A tool for visualizing protein motions in time-resolved crystallography.

Area of Science:

• Structural Biology
• Biophysics
• X-ray Crystallography

Background:

• Time-resolved serial femtosecond crystallography (TR-SFX) captures rapid protein structural changes.
• Analyzing global protein motions from TR-SFX data presents challenges.
• Novel tools are needed to correlate widespread electron density changes with protein dynamics.

Purpose of the Study:

• To develop and validate a method for quantifying time-dependent electron density changes in proteins.
• To correlate these changes throughout the protein structure using TR-SFX data.
• To assess the number and timescale of structural intermediates and identify rapid motions.

Main Methods:

• Utilized TR-SFX data from bacteriorhodopsin.
• Defined spherical volumes of difference electron density around selected atoms.
• Averaged positive and negative densities within volumes and systematically moved the volume through the protein.
• Correlated difference electron density amplitudes with time.

Main Results:

• Developed a method to quantify time-dependent electron density changes across the entire protein.
• Facilitated initial assessment of structural intermediates and their timescales.
• Highlighted sub-picosecond "quake-like" motions.
• Enabled comparison of structural models with experimental data via theoretical difference electron densities.

Conclusions:

• The new method effectively quantifies global protein electron density changes over time.
• It aids in understanding protein dynamics, identifying intermediates, and characterizing rapid motions.
• This tool enhances the analysis of TR-SFX data for structural biology research.