Extensive conformational heterogeneity within protein cores.

Area of Science:

• Biophysics
• Computational Biology
• Structural Biology

Background:

• Proteins exist as an ensemble of conformations at any temperature.
• Crystallographic structures are often treated as native states, overlooking protein flexibility.
• Characterizing protein conformational heterogeneity is experimentally challenging.

Purpose of the Study:

• To assess the degree of conformational heterogeneity in folded proteins.
• To build models describing protein thermodynamics and kinetics.
• To investigate protein flexibility using molecular dynamics simulations.

Main Methods:

• Construction of Markov state models for proteins (72–263 residues).
• Utilizing hundreds of microseconds of atomically detailed molecular dynamics simulations.
• Analysis of side-chain and backbone dynamics.

Main Results:

• Nearly every residue samples at least two rotameric states.
• Rotamer transition rates vary widely, from nanoseconds to microseconds.
• Substantial backbone dynamics occur on longer timescales than typically measured.
• Extensive protein rearrangements are consistent with experimental data (NMR, crystallography).

Conclusions:

• Proteins behave as dense fluids, not well-ordered solids.
• Significant structural fluctuations occur even in highly packed proteins.
• Molecular dynamics and Markov state models provide insights into protein flexibility.