Cryo-EM structure in situ reveals a molecular switch that safeguards virus against genome loss

The portal protein is a key component of many double-stranded DNA viruses, governing capsid assembly and genome packaging. Twelve subunits of the portal protein define a tunnel, through which DNA is translocated into the capsid. It is unknown how the portal protein functions as a gatekeeper, preventing DNA slippage, whilst allowing its passage into the capsid, and how these processes are controlled. A cryo-EM structure of the portal protein of thermostable virus P23-45, determined in situ in its procapsid-bound state, indicates a mechanism that naturally safeguards the virus against genome loss. This occurs via an inversion of the conformation of the loops that define the constriction in the central tunnel, accompanied by a hydrophilic–hydrophobic switch. The structure also shows how translocation of DNA into the capsid could be modulated by a changing mode of protein–protein interactions between portal and capsid, across a symmetry-mismatched interface.

Download Full-text

Cryo-EM analysis of a viral portal protein in situ reveals a switch in the DNA tunnel

10.1101/713933 ◽

2019 ◽

Author(s):

Oliver W. Bayfield ◽

Alasdair C. Steven ◽

Alfred A. Antson

Keyword(s):

Surface Properties ◽

Dynamic Processes ◽

Viral Capsid ◽

Capsid Assembly ◽

Genome Packaging ◽

Dna Viruses ◽

Portal Protein ◽

Double Stranded Dna ◽

Protein Functions

The portal protein is a key component of many double-stranded DNA viruses, governing capsid assembly and genome packaging. Twelve subunits of the portal protein form a ring with a central tunnel, through which DNA is translocated into the capsid. It is unknown how the portal protein functions as a gatekeeper, preventing DNA slippage, whilst allowing its passage into the capsid through its central tunnel, and how these processes can be controlled by capsid and motor proteins. A cryo-EM structure of a portal protein, determined in situ for immature capsids of thermostable bacteriophage P23-45, suggests how domain adjustments can be coupled with a switching of properties of the DNA tunnel. Of particular note is an inversion of the conformation of portal loops which define the tunnel’s constriction, accompanied by a switching of surface properties from hydrophobic to hydrophilic. These observations indicate how translocation of DNA into the viral capsid can be modulated by changes in the properties and size of the central tunnel and how the changing pattern of protein–capsid interactions across a symmetry-mismatched interface can facilitate these dynamic processes.

Download Full-text

The “In Situ” Proximity Ligation Assay to Probe Protein–Protein Interactions in Intact Tissues

Methods in Molecular Biology - Exocytosis and Endocytosis ◽

10.1007/978-1-4939-0944-5_27 ◽

2014 ◽

pp. 397-405 ◽

Cited By ~ 22

Author(s):

Arianna Bellucci ◽

Chiara Fiorentini ◽

Michela Zaltieri ◽

Cristina Missale ◽

PierFranco Spano

Keyword(s):

Protein Interactions ◽

Proximity Ligation Assay ◽

Protein Protein Interactions ◽

Proximity Ligation

Download Full-text

Adintoviruses: A Proposed Animal-Tropic Family of Midsize Eukaryotic Linear dsDNA (MELD) Viruses

Virus Evolution ◽

10.1093/ve/veaa055 ◽

2020 ◽

Cited By ~ 1

Author(s):

Gabriel J Starrett ◽

Michael J Tisza ◽

Nicole L Welch ◽

Anna K Belford ◽

Alberto Peretti ◽

...

Keyword(s):

Genome Packaging ◽

Metagenomic Sequence ◽

Dna Viruses ◽

Diverse Range ◽

Integrase Gene ◽

Data Mining Approach ◽

Double Stranded Dna ◽

Wide Range ◽

Linear Dsdna ◽

Dsdna Viruses

Abstract Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA (dsDNA) viruses. This supports the inference that at least some polintons are actually viruses capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of viruses with two genus-level divisions. We propose the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.

Download Full-text

Chemical toolbox for ‘live’ biochemistry to understand enzymatic functions in living systems

The Journal of Biochemistry ◽

10.1093/jb/mvz074 ◽

2019 ◽

Author(s):

Toru Komatsu ◽

Yasuteru Urano

Keyword(s):

Environmental Factors ◽

Protein Interactions ◽

Posttranslational Modifications ◽

Live Cell ◽

Living Systems ◽

Protein Protein Interactions ◽

Redox States ◽

Recent Advances ◽

Protein Functions ◽

Research Tools

Abstract In this review, we present an overview of the recent advances in chemical toolboxes that are used to provide insights into ‘live’ protein functions in living systems. Protein functions are mediated by various factors inside of cells, such as protein−protein interactions, posttranslational modifications, and they are also subject to environmental factors such as pH, redox states and crowding conditions. Obtaining a true understanding of protein functions in living systems is therefore a considerably difficult task. Recent advances in research tools have allowed us to consider ‘live’ biochemistry as a valid approach to precisely understand how proteins function in a live cell context.

Download Full-text

In Silico Recognition of Protein-Protein Interaction

Advanced Data Mining Technologies in Bioinformatics ◽

10.4018/978-1-59140-863-5.ch013 ◽

2011 ◽

pp. 248-268

Author(s):

Byung-Hoon Park ◽

Phuongan Dam ◽

Chongle Pan ◽

Ying Xu ◽

Al Geist ◽

...

Keyword(s):

Protein Interactions ◽

Regulatory Networks ◽

Machine Learning Techniques ◽

Translation Regulation ◽

Future Research ◽

Protein Protein Interactions ◽

Protein Protein Interaction ◽

Protein Levels ◽

Protein Functions ◽

Model Protein

Protein-protein interactions are fundamental to cellular processes. They are responsible for phenomena like DNA replication, gene transcription, protein translation, regulation of metabolic pathways, immunologic recognition, signal transduction, etc. The identification of interacting proteins is therefore an important prerequisite step in understanding their physiological functions. Due to the invaluable importance to various biophysical activities, reliable computational methods to infer protein-protein interactions from either structural or genome sequences are in heavy demand lately. Successful predictions, for instance, will facilitate a drug design process and the reconstruction of metabolic or regulatory networks. In this chapter, we review: (a) high-throughput experimental methods for identification of protein-protein interactions, (b) existing databases of protein-protein interactions, (c) computational approaches to predicting protein-protein interactions at both residue and protein levels, (d) various statistical and machine learning techniques to model protein-protein interactions, and (e) applications of protein-protein interactions in predicting protein functions. We also discuss intrinsic drawbacks of the existing approaches and future research directions.

Download Full-text

KISS: A Mammalian Two-Hybrid Method for In Situ Analysis of Protein–Protein Interactions

Methods in Molecular Biology - Two-Hybrid Systems ◽

10.1007/978-1-4939-7871-7_18 ◽

2018 ◽

pp. 269-278 ◽

Cited By ~ 2

Author(s):

Delphine Masschaele ◽

Sarah Gerlo ◽

Irma Lemmens ◽

Sam Lievens ◽

Jan Tavernier

Keyword(s):

Protein Interactions ◽

Hybrid Method ◽

In Situ Analysis ◽

Protein Protein Interactions ◽

Two Hybrid

Download Full-text

New advances in extracting and learning from protein–protein interactions within unstructured biomedical text data

Emerging Topics in Life Sciences ◽

10.1042/etls20190003 ◽

2019 ◽

Vol 3 (4) ◽

pp. 357-369

Author(s):

J. Harry Caufield ◽

Peipei Ping

Keyword(s):

Protein Interactions ◽

Protein Function ◽

Historical Context ◽

Specific Protein ◽

Basic Unit ◽

Biomedical Text ◽

Protein Protein Interactions ◽

Text Data ◽

Ppi Networks ◽

Protein Functions

Abstract Protein–protein interactions, or PPIs, constitute a basic unit of our understanding of protein function. Though substantial effort has been made to organize PPI knowledge into structured databases, maintenance of these resources requires careful manual curation. Even then, many PPIs remain uncurated within unstructured text data. Extracting PPIs from experimental research supports assembly of PPI networks and highlights relationships crucial to elucidating protein functions. Isolating specific protein–protein relationships from numerous documents is technically demanding by both manual and automated means. Recent advances in the design of these methods have leveraged emerging computational developments and have demonstrated impressive results on test datasets. In this review, we discuss recent developments in PPI extraction from unstructured biomedical text. We explore the historical context of these developments, recent strategies for integrating and comparing PPI data, and their application to advancing the understanding of protein function. Finally, we describe the challenges facing the application of PPI mining to the text concerning protein families, using the multifunctional 14-3-3 protein family as an example.

Download Full-text

Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure

Nature Communications ◽

10.1038/s41467-019-12341-z ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 6

Author(s):

Nicholas P. Stone ◽

Gabriel Demo ◽

Emily Agnello ◽

Brian A. Kelch

Keyword(s):

Major Capsid Protein ◽

Extreme Environment ◽

Structural Basis ◽

Genome Packaging ◽

Virus Capsid ◽

Dna Viruses ◽

Double Stranded Dna ◽

High Internal Pressure ◽

Extracellular Environment ◽

Catch Bonds

Abstract The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly.

Download Full-text