New experimental evidence for pervasive dynamics in proteins.

Area of Science:

• Biophysics
• Structural Biology
• Computational Biology

Background:

• Pico-nanosecond (ns) motions with Ångström (Å) amplitude are suggested by computational data but lack extensive experimental validation.
• Existing Nuclear Magnetic Resonance (NMR) relaxation experiments are limited in their sensitivity to distance fluctuations, underrepresenting protein dynamics.
• Understanding protein dynamics is crucial for protein function and entropy.

Purpose of the Study:

• To introduce and validate a novel NMR relaxation experiment for measuring amide proton transverse relaxation rates.
• To investigate protein dynamics in solution, specifically focusing on pico-ns motions.
• To provide experimental evidence for widespread protein motions and assess the accuracy of molecular dynamics simulations.

Main Methods:

• Utilized a novel NMR relaxation experiment to measure amide proton transverse relaxation rates in uniformly 15N-labeled protein domain GB1.
• Collected experimental data at two temperatures (283 K and 303 K).
• Computed relaxation rates from both crystal structures and a 200-ns molecular dynamics trajectory using a new program suite.

Main Results:

• A significant discrepancy was observed between experimental rates and those computed from the crystal structure.
• Calculating relaxation rates from molecular dynamics simulations showed substantial improvement in agreement with experimental data.
• The novel NMR experiment demonstrated sensitivity to distance fluctuations, unlike previous methods.

Conclusions:

• The study provides novel experimental evidence supporting the existence of widespread pico-ns motions in proteins.
• Molecular dynamics simulations, when properly parameterized, can accurately model these protein dynamics.
• This approach offers a new benchmark for refining theoretical force fields used in molecular dynamics calculations.