Current Protein and Peptide Science - Volume 18, Issue 11, 2017

Fungal pathogens affect a wide variety of hosts, such as human beings, plants, animals, and insects. The course of infection relies on the virulence grade of the fungus and the strength of the defense mechanisms of the host. Virulence factors are closely related to the cell surface; cell wall proteins have a crucial role in adhesion, hyphal development, hydrophobicity, biofilm formation, immunomodulation and surface variation. The enzymes involved in cell wall biosynthesis are not proper virulence factors, but they are necessary for cell function. The deletion of the genes encoding those enzymes often results in an attenuation of virulence. Secreted proteins and cell wall proteins are modified with sugar residues through the N- and O- glycosylation pathways. A set of glycosidases and glycosyltransferases from the Endoplasmic Reticulum and Golgi bodies determine the outcome of the protein. Proper protein glycosylation is important for folding, localization and protein function. In fungi, the glycoproteins are particularly enriched with mannose moieties. In this review, the role of mannosyltransferases from the Pmt, Ktr/Mnt, Mnn and Och1families for the full development of fungal virulence is summarized and discussed.

Paracoccidioides brasiliensis and P. lutzii cause human paracoccidioidomycosis (PCM). They are dimorphic ascomycetes that grow as filaments at mild temperatures up to 28°C and as multibudding pathogenic yeast cells at 37°C. Components of the fungal cell wall have an important role in the interaction with the host because they compose the cell outermost layer. The Paracoccidioides cell wall is composed mainly of polysaccharides, but it also contains proportionally smaller rates of proteins, lipids, and melanin. The polysaccharide cell wall composition and structure of Paracoccidioides yeast cells, filamentous and transition phases were studied in detail in the past. Other cell wall components have been better analyzed in the last decades. The present work gives to the readers a detailed updated view of cell wall-associated proteins. Proteins that have been localized at the cell wall compartment using antibodies are individually addressed. We also make an overview about PCM, the Paracoccidioides cell wall structure, secretion mechanisms, and fungal extracellular vesicles.

Protein glycosylation is a widely distributed posttranslational modification, though not exclusive to eukaryotic cells. The addition of glycans to proteins plays crucial roles in protein folding and secretion, cell-cell interaction, functional specificity and structural properties of both secreted and membrane-bound proteins. In this review, we emphasize the N-linked glycosylation pathway found in eukaryotic cells, the contribution of processing α-glycosidases, and the use of such enzymes as potential drug targets to control some medically relevant viral infections. Thus far, some inhibitors of the endoplasmic reticulum α -glucosidases such as castanospermine, 1-deoxyjirimycin and derivative molecules have been shown to control viral particles in both in vitro and in vivo models. Nonetheless, the mechanism used for these molecules to inhibit specific viral groups, without affecting the host cells, remains unknown. Furthermore, certain α-mannosidase inhibitors have proven to be helpful in cancer therapy, either improving the sensitivity to chemotherapeutic drugs or reducing metastasis of the tumor. Undeniably promising, the use of α-glycosidase inhibitors rises as an alternative to control both viral infections and cancer. Despite the significant progress in the field, it remains to be demonstrated whether those inhibitors are good candidates to control other pathogens and if so, a careful treatment of the data must be done before extrapolating their use to other systems.

Objective: The aim of this review is to examine the multiple activities of antimicrobial peptides (AMPs) in vertebrates. Content: The largest AMP families are the cathelicidins and defensins, but several peptides derived from bigger proteins have also been reported. Cathelicidins are characterized by a conserved Nterminal pro-region and a variable region that encodes the C-terminal mature peptide. The β-defensins comprise a large family of AMPs that have diversified their functions, apparently without losing their antimicrobial activity. Cathelicidins and β-defensins are present in all vertebrates studied so far; α- defensins are present in mammals, while -defensins are only present in some non-human primates. The AMPs are regulated by posttranslational modifications that mainly include proteolysis, amidation, ADP-ribosylation, glycosylation and phosphorylation. In addition to their antimicrobial effects, AMPs show activity against viral particles and interfere in different steps of virus replication. Moreover, AMPs may both promote and inhibit cancer growth: several vertebrate AMPs kill cancer cells, and some tumors grow in an environment wherein the expression of β-defensins is reduced; however, human cathelicidin and some β-defensins are overexpressed in several types of cancer and are correlated with tumor growth. AMPs are part of the complex network of cells and molecules that forms the vertebrate innate defense system and they induce adaptive responses. In addition, they participate in sperm maturation and male reproduction. Conclusion: AMPs are multifunctional peptides that participate in immune responses, wound healing, angiogenesis, toxin neutralization, iron metabolism, male reproduction, among other functions. However, AMPs may also contribute to excessive inflammation and tumorigenesis.

Predicting functions of proteins is a key issue in the post-genomic era. Some experimental methods have been designed to predict protein functions. However, these methods cannot accommodate the vast amount of sequence data due to their inherent difficulty and expense. To address these problems, a lot of computational methods have been proposed to predict the function of proteins. In this paper, we provide a comprehensive survey of the current techniques for computational prediction of protein functions. We begin with introducing the formal description of protein function prediction and evaluation of prediction methods. We then focus on the various approaches available in categories of supervised and unsupervised methods for predicting protein functions. Finally, we discuss challenges and future works in this field.

Natural heme proteins may have heme bound to poly-peptide chain as a cofactor via noncovalent forces or heme as a prosthetic group may be covalently bound to the proteins. Nature has used porphyrins in diverse functions like electron transfer, oxidation, reduction, ligand binding, photosynthesis, signaling, etc. by modulating its properties through diverse protein matrices. Synthetic chemists have tried to utilize these molecules in equally diverse industrial and medical applications due to their versatile electro-chemical and optical properties. The heme iron has catalytic activity which can be modulated and enhanced for specific applications by protein matrix around it. Heme proteins can be designed into novel enzymes for sterio specific catalysis ranging from oxidation to reduction. These designed heme-proteins can have applications in industrial catalysis and biosensing. A peptide folds around heme easily due to hydrophobic effect of the large aromatic ring of heme. The directional property of co-ordinate bonding between peptide and metal ion in heme further specifies the structure. Therefore heme proteins can be easily designed for targeted structure and catalytic activity. The central aromatic chemical entity in heme viz. porphyrin is a very ancient molecule. Its presence in the prebiotic soup and in all forms of life suggests that it has played a vital role in the origin and progressive evolution of living organisms. Porphyrin macrocycles are highly conjugated systems composed of four modified pyrrole subunits interconnected at their α -carbon atoms via methine (=CH−) bridges. Initial minimalist models of hemoproteins focused on effect of heme-ligand co-ordinate bonding on chemical reactivity, spectroscopy, electrochemistry and magnetic properties of heme. The great sensitivity of these spectroscopic features of heme to its surrounding makes them extremely useful in structural elucidation of designed heme-peptide complexes. Therefore heme proteins are easier to work on for designing novel proteins for industrial and medical applications.

Vaccine development is one of the greatest achievements of modern medicine. Vaccines made of live-attenuated pathogens can revert to virulent live strains, which causes safety concerns. On the other hand, the use of purified antigenic components as subunit vaccines is safer, but less effective, as these components induce lower levels of protective immunity. Multiple copy presentation of an antigenic determinant in a well-ordered and well-defined orientation on a nanosized particle can mimic the natural host-pathogen surface interaction to provide antigen stability and immunogenicity similar to that of conventional vaccines with improved safety. The icosahedral symmetry of plant viral capsid based nanoparticles is highly ordered and their multivalent structured protein nanostructures facilitate genetic modifications that result in the display of heterologous epitopes or antigens attached to coat proteins. These recombinant plant virus-based nanoparticles (PVNs) provide platforms for the induction of humoral and cellular immune responses to genetically fused antigens from pathogenic viruses, bacteria, tumors, and toxins in man and animals. Here, we comprehensively review the developments of several recombinant PVNs as prophylactic and/or therapeutic vaccines for the prevention or treatment of several microbial diseases, pathologies, and toxin poisoning.

Striatal-enriched tyrosine protein phosphatase (STEP) is expressed mainly in the brain. Its dysregulation is associated with Alzheimer's and Huntington's diseases, schizophrenia, fragile X syndrome, drug abuse and stroke/ischemia. However, an association between STEP and depressive disorders is still obscure. The review discusses the theoretical foundations and experimental facts concerning possible relationship between STEP dysregulation and depression risk. STEP dephosphorylates and inactivates several key neuronal signaling proteins such as extracellular signal-regulating kinase 1 and 2 (ERK1/2), stress activated protein kinases p38, the Src family tyrosine kinases Fyn, Pyk2, NMDA and AMPA glutamate receptors. The inactivation of these proteins decreases the expression of brain derived neurotrophic factor (BDNF) necessary for neurogenesis and neuronal survival. The deficit of BDNF results in progressive degeneration of neurons in the hippocampus and cortex and increases depression risk. At the same time, a STEP inhibitor, 8-(trifluoromethyl)-1,2,3,4,5-benzopentathiepin-6-amine hydrochloride (TC-2153), increases BDNF expression in the hippocampus and attenuated the depressivelike behavior in mice. Thus, STEP is involved in the mechanism of depressive disorders and it is a promising molecular target for atypical antidepressant drugs of new generation.

Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at the atomic and molecular levels. However, there are still some parameters including torsions in amino acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single stranded nucleic acids for which the force fields need further improvement, although there are several workers putting in constant efforts in these directions. The existing force fields are not efficient for studying the crowded environment inside the cells, since these interactions involve multiple factors in real time. Therefore, the improved force fields may provide the opportunities for their wider applications on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental biological and physiological processes at the molecular levels that may be further applied in various fields including biotechnology, fisheries, sustainable agriculture and biomedical research.