Mechanism of Phosphatidylglycerol Activation Catalyzed by Prolipoprotein Diacylglyceryl Transferase

Navigating the landscape of enzyme design: from molecular simulations to machine learning

Global environmental issues and sustainable development call for new technologies for fine chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the alternative to the traditional organic synthesis. However, it is challenging to navigate the vast sequence space to identify those proteins with admirable biocatalytic functions. The recent development of deep-learning based structure prediction methods such as AlphaFold2 reinforced by different computational simulations or multiscale calculations has largely expanded the 3D structure databases and enabled structure-based design. While structure-based approaches shed light on site-specific enzyme engineering, they are not suitable for large-scale screening of potential biocatalysts. Effective utilization of big data using machine learning techniques opens up a new era for accelerated predictions. Here, we review the approaches and applications of structure-based and machine-learning guided enzyme design. We also provide our view on the challenges and perspectives on effectively employing enzyme design approaches integrating traditional molecular simulations and machine learning, and the importance of database construction and algorithm development in attaining predictive ML models to explore the sequence fitness landscape for the design of admirable biocatalysts.

The Influence of Outer Membrane Protein on Ampicillin Resistance of Vibrio parahaemolyticus

The antibiotic resistance of the food-borne pathogen Vibrio parahaemolyticus has attracted researchers' attention in recent years, but its molecular mechanism remains poorly understood. In this study, 7 genes encoding outer membrane proteins (OMPs) were individually deleted in V. parahaemolyticus ATCC33846, and the resistance of these 7 mutants to 14 antibiotics was investigated. The results revealed that the resistance of the 7 mutants to ampicillin was significantly increased. Further exploration of 20-gene transcription changes by real time-qPCR (RT-qPCR) demonstrated that the higher ampicillin resistance might be attributed to the expression of β-lactamase and reduced peptidoglycan (PG) synthesis activity through reduced transcription of penicillin-binding proteins (PBPs), increased transcription of l,d-transpeptidases, downregulated d,d-carboxypeptidase, and alanine deficiency. This study provides a new perspective on ampicillin resistance in OMP mutants with respect to PG synthesis.

The Role of Pulmonary Surfactant Phospholipids in Fibrotic Lung Diseases

Diffuse parenchymal lung diseases (DPLD) or Interstitial lung diseases (ILD) are a heterogeneous group of lung conditions with common characteristics that can progress to fibrosis. Within this group of pneumonias, idiopathic pulmonary fibrosis (IPF) is considered the most common. This disease has no known cause, is devastating and has no cure. Chronic lesion of alveolar type II (ATII) cells represents a key mechanism for the development of IPF. ATII cells are specialized in the biosynthesis and secretion of pulmonary surfactant (PS), a lipid-protein complex that reduces surface tension and minimizes breathing effort. Some differences in PS composition have been reported between patients with idiopathic pulmonary disease and healthy individuals, especially regarding some specific proteins in the PS; however, few reports have been conducted on the lipid components. This review focuses on the mechanisms by which phospholipids (PLs) could be involved in the development of the fibroproliferative response.

Bacterial Lipoprotein Posttranslational Modifications. New Insights and Opportunities for Antibiotic and Vaccine Development

Lipoproteins are some of the most abundant proteins in bacteria. With a lipid anchor to the cell membrane, they function as enzymes, inhibitors, transporters, structural proteins, and as virulence factors. Lipoproteins activate the innate immune system and have biotechnological applications. The first lipoprotein was described by Braun and Rehn in 1969. Up until recently, however, work on lipoproteins has been sluggish, in part due to the challenges of handling proteins that are anchored to membranes by covalently linked lipids or are membrane integral. Activity in the area has quickened of late. In the past 5 years, high-resolution structures of the membrane enzymes of the canonical lipoprotein synthesis pathway have been determined, new lipoprotein types have been discovered and the enzymes responsible for their synthesis have been characterized biochemically. This has led to a flurry of activity aimed at developing novel antibiotics targeting these enzymes. In addition, surface exposed bacterial lipoproteins have been utilized as candidate vaccine antigens, and their potential to act as self-adjuvanting antigens is increasingly recognized. A summary of the latest developments in lipoproteins and their synthesis, as well as how this information is being exploited for therapeutic purposes is presented here.

Inhibition of Escherichia coli Lipoprotein Diacylglyceryl Transferase Is Insensitive to Resistance Caused by Deletion of Braun's Lipoprotein

Lipoprotein diacylglyceryl transferase (Lgt) catalyzes the first step in the biogenesis of Gram-negative bacterial lipoproteins which play crucial roles in bacterial growth and pathogenesis. We demonstrate that Lgt depletion in a clinical uropathogenic Escherichia coli strain leads to permeabilization of the outer membrane and increased sensitivity to serum killing and antibiotics. Importantly, we identify G2824 as the first-described Lgt inhibitor that potently inhibits Lgt biochemical activity in vitro and is bactericidal against wild-type Acinetobacter baumannii and E. coli strains. While deletion of a gene encoding a major outer membrane lipoprotein, lpp, leads to rescue of bacterial growth after genetic depletion or pharmacologic inhibition of the downstream type II signal peptidase, LspA, no such rescue of growth is detected after Lgt depletion or treatment with G2824. Inhibition of Lgt does not lead to significant accumulation of peptidoglycan-linked Lpp in the inner membrane. Our data validate Lgt as a novel antibacterial target and suggest that, unlike downstream steps in lipoprotein biosynthesis and transport, inhibition of Lgt may not be sensitive to one of the most common resistance mechanisms that invalidate inhibitors of bacterial lipoprotein biosynthesis and transport.

IMPORTANCE As the emerging threat of multidrug-resistant (MDR) bacteria continues to increase, no new classes of antibiotics have been discovered in the last 50 years. While previous attempts to inhibit the lipoprotein biosynthetic (LspA) or transport (LolCDE) pathways have been made, most efforts have been hindered by the emergence of a common mechanism leading to resistance, namely, the deletion of the gene encoding a major Gram-negative outer membrane lipoprotein lpp. Our unexpected finding that inhibition of Lgt is not susceptible to lpp deletion-mediated resistance uncovers the complexity of bacterial lipoprotein biogenesis and the corresponding enzymes involved in this essential outer membrane biogenesis pathway and potentially points to new antibacterial targets in this pathway.

Lipoproteins in Gram-negative bacteria: new insights into their biogenesis, subcellular targeting and functional roles

Bacterial lipoproteins are globular proteins anchored to a membrane by a lipid moiety. By discovering new functions carried out by lipoproteins, recent research has highlighted the crucial roles played by these proteins in the cell envelope of Gram-negative bacteria. Here, after discussing the wide range of activities carried out by lipoproteins in the model bacterium Escherichia coli, we review new insights into the essential mechanisms involved in lipoprotein maturation, sorting and targeting to their final destination. A special attention will also be given to the recent identification of lipoproteins on the surface of E. coli and of other bacteria. The renewed interest in lipoproteins is driven by the need to identify novel targets for antibiotic development.

Mode of action of lipoprotein modification enzymes-Novel antibacterial targets

Lipoproteins are characterized by a fatty acid moiety at their amino-terminus through which they are anchored into membranes. They fulfill a variety of essential functions in bacterial cells, such as cell wall maintenance, virulence, efflux of toxic elements including antibiotics, and uptake of nutrients. The posttranslational modification process of lipoproteins involves the sequential action of integral membrane enzymes and phospholipids as acyl donors. In recent years, the structures of the lipoprotein modification enzymes have been solved by X-ray crystallography leading to a greater insight into their function and the molecular mechanism of the reactions. The catalytic domains of the enzymes are exposed to the periplasm or external milieu and are readily accessible to small molecules. Since the lipoprotein modification pathway is essential in proteobacteria, it is a potential target for the development of novel antibiotics. In this review, we discuss recent literature on the structural characterization of the enzymes, and the in vitro activity assays compatible with high-throughput screening for inhibitors, with perspectives on the development of new antimicrobial agents.

Zinc-mediated conformational preselection mechanism in the allosteric control of DNA binding to the zinc transcriptional regulator (ZitR)

The zinc transcriptional regulator (ZitR) functions as a metalloregulator that fine tunes transcriptional regulation through zinc-dependent DNA binding. However, the molecular mechanism of zinc-driven allosteric control of the DNA binding to ZitR remains elusive. Here, we performed enhanced sampling accelerated molecular dynamics simulations to figure out the mechanism, revealing the role of protein dynamics in the zinc-induced allosteric control of DNA binding to ZitR. The results suggest that zinc-free ZitR samples distinct conformational states, only a handful of which are compatible with DNA binding. Remarkably, zinc binding reduces the conformational plasticity of the DNA-binding domain of ZitR, promoting the population shift in the ZitR conformational ensemble towards the DNA binding-competent conformation. Further co-binding of DNA to the zinc–ZitR complex stabilizes this competent conformation. These findings suggest that ZitR–DNA interactions are allosterically regulated in a zinc-mediated conformational preselection manner, highlighting the importance of conformational dynamics in the regulation of transcription factor family.