Reductive denaturation and oxidative renaturation of RNase A.
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Transcript of Reductive denaturation and oxidative renaturation of RNase A.
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Reductive denaturation and oxidative renaturation of RNase A
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Plausible mechanism for the thiol- or enzyme-catalyzed disulfide interchange reaction in a protein
protein disulfide isomerase
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Primary structure of porcine proinsulin
C-chain neededto direct properdisulfide bond
formation
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Determinants of Protein Folding
A. helices/sheets predominate in proteins because they fill space efficiently
B. protein folding is directed mainly by internal residues (protein folding is driven by hydrophobic forces)
C. protein structures are organized hierarchically
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Hierarchical organization of globular proteins (subdomains)
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Determinants of Protein Folding (cont.)
D. protein structures are highly adaptableE. secondary structure can be context-dependent
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NMR structure of protein GB1
“chameleon” sequence:AWTVEKAFKTF (unfolded
free in solution)
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Determinants of Protein Folding (cont.)
F. dependence of protein fold on primary sequence
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X-ray structure of Rop protein, a homodimer of motifs that associate to form a 4-helix bundle
created by changing 50%of the 56 residues in GB1
not all residues have equallyimportant roles in specifying
a specific fold
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The Levinthal Paradox
2n backbone torsions, n-residue protein: ~10n
structures
time to explore all structures: t = 10n/1013 s-1
for a 100-residue protein: t = 1087 s
Conclusion: proteins fold via an ordered pathway or setof pathways
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Experimental Methods to MonitorProtein Folding
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A stopped-flow device: 40 s dead-times
(UV/ VIS/ fluorescence /CD)
cold denatured proteins / T-jump
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UV absorbance spectra of the three aromatic amino acids, phenylalanine, tryptophan, and tyrosine
molarextinctioncoefficient
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Circular dichroism (CD) spectra of polypeptides
L and R differ (circularlypolarized light); measure ∆
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Pulsed H/D Exchange
X-H + D2O X-D + HOD
Used to follow the time course of protein folding by 2D NMR
a. Denatured protein in D2Ob. Dilute with H2O and allow to fold for time tf
c. Increase pH to initiate D-H exchange (10-40 ms)d. Lower pH; allow to completely folde. Determine which amide protons are protonated and deuterated
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Landscape Theory of Protein Folding
Polypeptides fold via a series of conformationaladjustments that reduce their free energy and entropy
until the native state is reached.
There is no single pathway or closely related setof pathways that a polypeptide must follow in folding
to its native state.
The sequence information specifying a particularfold is both distributed throughout the polypeptide
chain and highly overdetermined.
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Folding funnels: An idealized funnel landscape
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Folding funnels: The Levinthal “golf course” landscape
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Folding funnels: Classic folding landscape
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Folding funnels: Rugged energy surface
Closer mimicof an actual
foldingpathway
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Polypeptide backbone and disulfide bonds of native BPTI (58 residues, three disulfide bonds)
Folds via an orderedpathway: involves welldefined intermediates
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Renaturation of BPTI: protein primary structures evolved to specify efficient folding pathways as well as stable native
conformations
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Folding accessory proteins
A. Protein disulfide isomerases (PDI)B. Peptidyl prolyl cis-trans isomerasesC. Molecular chaperones
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Reactions catalyzed by protein disulfide isomerase (PDI). (a) Reduced PDI catalyzes the rearrangement of the non-native disulfide bonds.
A folding accessoryprotein
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Reactions catalyzed by protein disulfide isomerase (PDI). (b) The oxidized PDI-dependent synthesis of disulfide bonds in proteins.
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NMR structure of the a domain of human protein disulfide isomerase (PDI-a) in its oxidized form. (a) The polypeptide backbone is shown in ribbon form.
homodimer;eukaryotic; each
subunit consists offour domains
Cys 36 and 39 exposed
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NMR structure of the a domain of human protein disulfide isomerase (PDI-a) in its oxidized form. (b) The molecular structure as viewed from the bottom.
Cys 36 is locatedin a hydrophobic
patch
Oxidized PDI-a isless stable thanreduced PDI-a
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Peptidyl Prolyl Cis-Trans Isomerases (PPIs)
Xaa-Pro peptide bonds: ~10% cis
PPIs catalyze the otherwise slow interconversionof Xaa-Pro peptide bonds between their cis andtrans conformations; accelerate the folding ofPro-containing polypeptides.
Two families: cyclophilins and FKBP12 (based onknown inhibitors)
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Unfolded proteins in vivo have a great tendency toform intramolecular and intermolecular aggregates.
Molecular chaperones prevent/reverse improperassociations, especially in multidomain and multisubunit proteins.
Function by binding solvent-exposed hydrophobic surfaces reversibly to promote proper folding
Many chaperones are ATPases.
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Classes of Chaperones
A. Heat shock proteins 70: 70 kD monomeric proteins
B. Chaperonins: form large multisubunit cage-like assemblies
C. Hsp90: involved in signal transduction; very abundantin eukaryotes
D. Nucleoplasmins: acidic nuclear proteins involved innucleosome assembly
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Electron micrograph-derived 3D image of the Hsp60 (GroEL) chaperonin from the photosynthetic bacterium Rhodobacter sphaeroides.
Chaperonins
GroEL/ES system
14 identical ~60 kDsubunits in two rings;
creates a centralcavity
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X-ray structure of GroEL. (a) Side view perpendicular to the 7-fold axis.
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X-ray structure of GroEL. (b) Top view along the 7-fold axis.
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X-ray structure of GroES as viewed along its 7-fold axis.
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X-ray structure of the GroEL-GroES-(ADP)7 complex.
cis ring
trans ring
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X-ray structure of the GroEL-GroES-(ADP)7 complex.
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X-ray structure of the GroEL-GroES-(ADP)7 complex.
bound ADP shown in cis ring
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Domain movements in GroEL. (a) Ribbon diagram of a single subunit of GroEL in the X-ray structure of GroEL alone.
apical
intermediate
equatorial
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Domain movements in GroEL. (b) A GroEL subunit in the X-ray structure of GroEL-GroES-(ADP)7.
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Domain movements in GroEL. (c) Schematic diagram indicating the conformational changes in GroEL when it binds GroES.
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Apical domain of GroEL in complex with a tight-binding 12-residue polypeptide (SWMTTPWGFLHP).
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Movements of the polypeptide-binding helices of GroEL.
(a) (b)
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Reaction cycle of the GroEL/ES
chaperonin system
in protein folding.
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Models for GroEL/ES Action
A. Anfinsen cage model: folding within complex
B. Interative annealing: reversible release of partiallyfolded intermediates
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Rate of hydrogen-tritium exchange of tritiated RuBisCO.
Refolding of RiBisCO; requiresassistance to reach native state
black: no components
red: released only afternative state is reached
green: releasedafter one turnover
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Schematic diagram of the mechanism of stretch-induced hydrogen exchange by the GroEL/ES system.
exchange with solvent
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Protein Structure Prediction
Secondary structurea) Chou-Fasman method
Frequency at which a given aa occurs in an helix in a set of protein structures = f = n/n, where n = number of amino acid residues of the given type that occur in helices, and n = total number of residues of this type in the protein set
Propensity of a particular aa residue to occur in an helix =P = f/<f>, where <f> is the average value of f for all20 residues
P > 1: residue occurs with greater than average frequencyin an helix
Also applies to -structure
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Propensities and classifications of amino acid residues for helical and sheet conformations.
H = strong formerh = formerI = weak formeri = indifferentb = breakerB = strong breaker
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B. Reverse turns: Rose method
Occur on the surface of a protein; locationsof minimal hydropathy (exclude helical regions)
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Rationale for Observed Propensities
For -helix: appears related to the amount of side-chainhydrophobic surface buried in the protein
For Pro: low propensity caused by strain
For Gly: low propensity caused by reduced entropy andlack of hydrophobic stabilization
For Ala: high propensity caused by lack of a substituent;reduced entropic cost; minimal hydrophobic stabilization
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Computer-based Secondary Structure Algorithms
Combine three or more methods: accurate to ~75%
Jpred: public domain software
The moderate accuracy is caused by failure to take tertiaryinteractions into account (tertiary structure influencessecondary structure).
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Secondary structure prediction in adenylate kinase ( N-terminal 24 residues)
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Tertiary Structure Prediction
a. comparative or homology modelingb. fold recognition or threadingc. ab initio methods
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Structures of the second zinc finger motif of Zif268 (DNA-binding protein): X-ray structure.
ProteinDesign
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Structure of de novo designed peptide, FSD-1: NMR structure (a motif; 28 residues)
sequence hasonly 6 of the28 residues
identical to Zif268 (5 are similar)
group of Pheresidues replaces
zinc finger
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Comparison of the structures of the second zinc finger motif of Zif268 and FSD-1: best-fit superpositions of their backbones.
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Protein Dynamics
Proteins undergo structural motions that have functional significance.
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Conformational fluctuations (breathing motions) in the oxygen binding protein, myoglobin.
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Classes of Motions
1. atomic fluctuations (10-15-10-11 s; 0.01 - 1Å displacements) 2. collective motions (10-12-10-3 s; 0.01 - 5 Å displacements)3. triggered conformational changes (10-9 -103 s; 0.5 - 10 Å
displacements)
Techniques: crystallography, NMR, MD
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The mobility of the GroEL subunit in the X-ray structure of GroEL alone.
blue = least mobilered = most mobile
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The mobility of the GroEL subunit in the X-ray structure of the GroEL-GroES-(ADP)7 complex.
blue = least mobilered = most mobile
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The internal motions of myoglobin as determined by a molecular dynamics simulation: the C backbone and the heme group.
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The internal motions of myoglobin as determined by a molecular dynamics (MD) simulation: an helix.
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The hydrogen-tritium “exchange-out” curve for hemoglobin that has been pre-equilibrated with tritiated water.
Detectinginfrequent
motions (timescale of seconds)
Exchange rate ofa particular protoncorrelates with the
conformational mobility of itssurroundings
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Conformational Diseases: Amyloid and Prions
Alzheimer’s disease; transmissible spongiform encephalopathies (TSEs); amyloidoses
Common characteristic: formation of amyloid fibrils
The involved proteins assume two differentstable conformations (native and amyloid)
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Amyloid fibrils: an electron micrograph of amyloid fibrils of the protein PrP 27-30.
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Amyloid fibrils (PrP 27-30): Model (a) and isolated (b) sheet.
a b
Fibrils consist mainly of-sheets whose -strandsare perpendicular to the
fibril axis.
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Superposition of wild-type human lysozyme and its D67H mutant.
Lysozyme mutants
occur in familial visceral
amyloidosis
Amyloidogenic proteinsare mutant forms of
normally occuring proteins
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Evidence that the scrapie agent is a protein: scrapie agent is inactivated by treatment with diethylpyrocarbonate, which reacts with His sidechains.
Prion Diseases
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Evidence that the scrapie agent is a protein: scrapie agent is unaffected by treatment with hydroxylamine, which reacts with cytosine residues.
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Evidence that the scrapie agent is a protein: hydroxylamine rescues diethylpyrocarbonate-inactivated scrapie reagent.
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Prion protein conformations: NMR structure of human prion protein (PrPC). Note the disordered N-terminal tail residues (dots). PrP may be a cell-surface signal receptor.
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Prion protein conformations: a plausible model for the structure of PrPSc (very insoluble)
Prion hypothesis: PrPSc induces the conversion of
PrPC to PrpSc
Conversion may be mediatedby a molecular chaperone.
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END
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Figure 9-36 Molecular formula for iron-protoporphyrin IX (heme).
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Figure 9-37 Primary structures of some representative c-type cytochromes.
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Figure 9-38 Three-dimensional structures of the c-type cytochromes whose primary structures are displayed in Fig. 9-37.
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Figure 9-39 The two-structurally similar domains of rhodanese.