BBA Advances最新文献

{"title":"Are cellulases slow? Kinetic and thermodynamic limitations for enzymatic breakdown of cellulose","authors":"Peter Westh ,&nbsp;Jeppe Kari ,&nbsp;Silke Badino ,&nbsp;Trine Sørensen ,&nbsp;Stefan Christensen ,&nbsp;Nanna Røjel ,&nbsp;Corinna Schiano-di-Cola ,&nbsp;Kim Borch","doi":"10.1016/j.bbadva.2024.100128","DOIUrl":"10.1016/j.bbadva.2024.100128","url":null,"abstract":"<div><div>Cellulases are of paramount interest for upcoming biorefineries that utilize residue from agriculture and forestry to produce sustainable fuels and chemicals. Specifically, cellulases are used for the conversion of recalcitrant plant biomass to fermentable sugars in a so-called saccharification process. The vast literature on enzymatic saccharification frequently refers to low catalytic rates of cellulases as a main bottleneck for industrial implementation, but such statements are rarely supported by kinetic or thermodynamic considerations. In this perspective, we first discuss activation barriers and equilibrium conditions for the hydrolysis of cellulose and how these parameters influence enzymatic turnover. Next, we propose a simple framework for kinetic description of cellulolytic enzyme reactions and show how this can pave the way for comparative biochemical analyses of cellulases acting on their native, insoluble substrate. This latter analysis emphasizes that cellulases are characterized by extraordinarily low off-rate constants, while other kinetic parameters including specificity constants and rate constants for association and bond cleavage are quite like parameters reported for related enzymes acting on soluble substrates.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100128"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11699605/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142932750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phosphorylation of N-glycans in the brain: The case for a non-canonical pathway?","authors":"Lucija Sironić ,&nbsp;Nikol Mraz ,&nbsp;Gordan Lauc ,&nbsp;Thomas S. Klarić","doi":"10.1016/j.bbadva.2024.100134","DOIUrl":"10.1016/j.bbadva.2024.100134","url":null,"abstract":"<div><div>Asparagine-linked glycosylation (N-glycosylation) is a common co- and post-translational modification that refers to the addition of complex carbohydrates, called N-linked glycans (N-glycans), to asparagine residues within defined sequons of polypeptide acceptors. Some N-glycans can be modified by the addition of phosphate moieties to their monosaccharide residues, thus forming phospho-N-glycans (PNGs). The most prominent such carbohydrate modification is mannose-6-phosphate (M6P) which plays a well-established role in trafficking of acid hydrolases to lysosomes. However, comparatively little is known about potential alternative types of glycan phosphorylation, particularly when it comes to the brain which is especially rich in phosphorylated oligosaccharides. Combining data from the literature and novel insights derived from our own analyses of published datasets, here we present what is currently known about PNGs in the brain and the glycoproteins they modify. We show that brain PNGs exhibit several distinctive features that don't completely align with our current understanding of the canonical M6P pathway. Furthermore, we demonstrate that there are numerous differences in the way that lysosomal and non-lysosomal neural glycoproteins are modified by PNGs. Based on these observations, we put forward the hypothesis that, in addition to the conventional M6P pathway, the brain employs an alternative oligosaccharide phosphorylation mechanism for the modification of a discrete set of glycoproteins. Here we examine the evidence underpinning this hypothesis and discuss the implications that it raises. Overall, our work suggests that phosphorylation of N-glycans in the brain may be more complex and more diverse than previously recognised.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100134"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11732245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Capturing the micro-communities: Insights into biogenesis and architecture of bacterial biofilms","authors":"Harshita Agarwal ,&nbsp;Bharat Gurnani ,&nbsp;Bhumika Pippal ,&nbsp;Neha Jain","doi":"10.1016/j.bbadva.2024.100133","DOIUrl":"10.1016/j.bbadva.2024.100133","url":null,"abstract":"<div><div>Biofilm is an assemblage of microorganisms embedded within the extracellular matrix that provides mechanical stability, nutrient absorption, antimicrobial resistance, cell-cell interactions, and defence against host immune system. Various biomolecules such as lipids, carbohydrates, protein polymers (amyloid), and eDNA are present in the matrix playing significant role in determining the distinctive properties of biofilm. The formation of biofilms contributes to resistance against antimicrobial therapy in most of the human infections and exacerbates existing diseases. Therefore, this field requires several state-of-the-art techniques to fully understand the 3-D organization of biofilms, their cell behaviour and responses to pharmaceutical treatments. Here, we explore the assembly and regulation of biofilm biogenesis in the context of matrix components and highlight the significance of high-resolution imaging and analysing techniques for monitoring complex biofilm architecture. Our review also emphasizes the novelty and advancements in techniques to visualise biofilm structure and composition, providing valuable insights to understand biofilm-related infections.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100133"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein recognition methods for diagnostics and therapy","authors":"Ryne Montoya,&nbsp;Peter Deckerman,&nbsp;Mustafa O. Guler","doi":"10.1016/j.bbadva.2025.100149","DOIUrl":"10.1016/j.bbadva.2025.100149","url":null,"abstract":"<div><div>The fundamental biological processes involving highly specific interactions between proteins and other biological motifs are the pillars of protein recognition mechanisms. These interactions are crucial for biological systems, often having significant implications within diagnostics and therapy development. Protein recognition and specificity are reliant on structural compatibility, dynamic conformational changes, and biochemical interactions—all of which are grounded in fundamental molecular forces like hydrogen bonding, ionic interactions, and van der Waals forces. Advanced characterization tools have improved our understanding of protein interactions, revealing the kinetics and thermodynamics of these recognition mechanisms. In parallel, new computing methods, including artificial intelligence, molecular docking, and dynamical simulations, have increased prediction accuracy for molecular interactions, leading to well-defined interaction sites and binding kinetics information. Protein recognition is pivotal in diagnostic methods including ELISAs and biosensors, which are crucial within disease detection applications. In therapeutics, protein recognition plays an important role in drug development, enabling the design of small molecules, peptides, and monoclonal antibodies. Despite recent progress, there are many challenges remaining to fully understand protein recognition, particularly within the complex cell environment. These challenges require future work in protein recognition studies to enhance diagnostic and therapeutic applications. The researchers are using improved detection and screening methods to identify, assess, and optimize interactions for clinical translation.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100149"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143437617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"F-type lectins: Structural and functional aspects, and potential biomedical applications","authors":"Gerardo R. Vasta ,&nbsp;Mario A. Bianchet","doi":"10.1016/j.bbadva.2025.100166","DOIUrl":"10.1016/j.bbadva.2025.100166","url":null,"abstract":"<div><div>Among the multiple animal lectin families recognized to date, F-type lectins (FTLs), fucose-binding lectins characterized by an FTL domain (FTLD), constitute the most recent lectin family to be identified and structurally characterized. The structure of the FTL from the European eel <em>Anguilla anguilla</em> revealed a novel jellyroll lectin fold (the \"F-type\" fold) with unique fucose- and calcium-binding sequence motifs. The FTL lectin family comprises proteins that may exhibit single or multiple FTLD, in combination with structurally and functionally distinct domains, and can form oligomeric associations that display high-avidity multivalent binding. Differences in fine carbohydrate specificity among tandemly arrayed FTLDs present in any FTL polypeptide subunit, together with the expression of multiple FTL isoforms in a single individual supports a broad diversity in ligand recognition. Widely distributed in invertebrates, protochordates, ectothermic vertebrates, birds, and monotreme and marsupial mammals, the FTLD is also present in some bacterial proteins and viruses but absent in placental mammals. The taxonomically broad, and discontinuous distribution of the FTLD, suggests an extensive structural and functional diversification of this lectin family, including horizontal gene transfer in viruses and prokaryotic organisms, together with possible gene loss and/or cooption along the lineages leading to the mammals. FTLs’ biological roles range from pathogen recognition in innate immunity to fertilization, cell adhesion and cell aggregation, and as bacterial virulence factors, among others. The specificity of FTLs for fucosylated moieties should provide ample opportunities for novel applications in glycan and cell separation, and innovative diagnostic, preventive, and therapeutic approaches in cancer and infectious disease.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"8 ","pages":"Article 100166"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144330350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in total glycomic analysis including sialylated sub-glycan isomers by SALSA method","authors":"Masaki Kurogochi ,&nbsp;Chiharu Suzuki ,&nbsp;Hisatoshi Hanamatsu ,&nbsp;Jun-ichi Furukawa","doi":"10.1016/j.bbadva.2025.100144","DOIUrl":"10.1016/j.bbadva.2025.100144","url":null,"abstract":"<div><div>All eukaryotic cell surfaces are coated with various types of glycans, which are essential molecules in biological events. In this review, we summarize recent integrated glycomics studies using various biological samples. We introduce an improved sialic acid linkage-specific alkylamidation (SALSA) method for sialylated glycan analysis and an automated glycosphingolipid-glycan preparation system for large-scale glycomic analysis of human plasma/serum. Finally, we explain the importance of integrated glycomics of glycoconjugates through total glycomic analysis of human serum and mouse brain tissue, and discuss prospects for exploring glycans as effective biomarkers of biological phenomena.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100144"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143509572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The future of plant lectinology: Advanced technologies and computational tools","authors":"Vinicius J.S. Osterne ,&nbsp;Kyria S. Nascimento ,&nbsp;Benildo S. Cavada ,&nbsp;Els J.M. Van Damme","doi":"10.1016/j.bbadva.2025.100145","DOIUrl":"10.1016/j.bbadva.2025.100145","url":null,"abstract":"<div><div>Lectins play crucial roles in many biological processes and serve as tools in fields ranging from agriculture to biomedicine. While classical methods for lectin discovery and characterization were foundational for the field, they often lack sensitivity and throughput, limiting the detection of less abundant or weakly binding lectins, such as the stress-inducible or monovalent lectins. This review focuses on recent advancements in plant lectin research, particularly novel technologies that complement traditional approaches. Techniques such as glycan microarrays allow rapid assessment of lectin specificity across a diverse range of glycans by evaluating interactions with immobilized glycans on solid surfaces. Phage display libraries enable the identification of carbohydrate-mimetic peptides and the development of ligands for lectins by presenting diverse peptide libraries on bacteriophages. Genomic and transcriptomic analyses facilitate the exploration of the lectome in various plant species by scanning entire datasets to identify genes that contain lectin motifs—specific conserved amino acid sequences involved in carbohydrate recognition—and lectin domains, the larger structural regions that facilitate and stabilize these interactions. Additionally, computational methods—including molecular docking, molecular dynamics simulations, and machine learning pipelines—support predictions of lectin structures and binding properties, underpinning experimental efforts. These advanced techniques bring increased efficiency, accuracy, and a broader scope to lectin studies, with potential impacts across multiple fields. However, challenges such as data complexity and the need for experimental validation for computational methods remain. The future of lectin research will depend on the integration of these methods and the strengthening of interdisciplinarity to unlock the full potential of lectins.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100145"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143170982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a permethylation-based detection method for oligo/polysialic acid structures via tandem MALDI-TOF mass spectrometry","authors":"Kai Suzuki ,&nbsp;Di Wu ,&nbsp;Ken Kitajima ,&nbsp;Nao Yamakawa ,&nbsp;Takayuki Omoto ,&nbsp;Masaya Hane ,&nbsp;Chihiro Sato","doi":"10.1016/j.bbadva.2025.100155","DOIUrl":"10.1016/j.bbadva.2025.100155","url":null,"abstract":"<div><div>Oligo/polysialic acid (oligo/polySia) refers to a class of linear polymers composed of Sias, found extensively at the non-reducing ends of glycans across various organisms, from bacteria to vertebrates. Different types of oligo/polySia have been characterized, varying in Sia composition, α-ketosidic linkages to penultimate Sia residues, and degree of polymerization. Detection of oligo/polySia-capped glycans is typically achieved through western blotting or ELISA using specific antibodies or endo-N-acylneuraminidase. Additionally, a sensitive chemical approach involving the direct labeling of oligo/polySia with 1,2-diamino-4,5-methylenedioxybenzene, followed by separation and quantification via anion-exchange high-performance liquid chromatography, has been developed. However, detection through mass spectrometry (MS) has remained challenging due to the multiple negative charges and structural instability of these glycans. In this study, we applied a permethylation technique to convert carboxyl group of Sias into methyl esters, thereby neutralizing their negative charges, which allowed for improved MS analysis of sialylated glycans. We optimized both the permethylation and glycan purification processes. Consequently, we achieved the first successful detection of polySia structures using MALDI-TOF MS. There are more in-source decay ions in the MS profiling of permethylated α2,9-linked polySias compared to α2,8-linked polySias. Furthermore, we present the first examples of oligo/polySia sequencing by collision-induced dissociation on a TOF/TOF instrument, enabling us to differentiate between α2,8- and α2,9-linked polySias. We extended this approach to analyze oligo/polySia structures with <em>O</em>-linked glycans in polysialoglycoprotein from salmonid eggs. For the first time, the analysis of intact oligo/polySia structures with <em>O</em>-linked glycans were successfully detected using MALDI-TOF/TOF MS/MS with this optimized permethylation method.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100155"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143642499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toward spatial glycomics and glycoproteomics: Innovations and applications","authors":"Patcharaporn Boottanun ,&nbsp;Sayaka Fuseya ,&nbsp;Atsushi Kuno","doi":"10.1016/j.bbadva.2025.100146","DOIUrl":"10.1016/j.bbadva.2025.100146","url":null,"abstract":"<div><div>In this mini review, we provide an overview of the challenging field of spatial glycomics/glycoproteomics. Owing to their complexity, sophisticated analytical methods and innovative technologies are needed to advance this field. An agile development approach enables unraveling aberrant glycosylations, glycobiomarkers, and glycotargets for spatial imaging, diagnosis, and therapeutic purposes. We discuss glycopathology and tissue glycomic profiling using highly sensitive lectin-based analyses and introduce deep visual proteomics for glycomic/glycoproteomic sample preparation. Additionally, we highlight the importance of leveraging laser microdissection and artificial intelligence-driven visual software for cell-type assignment and automation techniques, which are crucial for advancing glycomics/glycoproteomics.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100146"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143376930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Porphyrin-based electrospun nanomaterials for life science applications","authors":"Ana C. Mendes ,&nbsp;Nuno M.M. Moura ,&nbsp;M. Amparo F․ Faustino ,&nbsp;M. Graça P.M.S. Neves ,&nbsp;Ioannis S. Chronakis","doi":"10.1016/j.bbadva.2025.100160","DOIUrl":"10.1016/j.bbadva.2025.100160","url":null,"abstract":"<div><div>Porphyrins are renowned for their utility in photocatalysis, electronics, sensors, solar cell dyes, and environmental remediation. However, their potential in life sciences applications remains underexplored, particularly in the context of encapsulation via electrospinning. This review examines recent advancements (2000–2025) in electrospinning techniques for encapsulating porphyrins, highlighting their unique properties, bioactivities, and versatile applications in life sciences. By combining the strengths of porphyrins and electrospinning technology, researchers can unlock transformative solutions for various life-science challenges, which include photodynamic therapy (PDT), composite materials for anti-microbial applications, sensors, and drug delivery. These efforts could push porphyrin-encapsulated materials from research concepts to applied societal solutions, addressing critical needs in healthcare and beyond to other fields.</div></div>","PeriodicalId":34672,"journal":{"name":"BBA Advances","volume":"7 ","pages":"Article 100160"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143874824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}