Hierarchy of Protein Structure 20 different amino acids: many combinations The order of amino acids:...
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Transcript of Hierarchy of Protein Structure 20 different amino acids: many combinations The order of amino acids:...
Hierarchy of Protein StructureHierarchy of Protein Structure
• 20 different amino acids: many combinations
The order of amino acids: Protein sequencePrimary Structure
Conformation varies depending on sequenceSecondary Structure
Overall structure of the chain in full 3DTertiary Structure
Protein SequencesProtein Sequences
A protein of n residues 20n possible sequences!
100 residue protein has 10020 possibilities 1.3 X 10130!
The latest estimates indicate on 40,000 sequences in the human genome THERE MUST BE RULES!
• 20 different amino acids: many combinations
N C
1 2 3 4
Amino terminus Carboxyl terminus
Residue number
Protein SequencesProtein Sequences
Minimum length for performing a function ~40
Molecular machines not perfect- errors
Function requires specific amino acid properties
Not all amino acids are equally useful
Abundant: Leu, Ala, Gly, Ser, Val, Glu
Rare: Trp, Cys, Met, His
Post-translational modifications Addition of co-factors- metals, hemes Chemical modification- phosphate, glycos.
*Length is generally 100-1000 residues*
Protein SequencesProtein SequencesThe pattern of amino acid side chains determines the secondary (and tertiary!!) structure
*Pattern is more important than exact sequence*
A T V R L L E W E D L
Reporting/Comparing Protein Sequences
A T V R L L E Y K D L5 10
h-CaM
b-CaM
conservative non-conservative
Secondary StructureSecondary Structure
Local structure of consecutive amino acids
Common regular secondary structures Helix Sheet turn
Amino acids have a greater propensity to form some secondary structures versus others
Chemical properties Spatial constraints
The Peptide BondThe Peptide Bond
-C - N-
O
=
-H-C = N-
O-
-
-H
Resonance structures
Peptide plane is flat angle ~180º
Partial double-bond:
Peptide bond
ackbone Conformationackbone Conformation
angle is fixed, and angles vary
Many / combinations cause atoms to collide
C
HR
Peptide planes
ackbone Conformationackbone Conformation
Side chains collision also limit /combinations
Backbone restricted Secondary structure limited
C
HR
C
H R
C
H R
Specific Secondary StructuresSpecific Secondary Structures
Three acceptable backbone combinations1. Right-hand helix: -helix (-40°, -60°) 2. Extended: antiparallel -sheet (140°, -140°)3. Left-hand helix (rarerare): -helix (45°, 45°)Glycine: special because it has no side chain!
Side chains positioned to minimize collisions amino acids prefer specific secondary structures
Hydrogen bonds between backbone atoms provide unique stability to secondary structures
Secondary Structure- Secondary Structure- Sheet Sheet
Oxygen Nitrogen
R Group
Hydrogen
Carbon Carbonyl C
H Bond
Secondary Structure- Secondary Structure- Helix Helix
H-bond
Secondary Structure- Secondary Structure- Turn Turn
1
43
2
Reverses direction of the chain