Proteins: structure, translation, etc.Proteins: structure, translation, etc.

Structure of proteins- amino acids, peptide bond, primary-quaternary structures, disulfide bond

Protein synthesis-protein translation, co-translational folding, stalling, etc.

Protein folding and unfolding- Levinthal paradox, acquisition of native structure, loss of structure

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glycine (G)

alanine (A)

valine (V) leucine (L)

Amino acid structuresAmino acid structures

serine (S) threonine (T)

cysteine

methionine (M)

phenylalanine (F) tyrosine (Y)

proline

isoleucine (I)

lysine (K)

tryptophan (W)

histidine (H)

asparticacid (D)

glutamicacid (E)

aspargine (N) glutamine (Q)

arginine (R)

3+

+2

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hydrophobic

MILV

FYW

C

P

small neutral

G(A*)ST

hydrophilic

EDNQ

KRH

Amino acid relationshipsAmino acid relationships

*A is alsofairly hydrophobic

Suggested amino acid substitutions

Amino acids connected by a line can be substituted with 95% confidenceAdapted from D. Bordo and P. Argos (1991) J. Mol. Biol. 217, 721-729.

Solvent exposed(SEA>30 Å2 , )

Interior(SEA<10 Å2, )

SEA, solvent exposed area

aromatic

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©Alberts et al. (1998)

You should know the structure of a polypeptide chain (protein)!

Peptide bond formationPeptide bond formation 2-4

The peptide bondThe peptide bond

R=side chainO=C-N-H is planar(double-bond character)

Phi (Φ) and Psi (ψ) angles can vary;their rotation allows polypeptidesto adopt their various structures(alpha-helices, beta-sheets, etc.)

Ri+1

Ri

cis conformation is rare except for proline

potential for steric hindrance

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Protein structure:Protein structure: overview overview Structural element Description

primary structure amino acid sequence of protein

secondary structure helices, sheets, turns/loops

super-secondary structure association of secondary structures

domain self-contained structural unit

tertiary structure folded structure of whole protein • includes disulfide bonds

quaternary structure assembled complex (oligomer) • homo-oligomeric (1 protein type) • hetero-oligomeric (>1 type)

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Protein structure:Protein structure: helices helices

alpha 3.10 pi

amino acidsper turn: 3.6 3.0 4.4

frequency ~97% ~3% rare

- alpha helices are about10 residues on average

- side chains are wellstaggered, preventingsteric hindrance

- helices can form bundles, coiled coils, etc.

H-bonding

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Protein structure:Protein structure: sheets sheets- the basic unit of abeta-sheet is called abeta-strand

- unlike alpha-helix, sheets can be formed from discontinuous regions of a polypeptide chain

- beta-sheets can formvarious higher-level structures, such as a beta-barrel

anti-parallel

parallel

‘twisted’

GreenFluorescent

Protein(GFP)

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Protein structure:Protein structure: sheets (detail) sheets (detail)

‘twisted’

- notice the difference in H-bonding pattern between parallel and anti-parallel beta-sheets

- also notice orientation of side chains relative to the sheets

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Protein structure:Protein structure: turns/loops turns/loops

ribonuclease A

- there are various types ofturns, differing in the number of residues andH-bonding pattern

- loops are typically longer;they are often called coils and do not have a ‘regular’,or repeating, structure

loop(usually exposed on surface)

alpha-helix beta-sheet

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Ramachandran plotRamachandran plot

Phi (Φ)

Psi (ψ)

- Phi (Φ) and Psi (ψ) rotate, allowing the polypeptide to assume its various conformations

- some conformations of the polypeptide backbone result in steric hindrance and are disallowed

- glycine has no side chain and is therefore conformationally highly flexible (it is often found in turns)

no stericclashes

permittedif atoms aremore closelyspaced

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Types of non-covalent interactionsTypes of non-covalent interactions

interaction naturebond length

“bond” strength example

ionic(salt bridge)

electrostatic 1.8-4.0 Å(3.0-10 Å for like charges)

1-6 kcal/mol

positive: K, R, H,N-terminusnegative: D, E,C-terminus

hydrophobic entropy - 2-3 hydrophobic side chains(M,I,L,V,F,W,Y,A,C,P)

H-bond H-bonding 2.6-3.5 2-10 H donor, O acceptor

van der Waals

attraction/repulsion

2.8-4.0 <1 closely-spaced atoms; if too close, repulsion

aromatic-aromatic

4.5-7.0 1-2 F,W,Y (stacked)

aromatic-amino group

H-bonding 2.9-3.6 2.7-4.9 N-H donor to F,W,Y

these all contribute to some extent to protein structure & stability;- important to understand extremophilic (or any other) proteins

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Protein-solvent interactionsProtein-solvent interactionshydrophilic amino acids (D, E, K, R, H, N, Q)

- these amino acids tend to interact extensively with solvent in context of the folded protein; the interaction is mostly ionic and H-bonding

- there are instances of hydrophilic residues being buried in the interior of the protein; often, pairs of these residues form salt bridges

hydrophobic amino acids (M, I, L, V, F, W, Y, A*, C, P)

- these tend to form the ‘core’ of the protein, i.e., are buried within the folded protein; some hydrophobic residues can be entirely (or partially) exposed

small neutral amino acids (G, A*, S, T)

- less preference for being solvent-exposed or not

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The disulfide bondThe disulfide bond

protein protein+

protein protein

• disulfide bond formation is a covalent modification; the oxidation reaction can either be intramolecular (within the same protein) or inter-molecular (within different proteins, e.g., antibody light and heavy chains). The reaction is reversible.

- most disulfide-bonded proteins are extracellular(e.g. lysozyme contains four disulfide bonds);the conditions inside the cytosol are reducing,meaning that the cysteines are usually in reduced form

- cellular enzymes (protein disulfide isomerases) assist

many proteins in forming proper disulfide bond(s)

oxidation

reduction+ 2 H+ + 2 e-

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Protein foldingProtein folding

“arguably the single most important process in biology”

in the test tube versus in the cell

~40 years ~20 years

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Folding of RNAse A in the test tubeFolding of RNAse A in the test tube

denaturation renaturation

Incubate proteinin guanidine

hydrochloride(GuHCl)or urea

100-folddilution of proteininto physiological

buffer

Anfinsen, CB (1973) Principles that govern the folding of protein chains. Science 181, 223-230.

- the amino acid sequence of a polypeptide is sufficient to specify its three-dimensional conformation

Thus: “protein folding is a spontaneous process that does not require the assistance of extraneous factors”

(aggregation)

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Levinthal paradoxLevinthal paradox

folding

denaturedprotein:

random coil106 possible

conformations

Native protein1 stable

conformation

in vitro in vivo

folding

t = secondst = seconds or much less

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• folding can be thoughtfolding can be thoughtto occur alongto occur along““energy surfaces or energy surfaces or landscapeslandscapes””

• limited number of limited number of secondary structure secondary structure elements: helices,elements: helices,sheets and turnssheets and turns

Protein folding theoryProtein folding theory

Dobson, CM (2001)Phil Trans R Soc Lond 356, 133-145

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Folding of lysozymeFolding of lysozyme

• hen lysozyme has 129 residues, hen lysozyme has 129 residues, consists of 2 domains (α and β)consists of 2 domains (α and β)

hydrophobic collapse

- upon dilution of unfolded protein in buffer, the protein will ‘collapse’ onto itself, trying to bury as many hydrophobic surfaces as possible

- in doing so, the protein may fold properly, or:

- misfold and aggregate

- go through a ‘trapped intermediate’ stage

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Protein synthesis: the ribosomeYusupov et al. (2001) Science 292, 883.

- whole 70S ribosome from Thermus thermophilus at 5.5Å

- small (30S) subunit: 16S RNA, ~20 proteins

- large (50S) subunit: 23S RNA, 5S RNA, >30 proteins

- high concentration in the cell (~ 50 μM)

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Protein synthesis cycleProtein synthesis cycle

interface view of 50S subunit

E-, P-, A-sitetRNAs and mRNA

1. acylation of tRNAs with respective amino acids

2. binding of tRNA charged with methionine to P-site on the AUG start codon (present on the mRNA)

3. next tRNA charged with appropriate amino acid binds A-site

4. transpeptidation (peptide bond formation) between P-site (N-terminal) amino acid and A-site amino acid leads to the growth of the polypeptide chain. The catalysis is by the peptidyltransferase, which consists only of RNA. The ribosome is thus a ribozyme.

5. the E-site represents the ‘exit’ site for the uncharged tRNA

6. release from tRNA and disassembly then occurs

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Elongation of the polypeptide chainElongation of the polypeptide chain

adapted from Selmer et al. (1999) Science 286: 2349-2352

- PT = peptidyltransferase site

- rRNAs are in grey

- proteins are in green

- polypeptide chain model is shown to traverse the ribosome channel from the PT site to the polypeptide exit site

- the channel/tunnel and exit site are quite narrow, meaning that there is likely to be little if any co-translational protein folding in the channel

- possibility of an alpha-helix forming? (“yes”)

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Co-translational protein foldingCo-translational protein folding

folding

assembly

Fact: - first ~30 amino acids of the polypeptide chain present within the ribosome is constrained (the N-terminus emerges first)

Assumption: as soon as the nascent chain is extruded, it will start to fold co-translationally (i.e., acquire secondary structures, super-secondary structures, domains) until the complete polypeptide is produced and extruded

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ObservingObserving co-translation co-translationalal folding folding

N-terminal domain

(~22 kDa)

C-terminal domain

(~40 kDa)

Experiment:1. translate firefly luciferase RNA in vitro in the presence of 35S-methionine for 2 min2. Prevent re-initiation of translation with aurintricarboxylic acid (ATCA): ‘synchronizing’3. at set timepoints, quench translation, incubate with proteinase K (digests unstructured/non-compact regions in proteins, but not folded domains/proteins)4. add denaturing (SDS) buffer, then perform SDS-PAGE (polyacrylamide gel electrophoresis)5. dry gel, observe by autoradiography

FireflyLuciferase(62 kDa)

3Result:

4 5 6 7 8 10 12no

ProK

withProK

min60 kDa40 kDa20 kDa

60 kDa40 kDa20 kDa

2

3 4 5 6 7 8 10 12 min2

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Antibiotics & protein synthesisAntibiotics & protein synthesis

antibiotic effect

cyclohexamide

inhibits the eukaryotic peptidyltransferase; prevents release of the polypeptide chain. Can be used to isolate ribosome-nascent chain complexes

chloramphenicol inhibits the prokaryotic peptidyltransferase

puromycin

causes premature chain termination and release from ribosome. Puromycin is similar to a tyrosyl-tRNA and acts as a substrate during elongation. Once added to the carboxyl end of the nascent chain, protein synthesis is aborted

tetracycline inhibits aminoacyl tRNA binding to the A-site

kanamycin causes misreading of the mRNA

streptomycin causes misreading of the mRNA

antibiotics can be useful tools for manipulating translation, folding

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ssrA RNA in bacteriassrA RNA in bacteria

Solution:- SsrA, or 10SA RNA is a small RNA (363 nt) that resembles a tRNA and can be charged with alanine. It is placed into the peptidyltransferase site by the protein SsrB

- SsrA can be used as a template, and codes a peptide, ANDENYALAA

- the fusion protein containing this sequence is recognized and degraded by the ClpAP or ClpPX proteases

Problem:- turnover (degradation) of mRNA occurs very quickly in bacteria, and the 3’ end of the mRNA has a higher probability of being degraded first

- if the stop codon is removed, there are no signals for mRNA release from the ribosome, and the mRNA will stall

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Nascent chain stalling in eukaryotesNascent chain stalling in eukaryotes- can make proteins that are of a defined length by translating an RNA that is truncated at the 3’ end (i.e., has no stop codon)

Steps:

1. linearize a vector encoding a gene of interest using a restriction enzyme, such that the cut is precisely where you want the polypeptide to end (before the stop codon)

2. make RNA using nucleotides and polymerase enzyme

3. add to an in vitro translation system (rabbit reticulocyte lysate), which has all of the required components to translate the RNA

4. if the RNA is not truncated, the full-length protein will be made and released; if the RNA is truncated, it will remain bound to the ribosome

Note: the protein can be labeled this way with 35S-methionine;co-translational folding still takes place

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Chain stalling:Chain stalling: in practice in practice

Goal: show that firefly luciferase can adopt a folded, functional conformation co-translationally

Experiment:

1. prepare DNA construct that encodes firefly luciferase and an extra 35 amino acids at its C-terminus

2. digest construct such that the last 2 amino acids and the stop codon are removed

3. prepare RNA using polymerase and nucleotides

4. in vitro translate the RNA in rabbit reticulocyte lysate

5. assay for firefly luciferase activity (light emission at 560 nm occurs when luciferin substrate is oxidatively decarboxylated)

Fact: only full-length firefly luciferase is functional

Problem? Hint: does this experiment show physiological relevance?

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Protein folding:Protein folding:in 3 different environmentsin 3 different environments

• ex vivo refolding rabbit reticulocyte lysate - rabbit reticulocyte lysate is an abundant source of molecular chaperones, many of which are ATP-dependent

• in vitro folding environments - protein folding (from denaturant), when possible, requires the proper environment: proper pH, salts, concentration of protein, temperature, stabilizing agents (e.g., other proteins, glycerol, etc.)

• in vivo folding - molecular chaperones, protein folding catalysts, proper redox environment, availability of binding partners

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Following the acquisitionFollowing the acquisitionofof (native) (native) structure structure

denaturation renaturation nativestructure?

• regain of 2º, 3º and 4º structures - by circular dichroism and

fluorescence measurements - by other criteria (e.g., native gel

electrophoresis, SEC,protease sensitivity assays, etc.)

• regain of activity - activity not necessarily enzymatic

Circulardichroism

unfolding

refolding

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Acquisition of native structure: Acquisition of native structure: examplesexamples

• actin - chemically denatured actin can be refolded by incubating it in rabbit reticulocyte lysate; native gel electrophoresis, and binding to DNAse I is used to assess folding

• various small proteins (RNAse A, lysozyme, etc.) - can be denatured chemically and refolded simply by dilution of the denaturing agent; activity assays are available, but folding can be monitored using spectroscopic techniques

• other - small-angle light x-ray scattering (SAXS), NMR are some other techniques used to monitor protein folding

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Protein denaturantsProtein denaturants• high temperatures

- cause protein unfolding, aggregation

• low temperatures - some proteins are sensitive to cold denaturation

• heavy metals (e.g., lead, cadmium, etc.) - highly toxic; efficiently induce the ‘stress response’

• proteotoxic agents (e.g., alcohols, cross-linking agents, etc.)

• oxygen radicals, ionizing radiation- cause permanent protein damage

• chaotropes (urea, guanidine hydrochloride, etc.)- highly potent at denaturing proteins;often used in protein folding studies

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Following the loss of structureFollowing the loss of structure• loss of secondary structure

- the far-UV circular dichroism spectrum of a protein changes at the so-called ‘melting temperature’ or Tm

- fluorescence characteristics will likely also change

• loss of tertiary structure - the far- and near-UV circular dichroism spectra of a protein change, but the Tm of both spectra may be different - fluorescence characteristics will likely also change

• loss of activity - the activity of a protein can be monitored over time

• aggregation - can measure light scattering (e.g., at 320 nm) spectrophoto-metrically, or by detecting the protein in a precipitate

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Loss of structure: Loss of structure: exampleexample

foldedunfolded

intermediate

Far-UVspectrum

Fluorescencespectrum

Noland et al. (1999) Biochemistry 38, 16136.

native

unfolded

2Murea

Urea (M)chymotrypsin

0no

0Yes

1Yes

2Yes

Bacterial luciferase (α subunit)

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