Biochemistry [JOURNAL]
Sun
200 papers
Riboflavin Biosynthesis: Mapping the Tagged Lines of a Complex Metabolic Design.
Hoffpauir ZA, Lamb AL
Biochemistry · 2026 May · PMID 42017481 · Full text
Nearly 150 years ago, riboflavin was first isolated as the water-soluble, yellow-green, fluorescent "lactochrome," a discovery that added the earliest bright stroke to what would become a complex metabolic mural. The rib...
Nearly 150 years ago, riboflavin was first isolated as the water-soluble, yellow-green, fluorescent "lactochrome," a discovery that added the earliest bright stroke to what would become a complex metabolic mural. The ribityl-isoalloxazine structure was fully defined nearly a century ago, and from the 1970s through the 1990s, a series of elegant biochemical studies began tracing the lines of biosynthesis with increasing definition, including isotopic labeling experiments (C, N) that effectively tagged substrate atoms to follow their movement through the pathway. In more recent years, presteady state analyses and high-resolution crystal structures have brought sharper focus to the proposed enzymatic mechanisms, adding depth and shading to the emerging picture. The purpose of this article is to define the current state of our understanding of the enzymatic mechanisms that compose the riboflavin biosynthetic pathway, bringing the latest evidence together as an updated rendering of this intricate biochemical (master)piece.
Development of Antagonist Peptides of the Crk/CrkL SH2 Domains by Modifying the Peripheral Amino Acid Residues of the YXXP Motif.
Park T, Roy A, Douglas JT … +6 more , Harned L, Neuenswander SA, Large N, Mudduluru G, Broward M, Johnson DK
Biochemistry · 2026 May · PMID 42009315 · Full text
Protein-protein interactions (PPIs) through the phosphotyrosine-Src homology 2 (SH2) interaction play critical roles in many signal transduction pathways. CT10 regulator of kinase (Crk) and Crk-like (CrkL) are structural...
Protein-protein interactions (PPIs) through the phosphotyrosine-Src homology 2 (SH2) interaction play critical roles in many signal transduction pathways. CT10 regulator of kinase (Crk) and Crk-like (CrkL) are structurally and functionally similar adaptor proteins that mediate PPIs through their SH2 domains. Crk and CrkL are essential in tumor cell migration and invasion and have been proposed as therapeutic targets. However, there are no Crk and CrkL inhibitors available. Previously, we designed a conserved heptapeptide that binds to Crk by analyzing the 15 YXXP motifs in p130Cas. The peptide bound to the SH2 domain of Crk (CrkSH2) and inhibited the CrkSH2-p130Cas interaction. Here, to design peptides with higher affinities, we performed two rounds of the structure-function relationship study in which the nonconserved amino acid residues were substituted with other l-amino acids based on molecular modeling results. The binding activities of the substituted peptides were determined by saturation transfer difference NMR (STD-NMR), fluorescence polarization (FP), and FP competition assays. Whereas none of the core amino acid substitutes improved the binding affinities, two terminal amino acid substitutes improved the binding affinities to Crk and CrkL and inhibited the Crk/CrkL-mediated PPIs. Our study demonstrates that substitution of amino acids at the -2 and +4 positions from the conserved phosphotyrosine improves the binding affinity of the YXXP motif-containing peptide to the SH2 domains of Crk and CrkL. Our study proposes modification or optimization of the peripheral amino acid residues of the YXXP motif to improve the YXXP-SH2 binding and develop inhibitors of Crk and CrkL.
Identification and Characterization of Novel Human IgG-Degrading Enzymes.
Tran E, Spraggon G, Jones DH … +1 more , Appling FD
Biochemistry · 2026 May · PMID 42009310 · Full text
The human immune response and factors that modulate it represent challenges and opportunities in many areas of medicine. Examples are the threat of transplant rejection and the reduction of this threat by the administrat...
The human immune response and factors that modulate it represent challenges and opportunities in many areas of medicine. Examples are the threat of transplant rejection and the reduction of this threat by the administration of a bacterially derived immune evasion enzyme. species secrete proteases of the IdeS/Mac family that efficiently degrade host immunoglobulin G (IgG) to help the bacteria evade the host's immune response. IdeS has recently received interest as a tool for transiently ablating circulating IgG in the context of diverse treatments, including transplantation and gene therapy. Given the wide-ranging utility of IdeS-mediated modulation of the human immune response, we sought to explore sequence-function relationships within the IdeS family in the hopes of identifying IdeS enzymes with therapeutic potential. To this end, we developed and applied a structural bioinformatics workflow and analytical strategy to identify and experimentally characterize novel IdeS homologs with activity against human IgG. Multiple IdeS-like enzymes with a range of human IgG degradation efficiencies were identified and characterized. The efficiencies of these enzymes exhibit a nontrivial dependence on the sequence of the IdeS-IgG binding site, highlighting the complexity of substrate recognition by IdeS. The workflow and data presented here inform basic IdeS enzymology, provide novel starting points for engineering IdeS variants for therapeutic use, and suggest general strategies for efficiently sampling protein sequence space to identify therapeutic enzymes.
Electrostatic Interactions with Extracellular Loop 1 Modulate Hormone-Specific Changes in Parathyroid Hormone 1 Receptor Activation and Signaling.
McArthur ES, Tscheu M, Crandall E … +9 more , Janssen MW, Jiang D, Cobb I, Ghimire M, Finegold N, Abraham S, Hudyma AL, Martin A, Culhane KJ
Biochemistry · 2026 May · PMID 41996540 · Publisher ↗
Parathyroid hormone 1 receptor (PTH1R) is a G protein-coupled receptor (GPCR) expressed in bone and kidney cells that is activated by two endogenous hormones, parathyroid hormone (PTH) and parathyroid hormone-related pep...
Parathyroid hormone 1 receptor (PTH1R) is a G protein-coupled receptor (GPCR) expressed in bone and kidney cells that is activated by two endogenous hormones, parathyroid hormone (PTH) and parathyroid hormone-related peptide (PTHrP). Hormone activation promotes G protein binding and downstream signaling from the Gs and Gq G protein isoforms. Flexible regions of PTH1R impact the stability of hormone and G protein interactions to modulate the downstream signaling. Extracellular loop 1 (ECL1) is one flexible region of PTH1R, which is abnormally long compared to other family B GPCRs and is implicated in positive allosteric modulation of PTH1R. However, a detailed understanding of how ECL1 interactions regulate PTH1R signaling is unknown. Therefore, we created a PTH1R mutant with ECL1 removed (ΔECL1 PTH1R) to investigate the role of the flexible loop in G protein binding and downstream signaling. Compared to WT, ΔECL1 PTH1R increased Gs interactions with the receptor and downstream signaling induced by PTH while decreasing those induced by PTHrP. However, ΔECL1 PTH1R increased both PTH and PTHrP Gq interactions and signaling compared to those induced by WT. The hormone-specific regulation of Gs signaling depends on charged residues in the C-terminal regions of PTH and PTHrP. The hormones have opposite electrostatic interactions with clusters of negative charges in ECL1, where ECL1 repels negative charges in PTH and stabilizes positive charges in PTHrP. Understanding the mechanism of ECL1 regulation of PTH1R signaling provides a clearer understanding of PTH and PTHrP interactions as future targets for drug development.
The Role of Metal Complexation in the Unfolding Energetics of a Nudix Hydrolase.
Alt N, Zhuang Y, Quirk S … +1 more , Hernandez R
Biochemistry · 2026 May · PMID 41995431 · Full text
Dihydroneopterin triphosphate pyrophosphatase (DHNTPase) catalyzes an essential step in bacterial folate biosynthesis. A characteristic of the enzyme is that it can be stabilized by divalent cations. To better characteri...
Dihydroneopterin triphosphate pyrophosphatase (DHNTPase) catalyzes an essential step in bacterial folate biosynthesis. A characteristic of the enzyme is that it can be stabilized by divalent cations. To better characterize the nature of its stabilization, we combine equilibrium denaturation with all-atom adaptive steered molecular dynamics (ASMD) on three forms of DHNTPase─viz apo (PDB: 5U7E), -bound (PDB: 5U7F), and -bound (PDB: 5U7H)─and identify the structural features that govern the native structure's resistance to unfolding. The metal-liganded forms of the enzyme were seen in experiments to unfold at a higher denaturant midpoint and with a slower rate than apo, indicating increased stability. ASMD yields the potential of mean force (PMF) profiles, and observables─such as native contacts , intrapeptide and protein-water H-bonds, residue distances, active-site spread, and site-resolved metal coordination─along a steered coordinate pulling the protein apart. Our findings support a pathway-specific mechanism in which the duration of active-site coherence (compact spread and intact coordination) is the dominant predictor of mechanical/chemical stability. Along the pulling coordinate, residues Glu 117 and Thr40, and metal-sulfate interactions are also seen to be levers for stabilization or disruption.
Covalent Inhibition of Isocitrate Lyase by Maleate Reveals Enolate Reactivity During Catalysis.
Fernando KGS, Murkin AS
Biochemistry · 2026 May · PMID 41989863 · Publisher ↗
Isocitrate lyase (ICL) from is a key enzyme of the glyoxylate shunt required for survival during latent infection and is absent in humans. Maleate has long been characterized as a reversible competitive inhibitor that m...
Isocitrate lyase (ICL) from is a key enzyme of the glyoxylate shunt required for survival during latent infection and is absent in humans. Maleate has long been characterized as a reversible competitive inhibitor that mimics the succinate product of catalysis. Here, we show that maleate instead functions as a slow, time-dependent covalent inactivator of ICL. Kinetic analysis supports a two-step mechanism involving reversible binding followed by irreversible modification of the catalytic cysteine residue, Cys191. Mass spectrometric analysis confirms covalent modification and, in the presence of glyoxylate, reveals an additional adduct incorporating both maleate and glyoxylate. Formation of this higher-mass species is consistent with enolate-like reactivity within the active site. Comparison with structurally related maleate analogues demonstrates that minimal substitution at the alkene abolishes covalent reactivity and alters the binding mode, highlighting the stringent geometric and electronic constraints imposed by the succinate-binding pocket. Together, these findings redefine the interaction of succinate analogues with ICL and provide mechanistic insight into active-site organization.
Crowder Induced Phase Separation Modulates the Huntingtin Protein Aggregation Landscape.
Mishra A, Banger S, Chowdhury PK
Biochemistry · 2026 May · PMID 41988802 · Publisher ↗
Macromolecular crowding is a defining feature of cellular environments and plays an important role in modulating protein aggregation. Here, we examine how mixed macromolecular crowders influence the aggregation of Huntin...
Macromolecular crowding is a defining feature of cellular environments and plays an important role in modulating protein aggregation. Here, we examine how mixed macromolecular crowders influence the aggregation of Huntingtin exon-1 protein with a pathogenic polyglutamine length (HD39Q). Using thioflavin-T (ThT) kinetics, we show that the binary mixtures of polyethylene glycol (PEG8), Dextran (40 and 70), and Ficoll 70 produce biphasic aggregation kinetics that deviate from classical single-step behavior. Confocal imaging using labeled proteins and crowders reveals that not only do the binary combinations of crowders give rise to phase separated conditions, but also these drive the aggregation in subtle but distinct ways based on the respective combinations. Moving beyond binary mixtures for a better in-cell mimic, ternary crowder systems were also studied. These generated hierarchically organized droplet architectures thereby further modulating aggregation pathways and associated protein localization. Comparative imaging of the aggregation of a few model proteins (bovine serum albumin, β-lactoglobulin, and lysozyme) demonstrates that aggregation and partitioning behavior depend strongly on both the properties of the biomolecule and phase composition. These findings highlight how mixed macromolecular crowding can reshape the aggregation landscape by adding complexity at both the spatial and temporal levels, thus making these more relevant for physiologically relevant processes.
Phage Display Driven Identification and Computational Mapping of Macrocyclic Peptides Targeting RhoA G17V.
Abraham S, Zhu C, Le LHS … +6 more , Alugubelli YR, Nonomura T, Huang Y, Hampton JT, Zhou Y, Liu WR
Biochemistry · 2026 May · PMID 41986244 · Full text
Mutant RhoA G17V is a clinically significant yet historically undruggable oncogenic GTPase that drives angioimmunoblastic T-cell lymphoma through a neomorphic interaction with the guanine nucleotide exchange factor Vav1....
Mutant RhoA G17V is a clinically significant yet historically undruggable oncogenic GTPase that drives angioimmunoblastic T-cell lymphoma through a neomorphic interaction with the guanine nucleotide exchange factor Vav1. Its rigid GTPase fold, absence of deep binding pockets, and transient protein-protein interfaces have hindered conventional small-molecule approaches, creating a critical need for alternative therapeutic modalities. Here, we report a systematic strategy to target RhoA G17V using macrocyclic peptides. Two complementary phage-displayed cyclic peptide libraries, an AcrK-mediated 10-mer cyclic library and a CAmCBT-cyclized 12-mer library, were subjected to high-stringency biopanning against recombinant RhoA G17V. While the 10-mer library yielded moderate-affinity binders, the 12-mer library enabled the discovery of Z1, a macrocyclic peptide with submicromolar affinity (K = 136 nM), representing the highest-affinity peptide reported for RhoA G17V to date. Computational docking combined with long-timescale molecular dynamics simulations revealed a stable peptide-protein interaction governed by cooperative hydrophobic and electrostatic interactions. Systematic alanine scanning mutagenesis experimentally validated the predicted binding determinants, confirming the key residues within the macrocycle. Collectively, this work establishes macrocyclic phage display as a powerful and generalizable platform for discovering high-affinity ligands against challenging mutant GTPases and lays a foundation for the development of precision peptide-based therapeutics.
Engineered Systems for the Characterization and Detection of Peptide-Based Quorum Sensing in Gram-Positive Bacteria.
Eisenbraun EL, Beebe NL, Nelson AE … +4 more , Prosser BN, Vulpis TD, Appel AE, Blackwell HE
Biochemistry · 2026 May · PMID 41984999 · Full text
Many questions remain about the biochemical mechanisms of quorum sensing (QS), particularly in Gram-positive bacterial pathogens that pose serious threats to human health such as . Methods to isolate and study the molecu...
Many questions remain about the biochemical mechanisms of quorum sensing (QS), particularly in Gram-positive bacterial pathogens that pose serious threats to human health such as . Methods to isolate and study the molecular components of these signaling systems are not straightforward. To date, most mechanistic investigations into QS systems have been accomplished in cells and, to a lesser extent, using chemical inhibitors. Herein, we report the development and characterization of a set of engineered strains that can be used to study the accessory gene regulator () QS circuits of a variety of Gram-positive bacteria. We cloned the QS machinery into as proof-of-concept to generate "sender" cells capable of autoinducing peptide (AIP) signal biosynthesis, "receiver" cells capable of signal transduction, and "full" cells containing the full QS system. We verified that the sender cells could produce the native AIP and that the receiver and full cells responded to both the AIP signal and a panel of known chemical modulators. The approach was readily transferable to study the QS systems of and , revealing interesting differences that could indicate underlying divergences in native QS mechanisms. We also demonstrate the ability of these strains to function as biosensors to detect the native AIPs of bacteria and produce a targeted antibiotic in response. These engineered systems should find utility for the study of QS in a range of fundamental and applied contexts.
Chain Entropy Modulates Cooperativity Selectively within Intermediate Subpopulations during Protein Unfolding.
Kaushik A, Udgaonkar JB
Biochemistry · 2026 May · PMID 41982069 · Publisher ↗
Protein unfolding invariably appears to be a cooperative transition; yet, the molecular basis by which structural elements could unfold in a coordinated manner remains unresolved. Here, the unfolding mechanism of the nat...
Protein unfolding invariably appears to be a cooperative transition; yet, the molecular basis by which structural elements could unfold in a coordinated manner remains unresolved. Here, the unfolding mechanism of the naturally occurring heterodimeric protein double-chain monellin (dcMN) was characterized using site-specific time-resolved FRET and fluorescence anisotropy decay measurements made under equilibrium conditions. Although ensemble-averaged measurements suggested an apparently cooperative transition, population-level analysis using the maximum entropy method coupled to time-resolved FRET revealed pronounced conformational heterogeneity, with partially contracted (N-like) coexisting with partially expanded (U-like) subpopulations during unfolding. Time-resolved fluorescence anisotropy decay measurements independently demonstrated that local motional constraints are lost gradually and asynchronously across different regions of the protein. The N-like subpopulations underwent cooperative expansion across both intra- and interchain segments, indicating coordinated responses when interchain coupling is maintained. In contrast, the U-like subpopulations displayed pronounced chain-specific, noncooperative behavior, consistent with independent unfolding of the two chains following loss of coupling. Comparison with a covalently linked single-chain variant demonstrates that chain connectivity suppresses heterogeneity and enforces coordinated unfolding. These results identify restriction of chain entropy arising from interchain coupling and covalent connectivity as a molecular determinant that governs whether heterogeneous intermediate subpopulations unfold cooperatively or in a chain-specific manner.
Cisplatin-Induced Oxidative Stress Regulates YAP to Modulate Epigenome Promoting the Survival of Osteosarcoma Cells.
Daiya A, Nayak C, Chowdhury R … +2 more , Chowdhury S, Mukherjee S
Biochemistry · 2026 May · PMID 41980058 · Publisher ↗
The widely used chemotherapeutic drug cisplatin (CDDP) is an integral part of the preoperative chemotherapy protocol for high-grade osteosarcoma (OS). However, despite an aggressive treatment regimen, drug refractoriness...
The widely used chemotherapeutic drug cisplatin (CDDP) is an integral part of the preoperative chemotherapy protocol for high-grade osteosarcoma (OS). However, despite an aggressive treatment regimen, drug refractoriness is a major hindrance to successful therapy. We previously identified key transcriptomic alterations that support the survival of OS cells following CDDP exposure. In the present study, our analyses further demonstrate that CDDP treatment promotes an adaptive, ROS-dependent enrichment of the repressive histone mark H3K27me3 at the upstream promoter regions of growth-associated genes such as CCNA2, as well as at the promoter of LATS1, a negative regulator of Yes-Associated Protein (YAP). This enrichment contributes to the transcriptional repression of these genes and is associated with growth arrest; notably, quenching of reactive oxygen species with -acetyl cysteine (NAC) reversed this effect. Furthermore, reduced LATS1 expression was associated with increased nuclear localization of YAP. Importantly, pharmacological inhibition or genetic ablation of YAP attenuated the CDDP-induced accumulation of repressive marks. Mechanistically, YAP was found to colocalize and coimmunoprecipitate with EZH2, the catalytic member of the Polycomb Repressive Complex 2 (PRC2), suggesting a potential role for YAP in facilitating EZH2-mediated transcriptional repression. Consistent with these observations, inhibition of YAP or pharmacological reversal of the repressive chromatin state using a histone deacetylase (HDAC) inhibitor enhanced the sensitivity of the OS cells to low-dose CDDP treatment. Overall, the present study demonstrates an interplay among oxidative stress, epigenetics, and YAP in modulating OS cell fate post-CDDP exposure.
Structural Landscape of Syanodin I Lasso Peptide.
Santos-Fernandez M, Jeanne Dit Fouque K, Karki U … +8 more , Blond A, Idir R, Asgharihosseinpour N, Zirah S, Chapagain P, Mebel AM, Hegemann JD, Fernandez-Lima F
Biochemistry · 2026 May · PMID 41979354 · Publisher ↗
Here, solution NMR, gas-phase hydrogen/deuterium back-exchange (HDbX)-trapped ion mobility spectrometry (TIMS), electron capture dissociation (ECD), quantum mechanical (QM) calculations, and molecular dynamics (MD) simul...
Here, solution NMR, gas-phase hydrogen/deuterium back-exchange (HDbX)-trapped ion mobility spectrometry (TIMS), electron capture dissociation (ECD), quantum mechanical (QM) calculations, and molecular dynamics (MD) simulations were combined for comprehensive structural elucidation of the lasso peptide syanodin I. NMR and ECD MS/MS confirmed an entangled lasso structure with Gln13 as the plug residue maintaining the lasso thread. A maximal /' ratio at Ala11 () was consistent with multiple long-range NOE correlations, identifying Ala11 in proximity to the macrolactam ring. ECD fragmentation patterns indicated a salt bridge between the C-terminus and the Gln13 side chain. TIMS resolved four distinct IMS bands for [M + 2H] ions of syanodin I and its branched-cyclic analog over a similar collision cross-sectional range. HDX-MS revealed mass shifts of ∼17 and ∼20 deuteriums for the lasso and branched-cyclic forms, respectively, consistent with the folded nature of the branched-cyclic C-terminal region. HDbX-TIMS-MS experiments ( ∼ 0.72 to ∼ 865 ms) resolved at least two distinct conformers within each IMS band, revealing intramolecular interactions inaccessible by TIMS alone. QM calculations determined the HDX rate and number of accessible hydrogens for Pro10 and Gln13; this information was used to inform the MD candidate assignment of the 2D-HDX-TIMS-MS results. This workflow provides a comprehensive framework for probing biomolecular conformational dynamics through complementary solution- and gas-phase approaches. The integration of solution-phase hydrogen/deuterium exchange (HDX) with ion mobility spectrometry-mass spectrometry (IMS-MS) offers powerful structural insights into the conformational dynamics of biological molecules.
Aromatic Residues in Mobile Regions Distal to the Active Site Support the Closed Conformation of DXPS.
Kramer LJ, Austin SL, Majumdar A … +3 more , Smith ND, Woodcock HL, Freel Meyers CL
Biochemistry · 2026 Apr · PMID 41972430 · Full text
The essential bacterial enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) is absent in humans, making the enzyme an attractive antimicrobial target. Its product DXP sits at a metabolic branchpoint and is required for...
The essential bacterial enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) is absent in humans, making the enzyme an attractive antimicrobial target. Its product DXP sits at a metabolic branchpoint and is required for biosynthesis of pyridoxal phosphate (PLP), thiamin diphosphate (ThDP), and isoprenoids. DXP is formed via decarboxylation of pyruvate and subsequent carboligation with d-glyceraldehyde-3-phosphate (d-GAP) in a ThDP-dependent manner. In the current mechanistic model, DXPS follows a ligand-gated mechanism. Pyruvate reacts with ThDP to form C2α-lactylThDP (LThDP), which coincides with a shift to a closed conformation. The flexible "spoon" and "fork" motifs become ordered and the catalytic residue H299 is placed within the active site, supporting LThDP formation and persistence in the closed conformation of the E-LThDP complex until binding of d-GAP. We aim to understand the molecular basis for stabilization of the E-LThDP complex in its closed conformation. We propose that the conserved aromatic residues Y288, F298, and F304 in the DXPS spoon and fork motifs form a cluster upon transition from the open to closed form, positioning H299 within the active site where it has roles in LThDP formation and persistence. We conducted mutagenesis studies to elucidate the roles of Y288, F298, and F304 in conformational cycling and catalysis. Variants (1) adopted open conformations, (2) displayed significantly reduced , (3) promoted LThDP decarboxylation, and (4) exhibited decreased affinity for the postdecarboxylation intermediate. Our results support a model in which conserved aromatic residues within the mobile, sequence-diverse spoon/fork motifs promote the closed conformation, supporting catalysis and LThDP persistence.
AI-Designed Peptides as Tools for Biochemistry.
Hong L, Vincoff S, Chatterjee P
Biochemistry · 2026 Apr · PMID 41961293 · Publisher ↗
Peptides occupy a unique niche as biochemical tools: they are small, modular reagents capable of perturbing protein function with a precision that is often inaccessible to small molecules or antibodies. Historically, the...
Peptides occupy a unique niche as biochemical tools: they are small, modular reagents capable of perturbing protein function with a precision that is often inaccessible to small molecules or antibodies. Historically, their broader use in biochemical research has been constrained by slow discovery workflows, limited control over specificity, and poor physicochemical properties. Recent advances in artificial intelligence have begun to change this landscape by enabling the rational, data-driven design of peptides tailored for specific experimental tasks. In this review, we focus on AI-designed peptides as practical tools for biochemistry. We survey sequence-based and structure-based design paradigms, highlighting how each supports distinct classes of peptide tools, including isoform- and motif-specific binders, multi-objective assay-ready reagents, and functional peptides that enable degradation, stabilization, or biophysical interrogation of proteins. By emphasizing experimental utility, design constraints, and appropriate use cases, we aim to provide a framework for selecting and deploying AI-designed peptides as on-demand reagents in modern biochemical research.
From Neoantigens to Nanocarriers: Modern Methods and Modalities in Using Peptides for Cancer Vaccination.
Treiterer AH, Robinson B, Huggins S … +1 more , Kimmel BR
Biochemistry · 2026 Apr · PMID 41954501 · Full text
The success of cancer vaccination depends on the ability of therapeutics to sustain prolonged immune activation, leading to the destruction of tumor cells. However, only a few therapeutic cancer vaccines have been FDA-ap...
The success of cancer vaccination depends on the ability of therapeutics to sustain prolonged immune activation, leading to the destruction of tumor cells. However, only a few therapeutic cancer vaccines have been FDA-approved due to challenges in targeting and eliciting a sufficiently strong immune response. Peptides have emerged as promising drugs owing to their ability to interact with cell-surface receptors and their low manufacturing cost. Despite the peptides' positive characteristics, additional research is needed to develop more effective methods for using peptides to stimulate the immune system for a sustained period to induce tumor cell regression. This review focuses on recent work in peptide-based vaccine design and development, aiming to determine the optimal formulation of peptide vaccines by identifying and isolating neoantigens for tumor targeting, thereby delivering peptide antigens to specific locations. The expansion of the current landscape of cancer treatments, including peptide vaccines and combination therapies, is revolutionizing the possibilities for patient care and treatment.
Discovery of SHANK1-PDZ Peptide-Fragment Inhibitors Using a Dynamic Ligation Screening Strategy.
Li Y, Gimenez D, Warriner SL … +1 more , Wilson AJ
Biochemistry · 2026 Apr · PMID 41944827 · Full text
The development of ligands that modulate protein-protein interactions (PPIs) remains an ongoing challenge in chemical biology and drug discovery. While several approaches have been elaborated to target α-helix-mediated P...
The development of ligands that modulate protein-protein interactions (PPIs) remains an ongoing challenge in chemical biology and drug discovery. While several approaches have been elaborated to target α-helix-mediated PPIs, methods for β-strand-mediated PPIs are less well developed. In addition to the shallow and extended interfaces characteristic of PPIs, β-strand-mediated PPIs exhibit topographical complexity, with side chains oriented above and below the plane of the strand, alongside hydrogen-bond donor and acceptor groups oriented perpendicular to the side chains. One class of β-strand-mediated PPIs involves the structurally conserved PDZ domains, which recognize protein partners through a β-strand containing a short consensus motif; canonical PDZ binding motifs (PBMs) recognize their substrates through a C-terminal carboxylate, offering a particularly challenging motif to mimic. Peptides and peptidomimetics represent a promising template for the design of ligands that target β-strand-mediated PPIs. In this work, we replaced segments of a peptide-based template using target/structure-agnostic fragments to achieve β-strand mimicry. Using reversible hydrazone exchange reactions allowed us to identify fragments at both the C- and N-terminus of an internal PDZ recognition motif with affinity for the SHANK1-PDZ domain. When combined into ligands bearing two different fragments, negative co-operativity was observed. In addition to broadening the acylhydrazone-fragment approach to screen for PDZ-binding ligands, this workflow for successive screening and combination of fragments should have broader applicability to other targets in future.
Register-Shifted Structures in Uracil:Adenine and Uracil:Guanine Base-Paired DNA.
Le Phan ST, Eni EE, Roallos MS … +4 more , Tran M, Young de Castro B, Parsons RF, van der Vaart A
Biochemistry · 2026 Apr · PMID 41944501 · Publisher ↗
Register-shifted structures in uracil-damaged dsDNA greatly extend lesion exposure by blocking the base-flipped uracil from re-entering the helix stack. Molecular dynamics simulations were performed to assess the occurre...
Register-shifted structures in uracil-damaged dsDNA greatly extend lesion exposure by blocking the base-flipped uracil from re-entering the helix stack. Molecular dynamics simulations were performed to assess the occurrence of register-shifted structures in U:A and U:G base-paired DNA for different sequence motifs and uracil base-flipping directions. Register-shifted structures were relatively common: significant populations were seen in 49 of 128 simulated sequences. They were about equally prevalent in U:A and U:G sequences, but uracil was preferentially flipped toward the major groove in U:A sequences and toward the minor groove in U:G sequences. The register-shifted base pair in U:G sequences commonly involved T:G mismatches. The majority of register shifts occurred in the 3' direction, and a few sequences formed register shifts over 2 and 3 base pairs. Register-shifted structures primarily occurred for sequences with UT motifs, which are known to be repaired slowly.
Deamidation Promotes AGE-Modifications in Human Lens γS-Crystallin.
Panja S, Nagaraj RH
Biochemistry · 2026 Jun · PMID 41944358 · Full text
Deamidation and advanced glycation end products (AGEs) are among the major post-translational modifications (PTMs) in eye lens proteins. Due to deamidation and AGE formation, proteins may aggregate and scatter light, con...
Deamidation and advanced glycation end products (AGEs) are among the major post-translational modifications (PTMs) in eye lens proteins. Due to deamidation and AGE formation, proteins may aggregate and scatter light, contributing to lens aging and cataract formation. So far, the relation between the two PTMs remains poorly understood. γS-crystallin (γSC), a major subtype of γ-crystallin, undergoes significant modifications through deamidation, especially at the surface-exposed asparagine residues, N14, N76, and N143. In this study, deamidation of γSC was mimicked by mutating asparagine residues to aspartic acid residues. The deamidation mimics were then incubated with a glycating mixture, and AGE formation in proteins was evaluated by LC-MS/MS. Results indicate that deamidation promotes the formation of both non-cross-linking (CML or CEL) and cross-linking AGEs (GOLD, MOLD, or pentosidine) in lysine residues. AGE formation in arginine residues (e.g., MG-H3) is mostly unaffected. Comparative analysis shows that N14D, N143D, and N14DN76DN143D (triple deamidated, TD) consistently accumulated more AGEs than native γSC. Oxidation with 2 mM GSSG led to increased disulfide-linked cross-linking in deamidated γSC. Upon glycation, the deamidated and oxidized γSC accumulated more AGEs than deamidated γSC; however, the specific AGE levels followed the same trend as deamidated γSC. The results suggest that deamidation promotes AGE formation in γSC, and further oxidation makes it even more susceptible to AGE modifications. The combined interdependent effects of deamidation, oxidation, and AGE modifications could therefore contribute to protein cross-linking and aggregation during lens aging and cataract formation.
Model Peptides Enable Comparisons of Substrate Binding Modes of Hsp70 Molecular Chaperones.
Bhasne K, Dörries L, Maqtedar A … +3 more , Mager ST, Clerico EM, Gierasch LM
Biochemistry · 2026 Apr · PMID 41942094 · Full text
Hsp70 molecular chaperones play a wide array of essential roles in the cell by exploiting their ability to bind incompletely folded client proteins. Our past study of the Hsp70, DnaK, bound to short peptides revealed ma...
Hsp70 molecular chaperones play a wide array of essential roles in the cell by exploiting their ability to bind incompletely folded client proteins. Our past study of the Hsp70, DnaK, bound to short peptides revealed many details of the interaction between a model substrate and the "pockets" of the canonical binding cleft within the chaperone substrate binding domain (SBD). A major finding was that peptides bound the SBD cleft in either N- to C- or C- to N- orientations with nearly equal frequencies. The current study asks key questions: What determines preferred orientation in the bound substrate? Also, are the binding behaviors observed for DnaK also found for mammalian homologues? Here, we use NMR and cross-linking methods developed in our past study and compare modes of binding to DnaK and the two major human cytoplasmic Hsp70s, Hsc70 and HspA1. Model peptides examined include a "palindromic" peptide, central residue variant peptides, and examples of naturally occurring Hsp70 clients. The results reveal that DnaK is agnostic to backbone orientation of the bound peptide, while Hsc70 modestly favors the C- to N- orientation, and HspA1 strongly favors the N- to C- orientation. Moreover, substrate affinities in general are similar for DnaK and Hsc70 and weaker for HspA1. The binding energy landscapes of these chaperones also differ, as the data suggest deeper energy wells for bound states in DnaK and HspA1 and a more rugged landscape for Hsc70. We speculate that these properties enable the chaperones to perform their physiological functions more effectively.
Controlled Seeding of β-Amyloid Fibrillation Reveals Propagation of Structural Polymorphisms in Cellular Environments.
Wang T, Sun Y, Lin YR … +2 more , Yao L, Qiang W
Biochemistry · 2026 Apr · PMID 41941608 · Full text
Molecular-level structural polymorphisms of β-amyloid (Aβ) aggregates in Alzheimer's disease patients are pathologically important. However, tracking the propagation and modulation of Aβ structural polymorphisms via app...
Molecular-level structural polymorphisms of β-amyloid (Aβ) aggregates in Alzheimer's disease patients are pathologically important. However, tracking the propagation and modulation of Aβ structural polymorphisms via approaches remains challenging. The successful application of cryogenic transmission electron microscopy (cryo-TEM) in this area relies on the availability of morphologically distinct micrographs, which then enable unambiguous three-dimensional structural reconstruction of individual fibrillar polymorphs to achieve optimal resolution. As a complementary approach, solid-state nuclear magnetic resonance (ssNMR) spectroscopy with guided isotope-labeling schemes can provide site-specific and quantitative information on the populations of individual polymorphs. Such ssNMR sample preparations require seeding, in which key parameters─including seed concentration and seeding time─must be carefully controlled for individual Aβ-cell systems to avoid the introduction of self-nucleated fibrillar polymorphs. In this work, we show that the application of controlled seeding combined with quantitative ssNMR spectroscopy reveals the propagation of molecular-level structural polymorphs, depending on the types of seeds and cells.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe