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folding
Review
The sequence dictates the 3D structure
Poten9al problems to finding the final na9ve structure
1. Exposed hydrophobic surfaces forcing aggrega9on – Solu9on: Chaperones
2. Incorrect disulfide bonds – Solu9on: PDI (Protein Disulfide Isomerases)
3. Isomeriza9on of proline residues, all X-Pro are made trans, some need to be
cis – Solu9on: PPI (Pep9dyl Proline cis-trans Isomerases )
Protein folding experiments
Proteins are marginally stable – important for biology (dynamics/func9on,
protein turnover)
Contribu9ons to free energy of folding of soluble proteins /
Factors governing stability of proteins:
ΔG = ΔH - TΔS
The covalent bonds are the same in U and F, so
plays no role (with the excep;on of disulfides).
Entropic (ΔS) – unfavorable – (many
conforma9ons in U, a single conforma9on in F
Hydrophobic effect – favorable - burial of
hydrophobic side chains, releases water results in
an increase ΔS
Enthalpic (ΔH) – favorable – forma9on of Non-
covalent interac9on in F : H-bonds, electrosta9c
vdW
Net result is a marginally stable protein.
Intramolecular chaperones
Proenzymes.
Prohormones.
Type I : N-terminal pep9de
Helps in folding – ter9ary structure
Type II : C-terminal pep9de
Helps in assembly - quaternary structure
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NaIvely (inherently, intrinsically)
Unstructured (disordered, unfolded)
Proteins
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NaIvely unstructured proteins
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NaIvely unstructured proteins
challenges the tradiIonal protein structure paradigm:
which states that a specific well-defined structure is required for the
correct func9on of a protein and that the structure defines the funcIon
of the protein.
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Example of inherently unstructured protein
BamCD complex
Components involved in the Assembly of beta-barrel membrane proteins
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9
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BamCD complex co-crystal structure
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Structural changes in BamD upon binding BamC
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An inherently unstructured
region of protein can cover a
large amount of protein
surface with few residues
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Potential control (regulation) mechanism for BAM?
By looking at how other structurally related proteins
(or even other machines) work,
you can find clues to how your protein may work
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Sequence signatures of disorder
• low content of bulky hydrophobic amino acids
• Thus disordered sequences cannot bury sufficient hydrophobic core to fold like
stable globular proteins.
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IdenIficaIon of intrinsically unstructured proteins
• once purified.
• Folded proteins have a high density (par9al specific volume of 0.72-0.74 mL/g) and
commensurately small radius of gyraIon. Hence, unfolded proteins can be
detected by methods that are sensi9ve to molecular size, density or hydrodynamic
drag, such as size exclusion chromatography, analyIcal ultracentrifugaIon, Small
angle X-ray scaRering (SAXS).
Since amino acid sequence determines 3-D structure, amino acid sequence should also
determine lack of 3-D structure
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Why are regions of sequence missing
in high-resolu9on crystal structures?
intrinsically disordered loops?
Many crystallographic structures have missing loops -- that is, ranges of amino acids
with no atomic coordinates in the model.
These "gaps" in the model are oien thought to be ar9facts of inadvertent disorder
in the crystal.
In some cases, these gaps may be aler9ng us to the presence of intrinsically
disordered loops in an otherwise folded protein.
Such gaps are the basis for the DISOPRED2 disorder predic9on server.
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Macromolecular crowding
It’s very crowded in the cell
Why don’t all the proteins aggregate and precipitate out of solution?
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Distribution of pI values for eukaryotic proteins by location in the cell.
Cytoplasmic proteins (CP)= red
Integral membrane proteins (MP) = blue
Nuclear proteins (NP)= green
β-augmentaIon
Amyloid-beta Precursor Protein (APP)
a large membrane protein in nerves.
Plays a role in neural growth and repair.
β-secretase
Amyloid-β pepIde
γ-secretase
pepsin
first enzyme to be discovered
(18th century)
second enzyme to be crystallized
(aier urease).
Beta-secretase These crystals played an
HIV protease important role in showing that
enzymes were proteins and that
they had a defined structure.
Pepsin works its best in strong
hydrochloric acid
Transmissible spongiform encephalopathies (TSEs)
Gly
Ubiqui9n Ligase
Proteasome:
Proteasome: cell's protein recyclers
19S regulatory
par9cle
7α
7α
19S regulatory
par9cle
Bacterial Signal pepIde pepIdase
SppA (protease IV)
E. coli SppA
cleaves signal pep9des
Novak & Dev 1988
• 618 residues
• Anchored to the inner
membrane
• sequence analysis
suggested
3 transmembrane segments
29-45, 398-414 and 421-441
E. coli SppA : soluble domain (Δ2–46, 1TM domain removed)
2.5Å resolu9on
extension
Ser409 / Lys209 region
at the interface
of 2 domains
Lys209
Ser409 globular
region
Gene duplicaIon:
2 domains: 56-316, 326-549
linker Only 18% idenIty,
rmsd= 2.5 Å
SppA is a tetrameric bowl shaped structure
Compartmentalized protease
Posi9vely charged
Axial hole
Hydrophobic
interior
Dimensions
SEC / light sca_ering
shows tetramer
4 acIve sites
SppA has structural similarity to
Ser/His/Asp protease ClpP
Larger SppA
Gram-nega9ve bacteria
Thylakoid
2.4 Å resolution
Dyad assembled from
neighboring protomers
Octamer in soluIon
SEC-MALS
AcIve site
assembled from 2 protomers
2.4 Å resolu9on
C-terminal pep9de found within BsSppA
Intramolecular chaperones