Identification of unknown proteins in X-ray crystallography and cryo-EM

Although experimental protein structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or as a contaminant. Regardless of the source of the pro...

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Bibliographic Details
Published inbioRxiv
Main Authors Chojnowski, Grzegorz, Simpkin, Adam J, Leonardo, Diego A, Seifert-Davila, Wolfram, Vivas-Ruiz, Dan E, Keegan, Ronan M, Rigden, Daniel J
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 18.04.2021
Subjects
Amino acid sequence
Contaminants
Crystal structure
Crystallography
Protein structure
Proteins
Snakes
Venom
X-ray crystallography
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Summary:Although experimental protein structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or as a contaminant. Regardless of the source of the problem, the unknown protein always requires tedious characterization. Here we present an automated pipeline for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. We present the method's application to characterize the crystal structure of an unknown protein purified from a snake venom. We also show that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures. Competing Interest Statement The authors have declared no competing interest.
DOI:10.1101/2021.04.18.440303