Principles of Protein Structure
Amino Acids - Basic Building Blocks of Proteins
Amino Acids Have
Molecular Chirality Molecular Chirality
Proteins are Polymers
Cis Proline in the Active Site of HCV NS2 Cis Pro 164
Cys 184
Glu 163 3.0 Å
4.1 Å 3.0 Å
3.2 Å
3.1 Å 3.1 Å His 143
Leu 217 (C-term)
Nature 2006 vol. 442 (7104) pp. 831-5
Cis trans Proline Isomerase • Cyclophilins are a family of proteins that catalyze the isomerization of peptide backbones at a proline • Critically important for protein folding • Cyclospronine is a potent immunosuppressant and an inhibitor of cyclophilins • Commonly used after organ transplant
Four Levels of Protein Structure Four Levels of Protein Structure • Primary, 1o! – Amino acid sequence; Covalent bonds"
• Secondary, 2o! – Local conformation of main-chain atoms (Φ and Ψ 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 Four Levels of Protein Structure Structure • Primary, 1o " TPEEKSAVTALWGKV" • Secondary, 2o!
• Tertiary, 3o!
• Quaternary, 4o!
α2
α1
β2
β1
β2
Side Chain Conformation
Protein Backbone Conformation
α Helices
α 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 H-bonded to C=O of residue n+4. • a-Helix has: – 3.6 residues per turn – Rise/residue = 1.5 Å – Rise/turn = 5.4Å
Secondary Structure: Alpha Helices Right handed
Left handed
310 and π Helices
310 helix H-bonds n and n+3 π helices H-bonds n and n+5
α Helix • R-groups in α-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
β 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.
β Sheet - 2 Orientations Parallel Not optimum Hbonds; less stable
Anti-parallel Optimum H-bonds; more stable
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 α2
α1
β2
β1
PDB File
Inter-atomic
Internal coordinates: bond lengths distances: (distance between bonded atoms)
Interatomic Distances Atomic coordinates
a1 = (a1x, a1y, a1z)
a2 = (a2x, a2y, a2z)
Bond length
b12 = ((a2x–a1x )2+(a2y–a1y )2 +(a2z–a1z )2)1/2
a2 b12
a1
PDB file 3e7l
Bonded distances don’t change much:
Bond Lengths Remain Constant
lengths: Chain A backbone
1.459±0.003 Å 1.527±0.003 Å 1.329±0.001 Å
Bond or “valence” angles: Internal coordinates: valence angles
(complement of angle formed by successive chemical bonds)
Bond Angles
Atomic coordinates
a1 = (a1x, a1y, a1z)
a2 = (a2x, a2y, a2z)
a3 = (a3x, a3y, a3z)
Bond vectors
b12 = (a2x–a1x, a2y–a1y, a2z–a1z)
b23 = (a3x–a2x, a3y–a2y, a3z–a2z)
Scalar product
b12"b23
= (a2x–a1x)(a3x–a2x)+(a2y–a1y)(a3y–a2y)+(a2z–a1z)(a3z–a2z)
a2 b12 a1
!123
b23
b12"b23 = b12b23 cos("–!123)
a3
cos!123 = –b12"b23/(b12b23) cos("–!123) = cos" cos!123 + sin" sin!123 = – cos!123
Distribution of Backbone Angles
PDB file 3e7l Distribution of backbone angles:
Valence angles: Chain A backbone
112.0±1.5° 116.4±0.5° 121.7±0.7°
Distribution of B-factors
Motifs, Topologies and Folds: β Sheet The arrangement of secondary structure elements that give rise to a folded entity
Motifs, Topologies and Folds: β Sheet
Motifs, Topologies and Folds: βαβ
Motifs, Topologies and Folds: α-helical
Motifs, Topologies and Folds: α-helical C
N Middle Domain of eIF4G - scaffold protein for translation initiation factors.
Protein Domains
• A folded unit of protein • normally formed around a hydrophobic core
• Tend to be globular • 150-250 amino acids
Protein Domains Many Eukaryotic proteins consist of multiple domains
•
Limited proteolysis can be used to experimentally determine domain limits.
Limited Trypsin Digestion in the Absence and Presence of dsRNA
Domain Swapping
Location of His 143, Glu 163, Cys 184
Glu
His
Cys
Cys
35Å
Glu His
HIV Protease
Retroviral aspartic protease - dimerization forms a single active site
Structural Comparison • Structural comparison requires a 3-Dimension search • Minimize the search by using just secondary structural elements - Potential problem? • DALI server http://ekhidna.biocenter.helsinki.fi/dali_server/ • PDBe/fold http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ ssmserver • VAST http://www.ncbi.nlm.nih.gov/Structure/VAST/
SCOP:Structural Classification Of Proteins SCOP database classifies domains not entire proteins
CATH:Class, Architecture, Topology, Homologous Superfamily
How to classify proteins with same general arrangement of secondary structure but are connected differently?
