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Keywords = YncE

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12 pages, 1198 KiB  
Article
AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement
by Lawrence Chai, Ping Zhu, Jin Chai, Changxu Pang, Babak Andi, Sean McSweeney, John Shanklin and Qun Liu
Crystals 2021, 11(10), 1227; https://doi.org/10.3390/cryst11101227 - 12 Oct 2021
Cited by 12 | Viewed by 5364
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Advances in Protein Crystallization and Crystallography)
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15 pages, 2162 KiB  
Article
Interactions of Bacillus subtilis Basement Spore Coat Layer Proteins
by Daniela Krajčíková, Veronika Bugárová and Imrich Barák
Microorganisms 2021, 9(2), 285; https://doi.org/10.3390/microorganisms9020285 - 30 Jan 2021
Cited by 7 | Viewed by 3670
Abstract
Bacillus subtilis endospores are exceptionally resistant cells encircled by two protective layers: a petidoglycan layer, termed the cortex, and the spore coat, a proteinaceous layer. The formation of both structures depends upon the proper assembly of a basement coat layer, which is composed [...] Read more.
Bacillus subtilis endospores are exceptionally resistant cells encircled by two protective layers: a petidoglycan layer, termed the cortex, and the spore coat, a proteinaceous layer. The formation of both structures depends upon the proper assembly of a basement coat layer, which is composed of two proteins, SpoIVA and SpoVM. The present work examines the interactions of SpoIVA and SpoVM with coat proteins recruited to the spore surface during the early stages of coat assembly. We showed that the alanine racemase YncD associates with two morphogenetic proteins, SpoIVA and CotE. Mutant spores lacking the yncD gene were less resistant against wet heat and germinated to a greater extent than wild-type spores in the presence of micromolar concentrations of l-alanine. In seeking a link between the coat and cortex formation, we investigated the interactions between SpoVM and SpoIVA and the proteins essential for cortex synthesis and found that SpoVM interacts with a penicillin-binding protein, SpoVD, and we also demonstrated that SpoVM is crucial for the proper localization of SpoVD. This study shows that direct contacts between coat morphogenetic proteins with a complex of cortex-synthesizing proteins could be one of the tools by which bacteria couple cortex and coat formation. Full article
(This article belongs to the Special Issue Bacillus subtilis as a Model Organism to Study Basic Cell Processes)
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