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 beta-bulges) 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 H-bonding.
A tug of war exists between conformational energies of the side chain and maximal H-bonding.
Two proteins exhibiting a twisting sheet
Bovine carboxypeptidase
Triose phosphate isomerase
Connections between adjacent 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
bends
type I and type II :hairpin turn between anti parallel sheets
Reverse Turns
Type I 2 = -60o, 2 = -30o
3 = -90o, 3 = 0o
Type II 2 = -60o, 2 = 120o
3 = 90o, 3 = 0o
two-residue turns
Protein Structure Terminology
Folding motifs (super secondary structure)
Certain amino sequences have patterns to their folding.
A. motif, B. hairpin C. 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 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 barrel motif
Carbonic anhydrase
H2CO3 - CO2 + H2O
Nucleotide binding-Rossmann Fold
Glyceraldehyde-3-phosphate 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 CX2CX13CX2CX14-
15CX5CX9CX2C. 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 CX2CX6CX5-6CX2CX6C. 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 ( bond)• Sheets and helices ( and bonds)• Tertiary structure (fibrous or globular)• Structure determination and fold space• Protein folding discussed after kinetics -lecture 19
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