
50% of structure of globular proteins are not
repeating structures
b bends
type I and type II :hairpin turn between anti
parallel sheets
Reverse Turns
Type I f2 = -60o, y2 = -30o
f3 = -90o, y3 = 0o
Type II f2 = -60o, y2 = 120o
f3 = 90o, y3 = 0o
two-residue turns
Protein Structure Terminology
Folding motifs (super secondary
structure)
Certain amino sequences have patterns to their folding.
A. bab motif,
B. b hairpin
C. aa motif
beta-alpha-beta
• parallel beta-strands connected by longer regions
containing alpha-helical segments
• almost always has a right-handed fold
Helix-turn-helix
•
•
•
•
•
loop regions connecting alpha-helical segments can have important functions
e.g. EF-hand and DNA-binding
EF hand loop ~ 12 residues
polar and hydrophobic a.a. conserved positions
Glycine is invariant at the sixth position
The calcium ion is octahedrally coordinated by carboxyl side chains, main
chain groups and bound solvent
Protein Folds
There is an estimate of about 10000 different folding
patterns in proteins
About half of the proteins fall into a few dozen folding
patterns.
Those proteins related by structure are called families.
A large Family are the c cytochromes (see Figure 6-31
pg 147 in FOB.)
The b barrel has several types of
structures that have been mimicked
in art.
A. rubredoxin
B. Human prealbumin or porins
C. Triose phosphate isomerase
Concanavalin A
Mostly a b barrel motif
Carbonic anhydrase
H2CO3 -  CO2 + H2O
Nucleotide binding-Rossmann
Fold
Glyceraldehyde-3phosphate
dehydrogenase
Binding NADH in the
Rossmann fold.
Zinc fingers
C2H2 zinc finger: It is characterized by the sequence CX2-4C....HX2-4H,
where C = cysteine, H = histidine, X = any amino acid.
C4 zinc finger: Its consensus sequence is CX2CX13CX2CX1415CX5CX9CX2C. The first four cysteine residues bind to a zinc ion and
the last four cysteine residues bind to another zinc ion
C6 zinc finger. It has the consensus sequence CX2CX6CX56CX2CX6C. The yeast's Gal4 contains such a motif where six cysteine
residues interact with two zinc ions
C2H2 zinc finger
Zinc Finger DNA-binding
Summary Chapter 6
• Four levels of protein structure
–
–
–
–
•
•
•
•
•
Primary
Secondary
Tertiary
Quaternary
Peptide bond (w bond)
Sheets and helices (f and y bonds)
Tertiary structure (fibrous or globular)
Structure determination and fold space
Protein folding discussed after kinetics -lecture 19