Rucete ✏ Lehninger Principles of Biochemistry In a Nutshell
4.4 Protein Denaturation and Folding
This chapter introduces the concept of proteostasis, the processes of protein denaturation and renaturation, the molecular basis of protein folding, the roles of chaperones, and how defects in folding cause disease.
Proteostasis: Maintaining the Cellular Protein Balance
• Proteostasis is the continual maintenance of a cell's active protein set through coordinated synthesis, folding, refolding, sequestration, and degradation pathways.
• Specialized enzymes and chaperones ensure correct protein folding, refold partially unfolded proteins, and target irreversibly misfolded proteins for degradation.
• Failures in proteostasis can lead to protein aggregation, loss of function, and diseases such as diabetes, Parkinson’s, and Alzheimer’s.
Protein Denaturation: Loss of Structure and Function
• Protein structure is adapted for specific cellular environments; changes in conditions can disrupt this structure.
• Denaturation is the loss of a protein’s three-dimensional structure and function, often resulting in partially folded states, not always complete unfolding.
• Most proteins denature cooperatively—loss of structure in one region destabilizes the whole molecule, leading to abrupt unfolding over a narrow temperature or condition range.
• Causes of denaturation include heat, extremes of pH, organic solvents (alcohol, acetone), solutes (urea, guanidine hydrochloride), and detergents. These agents disrupt noncovalent interactions without breaking covalent bonds.
• Denatured proteins often aggregate, forming disordered or, in some cases, ordered amyloid-like aggregates.
• Thermostable proteins in thermophiles resist denaturation via more charged residues, tight hydrophobic packing, and rigid folds.
Renaturation: Amino Acid Sequence Determines Structure
• Some proteins can renature spontaneously after denaturation, regaining their native conformation and biological activity (demonstrated by Anfinsen’s ribonuclease A experiment).
• This demonstrates that the amino acid sequence encodes all information for correct folding; however, only a minority of proteins can refold without assistance.
Mechanisms and Thermodynamics of Protein Folding
• Folding is not random but follows a hierarchical, stepwise process—secondary structures form first, followed by motifs, domains, and the final fold.
• Levinthal’s paradox shows that random folding would take astronomically long; instead, proteins fold rapidly via specific pathways and intermediates.
• The folding process is described by a free-energy funnel: unfolded proteins have high entropy and free energy; folding reduces conformational space and energy, forming intermediates until the native state is reached.
• Stability varies within proteins—some regions are highly stable, others are flexible or intrinsically disordered, enabling function or conformational change.
Chaperones and Assisted Folding
• Many proteins require chaperones—specialized proteins that bind and stabilize unfolded or partially folded polypeptides, preventing aggregation and assisting folding.
• Hsp70 chaperones (heat shock proteins) bind exposed hydrophobic regions, protect against heat stress, assist nascent chains, and use ATP for cycles of binding and release. Hsp70 can also deliver polypeptides to chaperonins.
• Chaperonins (e.g., GroEL/GroES in bacteria, Hsp60 in eukaryotes) provide a protected chamber for folding, preventing aggregation and constraining conformational search space.
• Protein disulfide isomerase (PDI) reshuffles disulfide bonds; peptide prolyl cis-trans isomerase (PPI) catalyzes isomerization of Pro peptide bonds, speeding folding.
Protein Misfolding and Disease
• Protein misfolding is common; cells degrade many misfolded polypeptides, but some escape quality control and form toxic aggregates.
• Amyloidoses (e.g., Alzheimer, Parkinson, Huntington diseases) involve misfolded proteins aggregating into amyloid fibers, rich in β-sheet, which damage tissues.
• Alzheimer’s: Amyloid-β peptide forms extracellular plaques; tau protein aggregates intracellularly. Inheritance of mutations can increase disease risk or change onset.
• Parkinson’s: Misfolded α-synuclein forms Lewy bodies; Huntington’s: Polyglutamine-expanded huntingtin aggregates in neurons; both show neurodegeneration if chaperone activity is insufficient.
• Cystic fibrosis: Deletion of Phe508 in CFTR causes improper folding, degradation, and loss of function. Corrector drugs can restore function by helping folding.
• Prion diseases: Misfolded PrP protein (PrPSc) induces misfolding of normal PrP (PrPC), leading to infectious neurodegenerative diseases (mad cow, Creutzfeldt-Jakob, kuru, etc.). Prions propagate by conformational conversion, not nucleic acids, causing fatal brain degeneration.
• The presence of aromatic residues and β-sheet structure is key to amyloid and prion aggregation and disease progression.
In a Nutshell
• Proteostasis requires active management of protein folding, refolding, and degradation to maintain cellular function.
• Denaturation destroys protein structure and function but can be reversible in some cases, showing that sequence encodes folding.
• Protein folding is hierarchical and rapid, often requiring chaperones, isomerases, and energy input.
• Protein misfolding underlies numerous human diseases, making folding and quality control fundamental to cell health and medicine.