Mass spectrometric approaches to study enveloped viruses: new possibilities for structural biology and prophylactic medicine

Proteomics in Influenza Research: The Emerging Role of Posttranslational Modifications

Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especially in posttranslational regulation of a variety of key biological processes. Protein posttranslational modifications (PTMs) increase the diversity of functionality of the organismal proteome and affect almost all aspects of pathogen biology, primarily by regulating the structure, function, and localization of the modified proteins. Considerable technical achievements in mass spectrometry-based proteomics have been made in a large number of proteome-wide surveys of PTMs in many different organisms. Herein we specifically focus on the proteomic studies regarding a variety of PTMs that occur in both the influenza viruses, mainly influenza A viruses (IAVs), and their hosts, including phosphorylation, ubiquitination and ubiquitin-like modification, glycosylation, methylation, acetylation, and some types of acylation. Integration of these data sets provides a unique scenery of the global regulation and interplay of different PTMs during the interaction between IAVs and their hosts. Various techniques used to globally profiling these PTMs, mostly MS-based approaches, are discussed regarding their increasing roles in mechanical regulation of interaction between influenza viruses and their hosts.

Differential S-Acylation of Enveloped Viruses

Post-translational modifications often regulate protein functioning. Covalent attachment of long chain fatty acids to cysteine residues via a thioester linkage (known as protein palmitoylation or S-acylation) affects protein trafficking, protein-protein and protein-membrane interactions. This post-translational modification is coupled to membrane fusion or virus assembly and may affect viral replication in vitro and thus also virus pathogenesis in vivo. In this review we outline modern methods to study S-acylation of viral proteins and to characterize palmitoylproteomes of virus infected cells. The palmitoylation site predictor CSS-palm is critically tested against the Class I enveloped virus proteins. We further focus on identifying the S-acylation sites directly within acyl-peptides and the specific fatty acid (e.g, palmitate, stearate) bound to them using MALDI-TOF MS-based approaches. The fatty acid heterogeneity/ selectivity issue attracts now more attention since the recently published 3D-structures of two DHHC-acyl-transferases gave a hint how this might be achieved.

S-Acylation of Proteins

Palmitoylation or S-acylation is the posttranslational attachment of fatty acids to cysteine residues and is common among integral and peripheral membrane proteins. Palmitoylated proteins have been found in every eukaryotic cell type examined (yeast, insect, and vertebrate cells), as well as in viruses grown in these cells. The exact functions of protein palmitoylation are not well understood. Intrinsically hydrophilic proteins, especially signaling molecules, are anchored by long-chain fatty acids to the cytoplasmic face of the plasma membrane. Palmitoylation may also promote targeting to membrane subdomains enriched in glycosphingolipids and cholesterol or affect protein-protein interactions.This chapter describes (1) a standard protocol for metabolic labeling of palmitoylated proteins and also the procedures to prove a covalent and ester-type linkage of the fatty acids, (2) a simple method to analyze the fatty acid content of S-acylated proteins, (3) two methods to analyze dynamic palmitoylation for a given protein, and (4) protocols to study cell-free palmitoylation of proteins.

Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications

In the current context of international conflicts and localized terrorist actions, there is unfortunately a permanent threat of attacks with unconventional warfare agents. Among these, biological agents such as toxins, microorganisms, and viruses deserve particular attention owing to their ease of production and dissemination. Mass spectrometry (MS)-based techniques for the detection and quantification of biological agents have a decisive role to play for countermeasures in a scenario of biological attacks. The application of MS to every field of both organic and macromolecular species has in recent years been revolutionized by the development of soft ionization techniques (MALDI and ESI), and by the continuous development of MS technologies (high resolution, accurate mass HR/AM instruments, novel analyzers, hybrid configurations). New possibilities have emerged for exquisite specific and sensitive detection of biological warfare agents. MS-based strategies for clinical application can now address a wide range of analytical questions mainly including issues related to the complexity of biological samples and their available volume. Multiplexed toxin detection, discovery of new markers through omics approaches, and identification of untargeted microbiological or of novel molecular targets are examples of applications. In this paper, we will present these technological advances along with the novel perspectives offered by omics approaches to clinical detection and follow-up.

Palmitoylation of influenza virus proteins

Influenza viruses contain two palmitoylated (S-acylated) proteins: the major spike protein HA (haemagglutinin) and the proton-channel M2. The present review describes the fundamental biochemistry of palmitoylation of HA: the location of palmitoylation sites and the fatty acid species bound to HA. Finally, the functional consequences of palmitoylation of HA and M2 are discussed regarding association with membrane rafts, entry of viruses into target cells by HA-mediated membrane fusion as well as the release of newly assembled virus particles from infected cells.