Protein Science最新文献

{"title":"MIF-MAPMS: Enhancing identification of myelin autoantigenic peptides in multiple sclerosis through multimodal information fusion.","authors":"Watshara Shoombuatong, Nalini Schaduangrat, Pramote Chumnanpuen, Lawankorn Mookdarsanit, Pakpoom Mookdarsanit","doi":"10.1002/pro.70695","DOIUrl":"10.1002/pro.70695","url":null,"abstract":"<p><p>Multiple sclerosis (MS) arises from an autoimmune response in which the immune system erroneously targets myelin autoantigens within the central nervous system, leading to myelin degradation and subsequent neurological dysfunction. Identifying myelin autoantigenic peptides (MAPs) is therefore critical for understanding MS pathogenesis and developing targeted therapies; however, conventional experimental approaches remain time-consuming and costly. Thus, computational methods that can perform in silico screening of T cell-specific MAP in MS (MAPMSs) using only peptide sequences are highly desirable. Existing computational methods primarily rely on a single modality, which often fails to capture key information of MAPMSs, leading to limited sequence representation and generalization ability. To address this limitation, we propose MIF-MAPMS, a novel multimodal information fusion framework that leverages multimodal information, including peptide format and SMILEs notation, for accurate MAPMS identification. This novel framework processes different modalities of compositional descriptors, molecular fingerprints, ESM-2 embeddings, and Mol2V embeddings using specific deep learning methods, leading to enriched MAPMS representation. Subsequently, the extracted embeddings are fused and passed through a multilayer perceptron (MLP), followed by a fully connected neural network for MAPMS identification. Both cross-validation and independent test results show that MIF-MAPMS attains significant improvements in MAPMS identification over the benchmark main and alternative datasets, with Matthew's correlation coefficient (MCC) of 0.931-0.968 and 0.812-0.928, providing 5.78%-8.04% and 1.22%-2.98% increases, respectively, compared to the existing method. Ablation studies further confirm the necessity of multimodal information fusion in improving MAPMS representation and the model's predictive performance. All codes and datasets are freely available online at https://github.com/lawankorn-m/MIF-MAPMS.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70695"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13347377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148412696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immunoglobulin binding protein (BiP) forms two types of dimers.","authors":"Karina New, Miguel I A Lagos-Espinoza, Nathalie Casanova-Morales, Roi Asor, John William Young, Zahra Alavi, Christian A M Wilson","doi":"10.1002/pro.70690","DOIUrl":"10.1002/pro.70690","url":null,"abstract":"<p><p>Immunoglobulin binding protein (BiP) is a chaperone protein that plays crucial roles in protein folding and transport by binding unfolded proteins in the substrate binding domain (SBD), an interaction allosterically linked to the nucleotide occupancy of the nucleotide binding domain (NBD). BiP also forms oligomers that influence its activity, particularly in binding polypeptide clients. Using single-molecule approaches and mechanical and enzymatic activity assays, BiP monomer stability and oligomerization were analyzed both alone and in response to nucleotides and peptides. We find that the formation of BiP dimers exhibits biphasic behavior as a function of BiP concentration, suggesting concentration-dependent changes in dimer dissociation constants. At low BiP concentrations, dimers were disrupted by peptide substrate and adenosine triphosphate (ATP) but remained unaffected by ADP or Adenosine 5'-O-(3-thio)triphosphate (ATPγS). At high concentrations, dimers are unaffected by peptides, but their assembly is inhibited by ATP and ATPγS to the same degree. These results suggest the formation of two distinct BiP dimers exhibiting unique binding affinities, kinetics, and potentially structures. We propose the existence of a high-affinity dimer binding site within the SBD of BiP, while the formation of a low-affinity dimer involves interactions between the lid and NBD of each protomer. Our findings demonstrate the importance of considering single-molecule characteristics when interpreting bulk studies on protein function and regulation.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70690"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13347316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148412704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SSEL-CPP: A SHAP-based feature-selection ensemble learning framework identifies molecular properties of cell-penetrating peptides.","authors":"Chan Woo Kwon, Minjun Kwon, Shaherin Basith, Sampa Misra, Yong Eun Jang, Gwang Lee","doi":"10.1002/pro.70704","DOIUrl":"10.1002/pro.70704","url":null,"abstract":"<p><p>Cell-penetrating peptides (CPPs) facilitate the intracellular delivery of therapeutic molecules. However, their accurate identification and design remain challenging because of the complexity of their structural and physicochemical characteristics. This study aimed to develop an interpretable predictive model that enables reliable CPP discovery and provides interpretable descriptors suggestive of the molecular properties underlying their activity. Peptide samples were represented using two-dimensional descriptors generated by Mordred. A novel two-stage feature selection method was introduced, combining a correlation-based filter with Shapley Additive exPlanations (SHAP). The model was trained on the CPP1708 dataset and built using an ensemble learning strategy integrating multiple machine learning algorithms. The ensemble framework, combining Extreme Gradient Boosting and Light Gradient Boosting Machine, identified five Mordred descriptors-5-ordered bonding information content (BIC5), Extended Topochemical Atom epsilon 5 (ETA_epsilon_5), averaged and centered Moreau-Broto autocorrelation of lag 0 weighted by ionization potential (AATSC0i), centered Moreau-Broto autocorrelation of lag 2 weighted by mass (ATSC2m), and first highest eigenvalue of Burden matrix weighted by gasteiger charge (BCUTc-1h)-as critical features for CPP prediction. The model achieved an accuracy of 82.0% and an area under the curve of 87.5% on the CPP1708 test set, outperforming existing predictors. This interpretable, high-performing prediction model supports the rational design of CPPs and advances peptide-based drug development. The SHAP-guided feature selection framework improves both efficiency and interpretability, with potential applications across diverse peptide classes. Furthermore, the identification of five mechanistic descriptors offers deeper insight into the structural, electronic, and physicochemical properties underpinning CPP activity.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70704"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13352142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148423430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanism-guided mutagenesis of Rft1 to test its role as a dolichol-linked oligosaccharide scramblase in cells.","authors":"George N Chiduza, Ken-Taro Sakata, Hannah G Wolfe, Faria Noor, Anant K Menon","doi":"10.1002/pro.70715","DOIUrl":"10.1002/pro.70715","url":null,"abstract":"<p><p>The membrane protein Rft1 is proposed to play an essential role in yeast and human cells by scrambling the glycolipid Man5GlcNAc2-PP-dolichol (M5-DLO) across the endoplasmic reticulum (ER) for protein N-glycosylation. While this activity has been demonstrated in liposomes reconstituted with purified Rft1, biochemical evidence of additional M5-DLO scramblases and the viability of Rft1-null Trypanosoma brucei suggest that scrambling may be a moonlighting function of Rft1 rather than its essential cellular role. To investigate this problem, we used AlphaFold3 and Chai-1 to model the conformational dynamics of yeast Rft1-M5-DLO complexes. The models suggest an alternating access mechanism, typical of Multidrug/Oligosaccharidyl-lipid/Polysaccharide (MOP) superfamily transporters, in which a cationic central cavity coordinates the anionic headgroup of M5-DLO, while the dolichol tail of the lipid is accommodated through a lateral portal formed by two transmembrane helices. We used the models to design mutations to disrupt the interaction between Rft1 and the M5-DLO headgroup, and to engineer a salt bridge to block the portal and stall transport. Using a Tet-off yeast reporter strain, we tested 26 central cavity mutants and identified 2 that supported cell growth poorly despite being well-expressed. Strikingly, the portal-blocking mutant which is predicted to lack scramblase activity supported robust growth. These data suggest that while M5-DLO binding is important for Rft1's essential function, scrambling activity is dispensable. We speculate that Rft1's essential role may be as an M5-DLO chaperone, capturing and routing M5-DLO propitiously on the cytoplasmic side of the ER to coordinate DLO biosynthesis.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70715"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13343734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of physiological oxidants on triggering amyloid formation of the cell cycle regulator protein p16^INK4A.","authors":"Briana R Smith, Nicholas J Magon, Aakriti Sethi, Shelby G Gray, Sarah G Heath, Vanessa K Morris, Christoph Göbl","doi":"10.1002/pro.70723","DOIUrl":"10.1002/pro.70723","url":null,"abstract":"<p><p>The tumor suppressor protein p16^INK4a plays a key role in cell cycle control and is frequently inactivated in human cancers. We previously discovered that oxidation of its single cysteine residue induces a structural transition from the functional monomeric form into inactive amyloid fibrils. Here, we investigate whether five physiologically relevant oxidants can trigger the conformational switch of the protein. Using time-resolved SDS-PAGE, thioflavin-T fluorescence assays, mass spectrometry, and electron microscopy, we show that peroxymonocarbonate and hypothiocyanous acid (HOSCN) efficiently induce cysteine-dependent dimerization with subsequent amyloid formation of recombinant p16. In contrast, hydrogen peroxide, hypochlorous acid, and taurine chloramine are less efficient and predominantly lead to the formation of amorphous aggregates. These findings demonstrate that physiological oxidants differ in their ability to induce amyloid transitions in p16, with potential implications for oxidative stress-mediated inactivation of this cell-cycle regulator protein.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70723"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13373305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RINAMI: Residue-attributed interpretable neural network for predicting absolute folding free energy by merging structure and sequence information.","authors":"Naoki Tomita, George Chikenji","doi":"10.1002/pro.70717","DOIUrl":"10.1002/pro.70717","url":null,"abstract":"<p><p>Recent advances in de novo protein design have enabled the generation of diverse novel proteins. However, a fundamental challenge remains: even when an amino acid sequence is designed with the target structure as the most stable conformation, there is currently no reliable computational method for assessing whether the target structure is sufficiently stabilized relative to alternative conformations. While experimental realization of the intended fold requires the target structure to be thermodynamically favored by a large free-energy gap, the absence of a quantitative measure of folding stability makes it difficult to distinguish reliable from unreliable designs. Here, we propose the Residue-attributed Interpretable Neural network for predicting Absolute folding free energy by Merging structure and sequence Information (RINAMI), a machine learning model that predicts the absolute folding free energy (ΔG) of proteins from their three-dimensional structures and amino acid sequences. RINAMI integrates structure- and sequence-based representations derived from ProteinMPNN and Evolutionary Scale Modeling 2 (ESM2) using a multi-head cross-attention mechanism that contextualizes sequence-derived signals within the structural environment. Benchmarking RINAMI on both natural and designed proteins from the Mega-scale and Maxwell datasets shows that it outperforms the tested existing approaches, achieving higher correlations with experimental measurements and improved or comparable prediction errors. An ablation study supports the contribution of sequence-structure integration for predictive accuracy. In addition, RINAMI exhibits strong interpretability by capturing key physicochemical effects, including the destabilizing effect of buried hydrophilic residues, the stabilizing effect of buried hydrophobic residues, and the characteristics of cysteine. Together, these results establish RINAMI as an accurate and interpretable framework for ΔG prediction and provide a practical computational tool for evaluating and prioritizing protein designs prior to experimental testing.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70717"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13351927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148423413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level.","authors":"Sören von Bülow, Kristoffer E Johansson, Kresten Lindorff-Larsen","doi":"10.1002/pro.70694","DOIUrl":"10.1002/pro.70694","url":null,"abstract":"<p><p>Deep-learning methods have transformed our ability to predict the three-dimensional structures of folded proteins from sequence, and coarse-grained simulations have made it possible to study intrinsically disordered proteins at the proteome scale. More than half of human proteins, however, contain mixtures of disordered regions and one or more folded domains, and the biological function of these multi-domain proteins (MDPs) depends on the interplay between the folded and disordered regions. Here, we developed AF-CALVADOS, a coarse-grained simulation model that is informed by AlphaFold to model the dynamics of intrinsically disordered proteins and MDPs containing mixtures of folded and disordered regions. AF-CALVADOS leverages information from AlphaFold 2 to model folded regions that we then integrate with the coarse-grained CALVADOS model. Our automated framework makes it possible to perform simulations of any soluble folded or disordered protein without manually defining the folded regions, enabling scaling to the proteome level. We validate AF-CALVADOS using experimental small-angle x-ray scattering data for more than 400 proteins and find that it performs well across proteins with varying amounts of ordered and disordered regions. We demonstrate the scalability of AF-CALVADOS by performing simulations of 12,483 intracellular human proteins and make the data freely available; we envisage that large-scale simulation data generated by AF-CALVADOS can be used to benchmark or train machine learning models for flexible, MDPs. The conformational ensembles can also be used to study sequence-dynamics-function relationships at scale, and can shed light on the interplay between folded and disordered regions. We illustrate this by analyzing the disordered regions in 1487 human transcription factors. AF-CALVADOS is available as part of the CALVADOS package at: github.com/KULL-Centre/CALVADOS. Single-chain simulations with AF-CALVADOS can be run via Google Colab: colab.research.google.com/github/KULL-Centre/_2025_buelow_AF-CALVADOS/blob/main/AF_CALVADOS.ipynb.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70694"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13351942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148423543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Activation parameters, enthalpy-entropy compensation and the temperature-dependent activity of enzymes.","authors":"Matthew J McLeod, Robert E Thorne","doi":"10.1002/pro.70722","DOIUrl":"10.1002/pro.70722","url":null,"abstract":"<p><p>The increase in enzyme-catalyzed reaction rates with temperature is typically modeled using Arrhenius or Eyring relations. Interpretation of extracted parameters is subject to multiple caveats. Here we analyze the impact of temperature variations of underlying activation or Eyring parameters and of temperature-dependent contributions to overall rates from steps other than a rate-limiting chemical step. Linear Arrhenius/Eyring behavior can still be observed when the underlying activation energy <math> <mrow><msub><mi>E</mi> <mi>a</mi></msub> </mrow> </math> or enthalpy <math><mrow><mi>Δ</mi> <msup><mi>H</mi> <mo>‡</mo></msup> </mrow> </math> and entropy <math><mrow><mi>Δ</mi> <msup><mi>S</mi> <mo>‡</mo></msup> </mrow> </math> vary with temperature. Modest variations-of the order of an H-bond energy over 60°C-lead to large fractional deviations of <math> <mrow><msub><mi>E</mi> <mi>a</mi></msub> </mrow> </math> , <math><mrow><mi>Δ</mi> <msup><mi>H</mi> <mo>‡</mo></msup> </mrow> </math> and <math><mrow><mi>Δ</mi> <msup><mi>S</mi> <mo>‡</mo></msup> </mrow> </math> values derived from linear fits from their underlying values and to deviations of Arrhenius prefactors <math><mrow><mi>A</mi></mrow> </math> by orders of magnitude. In a family of related enzymes with similar activation free energies <math><mrow><mi>Δ</mi> <msup><mi>G</mi> <mo>‡</mo></msup> </mrow> </math> , small differences in temperature-dependent contributions to overall rates will lead to apparent enthalpy-entropy compensation and may scramble enzyme ordering based on <math><mrow><mi>Δ</mi> <msup><mi>H</mi> <mo>‡</mo></msup> </mrow> </math> or <math><mrow><mi>Δ</mi> <msup><mi>S</mi> <mo>‡</mo></msup> </mrow> </math> . Similar considerations apply to interpretation of van 't Hoff plots of equilibrium measurements and related observations of enthalpy-entropy compensation. For enzymes exhibiting negative curvature and maximum rates well below the unfolding temperature, fits assuming <math><mrow><mi>Δ</mi> <msup><mi>H</mi> <mo>‡</mo></msup> <mfenced><mi>T</mi></mfenced> </mrow> </math> and <math><mrow><mi>Δ</mi> <msup><mi>S</mi> <mo>‡</mo></msup> <mfenced><mi>T</mi></mfenced> </mrow> </math> are connected by a negative heat capacity <math><mrow><mi>Δ</mi> <msubsup><mi>C</mi> <mi>p</mi> <mo>‡</mo></msubsup> <mfenced><mi>T</mi></mfenced> </mrow> </math> yield physically implausible values, suggesting the importance of other contributions to observed behavior. Complementary methods including pre-steady-state kinetics, kinetic isotope effect and viscosity-dependence measurements, multi-temperature static and time-resolved atomic-resolution structural studies, and simulations should play a key role in quantitatively interpreting temperature-dependent kinetic and equilibrium data from enzymatic systems.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70722"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13398508/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148579837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RCSB protein data Bank: Next-generation advanced search for exploration of experimental structures and computed structure models.","authors":"Yana Rose, Ronald Brown, Maria Voigt, Charmi Bhikadiya, Sebastian Bittrich, Jose M Duarte, Joan Segura, Rachel Kramer Green, Stephen K Burley","doi":"10.1002/pro.70731","DOIUrl":"10.1002/pro.70731","url":null,"abstract":"<p><p>The Protein Data Bank (PDB), established in 1971, is the primary global, open-access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research-focused RCSB.org web-portal provides access to these data alongside more than one million machine-learning-predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation-, sequence-, and 3D structure-based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand-guided structural motifs, for constructing geometry-driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure-function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70731"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13410952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148606956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"De novo design of proteinaceous binders targeting the LEDGF PWWP domain.","authors":"Thibault Vantieghem, Julie Delepine, Sam Noppen, Steven Beelen, Matúš Drexler, Jitka Holková, Josef Houser, Václav Veverka, Dominique Schols, Sergei V Strelkov","doi":"10.1002/pro.70726","DOIUrl":"10.1002/pro.70726","url":null,"abstract":"<p><p>Lens epithelium-derived growth factor p75 (LEDGF/p75) is a chromatin reader that recognizes di- or trimethylated Lys36 of histone H3 (H3K36me2/3)-modified nucleosomes and is implicated in diverse diseases, including cancer and human immunodeficiency virus (HIV) infection. Inhibiting the interaction between the Pro-Trp-Trp-Pro (PWWP) domain of LEDGF and chromatin through a small-molecule drug presents an attractive therapeutic opportunity, but the compounds developed to date bind entirely within the small H3K36me2/3 pocket and achieve only modest affinity. Here, we report de novo computational design and structural validation of proteinaceous binders that engage both this canonical pocket and adjacent DNA-interacting surfaces of the PWWP domain. Using a hotspot-driven workflow integrating RFdiffusion, ProteinMPNN, AlphaFold, molecular dynamics simulations and manual structural assessment, we generated four protein designs that were subjected to experimental validation. Biophysical analysis confirmed that one designed binder had a low-micromolar affinity for the LEDGF PWWP domain. Another designed binder revealed unexpected homodimerization which apparently interfered with its binding to the target in solution. Nevertheless, this binder could be co-crystallized with the PWWP domain. The resulting atomic structure at 2.1 Å resolution confirms correct engagement of the intended binding interface. This crystal structure enabled the construction of an expanded pharmacophore model that can instruct the design of next-generation small-molecule or peptide-based inhibitors targeting the LEDGF PWWP domain and related epigenetic readers. These results demonstrate that modern in silico design pipelines can directly yield functional proteinaceous binders without the need for additional experimental screening using phage display or related technologies.</p>","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 8","pages":"e70726"},"PeriodicalIF":5.6,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13393099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148562770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}