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Superimposition of Viral Protein Structures: A Means to Decipher the Phylogenies of Viruses

by Janne J. Ravantti, Ane Martinez-Castillo and Nicola G.A. Abrescia

Viruses 2020, 12(10), 1146; https://doi.org/10.3390/v12101146 - 9 Oct 2020

Cited by 16 | Viewed by 5879

Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is lost. Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and thoughts that have led to the current established structure-based phylogeny of viruses: starting from the original observation that the major capsid proteins of plant and animal viruses possess similar folds, to the idea that each virus has an innate “self”. This latter idea fueled the conceptualization of the PRD1-adenovirus lineage whose members possess a major capsid protein (innate “self”) with a double jelly roll fold. Based on this approach, long-range viral evolutionary relationships can be detected allowing the virosphere to be classified in four structure-based lineages. However, this process is not without its challenges or limitations. As an example of these hurdles, we finally touch on the difficulty of establishing structural “self” traits for enveloped viruses showcasing the coronaviruses but also the power of structure-based analysis in the understanding of emerging viruses Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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Open AccessArticle

Expression, Functional Characterization, and Preliminary Crystallization of the Cochaperone Prefoldin from the Thermophilic Fungus Chaetomium thermophilum

by Kento Morita, Yohei Y. Yamamoto, Ayaka Hori, Tomohiro Obata, Yuko Uno, Kyosuke Shinohara, Keiichi Noguchi, Kentaro Noi, Teru Ogura, Kentaro Ishii, Koichi Kato, Mahito Kikumoto, Rocio Arranz, Jose M. Valpuesta and Masafumi Yohda

Int. J. Mol. Sci. 2018, 19(8), 2452; https://doi.org/10.3390/ijms19082452 - 19 Aug 2018

Cited by 4 | Viewed by 6332

Abstract

Prefoldin is a hexameric molecular chaperone found in the cytosol of archaea and eukaryotes. Its hexameric complex is built from two related classes of subunits, and has the appearance of a jellyfish: Its body consists of a double β-barrel assembly with six long tentacle-like coiled coils protruding from it. Using the tentacles, prefoldin captures an unfolded protein substrate and transfers it to a group II chaperonin. Based on structural information from archaeal prefoldins, mechanisms of substrate recognition and prefoldin-chaperonin cooperation have been investigated. In contrast, the structure and mechanisms of eukaryotic prefoldins remain unknown. In this study, we succeeded in obtaining recombinant prefoldin from a thermophilic fungus, Chaetomium thermophilum (CtPFD). The recombinant CtPFD could not protect citrate synthase from thermal aggregation. However, CtPFD formed a complex with actin from chicken muscle and tubulin from porcine brain, suggesting substrate specificity. We succeeded in observing the complex formation of CtPFD and the group II chaperonin of C. thermophilum (CtCCT) by atomic force microscopy and electron microscopy. These interaction kinetics were analyzed by surface plasmon resonance using Biacore. Finally, we have shown the transfer of actin from CtPFD to CtCCT. The study of the folding pathway formed by CtPFD and CtCCT should provide important information on mechanisms of the eukaryotic prefoldin–chaperonin system. Full article

(This article belongs to the Special Issue Molecular Chaperones)

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