protein structure classification & determination Flashcards
Protein Structure DeterminationMethods
X-ray crystallography and NMR (Nuclear Magnetic Renosance)
X-ray crystallography steps
purify protein, crystallize protein, collect diffraction data, calculate electron density, fit residues into density
diffraction
spreading of light from X-rays to crystalline solid
X-ray crystallography pros
pros: no size limit, well established
X-ray crystallography cons
cons: difficult for membrane proteins, cannot “see” hydrogen atoms, not every protein can be crystallized
in x-ray structure resolution, the lower the number . . .
the better the resolution
NMR steps
Nuclear Magnetic Resonance
purify protein, dissolve protein, collect NMR data, assign NMR signals, calculate the structure
NMR Pros
Pros: no crystallizing protein, can get hydrogen atom positions
NMR Cons
Cons: difficult for insoluble proteins, works best with small proteins (<50 kd)
diffraction pattern in x-ray crystallography
crucial step in determining the atomic structure of a crystal
Intrinsically Disordered Proteins
proteins segments rhat lack definable structure
VERY flexible so you can’t capture information
AAs that make structures less defined: K, R, E, P
PDB ID
4 letter unique ID
first is a #
rest is letters
ex: 1PHD, 1GUO
domain
basic units for protein structure comparison/classification.
What is considered a structural domain?
- a domain is a compact, semi-independent units with an identifiable hydrophobic core
- a domain can be one continuous fragment OR two or more discontinuous fragments
SCOP classification
four major levels: class, fold, superfamily, and family
Key questions: what does it mean if two domains are at the same level? For example, fold level, family level
If they are similar at fold level, they are structurally similar. If they are similar at family level, they are evolutionary similar to each other and most likely related.
SCOP ID
onsists of four character/numbers
ex: a.2.54.5
a class in SCOP
all alpha proteins
b class in SCOP
all beta proteins
c class in SCOP
alpha and beta proteins (a/b)
mainly parallel beta sheets
d class in SCOP
alpha and beta proteins (a+b)
segregated alpha and beta regions; anti-parallel beta
