Exploring Protein Structures
Chemistry and Chemical Biology
Rutgers University
Four Levels of Protein Structure
• Primary, 1o
– Amino acid sequence; Covalent bonds
• Secondary, 2o
– Local conformation of main-chain atoms (F and Y
angles); non-covalent interactions (h-bonds)
• Tertiary, 3o
– 3-D arrangement of all the atoms in space (mainchain and side-chain); non-covalent interactions
• Quaternary, 4o
– 3-D arrangement of subunit chains, non-covalent
interactions
Four Levels of Protein Structure
• Primary, 1o
TPEEKSAVTALWGKV
• Secondary, 2o
• Tertiary, 3o
• Quaternary, 4o
a2
a1
b2
b1
b2
Tertiary
Secondary
Quaternary
Primary
Protein Folding & Protein Structure
Amino Acids
• Amino acid sequence
determines the 3D
structure of a protein
• 20 amino acids –
modifications do occur
post protein synthesis
• L- Amino Acids in normal
proteins “corn crib”
Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 68.
Protein Building Blocks: Amino Acids
Basic
Acidic
Side chain
Hydrophobic
Hydrophilic
C-alpha
Amino
group
From www.bachem.com
Carboxyl
group
Protein Building: Peptide Bonds
Side chain
Side chain
C-alpha
C-alpha
Amino
group
Carboxyl
group
- H2O
More amino acids
Peptide bond
Peptide Bond Formation
• Individual amino acids form a polypeptide chain
• Such a chain is a component of a hierarchy for
describing macromolecular structure
• The chain has its own set of attributes
Conformation of
the polypeptide chain
• Omega: Rotation around the peptide
bond Cn – N(n+1). It is planar and is
180 under ideal conditions
• Phi: is the angle around N – Ca
• Psi: is the angle around Ca – C
From Brandon and Tooze
• Values of phi and psi are constrained
to certain values based on steric
clashes of the R group.
• Ramachandran plot: Defines
characteristic patterns of torsion
angles
Ramachandran Plot
• allowed and
disallowed values for
phi and psi
• Gly and Pro are
exceptions
• Gly has no limitation
• Pro is constrained by
the fact its side chain
binds back to the
main chain
Gray = allowed conformations. bA, antiparallel b sheet; bP, parallel b
sheet; bT, twisted b sheet (parallel or anti-parallel); a, right-handed a
helix; L, left-handed helix; 3, 310 helix; p, p helix.
Secondary Structure: Alpha Helices
a Helix
a Helix
• If N-terminus is at bottom,
then all peptide N-H bonds
point “down” and all peptide
C=O bonds point “up”.
• N-H of residue n is Hbonded to C=O of residue
n+4.
• a-Helix has:
– 3.6 residues per turn
– Rise/residue = 1.5 Å
– Rise/turn = 5.4Å
a Helix
• R-groups in a-helices:
– extend radially from the core,
– shown in helical wheel diagram.
– Can have varied distributions
Polar
Hydrophobic
Amphipathic
Secondary Structure: Beta
Sheet
Antiparallel beta sheet
Parallel beta sheet
b Sheet
• Stabilized by H-bonds
between N-H & C=O
from adjacent
stretches of strands
• Peptide chains are
fully extended pleated
shape because
adjacent peptides
groups can’t be
coplanar.
b Sheet - 2 Orientations
Parallel
Not optimum Hbonds; less stable
Anti-parallel
Optimum H-bonds;
more stable
The Beta Turn – 2 Conformations
Only Difference
Tertiary Structure
• Charge based interactions
– 62R:163E
– 55E:170R
• Hydrophobic interactions
– 189V
– 201L
– 213I
– 215L
– 266L
• Disulfide bond
– 203C:259C
1HSA
Peptide bound to
Class I MHC
Quaternary Structure
a2
a1
b2
b1
Tertiary
Secondary
Quaternary
Primary
Summary: Protein Folding and
Protein Structure
References
• "Crystallization, X-ray studies, and site-directed cysteine
mutagenesis of the DNA-binding domain of OmpR", E.
Martínez-Hackert, S. Harlocker, M. Inouye, H. M. Berman
and A. M. Stock, Journal/Protein Sci., 5:1429-1433, 1996.
• http://www.cryst.bbk.ac.uk/ (School of Crystallography,
Birkbeck, University of London)
• "Introduction to protein structure", Brandon and Tooze, 3,
21, 1999.
• Voet, Donald and Judith G. Biochemistry. John Wiley &
Sons, 1990