Protein Folding and Chaperones

Summary

Protein folding is driven by the thermodynamic necessity to minimize free energy, a process conceptualized as the folding funnel. In vivo, this process is complicated by co-translational folding, where the N-terminal domains of a nascent chain begin to fold while the C-terminus is still being synthesized by the ribosome.

Key Points

1The folding funnel model explains how proteins navigate to their native state efficiently
2The hydrophobic effect drives initial collapse; hydrogen bonds stabilize the final structure
3Co-translational folding prevents inter-domain misfolding during ribosomal synthesis
4Hsp70 and chaperonins rescue misfolded proteins through ATP-dependent cycles
5Chaperones smooth the energy landscape without dictating final protein structure

Protein folding is one of the most fundamental processes in biology, converting linear amino acid sequences into functional three-dimensional structures. The cellular environment adds complexity that requires the assistance of molecular chaperones.

Thermodynamic Foundations

The Folding Funnel

The folding funnel or energy landscape theory resolves Levinthal's paradox—the observation that proteins fold in milliseconds despite the astronomical number of possible conformations.

Key concepts:

The funnel represents the free energy landscape

The native state is the global minimum

Proteins follow a biased search, not random exploration

Multiple parallel pathways lead to the same native structure

Driving Forces

The hydrophobic effect is the primary driving force:

Burying non-polar side chains releases ordered water molecules

This increases the entropy of the solvent, favoring folding

- Initial hydrophobic collapse forms the molten globule state

Enthalpic contributions stabilize the native state:

Hydrogen bonds optimize in the final structure

Van der Waals contacts pack the hydrophobic core

Salt bridges form between charged residues

Co-translational Folding

Vectorial Synthesis

Unlike in vitro refolding experiments, cellular proteins fold co-translationally:

N-terminal domains begin folding before C-terminal synthesis completes

This reduces the risk of inter-domain misfolding

The ribosomal exit tunnel restricts early conformational sampling

Ribosome-Associated Chaperones

The crowded cellular environment requires protection:

- Trigger Factor (bacteria): Binds near the exit tunnel, shielding hydrophobic segments

- NAC (Nascent polypeptide-Associated Complex, eukaryotes): Prevents premature ER targeting

- Ribosome-associated Hsp70: Assists folding of emerging domains

Chaperone Systems

Hsp70 Family

The most ubiquitous chaperone system:

1. Substrate binding: Hsp70 recognizes exposed hydrophobic segments

2. ATP-driven cycle: ATP binding releases substrate; hydrolysis promotes tight binding

3. Co-chaperones: Hsp40 (J-proteins) stimulate ATPase activity and deliver substrates

4. Nucleotide exchange factors: Reset the cycle by releasing ADP

Chaperonins (GroEL-GroES)

Provide a physical folding chamber:

Misfolded substrate binds to the GroEL apical domains

ATP and GroES binding create an enclosed, hydrophilic cavity

The protein folds in isolation for ~10 seconds

ATP hydrolysis triggers release

Hsp90

Specializes in signaling proteins:

Kinases, hormone receptors, transcription factors

Works downstream of Hsp70

Stabilizes near-native conformations

Chaperones and the Energy Landscape

Chaperones function by smoothing the energy landscape:

They rescue proteins from local minima (kinetic traps)

ATP hydrolysis provides energy to unfold misfolded intermediates

They do not dictate the final structure—this is encoded in the sequence

Proteostasis Failure

When the folding machinery is overwhelmed:

Misfolded proteins accumulate and aggregate

This leads to proteinopathies (Alzheimer's, Parkinson's, Huntington's)

The proteostasis network declines with age

References

Siderophore Biochemistry

Peptide Bond Hydrolysis Mechanism