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Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

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Measuring and modeling diffuse scattering in protein X-ray crystallography.

Andrew H Van Benschoten¹, Lin Liu¹, Ana Gonzalez²

¹Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;

Proceedings of the National Academy of Sciences of the United States of America

|April 2, 2016

Summary

This summary is machine-generated.

Measuring diffuse X-ray scattering from protein crystals reveals structural dynamics. Normal-modes (NM) and liquid-like motions (LLM) models accurately capture these protein motions, advancing structural biology.

Keywords:

diffuse scattering liquid-like motions normal modes protein dynamics structural biology

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Area of Science:

Structural Biology
X-ray Crystallography
Macromolecular Dynamics

Background:

X-ray diffraction (XRD) offers insights into macromolecular structural dynamics.
Bragg scattering yields static structures, while diffuse scattering captures charge density variations and correlations.
Collecting diffuse scattering data from protein crystals has been limited due to experimental challenges.

Purpose of the Study:

To present 3D diffuse intensity measurements from cyclophilin A and trypsin crystals.
To evaluate different models for describing protein motions using both Bragg and diffuse scattering data.
To establish a practical method for incorporating diffuse scattering data into structural refinement.

Main Methods:

Collected 3D diffuse X-ray scattering intensity data from protein crystals alongside standard Bragg data.
Tested translation-libration-screw (TLS), liquid-like motions (LLM), and normal-modes (NM) models for protein dynamics.
Refined LLM against diffuse data and compared TLS and NM models using Bragg data.

Main Results:

Diffuse scattering data were collected efficiently using standard X-ray diffraction techniques.
TLS models showed poor agreement with diffuse scattering data, despite similar Bragg intensities.
Both LLM and NM models demonstrated substantial agreement with the measured diffuse scattering data.

Conclusions:

This study presents a viable approach to increase the availability of diffuse scattering datasets for the biosciences.
Dynamics-informed normal-modes (NM) structural models can be refined to simultaneously fit both Bragg and diffuse scattering data.
The findings highlight the potential of diffuse scattering in characterizing macromolecular motions.