Protein folding Flashcards
Explain the formula for Gibbs energy
∆G = ∆H - T ∆S
∆H is positive because bonds are broken ➜ you need energy to break bonds.
∆S is positive because disorder increases in the unfolded state - atoms have more free choice of position.
Levels of protein structure
- Primary structure - amino acid sequence
- Secondary structure - local structural motifs
- Tertiary structure - domains
- Quaternary structure - domain-domain contacts
What are random coils?
unfolded proteins, they have free rotation around all bonds and very few intramolecular interactions. All molecules have different, random conformations.
What does the Ramachandran plot shows and what are torsion angles?
Is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure
–>The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide planar.
–> Values of the other backbone torsion angles y and F are limited
–>The geometry of the alpha helix is strongly defined in comparisson with the beta geometry.
How are tertiary structures classified? Name some examples.
FOLDS
- Rosmann fold
- Immunoglobulin
- Tim Barrel
What is the Anfinsen´s Dogma?
–> FOLDING CODE states that, at least for a small globular protein in its standard physiological environment, the native structure is determined only by the protein’s amino acid sequence
How does hydrophobic interactions between AA afects the folding process?
favorable hydrophobic interactions must overcome the unfavorable: + charge-charge + polar-polar + charge-polar interactions of the polar and charged AA.
This allows the ∆G of the folded state to become lower than the ∆G of the unfolded state.
What is the Levinthal´s paradox?
–> FOLDING SPEED protein folding is sped up and guided by the rapid formation of local interactions which then determine the further folding of the peptide; this suggests local amino acid sequences which form stable interactions and serve as nucleation points in the folding process. => specific pathway with folding intermediates.
Calculate how long would it take for a 100 AA long protein to fold?
Each residue 3 conformations, so, then there are 3^100 (5 x 1047) possible conformations.
Each chain moves within a femto second ( 10^-15), therefore we need 5 x 10^32 s to explore all confirmations.
32x106 s in a year –> 1x10^27 years to fold.
–> many proteins are bigger and the number is the age of the universe basically.
Kinds of bonds exist in a folded protein, and how to they help the folding process.
- Folding relies on the cooperation of many weak non-covalent interactions
- The folding process comprises mainly rotations around backbone C-C and N-C bonds.
- formation of “dipole interactions”, “hydrophobic interactions”, “hydrogen bridges”, “electrostatic interactions”
- formation of a few new covalent bonds like S-S bridges.
What are the energetic considerations of the bonds in a protein.
–> 2,4,10, 40 y una vuelta
–> Diego hiere y electrocuta a compañero
How do the following interactions help the folding process?
- hydrophobic interactions
- hydrogen bonds
- electrostatic interactions between charged side chains
- covalent
- HYDROPHOBIC INTERACTIONS –> exclude water and therefore increase entropy by increasing overall water mobility
- HYDROGEN BONDS –> A partially positive H-atom interacts with a partially negative atom (usually oxygen) Ideal distance 2.7 - 3 Å; Energy gained: 10 - 20 kJ/mol - only formed if water is excluded
- ELECTROST. BETWEEN CHARGED SIDE-CHAINS –> according to Coulombs law. any buried charged must be compensated by a counterion. ➜ion pairs contribute very little to protein stability
- COVALENT BONDS –> include S-S disulfide bonds (and the backbone!) 350 kJ/mol–1
What is the molten globule state?
is a partially folded state that may induce the advent of protein aggregation. MG states are important protein folding intermediates with a perturbed tertiary interaction and native-like compact secondary structures.
- Hydrophobic side chains form a core that excludes H2O
- Polar groups face the surface of the developing protein globule
- Any internal charged residues need complementary counterions
- depends on the side chain and backbone interactions
- Contacts can be formed in different orders.
Describe the oil dropplet and jigsaw description of the hydrophobic interior of a protein.
Oil dropplet: all hydrophobic residues are together.
Jigsaw: tight fitting, but with no specify chemistry.
–> mixture of both
Which types of folding were found from experimental folding studies?
TYPE I: small protein, fold fast with 2 states aprox. without intermediate.
TYPE II: large proteins fold in multiple phases.–> foldon units
What is MD simulation and what can you calculate with it?
- ZAM
- Foldons
MD: Molecular Dynamics
+Folding routes as determined by the zipping and assembly method (ZAM). Small pieces that fold fast come together +“foldons” – these are independent folding units controversial: the opposing view is a single pathway of folding MD simulation: Sum of potential foldings, it describes interactions with all atoms
What is the hydrophobic collapse model?
Is a process for the production of the 3-D conformation adopted by polypeptides and other molecules in polar solvents.
–>nascent polypeptide forms initial secondary structure (ɑ-helices and β-strands) creating localized regions of predominantly hydrophobic residues. The polypeptide interacts with water, thus placing thermodynamic pressures on these regions which then aggregate or “collapse” into a tertiary.
What is folding funnel? Describe the thermodynamic laws enhancing the folding process.
==> Protein fold towards a deep global energy minimum
- Hydrophobic collapse–> The inability of the solvent to interact with side chains leads to a decrease in entropy of the system.
- The series of shape changes gradually reduce Enthalpie ∆H and gain ∆S, resulting in the - ∆G
- ∆S Entropie is more dominant in larger proteins–> more release of free water
- The molten state can collapse onto “wrong” condense state, but to go back there is very high enthalpic ∆H barrier to overcome.
What are the states of the folding funnel during the proteinfolding process?
Denatured state: protein is unstructured; several possible conformational states high conformational ∆S.
Molten globule: folding progresses through formation of a ∆S low entropy, low- free energy intermediates
Transition state: native-like structurural emsemble state, rapidly searches the native state.
Native state: the lowest free energy structure.
What are Chaperones?
Chaperones are proteins that help to find other proteins to find their final active conformation, without being part of the final state and oppose aggregation of misfolded proteins.
How does GroEL/ES system im bacteria work?
- GroEL binds to partially folded or misfolded proteins.
- A cycle of ATP binding alloes GroES to bind
- –> forming a large hydrophillic chamber = the hydrophobic collaps, thus inducing substrate folding.
- ATP hydrolysis shifts GroEL to a more open “relaxed” state, which releases the folded protein.
What are the consequences of defective folding?
–>unfolded protein states may also be physiologically important. –>equilibria between many possible states - molecular chaperones protect these incompletely folded states - Ubiquitin “opens” folds to speed up degradation => PROTEOSTASIS
What is proteostasis and how does it works?
Proteostasis is achieved by a network of hundreds of proteins, including molecular chaperones and their regulators, which assist in de novo folding or refolding, and the ubiquitin−proteasome system (UPS) and autophagy system, which mediate the removal of irreversibly misfolded and aggregated proteins.
Describe the following diagram.
