Biochimica et biophysica acta. Proteins and proteomics最新文献

{"title":"Ndufs4 knockout mice with isolated complex I deficiency engage a futile adaptive brain response","authors":"Melissa A.E. van de Wal ,&nbsp;Cenna Doornbos ,&nbsp;Janne M. Bibbe ,&nbsp;Judith R. Homberg ,&nbsp;Clara van Karnebeek ,&nbsp;Martijn A. Huynen ,&nbsp;Jaap Keijer ,&nbsp;Evert M. van Schothorst ,&nbsp;Peter A.C. 't Hoen ,&nbsp;Mirian C.H. Janssen ,&nbsp;Merel J.W. Adjobo-Hermans ,&nbsp;Mariusz R. Wieckowski ,&nbsp;Werner J.H. Koopman","doi":"10.1016/j.bbapap.2024.141055","DOIUrl":"10.1016/j.bbapap.2024.141055","url":null,"abstract":"<div><div>Paediatric Leigh syndrome (LS) is an early-onset and fatal neurodegenerative disorder lacking treatment options. LS is frequently caused by mutations in the <em>NDUFS4</em> gene, encoding an accessory subunit of mitochondrial complex I (CI), the first complex of the oxidative phosphorylation (OXPHOS) system. Whole-body <em>Ndufs4</em> knockout (KO) mice (WB-KO mice) are widely used to study isolated CI deficiency, LS pathology and interventions. These animals develop a brain-specific phenotype <em>via</em> an incompletely understood pathomechanism. Here we performed a quantitative analysis of the sub-brain proteome in six-weeks old WB-KO mice <em>vs.</em> wildtype (WT) mice. Brain regions comprised of a brain slice (BrSl), cerebellum (CB), cerebral cortex (CC), hippocampus (HC), inferior colliculus (IC), and superior colliculus (SC). Proteome analysis demonstrated similarities between CC/HC, and between IC/SC, whereas BrSl and CB differed from these two groups and each other. All brain regions displayed greatly reduced levels of two CI structural subunits (NDUFS4, NDUFA12) and an increased level of the CI assembly factor NDUFAF2. The level of CI-Q module subunits was significantly more reduced in IC/SC than in BrSl/CB/CC/HC, whereas other OXPHOS complex levels were not reduced. Gene ontology and pathway analysis demonstrated specific and common proteome changes between brain regions.</div><div>Across brain regions, upregulation of cold-shock-associated proteins, mitochondrial fatty acid (FA) oxidation and synthesis (mtFAS) were the most prominent. FA-related pathways were predominantly upregulated in CB and HC. Based upon these results, we argue that stimulation of these pathways is futile and pro-pathological and discuss alternative strategies for therapeutic intervention in LS.</div></div><div><h3>Significance</h3><div>The <em>Ndufs4</em> knockout mouse model is currently the most relevant and most widely used animal model to study the brain-linked pathophysiology of human Leigh Syndrome (LS) and intervention strategies. We demonstrate that the <em>Ndufs4</em> knockout brain engages futile and pro-pathological responses. These responses explain both negative and positive outcomes of intervention studies in Leigh Syndrome mice and patients, thereby guiding novel intervention opportunities.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141055"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the cleavage sites of 3C-like protease in Gammacoronaviruses and Deltacoronaviruses","authors":"Mengxue Wang ,&nbsp;Xinyi Sun ,&nbsp;Shijiang Peng ,&nbsp;Feifan Wang ,&nbsp;Kangli Zhao ,&nbsp;Dang Wang","doi":"10.1016/j.bbapap.2024.141057","DOIUrl":"10.1016/j.bbapap.2024.141057","url":null,"abstract":"<div><div>Coronaviruses replicate by using the 3C-like protease (3CL^pro) to cleave polyprotein precursors and host proteins. However, current tools for identifying 3CL^pro cleavage sites are limited, particularly in <em>Gammacoronaviruses</em> (GammaCoV) and <em>Deltacoronaviruses</em> (DeltaCoV). This study aims to fill this gap by identifying 3CL^pro cleavage sites in these viruses to provide deeper insights into their pathogenic mechanisms. By integrating sequence alignments and structural model comparisons, we developed a position-specific scoring matrix (PSSM) based on self-cleavage motifs, revealing specific preferences for each residue. Utilizing AlphaFold2's predicted alignment error (PAE) and predicted local distance difference test (pLDDT), we found that most cleavage sequences are located in regions with high PAE and low pLDDT values. KEGG pathway analysis showed that potential host protein cleavage targets are mainly concentrated in pathways related to nucleo-cytoplasmic transport and endocytosis. Through <em>in vitro</em> cleavage experiments and mutational analysis, we identified and validated three high-scoring proteins—nucleoporin 58 (NUP58), cell division cycle 73 (CDC73), and signal transducing adaptor molecule 2 (STAM2). These findings suggest that 3CL^pro not only plays a vital role in viral replication but may also influence host cell functions by cleaving host proteins. This study provides an effective tool for identifying 3CL^pro cleavage sites, revealing the pathogenic mechanisms of coronaviruses, and offering new insights for developing potential therapeutic targets.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141057"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A distinct co-expressed sulfurtransferase extends the physiological role of mercaptopropionate dioxygenase in Pseudomonas aeruginosa PAO1","authors":"Chukwuemeka S. Adindu ,&nbsp;Katie Tombrello ,&nbsp;Luke A. Martz ,&nbsp;Tonya N. Zeczycki ,&nbsp;Holly R. Ellis","doi":"10.1016/j.bbapap.2024.141059","DOIUrl":"10.1016/j.bbapap.2024.141059","url":null,"abstract":"<div><div>Oxidation and assimilation of persulfides in bacteria is often catalyzed by a persulfide dioxygenase and sulfurtransferase in consecutive reactions. Enzymes responsible for the oxidation of persulfides have not been clearly defined in <em>Pseudomonas aeruginosa</em> PAO1. The characterized mercaptopropionate dioxygenase (MDO) in <em>P. aeruginosa</em> PAO1 has been proposed to catalyze the oxidation of 3-mercaptopropionate. However, the physiological role of MDO is uncertain given the expression of a sulfurtransferase (ST) enzyme on the same operon as the thiol dioxygenase. The <em>st</em> gene had a co-occurrence frequency with <em>mdo</em> of 0.94 demonstrating the co-expression and physiological link of the two genes. There are four tandem rhodanese domains in the ST enzyme with two of the domains containing potential catalytic Cys residues (Cys191 and Cys435) capable of forming a persulfide. Only Cys435 was accessible in thiol quantification assays, and results from H/D-X MS analyses further established the accessibility of the domain containing Cys435. Both thiosulfate and mercaptopyruvate served as sulfur donors to the ST enzyme, with Cys435 forming the persulfide intermediate. Kinetic investigations of MDO suggested the enzyme had a broader substrate specificity than previously identified, oxidizing both mercaptopropionate and mercaptopyruvate thiol and persulfide substrates. The results obtained from these investigations provide insight into the overall mechanism and physiological role of the <em>mdo</em> operon in sulfide oxidation and assimilation.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141059"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Incorporation of pyridoxal-5′-phosphate into the apoenzyme: A structural study of D-amino acid transaminase from Haliscomenobacter hydrossis","authors":"Alina K. Bakunova ,&nbsp;Ilya O. Matyuta ,&nbsp;Mikhail E. Minyaev ,&nbsp;Konstantin M. Boyko ,&nbsp;Vladimir O. Popov ,&nbsp;Ekaterina Yu. Bezsudnova","doi":"10.1016/j.bbapap.2024.141056","DOIUrl":"10.1016/j.bbapap.2024.141056","url":null,"abstract":"<div><div>Pyridoxal-5′-phosphate (PLP)-dependent transaminases are key enzymes of amino acid metabolism in cells and remarkable biocatalysts of stereoselective amination for process chemistry applications. As cofactor-dependent enzymes, transaminases are prone to cofactor leakage. Here we discuss the holoenzyme-apoenzyme interconversion and the kinetics of PLP incorporation into the apo form of a PLP-dependent transaminase from <em>Haliscomenobacter hydrossis</em>. PLP binding to the apoenzyme was slow in buffer, but was accelerated in the presence of substrates. Two crystal structures of the apoenzyme were obtained: the directly obtained apoenzyme (PDB ID: <span><span>7P8O</span><svg><path></path></svg></span>) and the one obtained by soaking crystals of the holoenzyme in a phenylhydrazine solution (PDB ID: <span><span>8YRU</span><svg><path></path></svg></span>). The mechanism of PLP association with the apoenzyme was proposed on the basis of structural analysis of these apo forms. Three rearrangement steps, including (I) anchoring of the PLP via the phosphate group, (II) displacement of two loops, and (III) Schiff-bonding between the PLP and the ε-amino group of the catalytic lysine residue, reconstituted the active holo form of the transaminase from <em>H. hydrossis</em>. The results obtained allowed us to determine in the active site a permanent part and elements that are assembled by PLP, these findings may be useful for transaminase engineering for biocatalysis.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141056"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of proton-coupled electron transfer from protein to heme in dehaloperoxidase","authors":"Mst Sharmin Aktar ,&nbsp;Nikhila Kashyap Dhanvantari Madhuresh ,&nbsp;Reza A. Ghiladi,&nbsp;Stefan Franzen","doi":"10.1016/j.bbapap.2024.141053","DOIUrl":"10.1016/j.bbapap.2024.141053","url":null,"abstract":"<div><div>At least two of the six methionine (Met) residues in dehaloperoxidase (DHP) are shown to act as electron donors in both autoreduction and protein-heme crosslinking. Autoreduction observed in the two isozymes, DHP-A and DHP-B, is explained by the high heme reduction potential and an endogenous source of electrons from methionine (Met) or cysteine (Cys). This study provides evidence of a connection to protein-heme crosslinking that occurs when DHP is activated by H₂O₂ in competition with substrate oxidation and autoreduction. The autoreduction yields of DHP-A and DHP-B are comparable and both are inversely proportional to DHP concentration. Both isoenzymes show an anti-cooperative effect on autoreduction kinetics associated with protein dimerization. Despite the presence of five tyrosine (Tyr) amino acids in DHP-A and four Tyr in DHP-B, the mass spectral evidence does not support a Tyr-heme or interprotein Tyr-Tyr crosslinking event as observed in some mammalian myoglobins. LC-MS and tandem MS/MS studies revealed three amino acids that were involved in the heme-protein crosslink, Cys73, Met63 and Met64. Cys73 facilitates dimer formation in DHP-A which also appears to slow the rate of autoreduction, but is not involved in covalent protein-heme crosslinking. Based on mutational studies, Met63 and 64 are involved in both covalent heme crosslinking and autoreduction. Proton-coupled electron transfer and crosslinking by Met to the heme may serve to regulate DHP function and protect it from uncontrolled oxidative damage.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141053"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phosphoproteome modulation by nucleoside diphosphate kinase affects photosynthesis & stress tolerance of Nostoc PCC 7120","authors":"Anurag Kirti ,&nbsp;Hema Rajaram","doi":"10.1016/j.bbapap.2024.141054","DOIUrl":"10.1016/j.bbapap.2024.141054","url":null,"abstract":"<div><div>Nucleoside diphosphate kinase (Ndk/NDK/NDPK) is known to possess pleiotropic functions, one of which is that as a protein kinase, and has been shown to be involved in stress tolerance in plants. To assess its role in the cyanobacterium <em>Nostoc</em> PCC 7120, which is hitherto unreported, recombinant strain overexpressing Ndk, An<em>ndk</em>^<em>+</em> was generated. Phosphoproteomic analysis of An<em>ndk</em>⁺ and its comparison with that of the vector control, AnpAM, revealed differential phosphorylation at S/T/Y sites of proteins belonging to varied functional groups, with over 17 % phosphoproteins involved in photosynthesis. A total of 177 phosphopeptides and 117 phosphoproteins were identified, including newly identified phosphopeptides in any cyanobacteria. Compared to AnpAM, the An<em>ndk</em>⁺ cells exhibited (i) lower photosynthetic efficiency and electron transport rate at low PAR (photosynthetically active radiation), (ii) no change in photochemical quenching across PAR, (iii) but distinct non-photochemical quenching [zero Y(NPQ) and high Y(NO) in An<em>ndk</em>⁺ and high Y(NPQ) and low (NO) in AnpAM], and (iv) increased tolerance to γ-radiation, oxidative, salt and DCMU stresses. The observed modulation of phosphoproteome linked to physiological changes upon overexpression of Ndk in <em>Nostoc</em> could be a combination of direct protein kinase activity of Ndk and/or indirectly through other protein kinases and phosphatases whose phosphorylation status is mediated by Ndk. This is the first report on a direct correlation between Ndk levels, phosphorylation status of proteins and stress tolerance in any cyanobacteria.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141054"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serratiopeptidase exhibits antibiofilm activity through the proteolytic function of N-terminal domain and versatile function of the C-terminal domain","authors":"Vishal Srivastava,&nbsp;Sheetal Bandhu,&nbsp;Shivam Mishra,&nbsp;Tapan K. Chaudhuri","doi":"10.1016/j.bbapap.2024.141046","DOIUrl":"10.1016/j.bbapap.2024.141046","url":null,"abstract":"<div><h3>Background</h3><p>Serratiopeptidase, a serine protease traditionally used as an oral anti-inflammatory drug has been found to show antibiofilm action. Structurally, it comprises of two distinct domains; viz-the N-terminal catalytic domain (N<em>cat</em>) and a C-terminal RTX (Repeat-In-Toxin) domain (C<em>rtx</em>). Understanding the antibiofilm action of the serratiopeptidase molecule, as well as the antibiofilm action of each of its two domains, was the objective of this study.</p></div><div><h3>Results</h3><p>Separate clones to express the complete recombinant serratiopeptidase protein and its variant containing a mutation in the catalytic site, the N-terminal catalytic domain and its mutant, and the C-terminal Repeat-In-Toxin domain were prepared, and the proteins were purified. The impact of these proteins on pre-existing biofilms, as well as their effect upon addition of these proteins during biofilm formation was investigated.</p></div><div><h3>Conclusions</h3><p>In our investigation, we have been able to analyze the antibiofilm action of serratiopeptidase in detail. Obtained results conclude that while N-terminally located proteolytic domain of serratiopeptidase conventionally acts against biofilms by hydrolytic activity, the C-terminal domain regulates or prevents biofilm formation by yet unknown mechanism in addition to its known function as an C-terminal located calcium modulated internal chaperone ensuring the proper folding and secretion of the molecule. The study's findings give new evidence that the C<em>rtx</em> domain plays a significant role in antibiofilm action. The proteolytic N<em>cat</em> domain breaks down pre-formed biofilms. The C-terminal domain, on the other hand, acts as an inhibitor of biofilm formation by regulating or preventing biofilm development.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141046"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1570963924000530/pdfft?md5=3a4d2c38465f942f4b2f8b47b6076387&pid=1-s2.0-S1570963924000530-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure and functional studies of Avt1, a novel peptide from the sea anemone Aulactinia veratra","authors":"Renad A. Albar ,&nbsp;Hayden L. Smith ,&nbsp;Karoline Sanches ,&nbsp;Dorothy C.C. Wai ,&nbsp;Muhammad Umair Naseem ,&nbsp;Tibor G. Szanto ,&nbsp;Gyorgy Panyi ,&nbsp;Peter J. Prentis ,&nbsp;Raymond S. Norton","doi":"10.1016/j.bbapap.2024.141050","DOIUrl":"10.1016/j.bbapap.2024.141050","url":null,"abstract":"<div><div>Sea anemones are a rich source of peptide toxins spanning a diverse range of biological activities, typically targeting proteins such as ion channels, receptors and transporters. These peptide toxins and their analogues are usually highly stable and selective for their molecular targets, rendering them of interest as molecular tools, insecticides and therapeutics. Recent transcriptomic and proteomic analyses of the sea anemone <em>Aulactinia veratra</em> identified a novel 28-residue peptide, designated Avt1. Avt1 was produced using solid-phase peptide synthesis, followed by oxidative folding and purification of the folded peptide using reversed-phase high-performance liquid chromatography. The liquid chromatography-mass spectrometry profile of synthetic Avt1 showed a pure peak with molecular mass 6 Da less than that of the reduced form of the peptide, indicating the successful formation of three disulfide bonds. The solution structure determined by NMR revealed that Avt1 adopts an inhibitor cystine knot (ICK) fold, in which a ring is formed by two disulfide bonds with a third disulfide penetrating the ring to create the pseudo-knot. This structure provides ICK peptides with high structural, thermal and proteolytic stability. Consistent with its ICK structure, Avt1 was resistant to proteolysis by trypsin, chymotrypsin and pepsin, although it was not a trypsin inhibitor. Avt1 at 100 nM showed no activity in patch–clamp electrophysiological assays against several mammalian voltage-gated ion channels, but has structural features similar to toxins targeting insect sodium ion channels. Although sequence homologues of Avt1 are found in a number of sea anemones, this is the first representative of this family to be characterised structurally and functionally.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141050"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CDR identification, epitope mapping and binding affinity determination of novel monoclonal antibodies generated against human apolipoprotein B-100","authors":"Tariga Sritrakarn ,&nbsp;Kanokwan Lowhalidanon ,&nbsp;Panida Khunkaewla","doi":"10.1016/j.bbapap.2024.141058","DOIUrl":"10.1016/j.bbapap.2024.141058","url":null,"abstract":"<div><div>In-house generated mAbs to apolipoprotein B-100 (apoB-100) clones hLDL-E8, hLDL-2D8 and hLDL-F5 were extensively studied to determine their complementarity-determining regions (CDRs), binding epitopes and affinity. RT-PCR revealed that all mAbs consisted of kappa light chains and gamma heavy chains. DNA sequencing and bioinformatic analysis showed that the variable gene and protein sequences of their CDRs shared over 50 % identity with the existing databases. The 3D structures of the mAb variable fragments (Fv) with a QSQE score above 0.7 were constructed using the SWISS-MODEL platform. The structural accuracy was confirmed by Ramachandran plots, with 99 % of amino acid residues falling within acceptable regions. Thrombolytic cleavage of apoB-100 and Western blot analysis demonstrated that hLDL-E8 and hLDL-F5 specifically bind to the T3 fragment (aa 1297–3249), whereas hLDL-2D8 binds to the T4 fragment (aa 1–1297). These findings were supported with epitope-binding assays using inhibition ELISA, which indicated that hLDL-E8 binds at different epitopes from hLDL-2D8 and has some overlap with hLDL-F5. Lastly, the binding affinity of the mAbs was examined by indirect ELISA. The average affinity constants (K_aff) for mAbs hLDL-2D8, hLDL-E8 and hLDL-F5 are 1.51 ± 0.69 × 10⁹ Mol⁻¹, 7.25 ± 3.56 × 10⁸ Mol⁻¹ and 4.39 ± 2.63 × 10⁶ Mol⁻¹, respectively. Additionally, the behavior of the antibodies in the dose-response curve revealed that hLDL-F5 may recognize two epitopes of apoB-100 or have very low binding affinity. In contrast, hLDL-2D8 and hLDL-E8 each recognize a single epitope. These findings provide information that will be useful when selecting mAbs for both laboratory and clinical research purposes.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141058"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From sequence to function: Exploring biophysical properties of bacteriophage BFK20 lytic transglycosylase domain from the minor tail protein gp15","authors":"Kristina Papayova ,&nbsp;Lucia Bocanova ,&nbsp;Vladena Bauerova ,&nbsp;Jacob Bauer ,&nbsp;Nora Halgasova ,&nbsp;Maria Kajsikova ,&nbsp;Gabriela Bukovska","doi":"10.1016/j.bbapap.2024.141044","DOIUrl":"10.1016/j.bbapap.2024.141044","url":null,"abstract":"<div><p>Bacteriophages have evolved different mechanisms of infection and penetration of bacterial cell walls. In <em>Siphoviridae</em>-like viruses, the inner tail proteins have a pivotal role in these processes and often encode lytic protein domains which increase infection efficiency. A soluble lytic transglycosylase (SLT) domain was identified in the minor tail protein gp15 from the BFK20 bacteriophage. Six fragments containing this SLT domain with adjacent regions of different lengths were cloned, expressed and purified. The biophysical properties of the two best expressing fragments were characterized by nanoDSF and CD spectroscopy, which showed that both fragments had a high refolding ability of 90 %. 3D modeling indicated that the bacteriophage BFK20 SLT domain is structurally similar to lysozyme. The degradation activity of these SLT proteins was evaluated using a lysozyme activity assay. BFK20 might use its transglycosylase activity to allow efficient phage DNA entry into the host cell by degrading bacterial peptidoglycan.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141044"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}