Biochemistry [JOURNAL]
Sun
200 papers
A High-Affinity but Low-Abundance Kanamycin Aptamer Reveals Hybridization-Limited Capture-SELEX.
Ding Y, Chen Q, Heng Y … +4 more , Chao EHP, Kaiyum YA, Johnson PE, Liu J
Biochemistry · 2026 Apr · PMID 41914599 · Publisher ↗
Kanamycin A, or simply referred to as kanamycin, is an aminoglycoside antibiotic with a narrow therapeutic window. Aptamers are useful recognition molecules for their detection and continuous monitoring. However, a short...
Kanamycin A, or simply referred to as kanamycin, is an aminoglycoside antibiotic with a narrow therapeutic window. Aptamers are useful recognition molecules for their detection and continuous monitoring. However, a short and high-affinity kanamycin aptamer that works under physiological conditions is still lacking. In this work, we revisited a previous aptamer selection done at pH 8, which had been abandoned due to poor sequence enrichment. Its top sequence, named KAN8-1, shows a of 51 nM at pH 7.5 for kanamycin as measured by isothermal titration calorimetry, and its affinities to kanamycin A and B are similar. Using NMR spectroscopy methods, the KAN8-1 aptamer undergoes ligand-induced folding and likely has a better-defined structure compared to the KAN6-1 aptamer, which was highly enriched in the pH 6 selection. Using the KAN8-1 aptamer, a strand-displacement biosensor was developed, and it has a limit of detection of 0.9 μM with excellent selectivity. This sensor also has a similar performance in serum. The reason for the poor enrichment of KAN8-1 was attributed to its low hybridization efficiency and poor hybridization stability to the capture strand as demonstrated by a fluorescence titration assay and melting analysis, which indicated a limitation of the capture-SELEX method.
Deciphering the Intratissue-Specific Collagen PTM Site-Specific Heterogeneity in Human Adrenal Extracellular Matrix.
Joshi A, Nigam A, Kremer JL … +3 more , Lotfi CFP, Mondal B, Basak T
Biochemistry · 2026 Apr · PMID 41910438 · Publisher ↗
Adrenal glands are one of the pivotal glands of the human endocrine system. Recently, the extracellular matrix (ECM) of the adrenal capsule and cortex was explored in two fractions: outer fraction (OF) and inner fraction...
Adrenal glands are one of the pivotal glands of the human endocrine system. Recently, the extracellular matrix (ECM) of the adrenal capsule and cortex was explored in two fractions: outer fraction (OF) and inner fraction (IF). A significant variation in the ECM proteins' levels, including collagens, was documented. Collagen undergoes a plethora of post-translational modifications (PTMs), exhibiting crucial roles such as cell-matrix interaction and cross-linking. However, the site-specific identification and characterization of collagen PTMs remain challenging and are unknown for the human adrenal gland. By applying our in-house proteomics pipeline, we identified 1044 4-hydroxyproline (4-HyP), 205 3-hydroxyproline (3-HyP), 106 hydroxylysine (HyK), 17 galactosyl-hydroxylysine (G-HyK), and 37 glucosyl galactosyl-hydroxylysine (GG-HyK) sites from abundant collagen chains of both fractions. Although the site-specificity of collagen PTMs (3-HyP, HyK, and G/GG-HyK) across fractions is conserved, the occupancies were different in a site-specific manner. The microheterogeneity observed in K of COL1A1 demonstrated that the hydroxylation level was higher in OF, while glycosylation levels were higher in IF. This points toward a change in the cross-linking of collagen I across both fractions. Furthermore, our analysis revealed that site-specific O-glycosylation, particularly GG-HyK, in basement membrane collagen-IV is higher, which may contribute to the secretion of steroids from the adrenal gland. In this study, we have annotated collagen PTMs, developed a COL1A1 PTM map, and quantitated site-specific PTMs in the human adrenal gland. Taken together, this work reveals the intratissue-specific site-specific collagen PTM heterogeneity although the ECM is stable, which is noteworthy, and lays the foundation for understanding their role in region-specific functions.
Strand Displacement Increases the Fidelity of DNA Polymerases.
Yudkina AV, Yakovlev AO, Rychkov DA … +2 more , Golyshev VM, Zharkov DO
Biochemistry · 2026 Apr · PMID 41906539 · Publisher ↗
Fidelity of DNA polymerases, defined as their ability to incorporate a correct dNMP opposite an undamaged template nucleotide, is a key factor in ensuring genome stability. Many DNA polymerases have been extensively inve...
Fidelity of DNA polymerases, defined as their ability to incorporate a correct dNMP opposite an undamaged template nucleotide, is a key factor in ensuring genome stability. Many DNA polymerases have been extensively investigated to understand the structural and biochemical basis of their fidelity. However, the great majority of these studies employed simple primer-template substrates, disregarding the possible effects of more complex DNA structures. Here, we have estimated the fidelity of a single dNMP incorporation by the Klenow fragment of DNA polymerase I (KF) and bacteriophage RB69 DNA polymerase (RBpol) during the strand displacement synthesis, a situation common in lagging strand replication and DNA repair. Although KF was more efficient than RBpol in the presence of a downstream strand, both polymerases demonstrated a 3-fold (up to an order of magnitude) increase in the fidelity compared with the primer-template system. To assess the dependence of fidelity on the energy spent on the disruption of the base pair ahead, we varied its strength using mismatches and synthetic base analogs. Both KF and RBpol generally traded efficiency for fidelity, making fewer errors when they had to disrupt stronger base pairs. Thus, the energetic penalty imposed by the downstream strand acts as a fidelity checkpoint, enhancing discrimination against incorrect nucleotides.
Early Kinetic Characterization of SARS-CoV-2 Main Protease Inhibitors: A Review and Guidance for Biochemical Assessments.
Voget R, Gütschow M
Biochemistry · 2026 Apr · PMID 41904986 · Publisher ↗
Optical, microplate reader-based assays are a standard tool for the initial biochemical analysis of SARS-CoV-2 main protease (M) inhibitor candidates. Such assays monitor M-catalyzed substrate proteolysis in order to inv...
Optical, microplate reader-based assays are a standard tool for the initial biochemical analysis of SARS-CoV-2 main protease (M) inhibitor candidates. Such assays monitor M-catalyzed substrate proteolysis in order to investigate the kinetic impact of inhibitors under examination on the catalytic reaction. This review outlines the numerous intricate considerations involved in establishing suitable assay protocols. Commonly employed M substrates that exploit different mechanisms for the optical detection of the cleavage reaction are introduced and compared with respect to their suitability for specific assay applications. The contribution of native or tagged forms of M and of the assay medium to representative kinetic data is debated. Protocols for high-throughput screening, IC investigation, elucidation of binding mode and modality, as well as for the determination of the kinetic parameters, , α, , , and /, are discussed with continuous reference to the underlying kinetic models. This review provides guidelines for the design and establishment of robust assays for precisely characterizing the kinetics of M inhibitor candidates. Typical confounders and false conclusions are demonstrated, along with strategies to circumvent these pitfalls.
Microproteins in Human Physiology and Pathology.
Du Z, Trifiro FA, Brunet MA … +1 more , Prensner JR
Biochemistry · 2026 Apr · PMID 41894539 · Full text
Microproteins are defined as polypeptides of 100-150 or fewer amino acids. With the integrated application of ribosome profiling (Ribo-Seq), mass spectrometry, and bioinformatic approaches, more microproteins have been i...
Microproteins are defined as polypeptides of 100-150 or fewer amino acids. With the integrated application of ribosome profiling (Ribo-Seq), mass spectrometry, and bioinformatic approaches, more microproteins have been identified as being encoded by small open reading frames (sORFs). The majority of microproteins are evolutionarily young and may represent species-specific events. This review highlights the current methods and their challenges for identification and characterization of novel microproteins. We will also summarize the biologically active microproteins that are involved in biological processes and essential for human physiology and pathology, followed by a discussion of their significant translational potential for diagnosis, prognosis, and therapeutic intervention in human diseases.
The Journey of Histones: Molecular Mechanisms of the Histone Chaperoning Cascade.
Cho C, Song JJ
Biochemistry · 2026 Apr · PMID 41891849 · Publisher ↗
In eukaryotes, genomic DNA is packaged into hierarchical higher-order chromatin structures. Regulation of this organization is essential for the faithful maintenance and controlled expression of genetic information. Asse...
In eukaryotes, genomic DNA is packaged into hierarchical higher-order chromatin structures. Regulation of this organization is essential for the faithful maintenance and controlled expression of genetic information. Assembly of the nucleosome─the fundamental unit of chromatin─depends on a tightly coordinated network of histone chaperones that escort histones from their initial synthesis through multiple intermediates to their final deposition into nucleosomes. This review provides an overview of the stepwise journey of histones and the regulatory mechanisms that govern this process. We also highlight major outstanding questions and discuss future directions in the field.
Direct RNA Sequencing Reveals Stress-Dependent and Pathway-Specific rRNA Modification Reprogramming during 50S Biogenesis.
Gracia Mazuca LA, Rodarte S, Weislow IS … +2 more , Mohl JE, Koculi E
Biochemistry · 2026 Apr · PMID 41891765 · Publisher ↗
Ribosomal RNA (rRNA) modification and processing are essential steps in the ribosome assembly. Using Oxford Nanopore direct RNA sequencing, we simultaneously detect and quantify -methyladenosine (mA), pseudouridine (Ψ),...
Ribosomal RNA (rRNA) modification and processing are essential steps in the ribosome assembly. Using Oxford Nanopore direct RNA sequencing, we simultaneously detect and quantify -methyladenosine (mA), pseudouridine (Ψ), 2'--methyluridine, 1-methylguanosine, 7-methylguanosine, dihydrouridine, 3-methylpseudouridine, and 5-methyluridine modification in 23S rRNA of the mature 50S large subunit (LSU) from cells expressing either wild-type DbpA or the helicase-inactive R331A DbpA variant and in two LSU assembly intermediates, 35S and 45S, which accumulate along distinct maturation pathways in R331A DbpA-expressing cells. Furthermore, we analyze the 3'-end processing of 23S and 5S rRNAs across these particles. Many 23S rRNA modifications are incorporated at similar levels in LSU assembly intermediates and mature 50S subunits from both wild-type and R331A DbpA-expressing cells, indicating that these modifications are incorporated prior to intermediate accumulation and are not preferentially reprogrammed under R331A DbpA-induced assembly stress. A subset of three modifications exhibits altered incorporation patterns. mA 2507 incorporation is reduced in the 50S LSU from R331A DbpA-expressing cells compared with the cells expressing wild-type DbpA, whereas Ψ 2508 is increased. In addition, Ψ 2608 is reduced in the 50S subunit from R331A DbpA-expressing cells compared with the 35S and 45S intermediates from the same cells and the 50S subunit from wild-type cells. Because the 35S and 45S pathways account for only ∼40% of ribosome assembly in R331A DbpA-expressing cells, these findings demonstrate that Ψ 2608 incorporation is selectively reprogrammed across alternative assembly routes, revealing an additional regulatory layer in ribosome biogenesis.
Detergent Exchange from Lipid Nanoparticles into Detergent Micelles Unlocks a Tool for Biochemical and Kinetic Characterization of Membrane Proteins.
Koweek RS, Knox HL, Dodge GJ … +2 more , Imperiali B, Allen KN
Biochemistry · 2026 Apr · PMID 41888052 · Publisher ↗
Bacterial membrane proteins make up ∼ 30% of the prokaryotic genome and play key roles in infection and virulence. Membrane protein chemistry has advanced in recent years, including purification strategies that mimic nat...
Bacterial membrane proteins make up ∼ 30% of the prokaryotic genome and play key roles in infection and virulence. Membrane protein chemistry has advanced in recent years, including purification strategies that mimic nativelike lipid environments, such as lipid nanoparticles, amphipols, and nanodiscs. The use of styrene maleic acid copolymers (SMALPs) to form a lipid nanoparticle has become increasingly common in membrane protein purification, especially for proteins which are not amenable to detergent extraction from the cellular membrane fraction. Yet, for some biochemical and biophysical methods, it is preferable to use detergent-solubilized protein. Here we show a general exchange screening method to transfer membrane proteins from lipid nanoparticles to detergent micelles while retaining protein fold, homogeneity, and function. Conditions were first optimized for copolymer dispersion and recovery into detergents, and analytical methods were employed to assess activity and quality of detergent-solubilized proteins. Thirteen protein targets were purified in copolymer based on a 16-polymer screen. This selection was followed by an eight-detergent screen in the presence of calcium and magnesium ions for optimal dissolution of the nanoparticle, producing detergent-stabilized protein. In all membrane proteins assessed, homogeneity and folding were retained from the initial purification in lipid nanoparticles through a detergent-exchange protocol. For membrane enzymes that have proven to be experimentally intractable when detergent solubilized, we were able to observe catalytic activity using the detergent-exchanged material. The use of this protocol to purify membrane proteins provides greater versatility for biochemical and kinetic characterization than was previously accessible.
Signaling Bias as a Framework for Therapeutically Relevant Orthosteric Agonists: The β Adrenergic Receptor Paradigm.
Georgiou K, Kolocouris A
Biochemistry · 2026 Apr · PMID 41885235 · Full text
Abstract loading — click title to view on PubMed.
Stepwise Assembly of the Capsular Polysaccharide A Repeating Unit in .
Scarbrough BA, Moneghan CE, Salamat S … +5 more , Dooda MK, Murray AH, Costelloe JS, Jorgenson MA, Troutman JM
Biochemistry · 2026 Apr · PMID 41880207 · Full text
Bacterial surface polysaccharides are versatile structures that provide specificity to the behavior and interactions of a given bacterial strain. One surface polysaccharide displayed on the organism , Capsular Polysaccha...
Bacterial surface polysaccharides are versatile structures that provide specificity to the behavior and interactions of a given bacterial strain. One surface polysaccharide displayed on the organism , Capsular Polysaccharide A, has been implicated as a potential therapeutic for autoimmune disorders. This polymer is composed of repeating units of the tetrasaccharide 2-acetamido-4-amino-2,4,6-trideoxygalactopyranose (AATGal), 4,6--pyruvate-galactopyranose (PyrGal), -acetylgalactosamine (GalNAc), and galactofuranose (Gal). While this and other bacterial surface polysaccharides are attractive to study and apply to biomedicine, it can be difficult to acquire quick, inexpensive access to these pure materials. In this work, we developed a recombinant expression system in for the stepwise production of the CPSA polymer. A series of sequential plasmids were prepared, each incorporating successive genes required for CPSA biosynthesis. Using these iterative plasmids, we were able to observe production of the CPSA repeating unit and precursors by liquid chromatography mass spectrometry (LC-MS) analysis of cell lysates. We found that it was critical to include the CPSA polymerase but not the flippase, indicating that a native flippase could support polymer production. We also provide evidence that the CPSA polymer produced by can be ligated to LPS by the WaaL ligase, and deletion of this gene led to the formation of a water-soluble polymer. Overall, this work describes the first recombinant system for CPSA production and outlines a key strategy for the production of complex glycopolymers.
A Push-Pull Loop Motif Controls Product Distribution in GH5 Endocellulases.
Li ZL, Liu XY, Li ZM
Biochemistry · 2026 Apr · PMID 41879430 · Publisher ↗
Endocellulases are central to cellulose deconstruction but are commonly viewed as stochastic catalysts whose product distributions are difficult to control. Here, we report a loop encoded mechanism that governs cleavage-...
Endocellulases are central to cellulose deconstruction but are commonly viewed as stochastic catalysts whose product distributions are difficult to control. Here, we report a loop encoded mechanism that governs cleavage-site selection in GH5 endocellulases. By comparing two closely related enzymes with distinct product profiles, we show that a short loop near the binding cleft determines substrate positioning and hydrolytic outcomes. Molecular dynamics simulations reveal that a triaspartate loop (DDD) promotes deep substrate binding and favors central bond cleavage, whereas an alternative loop (DND) conformation restricts substrate entry and leads to nonspecific hydrolysis. Minimal loop substitutions are sufficient to reversibly switch product distributions without altering the catalytic core, and the same behavior is retained on regenerated amorphous cellulose. These results demonstrate that endocellulase product profiles can be rationally programmed through loop engineering and functionally coupled to phosphorylated sugar biosynthesis requiring controlled oligosaccharide inputs.
A High-Potency Protein That Normalizes Body Weight in DIO Mice through Triple Agonism at FGF21, GLP1, and GIP Receptors.
Brunel FM, Parlee SD, Li P … +6 more , Lu W, Chabenne J, Perez-Tilve D, Finan B, Kharitonenkov A, DiMarchi RD
Biochemistry · 2026 Apr · PMID 41861089 · Publisher ↗
Obesity and its associated metabolic syndrome present significant therapeutic challenges, with current pharmacological interventions often falling short of replicating the multifaceted benefits of bariatric surgery. Rece...
Obesity and its associated metabolic syndrome present significant therapeutic challenges, with current pharmacological interventions often falling short of replicating the multifaceted benefits of bariatric surgery. Recent advances in incretin-based therapies, particularly GLP-1 and GIP coagonists, have demonstrated substantial improvements in glycemic control and weight management, yet residual cardiovascular risk and lipid abnormalities persist. Fibroblast growth factor 21 (FGF21) has emerged as a promising protein to complement incretin pharmacology due to its potent lipid-lowering effects and favorable safety profile. This study describes the engineering of a balanced, long-acting triple agonist that simultaneously targets FGF21, GLP-1, and GIP receptors. Through strategic N- and C-terminal modifications and lipid conjugation, a novel optimized FGF21 analogue is engineered to exhibit enhanced potency, stability, and sustained pharmacokinetics compared to native protein. In Diet-Induced Obesity (DIO) mice, this FGF21 analogue achieves near normalization of body weight, superior to benchmark GLP-1 agonists, and demonstrates additive efficacy when combined with a GLP-1/GIP receptor coagonist. Based on this additivity, a unimolecular triagonist is engineered, and mechanistic studies confirm balanced receptor activity at the FGF21 and incretin receptors to achieve combinational pharmacology, with significant reductions in body fat, improved glucose tolerance, and extended duration of action. These findings position the FGF21/GLP-1/GIP triagonist as a first-in-class candidate for next-generation metabolic disease therapy, potentially approximating the efficacy of surgical intervention while addressing lipid disorders inadequately managed by current incretin therapies.
Cellular Prion Protein Engages the -Methyl-d-Aspartate Receptor through N- and C-Terminal Domains.
Mayfield JE, Wang J, Tovell H … +3 more , Taylor SS, Gonias SL, Sigurdson CJ
Biochemistry · 2026 Apr · PMID 41860118 · Publisher ↗
Nonpathogenic cellular prion protein (PrP) is expressed by neurons and other cells, regulating neurite outgrowth, cell survival, myelin maintenance, and immunity, yet the PrP-protein interaction network and signaling pat...
Nonpathogenic cellular prion protein (PrP) is expressed by neurons and other cells, regulating neurite outgrowth, cell survival, myelin maintenance, and immunity, yet the PrP-protein interaction network and signaling pathways that underlie PrP function remain incompletely understood. PrP is glycophosphatidylinositol-anchored in lipid rafts and reportedly interacts with membrane-bound proteins at the cell surface, including the -methyl-d-aspartate receptor (NMDA-R), triggering cell-signaling responses. PrP may also be glycosylphosphatidylinositol (GPI)-anchored in extracellular vesicles or released from cells by proteases to interact with plasma membrane proteins in target cells. To identify PrP binding sites for the NMDA-R in an unbiased manner, we generated extracts from HEK293T cells transfected with the GluN1 and GluN2B NMDA-R subunits and performed a targeted series of co-immunoprecipitation experiments, peptide arrays, and protein structure analyses. We identified two sites in PrP that bind to the NMDA-R. One site was located in the N-terminal disordered region of PrP. This site is in a lysine-rich segment that incorporates the sequence previously identified as the biologically active PrP-derived peptide, P3. The second site was located in the C-terminal structured region of PrP within the α1 helix and β1 strand. PrP bound GluN1-GluN2B complexes as well as GluN1 in isolation. Notably, the N-linked glycans in PrP inhibited binding to GluN1. Mutation of PrP to incorporate a third glycosylation site further inhibited binding to GluN1. These results demonstrate binding sites in PrP that may mediate interaction with the NMDA-R when PrP is membrane-anchored to the cell of origin, released in extracellular vesicles, or shed from the cell surface by proteases.
Comparison of Pleated and Rippled β-Sheet Assembly of Sequence Isomers of an Amphipathic Self-Assembling Peptide.
Jones CW, Chen J, Panda R … +6 more , Jalali S, Cardani LP, Guo Y, Arnold IM, Dias CL, Nilsson BL
Biochemistry · 2026 Apr · PMID 41859952 · Full text
Supramolecular β-sheet peptide nanomaterials are of critical interest due to their relevance in amyloid disorders and are increasingly valued for applications in regenerative medicine, tissue engineering, and antimicrobi...
Supramolecular β-sheet peptide nanomaterials are of critical interest due to their relevance in amyloid disorders and are increasingly valued for applications in regenerative medicine, tissue engineering, and antimicrobial design. Amphipathic peptides, particularly those with alternating hydrophobic and hydrophilic residues, readily form amyloid-like pleated β-sheet fibrils. It has been demonstrated that the amino acid sequence order of isomeric peptides dramatically influences the self-assembly propensity of the resulting sequences as well as the morphology of the assembled pleated β-sheet nanomaterials. This was substantiated by our previous investigations of the peptides Ac-(FKFE)-NH (L1), Ac-(FK)(FE)-NH (L2), Ac-KE(F)KE-NH2 (L3), Ac-(KFFE)-NH (L4), and Ac-FF(KE)FF-NH (L5). Recently, interest in the Pauling and Corey rippled β-sheet motif, composed of coassembled enantiomeric l- and d-peptides in which the l- and d-enantiomers are organized in an alternating fashion, has been revitalized, although understanding of the rippled β-sheet fold lags far behind that of the naturally occurring pleated β-sheet. Herein, we interrogate the scope of rippled β-sheet formation by extending our previous study of the L1-L5 peptides to enantiomeric mixtures of these sequences to understand the effect of sequence order on rippled β-sheet formation. These integrated experimental and computational studies confirm that enantiomeric mixtures of these peptides have a significantly higher propensity to coassemble into putative rippled β-sheets than single enantiomers have to self-assemble into pleated β-sheets under the same solvent and concentration conditions. These findings extend our understanding of the rippled β-sheet motif and highlight the potential to exploit stereochemically diverse peptides in the design of next-generation biomaterials.
Structural Insights into L-Type Voltage-Gated Ca Channel (Ca1.2) Activation by CaBP1.
Salveson I, Anderson DE, Bej A … +4 more , Nieves-Cintron M, Navedo M, Hell JW, Ames JB
Biochemistry · 2026 May · PMID 41859936 · Full text
The L-type voltage-gated Ca channel (Ca1.2) controls gene expression, cardiac function, and neuronal excitability. Mutations in Ca1.2 that disrupt channel function are implicated in cardiac arrhythmias, vascular dysfunct...
The L-type voltage-gated Ca channel (Ca1.2) controls gene expression, cardiac function, and neuronal excitability. Mutations in Ca1.2 that disrupt channel function are implicated in cardiac arrhythmias, vascular dysfunction, Timothy Syndrome, and epilepsy. Calcium-binding protein 1 (CaBP1) binds to the IQ-motif in Ca1.2 (residues 1640-1665), blocks Ca-dependent inactivation (CDI), and promotes Ca-dependent facilitation (CDF). CaBP1 is 56% identical in sequence to calmodulin (CaM), and both proteins bind competitively to the IQ-motif. Our binding studies reveal that Ca binding to CaBP1 is enhanced more than 40-fold when CaBP1 is bound to the IQ peptide. Also, the IQ peptide binds to Ca-bound CaBP1 (dissociation constant of 45 ± 10 nM) with 100-fold higher affinity than IQ binding to Ca-free CaBP1. We present NMR structures of Ca-CaBP1 bound to the IQ peptide, which reveal CaBP1 residues (A107, F111, M128, L131, I144, and M165) that contact IQ residues (I1654, Y1657, and F1658). Also, IQ residue K1662 forms a salt bridge with CaBP1 residue D140, which may explain why a K1662 charge reversal mutation causes 4-fold weaker IQ binding to CaBP1. Electrophysiology studies suggest that CaBP1 acts to increase the Ca1.2 channel open probability (Po). We propose that Ca binding to the third and fourth EF-hands of CaBP1 and the binding of Ca-bound CaBP1 to the IQ-motif are important for Ca1.2 channel activation.
Human Endonuclease G Preferentially Cleaves Oxidatively Damaged DNA.
Lu WT, Chen YP, Yang WZ … +2 more , Yuan HS, Lin JLJ
Biochemistry · 2026 May · PMID 41854021 · Full text
Endonuclease G (EndoG) is a conserved endonuclease implicated in mitochondrial DNA (mtDNA) replication, maintenance of mtDNA integrity under oxidative stress, and the removal of nuclear and paternal mtDNA during apoptosi...
Endonuclease G (EndoG) is a conserved endonuclease implicated in mitochondrial DNA (mtDNA) replication, maintenance of mtDNA integrity under oxidative stress, and the removal of nuclear and paternal mtDNA during apoptosis and early embryogenesis. Despite its biological significance, the substrates targeted by EndoG and its cleavage preferences remain unclear. Here, we characterize human EndoG (hEndoG) across diverse nucleic acid substrates, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), nicked and gapped dsDNA, modified dsDNA containing 8-oxoguanine (oxoG-DNA) and hydroxymethylated cytosine (5hmC-DNA), single-stranded RNA (ssRNA), and RNA/DNA hybrids. We show that hEndoG binds most of these substrates with only modest differences in affinity (∼10-fold), yet displays a particularly strong preference for cleaving oxidatively damaged DNA, including nicked and gapped dsDNA, and oxoG-DNA. Notably, hEndoG preferentially cleaves the strand opposite the gapped or nicked site, and it targets the complementary strand to the modified base in oxoG-DNA and 5hmC-DNA. Our structural modeling of hEndoG bound to ssDNA and dsDNA indicates that ssDNA is a favored substrate because its flexibility allows kinked conformations that position the scissile phosphate near the catalytic Mg in the His-Me finger motif. Together, these findings support a critical role for hEndoG in preserving mitochondrial genome integrity under conditions of oxidative stress by selectively targeting and removing oxidatively damaged DNA.
Revealing and Exploiting the Biochemistry of -GlcNAc through Protein Semisynthesis.
Ampomah GB, Pratt MR
Biochemistry · 2026 Apr · PMID 41849190 · Full text
-GlcNAcylation is a dynamic posttranslational modification regulated by the enzymes -GlcNAc transferase (OGT) and -GlcNAc hydrolase (OGA). It involves the attachment of -acetylglucosamine to serine or threonine residues...
-GlcNAcylation is a dynamic posttranslational modification regulated by the enzymes -GlcNAc transferase (OGT) and -GlcNAc hydrolase (OGA). It involves the attachment of -acetylglucosamine to serine or threonine residues of proteins in the cytosol, nucleus, and mitochondria. As a dynamic and abundant modification, -GlcNAcylation functions as a sensor of the cell's metabolic state. Fluctuations in -GlcNAc levels of the adenosine (-GlcNAc) signal cellular stress or metabolic changes and have been implicated in various human diseases. The overall impact of this modification is protein-dependent, underscoring the importance of studying its biochemical consequences in a protein- and site-specific manner. To achieve this, enzymatic and chemical strategies have been developed to incorporate -GlcNAc into peptides and proteins. These synthetic glycopeptides and glycoproteins have been instrumental in elucidating how -GlcNAcylation influences protein structure, function, and diverse biochemical pathways. Recently, the -GlcNAcylation has also emerged as a tool for glycosylation-assisted folding of proteins and as a solubility tag for the chemical synthesis of glycopeptides and proteins. Here, we overview the current methods enabling the preparation of specific -GlcNAc-modified proteins and highlight recent developments.
Nuclear Receptors as Orchestrators of Regulatory Cell Death.
Ai YL, Wu Q, Chen HZ
Biochemistry · 2026 Apr · PMID 41848505 · Publisher ↗
Recently, a growing number of novel types of regulated cell death have been reported, including pyroptosis, necroptosis, and ferroptosis, among others. These types of cell death play crucial roles in a wide array of phys...
Recently, a growing number of novel types of regulated cell death have been reported, including pyroptosis, necroptosis, and ferroptosis, among others. These types of cell death play crucial roles in a wide array of physiological functions such as metabolism, tissue injury and repair, chronic disease progression, and immune protection. However, specifically targeting cell death pathways for therapeutic purposes remains a challenge due to the unresolved complexities in pharmacological intervention. Nuclear receptor superfamily members, a class of prominent targets in drug discovery, are involved in diverse physiological and pathological processes. Investigating the regulatory functions between nuclear receptors and cell death is essential for understanding their roles in cell death and developing novel treatment methods for cell death-related diseases. This review discusses the mechanisms and functional significance of nuclear receptors in cell death across various physiological and pathological conditions, summarizes current ligands and compounds that facilitate targeting nuclear receptors to modulate cell death, and aims to promote the development of novel pharmacological strategies.
Design Strategies for Advanced Biomaterials Functionalized with Bioactive Peptides.
Trickett SM, López-Silva TL
Biochemistry · 2026 Apr · PMID 41843899 · Publisher ↗
A vast library of bioactive peptides provides a versatile toolkit for engineering biological functionality into materials. This peptide repertoire encompasses a broad range of bioactivities, including cell adhesion, prot...
A vast library of bioactive peptides provides a versatile toolkit for engineering biological functionality into materials. This peptide repertoire encompasses a broad range of bioactivities, including cell adhesion, protease lability, signaling activation, and immunomodulation. As a result, these peptides have been widely used in biomaterial design to instruct cell behavior and control biological outcomes. Given the complexity and highly dynamic nature of native cellular microenvironments, emerging approaches focus on developing multifunctional and stimuli-responsive biomaterials that better recapitulate these biological systems. Designing such materials requires integrating biochemical mechanisms that drive specific cellular responses while optimizing material properties to enhance desired functionality. In this review, we describe emerging design strategies and key considerations for peptide-functionalized materials, with an emphasis on the molecular interactions and biochemical mechanisms that inform their design. We discuss how synergistic cues, peptide structural conformation, and modes of motif presentation are used to regulate cell-material interactions and downstream signaling. We also highlight molecular- and material-based strategies to impart endogenous and exogenous stimulus-responsive behavior, as well as the influence of intrinsic material properties on peptide bioactivity. Advances in computational and data-driven approaches for the discovery and optimization of de novo bioactive peptides and biomaterials, coupled with new insights into biological mechanisms and protein structures, are accelerating the design of materials that more closely recapitulate natural environments for diverse biomedical applications.
Thyroid Peroxidase Gene Mutations Associated with Thyroid Disorders.
Zubkov AV, Butova LG
Biochemistry (Mosc) · 2026 Jan · PMID 41843886 · Publisher ↗
The gene belongs to the group of genes responsible for the biosynthesis of thyroid hormones and encodes thyroid peroxidase, a key enzyme involved in this process. Mutations in these genes can result in thyroid dysfuncti...
The gene belongs to the group of genes responsible for the biosynthesis of thyroid hormones and encodes thyroid peroxidase, a key enzyme involved in this process. Mutations in these genes can result in thyroid dysfunction characterized by reduced levels of thyroid hormones. Hypothyroidism caused by pathogenic variants typically presents as permanent hypothyroidism and is frequently associated with endemic goiter. This analytical review summarizes and systematizes data from the studies conducted in different regions of the world on mutations identified in the gene in patients with hypothyroidism. Particular attention is given to mutations within structural and functional domains of thyroid peroxidase, which has a unique molecular architecture within its family.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe