Protein folding is a complex process that transforms a linear amino acid sequence into a functional 3D structure. This intricate dance involves hydrophobic collapse, secondary structure formation, and final tertiary arrangement, guided by an energy landscape to overcome Levinthal's paradox.

Misfolding can lead to loss of function, toxic gain of function, or aggregation, causing diseases like Alzheimer's. Protein stability depends on various interactions, and understanding these principles allows for engineering more stable proteins and developing treatments for misfolding-related disorders.

Protein Folding Process and Influencing Factors

Process of protein folding

• Primary structure determines folding as amino acid sequence dictates final 3D structure through specific interactions
• Hydrophobic collapse initiates rapid compaction of hydrophobic residues to core forming a molten globule
• Secondary structure formation involves alpha helices and beta sheets stabilized by hydrogen bonding patterns
• Tertiary structure formation finalizes 3D arrangement of secondary structures through various intramolecular interactions
• Factors influencing folding include temperature affecting kinetics, pH altering charge distribution, ionic strength modulating electrostatic interactions, and presence of ligands or cofactors stabilizing specific conformations
• Energy landscape theory posits proteins fold through multiple pathways to native state, visualized as a funnel-like energy surface
• Levinthal's paradox highlights impossibility of random folding, implying directed folding process must exist to achieve biologically relevant timescales

Role of chaperones

• Molecular chaperones assist in proper folding by preventing aggregation of partially folded proteins and providing isolated environment
• Hsp70 family binds to exposed hydrophobic regions, shielding them from unwanted interactions
• Hsp60 (GroEL/GroES) provides enclosed folding chamber allowing proteins to fold without interference
• Hsp90 assists in late-stage folding, particularly for signaling proteins and transcription factors
• Chaperone-mediated quality control involves recognition of misfolded proteins, refolding attempts, and targeting for degradation if refolding fails (ubiquitin-proteasome system)

Protein Misfolding, Aggregation, and Stability

Consequences of protein misfolding

• Loss of protein function impairs cellular processes (enzyme catalysis, signal transduction)
• Gain of toxic function leads to harmful interactions with other cellular components (membrane disruption, sequestration of essential proteins)
• Formation of protein aggregates results in amyloid fibrils (Alzheimer's disease) or inclusion bodies (Huntington's disease)
• Cellular stress responses triggered include unfolded protein response in ER and heat shock response in cytosol
• Diseases associated with protein misfolding encompass neurodegenerative disorders (Alzheimer's, Parkinson's), cystic fibrosis (CFTR protein), and type II diabetes (amylin aggregation)

Principles of protein stability

• Thermodynamic stability quantified by Gibbs free energy of unfolding ($\Delta G$) represents equilibrium between folded and unfolded states
• Factors affecting protein stability include hydrogen bonding (backbone and side chains), Van der Waals interactions (close packing), electrostatic interactions (salt bridges), and hydrophobic effect (core formation)
• Denaturation causes loss of higher-order structure through heat (disrupts hydrogen bonds), extreme pH (alters charge distribution), or chemical denaturants (urea, guanidinium chloride)
• Protein stability curve shows temperature dependence of $\Delta G$, revealing cold denaturation phenomenon at low temperatures
• Stabilizing strategies employed in nature and protein engineering include disulfide bonds (covalent crosslinks), salt bridges (electrostatic interactions), and rational design for enhanced stability (thermophilic enzymes)