Hydrogen atoms in proteins: positions and dynamics

Area of Science:

• Structural Biology
• Biophysics
• Computational Chemistry

Background:

• Hydrogen atoms comprise approximately 50% of atoms in proteins.
• Hydrogen's contribution to the complex protein energy landscape is significant.
• Accurate hydrogen atom positioning is vital for understanding protein dynamics.

Purpose of the Study:

• To investigate the positions and dynamics of hydrogen atoms in myoglobin using neutron crystallography.
• To assess the reliability of computational methods for predicting hydrogen atom coordinates.
• To analyze the mean-square displacements of hydrogen atoms and their contribution to protein dynamics.

Main Methods:

• Neutron crystal structure analysis of myoglobin.
• Comparison of experimental hydrogen atom coordinates with computational predictions.
• Analysis of mean-square displacements using Debye-Waller factors.
• Comparison with dynamic mean-square displacements from incoherent neutron scattering.

Main Results:

• Over 70% of mobile hydrogen atom coordinates were predicted with errors exceeding 0.2 Å.
• Mean-square displacements of hydrogen atoms were categorized into three distinct classes.
• Side-chain hydrogen atoms were identified as major contributors to dynamic displacements on timescales faster than 100 ps.

Conclusions:

• Current computational methods show significant inaccuracies in predicting hydrogen atom positions in proteins.
• Neutron crystallography provides crucial experimental data for validating and improving protein structure models.
• Understanding hydrogen atom dynamics is essential for elucidating protein function and energy landscapes.