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Plasminogen (Plg) is the inactive form of plasmin (Plm) that exists in two major glycoforms, referred to as glycoforms I and II (GI and GII). In the circulation, Plg assumes an activation-resistant "closed" conformation via interdomain interactions and is mediated by the lysine binding site (LBS) on the kringle (KR) domains. These inter-domain interactions can be readily disrupted when Plg binds to lysine/arginine residues on protein targets or free L-lysine and analogues. This causes Plg to convert into an "open" form, which is crucial for activation by host activators. In this study, we investigated how various ligands affect the kinetics of Plg conformational change using small-angle X-ray scattering (SAXS). We began by examining the open and closed conformations of Plg using size-exclusion chromatography (SEC) coupled with SAXS. Next, we developed a high-throughput (HTP) 96-well SAXS assay to study the conformational change of Plg. This method enables us to determine the Kopen value, which is used to directly compare the effect of different ligands on Plg conformation. Based on our analysis using Plg GII, we have found that the Kopen of ε-aminocaproic acid (EACA) is approximately three times greater than that of tranexamic acid (TXA), which is widely recognized as a highly effective ligand. We demonstrated further that Plg undergoes a conformational change when it binds to the C-terminal peptides of the inhibitor α2-antiplasmin (α2AP) and receptor Plg–RKT. Our findings suggest that in addition to the C-terminal lysine, internal lysine(s) are also necessary for the formation of open Plg. Finally, we compared the conformational changes of Plg GI and GII directly and found that the closed form of GI, which has an N-linked glycosylation, is less stable. To summarize, we have successfully determined the response of Plg to various ligand/receptor peptides by directly measuring the kinetics of its conformational changes. [ABSTRACT FROM AUTHOR]

The protein NINJ1 drives membrane rupture associated with certain types of cell death. Investigation of NINJ1 reveals mechanistic details of how it functions, raising the possibility of developing new therapeutics.Insights into a mechanism that ruptures the plasma membrane. [ABSTRACT FROM AUTHOR]

To control infections phagocytes can directly kill invading microbes. Macrophage‐expressed gene 1 (Mpeg1), a pore‐forming protein sometimes known as perforin‐2, is reported to be essential for bacterial killing following phagocytosis. Mice homozygous for the mutant allele Mpeg1tm1Pod succumb to bacterial infection and exhibit deficiencies in bacterial killing in vitro. Here we describe a new Mpeg mutant allele Mpeg1tm1.1Pib on the C57BL/6J background. Mice homozygous for the new allele are not abnormally susceptible to bacterial or viral infection, and irrespective of genetic background show no perturbation in bacterial killing in vitro. Potential reasons for these conflicting findings are discussed. In further work, we show that cytokine responses to inflammatory mediators, as well as antibody generation, are also normal in Mpeg1tm1.1Pib/tm1.1Pib mice. We also show that Mpeg1 is localized to a CD68‐positive endolysosomal compartment, and that it exists predominantly as a processed, two‐chain disulfide‐linked molecule. It is abundant in conventional dendritic cells 1, and mice lacking Mpeg1 do not present the model antigen ovalbumin efficiently. We conclude that Mpeg1 is not essential for innate antibacterial protection or antiviral immunity, but may play a focused role early in the adaptive immune response. [ABSTRACT FROM AUTHOR]

Macrophages are an ancient blood cell lineage critical for homeostasis and defence against pathogens. Although their numbers were long thought to be sustained solely by haematopoietic organs, it has recently become clear that their proliferation, or self‐renewal, also plays a major role. In the Drosophila larva, macrophages undergo a phase of rapid self‐renewal, making this an attractive model for elucidating the signals and regulatory mechanisms involved. However, a central self‐renewal pathway has not been identified in this system. Here, we show that the PDGF‐ and VEGF‐receptor related (Pvr) pathway fulfils this role. Our data show that two of the three known Pvr ligands, PDGF‐ and VEGF‐related factor 2 (Pvf2) and Pvf3, are major determinants of overall macrophage numbers, yet they each act in a temporally independent manner and via distinct mechanisms. While Pvf3 is needed prior to the self‐renewal period, we find that Pvf2 is critical specifically for expanding the larval macrophage population. We further show that Pvf2 is a potent macrophage mitogen that is kept at limiting quantities by its transient expression in a remarkably small number of blood cells. Together, these data support a novel mechanism for the regulation of macrophage self‐renewal rates by the dynamic transcriptional control of Pvf2. Given the strong parallels that exist between Drosophila and vertebrate macrophage systems, it is likely that a similar self‐renewal control mechanism is at play across animal phyla. [ABSTRACT FROM AUTHOR]

Natural killer cells and cytotoxic T lymphocytes accomplish the critically important function of killing virus-infected and neoplastic cells. They do this by releasing the pore-forming protein perforin and granzyme proteases from cytoplasmic granules into the cleft formed between the abutting killer and target cell membranes. Perforin, a 67-kilodalton multidomain protein, oligomerizes to form pores that deliver the pro-apoptopic granzymes into the cytosol of the target cell (1-6). The importance of perforin is highlighted by the fatal consequences of congenital perforin deficiency, with more than 50 different perforin mutations linked to familial haemophagocytic lymphohistiocytosis (type 2 FHL) (7). Here we elucidate the mechanism of perforin pore formation by determining the X-ray crystal structure of monomeric murine perforin, together with a cryo-electron microscopy reconstruction of the entire perforin pore. Perforin is a thin 'key-shaped' molecule, comprising an amino-terminal membrane attack complex perforinlike (MACPF)/cholesterol dependent cytolysin (CDC) domain (8,9) followed by an epidermal growth factor (EGF) domain that, together with the extreme carboxy-terminal sequence, forms a central shelf-like structure. A C-terminal C2 domain mediates initial, [Ca.sup.2+]-dependent membrane binding. Most unexpectedly, however, electron microscopy reveals that the orientation of the perforin MACPF domain in the pore is inside-out relative to the subunit arrangement in CDCs (10,11). These data reveal remarkable flexibility in the mechanism of action of the conserved MACPF/CDC fold and provide new insights into how related immune defence molecules such as complement proteins assemble into pores., The sequence similarity between perforin and complement components C6-C9 of the membrane attack complex strongly suggests that two major branches of the mammalian immune system utilize a pore-forming MACPF fold [...]

Approximately 2% of mammalian genes encode proteases. Comparative genomics reveals that those involved in immunity and reproduction show the most interspecies diversity and evidence of positive selection during evolution. This is particularly true of granzymes, the cytotoxic proteases of natural killer cells and CD8+ T cells. There are 5 granzyme genes in humans and 10 in mice, and it is suggested that granzymes evolve to meet species-specific immune challenge through gene duplication and more subtle alterations to substrate specificity. We show that mouse and human granzyme B have distinct structural and functional characteristics. Specifically, mouse granzyme B is 30 times less cytotoxic than human granzyme B and does not require Bid for killing but regains cytotoxicity on engineering of its active site cleft. We also show that mouse granzyme A is considerably more cytotoxic than human granzyme A. These results demonstrate that even 'orthologous' granzymes have species-specific functions, having evolved in distinct environments that pose different challenges.

Author(s): Adrienne W. Paton (corresponding author) [1]; Travis Beddoe [2]; Cheleste M. Thorpe [3]; James C. Whisstock [2]; Matthew C. J. Wilce [2]; Jamie Rossjohn [2]; Ursula M. Talbot [1]; [...]

Protein structure fundamentally underpins the function and processes of numerous biological systems. Fold recognition algorithms offer a sensitive and robust tool to detect structural, and thereby functional, similarities between distantly related homologs. In the era of accurate structure prediction owing to advances in machine learning techniques and a wealth of experimentally determined structures, previously curated sequence databases have become a rich source of biological information. Here, we use bioinformatic fold recognition algorithms to scan the entire AlphaFold structure database to identify novel protein family members, infer function and group predicted protein structures. As an example of the utility of this approach, we identify novel, previously unknown members of various pore-forming protein families, including MACPFs, GSDMs and aerolysin-like proteins. Author summary: Virtually every cellular process in all organisms on Earth is driven by molecular nano-machines known as proteins. The diverse functions of proteins are the result of the unique three-dimensional shape adopted by a given protein molecule. It is therefore important to determine the shape of a given protein, which unlike DNA and our genes, cannot be known from its sequence alone. Since two proteins with similar shapes typically have a similar function, knowing a protein shape provides crucial clues about its function. By virtue of decades of experimental work and advances in artificial intelligence, this complex shape can now be computationally predicted for any protein whose composition is known. Scientists have used these and other methods to produce enormous libraries of protein shapes consisting of nearly a million unique entries. However, these libraries are too large and too complex for researchers to 'read'. We use shape-comparison algorithms to carefully check these shape-libraries to gain insight into the potential function and biological role of previously unknown proteins. Furthermore, we identified new members of protein families using this technique. We show that shape-matching algorithms and computationally generated shape-libraries can be used effectively together to yield new insights and expedite scientific endeavours. [ABSTRACT FROM AUTHOR]

Research reveals that chimeras of the alpha(sub)1-antitrypsin efficiently inhibit papain-like cysteine protease and that the inhibition is a function of the length of the reactive center loop. Data indicate that the inhibition requires insertion of the reactive center loop into the body of the cysteine protease body.

Amino acid substitution studies reveal that the F-helix of the serpin alpha(sub)1-antitrypsin Abeta-sheet is highly disrupted in conformation, suggesting that the F-helix plays a role in the early conformational changes of the protein unfolding. The substitution of Tyr160 to alanine leads to loss of hydrogen bond and protein stability but restored by tryptophan.

The mouse SQN-5 serpin inhibits both chymotrypsin-like serine and the papain-like cysteine proteinases through a reactive site loop-dependent inhibitory mechanism. Data indicate that the human and mouse serpin genes seem to have originated from a common ancestor.