Visualizing how inclusion of higher reciprocal space in SWAXS data analysis improves shape restoration of biomolecules: case of lysozyme

Abstract

Query remains whether use of increased resolution data from X-ray scattering aids in better understanding of the dynamic shape of the biomolecule in solution? To address this, we acquired Small/Wide angle X-ray scattering (SWAXS) data in the q range of 0.008 − 1.72 Å⁻¹ from dilute solutions of lysozyme (0.9 to 5 mg/ml). Samples lacked any interparticulate effect and datasets showed Bragg peaks at q∼0.325, 0.65 and 1.4 Å⁻¹, as reported before by other authors. Considering an averaged profile, we estimated shape parameters and distance distribution profiles of interatomic vectors by gradually increasing input q_max value. Interestingly, use of higher resolution led to emergence of new peaks amongst smaller vectors. Deconvolution of these peaks provided positions of smaller peaks which correlated well with an earlier theoretical work. These peaks arise from secondary structures or due to non-uniform internal motions within the larger shape of this protein. Dummy residue modeling considering uniform density yielded model(s) with holes or cavities when considering higher q values implying limitations of this method. Employing normal mode calculations, we searched for better fitting model of lysozyme using differentially ranged SWAXS data and a crystal structure of lysozyme as starting structure. Comparison of refined models with structures from crystallography and NMR data showed that use of data till mid q region resulted in adjustments near the center of mass of starting structure, and inclusion of higher resolution induced pan-structure adjustments. We conclude that high resolution SWAXS data analysis provides additional dimension towards understanding biomolecular structural dynamics.

Communicated by Ramaswamy H. Sarma

Keywords:

• Small/wide angle X-ray scattering
• lysozyme
• reciprocal space
• real space
• shape restoration

Acknowledgements

This work was mainly supported by CSIR 12 Five Year Plan Project UNSEEN from CSIR INDIA to Ashish. Samples were prepared as routine measure to characterize beam intensity for experiments at different beamlines or for in-house experiments. Research scholars at that time, Yogendra S. Rathore and Ashish K. Solanki are acknowledged for performing some parts of sample preparation. Consistent support of faculty and staff of CSIR-IMTECH in pursuing research activities is acknowledged. Use of the National Synchrotron Light Source, Brookhaven National Laboratory, was supported by the United States Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract DE-AC02-98CH10886. This is IMTECH communication number 026/2021.

Disclosure statement

No potential conflict of interest was reported by the authors.