9.2 Protein Dynamics and Protein Folding

Proteostasis

Continual maintenance of the active set of cellular proteins required under a give set of conditions

Native Proteins

Proteins that are synthesized, forms intermediates, or chaperone assisted folding

Misfolded Protein

Reformed or form aggregates that leads to diseased state or degradation

Protein folding sequence

Transcription of DNA into RNA; RNA to protein; Protein to supramolecular complex

Thermodynamic terms that influences stability

Entropy, Free Energy, and Enthalpy

Bonding interactions/factors that influence stability

H-bonds, Ionic bonds, Hydrophobic interactions, Van der Waals interactions, Disulphide bonds

Recall importance of AA sequence, denaturation, and renaturation

AA sequence determines structure and function

Denaturation: allows upkeep of protein and breakdown of improper proteins; loss of 3D structure sufficient to cause loss of function

Renaturation: process by which certain denatured proteins regain their native structure and biological activity

Protein stability depends on the balance of three factors

1. unfavorable conformational entropy (delta S is negative) change → folding

2. favorable enthalpy (delta H is negative) from intramolecular noncovalent interactions

3. favorable entropy (delta S is positive) from burying hydrophobic residues in water

Anfinsen experiment

Used Urea and B-mercaptoethanol; showed that AA sequence contains all info to fold the protein

Stepwise process of protein folding

Local secondary structures fold first, longer range interactions follow, continues until entire protein is folded

Levinthal’s paradox

It’s mathematically impossible for protein folding to occur by randomly trying every confirmation until the lowest energy is found

Energy well/Free-energy tunnel

proteins have a sequence and have no choice but to fold due to the loss of free energy

A model that shows how multiple pathways can lead proteins to fold into one conformation. Caveat: Doesn’t consider stable intermediate states leading to final fold.

van der Waals interactions operate over

short distances (attractive force is proportional to distance) ^-6

van der Waals result from the overlap of

short lived, highly fluctuating dipoles of nonbonding electron orbitals

Inside the densely packed protein interior, numerous van der Waals interaction sum up and contribute to the

stability of a folded protein

Hydrogen bonding is/is not a driving force for protein folding because H-bonds with water are broken to make intramolecular H-bonds

IS NOT

Formation of extended H-bond networks (especially in a-helices or B-sheets) compensate for

loss of AA-water bonds, so H-bonding changes do not effect free energy much

Contribution of noncovalent interactions, particularly hydrogen bonding, to enthalpy of folding is offset by

protein folding decreases interactions between the protein and water

Hydrophobic interactions is a major contribution to

protein folding and stability; water around unfolded protein is ordered and structured

Proteins fold with hydrophobic residues on the

interior

Protein folding increases entropy of the

protein-water system because water is less ordered (delta S is positive)

Once a protein folds, the protein structure can be stabilized by the formation of

disulfide (-S-S-) bonds between sulfhydryls (-SH) of cysteine

Chaperonins (GroEL & GroES)

helper proteins that “assist” polypeptide folding into native structure (or prevent improper folding or aggregation)

Hsp; Two types

Heat shock protein; binds to hydrophobic regions of unfolded proteins and guides it towards chaperonins

HPS 40 & 70

Amyloid fibers/peptides/fibril

Misfolded proteins self-associates to form these

Alzheimer disease

Amyloid deposition by neurons involving the amyloid-beta peptide

Parkinson disease

misfolded alpha-synuclein aggregates that forms spherical masses called Lewy bodies

Huntington disease

Aggregation of huntingtin (Contains long polyglutamine repeats)

Prion disease

Prion protein (PrP) = misfolded brain protein; misfold forms prions that interacts with other normal proteins, causing aggregation