Current Protein and Peptide Science - Volume 19, Issue 2, 2018

Antibiotic resistance in gram-negative bacteria has emerged as a major health threat that occurs because these bacteria actively produce β-lactamases responsible for the inactivation of β-lactam antibiotics. The first β lactamase was reported in E. coli back in 1940, before the release of the first antibiotic penicillin in clinical settings. Later on, large numbers of β-lactamases have been discovered in Gram-positive, Gram-negative bacteria as well as mycobacteria. Currently, numerous three-dimensional structures of serine and metallo-β-lactamases have been solved. The serine β-lactamases essentially consist of two structural domains (an all α and an α/β domain) and the active site is located at the groove between the two domains. The catalysis of serine β-lactamase proceeds via acylation and deacylation reactions. The three dimensional structure of metallo-β-lactamases displayed a common four layer “αβ/βα” motif, with a central “ββ”- sandwich by Zn2+ ion(s), and two α-helices are located on the either side. The active site of metallo-β-lactamases contain either 1 or 2 Zn2+ ions, which is coordinated to metal ligating amino acids and polarized water molecule(s) necessary for the hydrolysis of β-lactam antibiotics. Keeping the above views in mind, in this review we have shed light on the current knowledge of the structures and mechanisms of catalysis of serine and metallo-β-lactamases. Moreover, mutational studies on β-lactamases highlight the importance of the active site residues and residues in the vicinity to the active site pocket in the catalysis. To combat bacterial infections more effeciently novel inhibitors of β-lactamase in combination with antibiotics have been used which also form the theme of the review.

X-box binding protein 1 (XBP-1) is a key regulator of the unfolded protein response (UPR), which is activated in response to endoplasmic reticulum (ER) stress. Cells contain two protein isoforms of XBP-1, the active isoform (XBP-1S) and the inactive isoform (XBP-1U). Induction of UPR leads to the generation of XBP-1S while XBP-1U is dominant in ER stress-free cells. XBP-1S is a transcriptional activator and regulates the expression of a subset of UPR genes. Importantly, recent studies have demonstrated the essential role of XBP-1S in various human diseases, such as viral infections. Many viruses have evolved to manipulate UPR/XBP-1 of the infected cells to promote viral survival and replication. In this review, we will summarize the current findings on the involvement of XBP-1 in viral infection/ replication and discuss the potential anti-viral strategies by targeting XBP-1.

Cells possess protein quality control mechanisms to maintain proper cellular homeostasis. In eukaryotes, the roles of the ubiquitination and proteasome-mediated degradation of cellular proteins is well established. Recent studies have elucidated protein tagging mechanisms in prokaryotes, involving transfer messenger RNA (tmRNA) and pupylation. In this review, newer insights and bioinformatics analysis of two distinct bacterial protein tagging machineries are discussed. The machinery for tmRNAmediated tagging is present in several eubacterial representatives, e.g. Escherichia coli, Mycobacterium tuberculosis, Bacillus subtilis etc., but not in two archaeal representatives, such as Thermoplasma acidophilum and Sulfolobus solfataricus. On the other hand, the machinery involving tagging with the prokaryotic ubiquitin-like protein (Pup) is absent in most bacteria but is encoded in some eubacterial representatives, e.g. Mycobacterium tuberculosis and Mycobacterium leprae. Furthermore, molecular details on the relationship between protein tagging and enzymes involved in protein degradation in bacteria during infection are emerging. Several pathogenic bacteria that do not express the major ATP-dependent proteases, Lon and Caseinolytic protease (ClpP), are avirulent. Also, some ATP-independent peptidases, such as PepA and PepN, modulate the infection process. The roles of bacterial proteins involved in tagging and degradation during infection are discussed. These aspects add a new dimension to better understanding of the peculiarities of host-pathogen interactions.

Runt-related transcription factor 1 (RUNX1), a member of the RUNX family, is one of the key regulatory proteins in vertebrates. RUNX1 is involved in embryonic development, hematopoiesis, angiogenesis, tumorigenesis and immune response. In the past few decades, studies mainly focused on the effect of RUNX1 on acute leukemia and cancer. Only few studies about the function of RUNX1 in the pathological process of pulmonary diseases have been reported. Recent studies have demonstrated that RUNX1 is highly expressed in both mesenchymal and epithelial compartments of the developing and postnatal lung and that it plays a critical role in the lipopolysaccharide induced lung inflammation by regulating the NF-ΚB pathway. RUNX1 participates in the regulation of the NF-ΚB signaling pathway through interaction with IkB kinase complex in the cytoplasm or interaction with the NF-ΚB subunit P50. NF-ΚB is well-known signaling pathway necessary for inflammatory response in the lung. This review is to highlight the RUNX1 structure, isoforms and to present the mechanism that RUNX1 regulates NF-ΚB. This will illustrate the great potential role of RUNX1 in the inflammation signaling pathway in pulmonary diseases.

Diabetes is a metabolic disorder with multiple complications, including cardiomyopathy, retinopathy, nephropathy and neuropathy. Diabetic complications are the major cause of disability and death in diabetic patients. Apelin, a recently identified adipokine peptide, has been found to play important roles in diabetic complications. Here we summarize the current knowledge on the role of apelin in the pathogenesis of different diabetic complications. We also propose that similar to insulin resistance or leptin resistance, diabetics may also show apelin resistance. Potential clinical application of apelin and its analogue peptides in treating diabetic complications is discussed.

Plant cell walls are composite structures surrounding cells and involved in both mechanical support and perception of their environment. They are mainly composed of polysaccharides (90-95% of their mass) and proteins (5-10%). The cell wall proteins (CWPs) contribute to the arrangements and modifications of polymer networks and to cell-to-cell communication. The structure and composition of cell walls are not uniform in the whole plants, but rather specialized in different cell types to fulfil different functions. As examples, two kinds of cells are covered with extracellular structures composed of lipids: epidermal cells of aerial organs synthesize a cuticle on their outside surface whereas endodermal root cells form a suberin surrounding strip. In both cases, these particular hydrophobic layers contribute to the protection of the cells against attacks by pathogens or abiotic stresses and regulate physiological processes. If the intracellular biosynthesis of the molecules forming these layers starts to be welldescribed, the mechanisms of their assembly beyond the plasma membrane remain largely unknown. In this review, this issue is addressed on the basis on cell wall proteomics data which has allowed the identification of many CWPs possibly related to lipid metabolism during the last years, in particular in Arabidopsis thaliana and tomato. These data are combined with transcriptomics and genetics studies. The main known roles of extracellular proteins related to lipid metabolism are discussed.

Selection of proper targets for the X-ray crystallography will benefit biological research community immensely. Several computational models were proposed to predict propensity of successful protein production and diffraction quality crystallization from protein sequences. We reviewed a comprehensive collection of 22 such predictors that were developed in the last decade. We found that almost all of these models are easily accessible as webservers and/or standalone software and we demonstrated that some of them are widely used by the research community. We empirically evaluated and compared the predictive performance of seven representative methods. The analysis suggests that these methods produce quite accurate propensities for the diffraction-quality crystallization. We also summarized results of the first study of the relation between these predictive propensities and the resolution of the crystallizable proteins. We found that the propensities predicted by several methods are significantly higher for proteins that have high resolution structures compared to those with the low resolution structures. Moreover, we tested a new meta-predictor, MetaXXC, which averages the propensities generated by the three most accurate predictors of the diffraction-quality crystallization. MetaXXC generates putative values of resolution that have modest levels of correlation with the experimental resolutions and it offers the lowest mean absolute error when compared to the seven considered methods. We conclude that protein sequences can be used to fairly accurately predict whether their corresponding protein structures can be solved using X-ray crystallography. Moreover, we also ascertain that sequences can be used to reasonably well predict the resolution of the resulting protein crystals.

The lipid bilayer of the plasma membrane is a selective impermeable barrier for the internalization of most macromolecules. Cell penetrating peptides (CPPs) could cross the plasma membrane barrier to deliver various molecules into cells and are considered as a promising tool to deliver macromolecular drugs. However, the exact cellular uptake mechanisms of CPPs are still ambiguous. It was reported that the exact cellular uptake pathway was determined by numerous factors such as the amino acid sequences (hydrophobicity and net charge), extracellular CPP concentration, cargoes' properties, cell type and the temperature. No matter what kind of mechanisms, the electrostatic interaction between the positive charged amino acids and the membrane with negatively charged glycosaminoglycans (GAGs), especially heparan sulphate proteoglycans (HSPGs), was supposed to be the first crucial step for CPPs uptake. The first recognition triggers cytoskeletal remodeling via activating Rho/Rac GTPases and kinase C, followed by the cell surface microdomains changing, ligand binding and cellular uptake. This review briefly discusses the classification, structure-activity relationships, cellular uptake mechanisms and biomedical applications of CPPs.

Adipose triglyceride lipase (ATGL) is the key-enzyme for the release of fatty acids (FAs) from triacylglycerol (TG) stores during intracellular lipolysis producing FAs used for energy production. There is growing evidence that the products and intermediates from lipolytic breakdown during the FA mobilization process also have fundamental regulatory functions affecting cell signaling, gene expression, metabolism, cell growth, cell death, and lipotoxicity. Regulation of ATGL is therefore vital for maintaining a defined balance between lipid storage and mobilization. This review addresses the regulation of ATGL activity at the post-translational level with special emphasis on protein-mediated interaction at the site of hydrolytic action, namely to the lipid droplet.