{"title":"Acyltransferases that Modify Cell Surface Polymers Across the Membrane.","authors":"Bailey J Schultz, Suzanne Walker","doi":"10.1021/acs.biochem.4c00731","DOIUrl":"10.1021/acs.biochem.4c00731","url":null,"abstract":"<p><p>Cell surface oligosaccharides and related polymers are commonly decorated with acyl esters that alter their structural properties and influence their interactions with other molecules. In many cases, these esters are added to polymers that are already positioned on the extracytoplasmic side of a membrane, presenting cells with a chemical challenge because the high-energy acyl donors used for these modifications are made in the cytoplasm. How activated acyl groups are passed from the cytoplasm to extra-cytoplasmic polymers has been a longstanding question. Recent mechanistic work has shown that many bacterial acyl transfer pathways operate by shuttling acyl groups through two covalent intermediates to their final destination on an extracellular polymer. Key to these and other pathways are cross-membrane acyltransferases─enzymes that catalyze transfer of acyl groups from a donor on one side of the membrane to a recipient on the other side. Here we review what has been learned recently about how cross-membrane acyltransferases in polymer acylation pathways function, highlighting the chemical and biosynthetic logic used by two key protein families, membrane-bound <i>O</i>-acyltransferases (MBOATs) and acyltransferase-3 (AT3) proteins. We also point out outstanding questions and avenues for further exploration.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1728-1749"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12021268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Coarse-Grained Molecular Dynamics Simulations Reveal Potential Role of Cardiolipin in Lateral Organization of Proteorhodopsin.","authors":"Alexander Wroe, Eric Sefah, Blake Mertz","doi":"10.1021/acs.biochem.4c00831","DOIUrl":"10.1021/acs.biochem.4c00831","url":null,"abstract":"<p><p>Proteorhodopsin (PR) is a microbial light-harvesting proton pump protein that is ubiquitous in marine ecosystems and is critical for biological solar energy conversion. A unique characteristic of PR is that its function can be directly affected by changes in the surrounding cellular membrane environment. Cardiolipin (CL) is a commonly found lipid in mitochondria and bacterial cell membranes and plays a prominent role in the function of numerous integral membrane proteins, due to its bulky conical shape and ionizable nature of its headgroup. CL can directly interact with other microbial rhodopsins and modulate their function; however, the potential role of CL in the function of PR is unclear. In this study, we used the MARTINI coarse-grained force field to characterize the interactions of CL with PR in a model bilayer via coarse-grained molecular dynamics (MD) simulations. Our simulations show that both electrostatic and nonpolar forces drive residue-specific interactions of CL with proteorhodopsin, especially for the asymmetrical -1 charge state of CL. Several CL binding sites were identified, with lipid-protein interactions occurring on the μs time scale. These binding sites are proximal to key functional areas and regions of oligomerization on PR, suggesting that CL could play a role in modulating proton pumping of proteorhodopsin.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1887-1894"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12004449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Click Lipid Nanoparticles for the Delivery of mRNA to Metabolically Labeled Cancer Cells.","authors":"Zhengzhong Tan, Lining Zheng, Yang Bo, Nurila Kambar, Hua Wang, Cecilia Leal","doi":"10.1021/acs.biochem.4c00699","DOIUrl":"10.1021/acs.biochem.4c00699","url":null,"abstract":"<p><p>Lipid nanoparticle (LNP)-based mRNA delivery has a lot of potential in combating a wide range of diseases, but delivering mRNA to specific cell types continues to be challenging. Despite recent advances in organ and cell specificity, the majority of clinical LNP systems cannot fully release their payload to a targeted site. Incorporating active targeting moieties into LNPs is highly desired to expand nanomedicine applications. In this Letter, we developed LNPs that harness the power of bioorthogonal \"click\" azide-alkyne chemical reactions. We show that the plasma membranes of cancer cells can be labeled with azide groups by metabolic sugar labeling, and these azide groups can react with dibenzocyclooctyne (DBCO) on LNPs to achieve specific binding. To achieve this, we synthesized new and versatile lipids by functionalizing DBCO groups to phospholipids with or without a poly(ethylene glycol) (PEG) linker. The DBCO lipids were successfully formulated into DBCO-LNPs comprising other standard lipid compounds. When using these DBCO-LNPs to deliver mRNA to metabolically labeled cells, DBCO-LNPs showed a remarkable ability to preferentially deliver mRNA to azide-labeled cells. Removing PEG linkers from DBCO lipids enables better integration and retention in the LNP, and the higher the amount of DBCO lipid, the stronger the targeting effect. This work demonstrates that cell-specific targeting can be achieved utilizing azide-alkyne ″click″ chemistry and could inspire the development of the next generation of LNPs for active cyto-tropic nanomedicines.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1807-1816"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Molecular Pharmacology of the Antibiotic Fosfomycin, an Inhibitor of Peptidoglycan Biosynthesis.","authors":"Dennis H Kim, Watson J Lees","doi":"10.1021/acs.biochem.4c00522","DOIUrl":"10.1021/acs.biochem.4c00522","url":null,"abstract":"<p><p>The antibiotic fosfomycin is an epoxy-phosphonate natural product with a broad spectrum of antibacterial activity and distinct mechanism of action that has been in clinical use for 50 years. Fosfomycin is an irreversible covalent inhibitor of UDP-GlcNAc enolpyruvyl transferase (MurA), which catalyzes the first committed step in bacterial peptidoglycan biosynthesis. Fosfomycin binds to the active site of MurA in competition with substrate phosphoenolpyruvate (PEP) and undergoes the ring-opening nucleophilic attack of an active-site cysteine. MurA and its related enolpyruvyl transferase, 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase (AroA), are the only known enzymes to catalyze the unusual enolpyruvyl transfer from PEP, and each is the target of an important inhibitor. Specifically, MurA is inactivated by fosfomycin, and EPSP synthase (AroA) of the shikimate pathway is the target of the herbicide glyphosate. Commonalities and differences in enzymatic reaction mechanisms of MurA and EPSP synthase provide a molecular rationale for the specificity of their respective inhibitors. With its distinct mode of molecular action and clinical activity against multidrug-resistant bacteria, fosfomycin continues to motivate the discovery and development of novel inhibitors of MurA.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1720-1727"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lucy Martin, Daniela P Freitas, Emmanuelle Boll, Alain Brans, Justine Mortelecque, François-Xavier Cantrelle, Pierre Dourlen, Cláudio M Gomes, Clément Danis, Isabelle Landrieu
{"title":"Conformation-Driven Phase Separation in the Linker Domain of Focal Adhesion Kinases.","authors":"Lucy Martin, Daniela P Freitas, Emmanuelle Boll, Alain Brans, Justine Mortelecque, François-Xavier Cantrelle, Pierre Dourlen, Cláudio M Gomes, Clément Danis, Isabelle Landrieu","doi":"10.1021/acs.biochem.4c00677","DOIUrl":"10.1021/acs.biochem.4c00677","url":null,"abstract":"<p><p>Protein tyrosine kinase 2 (Pyk2), also known as focal adhesion kinase 2, and focal adhesion kinase 1 (Fak1) are two related nonreceptor tyrosine kinases (hereafter referred to as FAKs). Here, we focused on characterizing a linker region of the FAK proteins (hereafter referred to as FAK KFL for Kinase FAT Linker), which in the case of Pyk2 has previously been shown to play a functional role in calcium sensing through its interaction with calmodulin. Using structural nuclear magnetic resonance spectroscopy, we provide chemical shift assignments for the FAK KFLs, defining their conformational properties. Analysis of the FAK KFL conformations revealed their predominantly disordered nature, except for well-defined segments with a significant tendency to form α-helices, which were modeled to form homodimeric interfaces. In addition, we showed that the FAK KFL segments form condensates in vitro under high crowding conditions. By directly comparing the conformational properties of the Pyk2 and Fak1 KFL domains and providing structural data, this study provides valuable insights into the structural basis of FAK KFL interactions. Furthermore, the results show that disordered segments in proteins within the focal adhesion complex undergo phase separation, a process of potential biological significance due to protein clustering.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1797-1806"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Druggable Transcriptome Project: From Chemical Probes to Precision Medicines.","authors":"Matthew D Disney","doi":"10.1021/acs.biochem.5c00006","DOIUrl":"10.1021/acs.biochem.5c00006","url":null,"abstract":"<p><p>RNA presents abundant opportunities as a drug target, offering significant potential for small molecule medicine development. The transcriptome, comprising both coding and noncoding RNAs, is a rich area for therapeutic innovation, yet challenges persist in targeting RNA with small molecules. RNA structure can be predicted with or without experimental data, but discrepancies with the actual biological structure can impede progress. Prioritizing RNA targets supported by genetic or evolutionary evidence enhances success. Further, small molecules must demonstrate binding to RNA in cells, not solely in vitro, to validate both the target and compound. Effective small molecule binders modulate functional sites that influence RNA biology, as binding to nonfunctional sites requires recruiting effector mechanisms, for example degradation, to achieve therapeutic outcomes. Addressing these challenges is critical to unlocking RNA's vast potential for small molecule medicines, and a strategic framework is proposed to navigate this promising field, with a focus on targeting human RNAs.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1647-1661"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12005196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zahra Raza, Nehad S El Salamouni, Andrew B McElroy, Danielle Skropeta, Michael J Kelso, Aaron J Oakley, Nicholas E Dixon, Haibo Yu
{"title":"Active Site Plasticity of the Bacterial Sliding Clamp.","authors":"Zahra Raza, Nehad S El Salamouni, Andrew B McElroy, Danielle Skropeta, Michael J Kelso, Aaron J Oakley, Nicholas E Dixon, Haibo Yu","doi":"10.1021/acs.biochem.4c00686","DOIUrl":"10.1021/acs.biochem.4c00686","url":null,"abstract":"<p><p>The rise of antibiotic resistance poses a severe global threat, specifically due to the emergence of multiresistant bacteria (ESKAPE pathogens), which are responsible for countless deaths globally. Consequently, the development of novel antibiotics is in dire need. Targeting proteins essential to DNA replication is a promising pathway, making the β-sliding clamp (β-SC) an attractive target. Currently, there are no antibiotics on the market that target the β-SC. However, numerous compounds are being investigated to create an antibiotic with high potency against a broad range of bacterial species. Interestingly, most proposed compounds do not bind to the entire active site, which may reduce their potential as high-potency inhibitors. This is due to the active site residue Met at position 362, adopting a \"closed\" conformation, preventing inhibitors access into Subsite II of the active site. This study explored the effect of key residues on the plasticity of the β-SC active site using molecular dynamics and metadynamics simulations under different physiological states. Our results show that the Met gate exhibits flexibility and both open and closed states are thermodynamically and kinetically accessible.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1762-1769"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Targeting Polymeric Nanoparticles to Specific Cell Populations in the Liver.","authors":"Lauren Harkins, Silvia Vilarinho, W Mark Saltzman","doi":"10.1021/acs.biochem.4c00712","DOIUrl":"10.1021/acs.biochem.4c00712","url":null,"abstract":"<p><p>Nanoparticles (NPs) are beneficial for delivery of drugs in a variety of settings, serving to protect their cargo and allow for sustained release. Polymeric NPs offer several advantages as therapeutics carriers due to their tunable characteristics like size and shape, ease of manufacturing, and biocompatibility. Despite this, there are no polymeric NPs that are approved for treatment of liver diseases. This is surprising since─when administered intravenously─the majority of NPs accumulate in cells in the liver. NP characteristics like size and surface charge can be altered to affect distribution to the liver, and even cellular distribution, but the conjugation of targeting ligands onto the NP surface for specific receptors on the cells is an important approach for enhancing cell specific delivery. Enhancing cell-specific targeting of conjugated NPs in the liver has two major hurdles: 1) avoiding accumulation of NPs in the liver resident macrophages known as Kupffer cells, which are optimized to phagocytose particulates, and 2) overcoming the transport barriers associated with architectural changes of the diseased liver. To identify the structures and mechanisms most important in NP design, NP administration during ex vivo perfusion (EVP)─achieved by anatomically isolating an organ by perfusing it outside the body─may be the most important and efficient approach. However, EVP is currently underutilized in the NP field, with limited research published on NPs delivered during liver EVP, and therefore representing an opportunity for future investigations.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1685-1697"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genome-Wide Analysis of Stable RNA Secondary Structures across Multiple Organisms Using Chemical Probing Data: Insights into Short Structural Motifs and RNA-Targeting Therapeutics.","authors":"Jingxin Wang","doi":"10.1021/acs.biochem.4c00764","DOIUrl":"10.1021/acs.biochem.4c00764","url":null,"abstract":"<p><p>Small molecules targeting specific RNA-binding sites, including stable and transient RNA structures, are emerging as effective pharmacological approaches for modulating gene expression. However, little is understood about how stable RNA secondary structures are shared across organisms, which is an important factor in controlling drug selectivity. In this study, I provide an analytical pipeline named RNA secondary structure finder (R2S-Finder) to discover short, stable RNA structural motifs in humans, <i>Escherichia coli</i> (<i>E. coli</i>), SARS-CoV-2, and Zika virus by leveraging existing in vivo and in vitro genome-wide chemical RNA-probing datasets. I found several common features across the organisms. For example, apart from the well-documented tetraloops, AU-rich tetraloops are widely present in different organisms. I also validated that the 5' untranslated region (UTR) contains a higher proportion of stable structures than the coding sequences in humans and Zika virus. In general, stable structures predicted from in vitro (protein-free) and in vivo datasets are consistent across different organisms, indicating that stable structure formation is mostly driven by RNA folding, while a larger variation was found between in vitro and in vivo data for certain RNA types, such as human long intergenic noncoding RNAs (lincRNAs). Finally, I predicted stable three- and four-way RNA junctions that exist under both in vivo and in vitro conditions and can potentially serve as drug targets. All results of stable structures, stem-loops, internal loops, bulges, and <i>n</i>-way junctions have been collated in the R2S-Finder database (https://github.com/JingxinWangLab/R2S-Finder), which is coded in hyperlinked HTML pages and tabulated in CSV files.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1817-1827"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12005188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Indalo Domene-Serrano, Raquel Cuadros, Vega García-Escudero, Francisco Vallejo-Bedia, Ismael Santa-María, Laura Vallés-Saiz, Félix Hernandez, Jesús Avila
{"title":"Shapeshifter W-Tau Peptide Inhibits Tau Aggregation and Disintegrates Paired Helical Filaments.","authors":"Indalo Domene-Serrano, Raquel Cuadros, Vega García-Escudero, Francisco Vallejo-Bedia, Ismael Santa-María, Laura Vallés-Saiz, Félix Hernandez, Jesús Avila","doi":"10.1021/acs.biochem.4c00809","DOIUrl":"10.1021/acs.biochem.4c00809","url":null,"abstract":"<p><p>Tauopathies comprise a range of neurodegenerative conditions characterized by the aberrant accumulation of tau protein clumps in the brain. These aggregates are formed by different tau splicing isoforms. Here, we analyzed the role of a specific intron-derived peptide called the W-Tau peptide on the polymerization-depolymerization of tau filaments. This peptide originates from a new isoform of the tau protein, named W-Tau, which is formed due to the retention of intron 12. AlphaFold3 (AF3)-based <i>in silico</i> investigations suggested that the W-Tau peptide interacts with tau monomers. Our <i>in vitro</i> experiments confirmed these predictions and showed that the W-Tau peptide inhibited tau aggregation. In addition, the W-Tau peptide disrupted preexisting paired helical filaments (PHFs) isolated from postmortem brain samples of patients with Alzheimer's disease, thereby supporting its potential therapeutic value. The effectiveness of the W-Tau peptide was demonstrated by the decrease in tau aggregation observed after cotransfection of the W-Tau peptide and PHF seeds, as demonstrated by analysis involving a fluorescence resonance energy transfer (FRET) cell biosensor. The W-Tau peptide breaks PHFs by selectively attaching to their ends, causing the structures to unwind and convert into circle-like formations. Considering the potential neuroprotective effects against tauopathies, the W-Tau isoform and its peptide are interesting candidates for future therapeutic interventions.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1841-1851"},"PeriodicalIF":2.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12004447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143717576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}