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Protein Structure
Protein Structure
Protein Structure
Basics of protein
structure
Protein Structure
Protein core - usually conserved.
Protein loops - variable regions
Surface loops
Hydrophobic core
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Supersecondary structures
Assembly of secondary structures which are
shared by many structures.
Beta-alpha-beta unit
Beta
5 hairpin
Helix hairpin
Hemoglobin (1bab)
http://scop.berkeley.edu/count.html
similar structures
conserved sequences
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Comments
X-ray crystallography is the most widely
used method.
Quaternary structure of large proteins
(ribosomes, virus particles, etc) can be
determined by electron microscopes
(cryoEM).
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Protein Databases
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PDB - model
A model defines the 3D positions of atoms in
one or more molecules.
There are models of proteins, protein
complexes, proteins and DNA, protein
segments, etc
The models also include the positions of ligand
molecules, solvent molecules, metal ions, etc.
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http://www.pdb.org/pdb/home/home.do
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Atom
identity
Atom
number
ATOM:
Usually protein
or DNA
HETATM:
Usually Ligand,
ion,
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chain
The coordinates
for each residue in
the structure
Residue
number
Structural Alignment
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Human Hemoglobin
alpha-chain
pdb:1jebA
Human Myoglobin
pdb:2mm1
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:Solution
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:Good result
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:Kinds of transformations
Rotation
Translation
Scaling
and more.
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:Translation
Y
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:Rotation
Y
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Scale:
Y
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Gly
Thr
Glu
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Ala
The aim:
Given two proteins
Find the transformation that produces
the best Superimposition of one protein
onto the other
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Correspondence is Unknown
Given two configurations of points in the three
dimensional space:
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Question:
how do we asses the
quality of the
transformation?
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rmsd(P,Q) = i|pi
- qi |2 /n
i|T(pi) - qi |2 /n
Find the highest number of atoms aligned with the lowest RMSD
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Pitfalls of RMSD
all atoms are treated equally
(residues on the surface have a higher degree of
freedom than those in the core)
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Rigid alignment
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Flexible alignment
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Does the fact that all proteins have alphahelix indicates that they are all evolutionary
related?
No. Alpha helices reflect physical constraints,
as do beta sheets.
For structures it is difficult sometimes
to separate convergent evolution from
evolutionary relatedness.
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