AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement

Lawrence Chai,Ping Zhu,Babak Andi,Jin Chai,Sean McSweeney,Qun Liu,Changxu Pang,John Shanklin

doi:10.3390/cryst11101227

Abstract

Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to find suitable templates for phasing. However, sequence information is not always available, such as when proteins are crystallized with unknown binding partner proteins or when the crystal is of a contaminant. The recent development of AlphaFold published the predicted protein structures for every protein from twenty distinct species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough to enable sequence-independent phasing of diffraction data from two crystallization contaminants of unknown sequence. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained, which allowed the identification and structure determination of YncE and YadF. Our results demonstrate the general utility of the AlphaFold-predicted structure database with respect to sequence-independent crystallographic phasing.

Highlights

Using a relatively straightforward workflow, we showed that predicted AlphaFold structures can be used to phase both structures without any protein sequence information
We used CCP4 beyond 80%, we were unable to solve the structure using the Protein Data Bank (PDB) as search models, sugonline servers to search for contaminants but did not find a clear solution
We demonstrated that AlphaFold-predicted E. coli structures can be useful for molecular replacement to identify unknown crystallized contaminant proteins and to determine their structures

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Crystallographic phasing requires the retrieval of phase information that is lost during diffraction experiments. When there are no homology models, such phase information is recovered experimentally using isomorphous replacement preferably with their anomalous signals [1,2]. With the accumulation of experimentally determined structures, molecular replacement [3,4] has become a routine method for crystallographic phasing.

Methods

Results

Discussion

Conclusion