Molecular-replacement phasing using predicted protein structures from AWSEM-Suite.

Shikai Jin,George N Phillips,Xingcheng Lin,Mingchen Chen,Nicholas P Schafer,Xun Chen,Peter G Wolynes,Mitchell D Miller

doi:10.1107/s2052252520013494

Abstract

The phase problem in X-ray crystallography arises from the fact that only the intensities, and not the phases, of the diffracting electromagnetic waves are measured directly. Molecular replacement can often estimate the relative phases of reflections starting with those derived from a template structure, which is usually a previously solved structure of a similar protein. The key factor in the success of molecular replacement is finding a good template structure. When no good solved template exists, predicted structures based partially on templates can sometimes be used to generate models for molecular replacement, thereby extending the lower bound of structural and sequence similarity required for successful structure determination. Here, the effectiveness is examined of structures predicted by a state-of-the-art prediction algorithm, the Associative memory, Water-mediated, Structure and Energy Model Suite (AWSEM-Suite), which has been shown to perform well in predicting protein structures in CASP13 when there is no significant sequence similarity to a solved protein or only very low sequence similarity to known templates. The performance of AWSEM-Suite structures in molecular replacement is discussed and the results show that AWSEM-Suite performs well in providing useful phase information, often performing better than I-TASSER-MR and the previous algorithm AWSEM-Template.

Highlights

For more than 60 years, the rationalization of protein crystallogenesis and the finding of readily usable solutions for the phase problem have been important technical challenges for protein crystallographers (Abergel, 2013)
To explore the capability of the algorithm to make phase predictions where there are only low-quality templates, in this paper we focus on making predictions for distantly related protein targets, where the protein structures available have less than 30% sequence identity
Ten of the cases solved by AWSEM-Suite failed in the I-TASSER-MR trial, so that an overall 25% higher success rate is achieved if both methods are used

Summary

Introduction

For more than 60 years, the rationalization of protein crystallogenesis and the finding of readily usable solutions for the phase problem have been important technical challenges for protein crystallographers (Abergel, 2013). In X-ray crystallography, the crystallographer seeks to obtain an electrondensity map from the diffraction pattern produced by X-rays. The X-ray diffraction experiment, only records the intensities of the diffracted waves and not their relative phases. The so-called ‘phase problem’ results since such phases are not measured directly but are still required for the calculation of the electron-density map. Molecular replacement is an approach that does not require any further experiments such as isomorphous replacement or anomalous dispersion to estimate the necessary phase information. Molecular replacement is often the most economical and the fastest method for solving the phase problem in X-ray structure determination. Molecular replacement accounts for around 80% of the molecular structures deposited in the Protein Data Bank (PDB) to 2017 (Wang, Virtanen et al, 2017)

Methods

Results

Conclusion