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Reductive denaturation and oxidative renaturation of RNase A. Plausible mechanism for the thiol- or enzyme-catalyzed disulfide interchange reaction in a protein. protein disulfide isomerase. C-chain needed to direct proper disulfide bond formation. Primary structure of porcine proinsulin.

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Plausible mechanism for the thiol or enzyme catalyzed disulfide interchange reaction in a protein l.jpg
Plausible mechanism for the thiol- or enzyme-catalyzed disulfide interchange reaction in a protein

protein disulfide isomerase


Primary structure of porcine proinsulin l.jpg

C-chain needed disulfide interchange reaction in a protein

to direct proper

disulfide bond

formation

Primary structure of porcine proinsulin


Slide4 l.jpg

Determinants of Protein Folding disulfide interchange reaction in a protein

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


Hierarchical organization of globular proteins subdomains l.jpg
Hierarchical organization of globular proteins (subdomains) disulfide interchange reaction in a protein


Slide6 l.jpg

Determinants of Protein Folding (cont.) disulfide interchange reaction in a protein

D. protein structures are highly adaptable

E. secondary structure can be context-dependent


Nmr structure of protein gb1 l.jpg

“chameleon” sequence: disulfide interchange reaction in a protein

AWTVEKAFKTF (unfolded

free in solution)

NMR structure of protein GB1


Slide8 l.jpg

Determinants of Protein Folding (cont.) disulfide interchange reaction in a protein

F. dependence of protein fold on primary sequence


X ray structure of rop protein a homodimer of aa motifs that associate to form a 4 helix bundle l.jpg

created by changing 50% disulfide interchange reaction in a protein

of the 56 residues in GB1

not all residues have equally

important roles in specifying

a specific fold

X-ray structure of Rop protein, a homodimer of aa motifs that associate to form a 4-helix bundle


Slide10 l.jpg

The Levinthal Paradox disulfide interchange reaction in a protein

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 set

of pathways


Slide11 l.jpg

Experimental Methods to Monitor disulfide interchange reaction in a protein

Protein Folding


A stopped flow device 40 m s dead times l.jpg

(UV/ VIS/ fluorescence /CD) disulfide interchange reaction in a protein

cold denatured proteins / T-jump

A stopped-flow device: 40 ms dead-times


Uv absorbance spectra of the three aromatic amino acids phenylalanine tryptophan and tyrosine l.jpg

molar disulfide interchange reaction in a protein

extinction

coefficient

UV absorbance spectra of the three aromatic amino acids, phenylalanine, tryptophan, and tyrosine


Circular dichroism cd spectra of polypeptides l.jpg

e disulfide interchange reaction in a proteinL and eR differ (circularly

polarized light); measure ∆e

Circular dichroism (CD) spectra of polypeptides


Slide15 l.jpg

Pulsed H/D Exchange disulfide interchange reaction in a protein

X-H + D2OX-D + HOD

Used to follow the time course of protein folding by 2D NMR

a. Denatured protein in D2O

b. 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 fold

e. Determine which amide protons are protonated and deuterated


Slide16 l.jpg

Landscape Theory of Protein Folding disulfide interchange reaction in a protein

Polypeptides fold via a series of conformational

adjustments that reduce their free energy and entropy

until the native state is reached.

There is no single pathway or closely related set

of pathways that a polypeptide must follow in folding

to its native state.

The sequence information specifying a particular

fold is both distributed throughout the polypeptide

chain and highly overdetermined.


Folding funnels an idealized funnel landscape l.jpg
Folding funnels: An idealized funnel landscape disulfide interchange reaction in a protein


Folding funnels the levinthal golf course landscape l.jpg
Folding funnels: The Levinthal “golf course” landscape disulfide interchange reaction in a protein


Folding funnels classic folding landscape l.jpg
Folding funnels: Classic folding landscape disulfide interchange reaction in a protein


Folding funnels rugged energy surface l.jpg

Closer mimic disulfide interchange reaction in a protein

of an actual

folding

pathway

Folding funnels: Rugged energy surface


Polypeptide backbone and disulfide bonds of native bpti 58 residues three disulfide bonds l.jpg

Folds via an ordered disulfide interchange reaction in a protein

pathway: involves well

defined intermediates

Polypeptide backbone and disulfide bonds of native BPTI (58 residues, three disulfide bonds)


Slide22 l.jpg
Renaturation of BPTI: disulfide interchange reaction in a proteinprotein primary structures evolved to specify efficient folding pathways as well as stable native conformations


Slide23 l.jpg

Folding accessory proteins disulfide interchange reaction in a protein

A. Protein disulfide isomerases (PDI)

B. Peptidyl prolyl cis-trans isomerases

C. Molecular chaperones


Slide24 l.jpg

A folding accessory disulfide interchange reaction in a protein

protein

Reactions catalyzed by protein disulfide isomerase (PDI). (a) Reduced PDI catalyzes the rearrangement of the non-native disulfide bonds.


Slide25 l.jpg
Reactions catalyzed by protein disulfide isomerase (PDI). ( disulfide interchange reaction in a proteinb) The oxidized PDI-dependent synthesis of disulfide bonds in proteins.


Slide26 l.jpg

homodimer; disulfide interchange reaction in a protein

eukaryotic; each

subunit consists of

four domains

Cys 36 and 39 exposed

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.


Slide27 l.jpg

Cys 36 is located disulfide interchange reaction in a protein

in a hydrophobic

patch

Oxidized PDI-a is

less stable than

reduced PDI-a

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.


Slide28 l.jpg

Peptidyl Prolyl Cis-Trans Isomerases (PPIs) disulfide interchange reaction in a protein

Xaa-Pro peptide bonds: ~10% cis

PPIs catalyze the otherwise slow interconversion

of Xaa-Pro peptide bonds between their cis and

trans conformations; accelerate the folding of

Pro-containing polypeptides.

Two families: cyclophilins and FKBP12 (based on

known inhibitors)


Slide29 l.jpg

Unfolded proteins disulfide interchange reaction in a proteinin vivo have a great tendency to

form intramolecular and intermolecular aggregates.

Molecular chaperones prevent/reverse improper

associations, especially in multidomain and

multisubunit proteins.

Function by binding solvent-exposed hydrophobic

surfaces reversibly to promote proper folding

Many chaperones are ATPases.


Slide30 l.jpg

Classes of Chaperones disulfide interchange reaction in a protein

A. Heat shock proteins 70: 70 kD monomeric proteins

B. Chaperonins: form large multisubunit cage-like assemblies

C. Hsp90: involved in signal transduction; very abundant

in eukaryotes

D. Nucleoplasmins: acidic nuclear proteins involved in

nucleosome assembly


Slide31 l.jpg

Chaperonins disulfide interchange reaction in a protein

GroEL/ES system

14 identical ~60 kD

subunits in two rings;

creates a central

cavity

Electron micrograph-derived 3D image of the Hsp60 (GroEL) chaperonin from the photosynthetic bacterium Rhodobacter sphaeroides.


X ray structure of groel a side view perpendicular to the 7 fold axis l.jpg
X-ray structure of disulfide interchange reaction in a proteinGroEL. (a) Side view perpendicular to the 7-fold axis.


X ray structure of groel b top view along the 7 fold axis l.jpg
X-ray structure of disulfide interchange reaction in a proteinGroEL. (b) Top view along the 7-fold axis.


X ray structure of groes as viewed along its 7 fold axis l.jpg
X-ray structure of disulfide interchange reaction in a proteinGroES as viewed along its 7-fold axis.


X ray structure of the groel groes adp 7 complex l.jpg

cis ring disulfide interchange reaction in a protein

trans ring

X-ray structure of the GroEL-GroES-(ADP)7 complex.


X ray structure of the groel groes adp 7 complex36 l.jpg
X-ray structure of the GroEL-GroES-(ADP) disulfide interchange reaction in a protein7 complex.


X ray structure of the groel groes adp 7 complex37 l.jpg

bound ADP shown disulfide interchange reaction in a protein

in cis ring

X-ray structure of the GroEL-GroES-(ADP)7 complex.


Slide38 l.jpg

apical disulfide interchange reaction in a protein

intermediate

equatorial

Domain movements in GroEL. (a) Ribbon diagram of a single subunit of GroEL in the X-ray structure of GroEL alone.


Domain movements in groel b a groel subunit in the x ray structure of groel groes adp 7 l.jpg
Domain movements in GroEL. ( disulfide interchange reaction in a proteinb) A GroEL subunit in the X-ray structure of GroEL-GroES-(ADP)7.


Slide40 l.jpg
Domain movements in GroEL. ( disulfide interchange reaction in a proteinc) Schematic diagram indicating the conformational changes in GroEL when it binds GroES.


Apical domain of groel in complex with a tight binding 12 residue polypeptide swmttpwgflhp l.jpg
Apical domain of GroEL in complex with a tight-binding 12-residue polypeptide (SWMTTPWGFLHP).


Movements of the polypeptide binding helices of groel l.jpg

(a) 12-residue polypeptide (SWMTTPWGFLHP).

(b)

Movements of the polypeptide-binding helices of GroEL.


Reaction cycle of the groel es chaperonin system in protein folding l.jpg
Reaction cycle of 12-residue polypeptide (SWMTTPWGFLHP).the GroEL/ES chaperonin system in protein folding.


Slide44 l.jpg

Models for GroEL/ES Action 12-residue polypeptide (SWMTTPWGFLHP).

A. Anfinsen cage model: folding within complex

B. Interative annealing: reversible release of partially

folded intermediates


Rate of hydrogen tritium exchange of tritiated rubisco l.jpg

Refolding of RiBisCO; requires 12-residue polypeptide (SWMTTPWGFLHP).

assistance to reach native state

black: no components

red: released only after

native state is reached

green: released

after one turnover

Rate of hydrogen-tritium exchange of tritiated RuBisCO.


Schematic diagram of the mechanism of stretch induced hydrogen exchange by the groel es system l.jpg

exchange with solvent 12-residue polypeptide (SWMTTPWGFLHP).

Schematic diagram of the mechanism of stretch-induced hydrogen exchange by the GroEL/ES system.


Slide47 l.jpg

Protein Structure Prediction 12-residue polypeptide (SWMTTPWGFLHP).

Secondary structure

a) Chou-Fasman method

Frequency at which a given aa occurs in an a helix in a set of protein structures = fa = na/n, where na = number of amino acid residues of the given type that occur in a helices, and n = total number of residues of this type in the protein set

Propensity of a particular aa residue to occur in an a helix =

Pa = fa/<fa>, where <fa> is the average value of fa for all

20 residues

Pa > 1: residue occurs with greater than average frequency

in an a helix

Also applies to b-structure


Propensities and classifications of amino acid residues for a helical and b sheet conformations l.jpg

H 12-residue polypeptide (SWMTTPWGFLHP). = strong former

h = former

I = weak former

i = indifferent

b = breaker

B = strong breaker

Propensities and classifications of amino acid residues for a helical and b sheet conformations.


Slide49 l.jpg

B. Reverse turns: 12-residue polypeptide (SWMTTPWGFLHP).Rose method

Occur on the surface of a protein; locations

of minimal hydropathy (exclude helical regions)


Slide50 l.jpg

Rationale for Observed Propensities 12-residue polypeptide (SWMTTPWGFLHP).

For a-helix: appears related to the amount of side-chain

hydrophobic surface buried in the protein

For Pro: low a propensity caused by strain

For Gly: low a propensity caused by reduced entropy and

lack of hydrophobic stabilization

For Ala: high a propensity caused by lack of a g substituent;

reduced entropic cost; minimal hydrophobic stabilization


Slide51 l.jpg

Computer-based Secondary Structure Algorithms 12-residue polypeptide (SWMTTPWGFLHP).

Combine three or more methods: accurate to ~75%

Jpred: public domain software

The moderate accuracy is caused by failure to take tertiary

interactions into account (tertiary structure influences

secondary structure).


Secondary structure prediction in adenylate kinase n terminal 24 residues l.jpg
Secondary structure prediction in adenylate kinase ( 12-residue polypeptide (SWMTTPWGFLHP). N-terminal 24 residues)


Slide53 l.jpg

Tertiary Structure Prediction 12-residue polypeptide (SWMTTPWGFLHP).

a. comparative or homology modeling

b. fold recognition or threading

c. ab initio methods


Structures of the second zinc finger motif of zif268 dna binding protein x ray structure l.jpg

Protein 12-residue polypeptide (SWMTTPWGFLHP).

Design

Structures of the second zinc finger motif of Zif268 (DNA-binding protein): X-ray structure.


Structure of de novo designed peptide fsd 1 nmr structure a bba motif 28 residues l.jpg

sequence has 12-residue polypeptide (SWMTTPWGFLHP).

only 6 of the

28 residues

identical to Zif268 (5 are similar)

group of Phe

residues replaces

zinc finger

Structure of de novo designed peptide, FSD-1: NMR structure (a bba motif; 28 residues)


Slide56 l.jpg
Comparison of the structures of the second zinc finger motif of Zif268 and FSD-1: best-fit superpositions of their backbones.


Slide57 l.jpg

Protein Dynamics of Zif268 and FSD-1: best-fit superpositions of their backbones.

Proteins undergo structural motions that have

functional significance.


Conformational fluctuations breathing motions in the oxygen binding protein myoglobin l.jpg
Conformational fluctuations (breathing motions) in the oxygen binding protein, myoglobin.


Slide59 l.jpg

Classes of Motions oxygen binding protein, myoglobin.

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


The mobility of the groel subunit in the x ray structure of groel alone l.jpg

blue = least mobile oxygen binding protein, myoglobin.

red = most mobile

The mobility of the GroEL subunit in the X-ray structure of GroEL alone.


The mobility of the groel subunit in the x ray structure of the groel groes adp 7 complex l.jpg

blue = least mobile oxygen binding protein, myoglobin.

red = most mobile

The mobility of the GroEL subunit in the X-ray structure of the GroEL-GroES-(ADP)7 complex.


Slide62 l.jpg
The internal motions of myoglobin as determined by a molecular dynamics simulation: the Ca backbone and the heme group.


The internal motions of myoglobin as determined by a molecular dynamics md simulation an a helix l.jpg
The internal motions of myoglobin as determined by a molecular dynamics (MD) simulation: an a helix.


Slide64 l.jpg

Detecting molecular dynamics (MD) simulation: an

infrequent

motions (time

scale of seconds)

Exchange rate of

a particular proton

correlates with the

conformational

mobility of its

surroundings

The hydrogen-tritium “exchange-out” curve for hemoglobin that has been pre-equilibrated with tritiated water.


Slide65 l.jpg

Conformational Diseases: Amyloid and Prions molecular dynamics (MD) simulation: an

Alzheimer’s disease; transmissible spongiform encephalopathies (TSEs); amyloidoses

Common characteristic: formation of amyloid fibrils

The involved proteins assume two different

stable conformations (native and amyloid)



Amyloid fibrils prp 27 30 model a and isolated b b sheet l.jpg

a of the protein PrP 27-30.

b

Fibrils consist mainly of

b-sheets whose b-strands

are perpendicular to the

fibril axis.

Amyloid fibrils (PrP 27-30): Model (a) and isolated (b) b sheet.


Superposition of wild type human lysozyme and its d67h mutant l.jpg

Amyloidogenic proteins of the protein PrP 27-30.

are mutant forms of

normally occuring proteins

Lysozyme mutants

occur in familial visceral

amyloidosis

Superposition of wild-type human lysozyme and its D67H mutant.


Slide69 l.jpg

Prion of the protein PrP 27-30.Diseases

Evidence that the scrapie agent is a protein: scrapie agent is inactivated by treatment with diethylpyrocarbonate, which reacts with His sidechains.


Slide70 l.jpg

Evidence that the scrapie agent is a of the protein PrP 27-30.protein: scrapie agent is unaffected by treatment with hydroxylamine, which reacts with cytosine residues.


Slide71 l.jpg
Evidence that the scrapie agent is a of the protein PrP 27-30.protein: hydroxylamine rescues diethylpyrocarbonate-inactivated scrapie reagent.


Slide72 l.jpg

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.


Prion protein conformations a plausible model for the structure of prp sc very insoluble l.jpg

Prion hypothesis: PrP protein (PrPSc

induces the conversion of

PrPC to PrpSc

Conversion may be mediated

by a molecular chaperone.

Prion protein conformations: a plausible model for the structure of PrPSc (very insoluble)


Slide74 l.jpg

END protein (PrP


Figure 9 36 molecular formula for iron protoporphyrin ix heme l.jpg
Figure 9-36 protein (PrP Molecular formula for iron-protoporphyrin IX (heme).


Figure 9 37 primary structures of some representative c type cytochromes l.jpg
Figure 9-37 protein (PrP Primary structures of some representative c-type cytochromes.


Slide77 l.jpg
Figure 9-38 protein (PrP Three-dimensional structures of the c-type cytochromes whose primary structures are displayed in Fig. 9-37.


Figure 9 39 the two structurally similar domains of rhodanese l.jpg
Figure 9-39 protein (PrP The two-structurally similar domains of rhodanese.


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