ACS Bio & Med Chem Au最新文献

{"title":"New Catalytic Residues and Catalytic Mechanism of the RNase T1 Family","authors":"Katsuki Takebe, Mamoru Suzuki, Yumiko Hara, Takuya Katsutani, Naomi Motoyoshi, Tadashi Itagaki, Shuhei Miyakawa, Kuniaki Okamoto, Kaori Fukuzawa, Hiroko Kobayashi","doi":"10.1021/acsbiomedchemau.4c00046","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00046","url":null,"abstract":"The ribonuclease T1 family, including RNase Po1 secreted by <i>Pleurotus ostreatus</i>, exhibits antitumor activity. Here, we resolved the Po1/guanosine-3′-monophosphate complex (3′GMP) structure at 1.75 Å. Structure comparison and fragment molecular orbital (FMO) calculation between the apo form and the Po1/3′GMP complex identified Phe38, Phe40, and Glu42 as the key binding residues. Two types of the RNase/3′GMP complex in RNasePo1 and RNase T1 were homologous to Po1, and FMO calculations elucidated that the biprotonated histidine on the β3 sheet (His36) on the β3 sheet and deprotonated Glu54 on the β4 sheet were advantageous to RNase activity. Moreover, tyrosine (Tyr34) on the β3 sheet was elucidated as a crucial catalytic residues. Mutation of Tyr34 with phenylalanine decreased RNase activity and diminished antitumor efficacy compared to that in the wild type. This suggests the importance of RNase activity in antitumor mechanisms.","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design, Synthesis, and Biological Evaluation of Darunavir Analogs as HIV-1 Protease Inhibitors","authors":"Muhammad Asad Ur Rehman, Hathaichanok Chuntakaruk, Soraat Amphan, Aphinya Suroengrit, Kowit Hengphasatporn, Yasuteru Shigeta, Thanyada Rungrotmongkol, Kuakarun Krusong, Siwaporn Boonyasuppayakorn, Chanat Aonbangkhen, Tanatorn Khotavivattana","doi":"10.1021/acsbiomedchemau.4c00040","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00040","url":null,"abstract":"Darunavir, a frontline treatment for HIV infection, faces limitations due to emerging multidrug resistant (MDR) HIV strains, necessitating the development of analogs with improved activity. In this study, a combinatorial in silico approach was used to initially design a series of HIV-1 PI analogs with modifications at key sites, P1′ and P2′, to enhance interactions with HIV-1 PR. Fifteen analogs with promising binding scores were selected for synthesis and evaluated for the HIV-1 PR inhibition activity. The variation of P2′ substitution was found to be effective, as seen in <b>5aa</b> (1.54 nM), <b>5ad</b> (0.71 nM), <b>5ac</b> (0.31 nM), <b>5ae</b> (0.28 nM), and <b>5af</b> (1.12 nM), featuring halogen, aliphatic, and alkoxy functionalities on the phenyl sulfoxide motif exhibited superior inhibition against HIV-1 PR compared to DRV, with minimal cytotoxicity observed in Vero and 293T cell lines. Moreover, computational studies demonstrated the potential of selected analogs to inhibit various HIV-1 PR mutations, including I54M and I84V. Further structural dynamics and energetic analyses confirmed the stability and binding affinity of promising analogs, particularly <b>5ae</b>, which showed strong interactions with key residues in HIV-1 PR. Overall, this study underscores the importance of flexible moieties and interaction enhancement at the S2′ subsite of HIV-1 PR in developing effective DRV analogs to combat HIV and other global health issues.","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Directed Evolution of Candidatus Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase for the Genetic Incorporation of Two Different Noncanonical Amino Acids in One Protein","authors":"Chia-Chuan D. Cho, Waye Michelle Leeuwon, Wenshe Ray Liu","doi":"10.1021/acsbiomedchemau.4c00028","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00028","url":null,"abstract":"The genetic code expansion technique is a powerful chemical biology tool to install noncanonical amino acids (ncAAs) in proteins. As a key enzyme for this technique, pyrrolysyl-tRNA synthetase (PylRS), coupled with its cognate amber suppressor tRNA^Pyl, has been engineered for the genetic incorporation of more than 200 ncAAs. Using PylRS clones from different archaeal origins, two ncAAs have also been genetically encoded in one protein. In this work, we show that the C41AU mutant of tRNA^Pyl from <i>Candidatus Methanomethylophilus alvus</i> (CmatRNA^Pyl) is catalytically inert toward PylRS from <i>Methanosarcina mazei</i> (MmPylRS) but has weak activity toward PylRS from <i>Ca. M. alvus</i> (CmaPylRS). To improve the catalytic efficiency of CmaPylRS toward CmatRNA^Pyl-C41AU, we conducted a directed evolution of CMaPylRS by randomizing its coding sequence, followed by the screening of active mutant clones. After three rounds of randomization and screening, we identified 4 mutations, Y16F/N57D/E161G/N182I, that improve the catalytic efficiency of CMaPylRS toward CMatRNA^Pyl-C41AU. This new clone, named R3–14, coupling with CmatRNA^Pyl-C41AU to recognize an amber codon, has been successfully used together with an evolved MmPylRS clone, coupling with a mutant <i>M. mazei</i> tRNA^Pyl to recognize an ochre codon, to genetically incorporate two different ncAAs, <i>N</i>^ε-(<i>t</i>-butoxycarbonyl)-lysine and <i>N</i>^ε-acetyl-lysine, into one model protein.","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"2674 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a Polymersome Blood Ammonia Assay Coupled with a Portable Near-Infrared Fluorometer","authors":"Marie-Lynn Al-Hawat, Justine Caron, Sarah Djebbar, Simon Matoori","doi":"10.1021/acsbiomedchemau.4c00013","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00013","url":null,"abstract":"Ammonia is a key biomarker in inborn and acquired liver disease. As clinical point-of-care blood ammonia assays are lacking, we developed a polymersome formulation for point-of-care blood ammonia sensing combined with a portable fluorometer. A pH-sensitive near-infrared (NIR) fluorescent dye was identified, which showed a strong fluorescence increase at acidic pH values. Building on reports on ammonia-selective PS-<i>b</i>-PEG polymersomes, these polymersomes were loaded with the NIR dye. These NIR fluorescent polymersomes sensed ammonia in a clinically relevant range in ammonia-spiked fresh whole blood with high linearity (<i>R</i>² = 0.9948) after 5 min using a conventional tabletop plate reader. Subsequently, the assay was tested with a portable fluorometer. An ammonia-dependent fluorescence increase was detected in ammonia-spiked fresh mouse blood after 5 min using the portable fluorometer. The NIR dye-loaded PS-<i>b</i>-PEG polymersomes rapidly sensed ammonia with high linearity in whole blood. This assay was successfully combined with a portable fluorometer and only required 3 μL of blood. These findings motivate a further development and clinical translation of this point-of-care blood ammonia assay.","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141870566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selagibenzophenone B and Its Derivatives: SelB-1, a Dual Topoisomerase I/II Inhibitor Identified through In Vitro and In Silico Analyses","authors":"Serhat Dönmez,&nbsp;Ringaile Lapinskaite,&nbsp;Hazal Nazlican Atalay,&nbsp;Esra Tokay,&nbsp;Feray Kockar,&nbsp;Lukas Rycek*,&nbsp;Mehmet Özbil* and Tugba Boyunegmez Tumer*,&nbsp;","doi":"10.1021/acsbiomedchemau.4c0002710.1021/acsbiomedchemau.4c00027","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00027https://doi.org/10.1021/acsbiomedchemau.4c00027","url":null,"abstract":"<p >The development of multitargeted drugs represents an innovative approach to cancer treatment, aiming to enhance drug effectiveness while minimizing side effects. Herein, we sought to elucidate the inhibitory effect of selagibenzophenone B derivatives on the survival of cancer cells and dual topoisomerase I/II enzyme activity. Results demonstrated that among the compounds, <b>SelB-1</b> selectively inhibited the proliferation and migration of prostate cancer cells while exhibiting minimal effects on healthy cells. Furthermore, <b>SelB-1</b> showed a dual inhibitory effect on topoisomerases. Computational analyses mirrored the results from enzyme inhibition assays, demonstrating the compound’s strong binding affinity to the catalytic sites of the topoisomerases. To our surprise, <b>SelB-1</b> did not induce apoptosis in prostate cancer cells; instead, it induced autophagic gene expression and lipid peroxidation while reducing GSH levels, which might be associated with ferroptotic death mechanisms. To summarize, the findings suggest that <b>SelB-1</b> possesses the potential to serve as a dual topoisomerase inhibitor and can be further developed as a promising candidate for prostate cancer treatment.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"4 4","pages":"178–189 178–189"},"PeriodicalIF":3.8,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsbiomedchemau.4c00027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142011011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selagibenzophenone B and Its Derivatives: SelB-1, a Dual Topoisomerase I/II Inhibitor Identified through In Vitro and In Silico Analyses","authors":"Serhat Dönmez, Ringaile Lapinskaite, Hazal Nazlican Atalay, Esra Tokay, Feray Kockar, Lukas Rycek, Mehmet Özbil, Tugba Boyunegmez Tumer","doi":"10.1021/acsbiomedchemau.4c00027","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00027","url":null,"abstract":"The development of multitargeted drugs represents an innovative approach to cancer treatment, aiming to enhance drug effectiveness while minimizing side effects. Herein, we sought to elucidate the inhibitory effect of selagibenzophenone B derivatives on the survival of cancer cells and dual topoisomerase I/II enzyme activity. Results demonstrated that among the compounds, <b>SelB-1</b> selectively inhibited the proliferation and migration of prostate cancer cells while exhibiting minimal effects on healthy cells. Furthermore, <b>SelB-1</b> showed a dual inhibitory effect on topoisomerases. Computational analyses mirrored the results from enzyme inhibition assays, demonstrating the compound’s strong binding affinity to the catalytic sites of the topoisomerases. To our surprise, <b>SelB-1</b> did not induce apoptosis in prostate cancer cells; instead, it induced autophagic gene expression and lipid peroxidation while reducing GSH levels, which might be associated with ferroptotic death mechanisms. To summarize, the findings suggest that <b>SelB-1</b> possesses the potential to serve as a dual topoisomerase inhibitor and can be further developed as a promising candidate for prostate cancer treatment.","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"108 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141783709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioproduction Platform to Generate Functionalized Disulfide-Constrained Peptide Analogues","authors":"Sunhee Hwang, Aaron T. Balana, Bryan Martin, Michael Clarkson, Paola Di Lello, Hao Wu, Yanjie Li, Jakob Fuhrmann, Yavuz Dagdas, Patrick Holder, Christina I. Schroeder, Stephen E. Miller, Xinxin Gao","doi":"10.1021/acsbiomedchemau.4c00026","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00026","url":null,"abstract":"Disulfide-constrained peptides (DCPs) have gained increased attention as a drug modality due to their exceptional stability and combined advantages of large biologics and small molecules. Chemical synthesis, although widely used to produce DCPs, is associated with high cost, both economically and environmentally. To reduce the dependence on solid phase peptide synthesis and the negative environmental footprint associated with it, we present a highly versatile, low-cost, and environmentally friendly bioproduction platform to generate DCPs and their conjugates as well as chemically modified or isotope-labeled DCPs. Using the DCP against the E3 ubiquitin ligase Zinc and Ring Finger 3, MK1-3.6.10, as a model peptide, we have demonstrated the use of bacterial expression, combined with Ser ligation or transglutaminase-mediated XTEN ligation, to produce multivalent MK1-3.6.10 and MK1-3.6.10 with N-terminal functional groups. We have also developed a bioproduction method for the site-specific incorporation of unnatural amino acids into recombinant DCPs by the amber codon suppression system. Lastly, we produced ¹⁵N/¹³C-labeled MK1-3.6.10 with high yield and assessed the performance of a semiautomated resonance assignment workflow that could be used to accelerate binding studies and structural characterization of DCPs. This study provides a proof of concept to generate functionalized DCPs using bioproduction, providing a potential solution to alleviate the reliance on hazardous chemicals, reduce the cost, and expedite the timeline for DCP discovery.","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141614418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioproduction Platform to Generate Functionalized Disulfide-Constrained Peptide Analogues","authors":"Sunhee Hwang,&nbsp;Aaron T. Balana,&nbsp;Bryan Martin,&nbsp;Michael Clarkson,&nbsp;Paola Di Lello,&nbsp;Hao Wu,&nbsp;Yanjie Li,&nbsp;Jakob Fuhrmann,&nbsp;Yavuz Dagdas,&nbsp;Patrick Holder,&nbsp;Christina I. Schroeder,&nbsp;Stephen E. Miller* and Xinxin Gao*,&nbsp;","doi":"10.1021/acsbiomedchemau.4c0002610.1021/acsbiomedchemau.4c00026","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00026https://doi.org/10.1021/acsbiomedchemau.4c00026","url":null,"abstract":"<p >Disulfide-constrained peptides (DCPs) have gained increased attention as a drug modality due to their exceptional stability and combined advantages of large biologics and small molecules. Chemical synthesis, although widely used to produce DCPs, is associated with high cost, both economically and environmentally. To reduce the dependence on solid phase peptide synthesis and the negative environmental footprint associated with it, we present a highly versatile, low-cost, and environmentally friendly bioproduction platform to generate DCPs and their conjugates as well as chemically modified or isotope-labeled DCPs. Using the DCP against the E3 ubiquitin ligase Zinc and Ring Finger 3, MK1-3.6.10, as a model peptide, we have demonstrated the use of bacterial expression, combined with Ser ligation or transglutaminase-mediated XTEN ligation, to produce multivalent MK1-3.6.10 and MK1-3.6.10 with N-terminal functional groups. We have also developed a bioproduction method for the site-specific incorporation of unnatural amino acids into recombinant DCPs by the amber codon suppression system. Lastly, we produced ¹⁵N/¹³C-labeled MK1-3.6.10 with high yield and assessed the performance of a semiautomated resonance assignment workflow that could be used to accelerate binding studies and structural characterization of DCPs. This study provides a proof of concept to generate functionalized DCPs using bioproduction, providing a potential solution to alleviate the reliance on hazardous chemicals, reduce the cost, and expedite the timeline for DCP discovery.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"4 4","pages":"190–203 190–203"},"PeriodicalIF":3.8,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsbiomedchemau.4c00026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142010328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mass Spectrometry-Based Protein Footprinting Defines the Binding Pocket of Crotonylated H3K14 in the PHD1 Domain of BAF45D within the BAF Chromatin Remodeling Complex","authors":"Marissa R. Martinez,&nbsp;Janna Kiselar,&nbsp;Benlian Wang,&nbsp;Dipti Sadalge,&nbsp;Laura Zawadzke,&nbsp;Asad Taherbhoy,&nbsp;Derek Musser,&nbsp;Yunji Davenport,&nbsp;Jeremy Setser,&nbsp;Mark R. Chance* and Steve Bellon*,&nbsp;","doi":"10.1021/acsbiomedchemau.4c0000910.1021/acsbiomedchemau.4c00009","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00009https://doi.org/10.1021/acsbiomedchemau.4c00009","url":null,"abstract":"<p >The BRG-/BRM-associated factor (BAF) chromatin remodeling complex is a central actor in transcription. One mechanism by which BAF affects gene expression is via its various histone mark readers, including double plant homeodomains (DPF), located in the BAF45D subunit. DPF domains recognize lysine acetyl and acylations, including crotonylation, localized at promoters and enhancers. Despite a significant degree of conservation between DPF domains, attempts to crystallize BAF45D with a crotonylated histone 3 peptide (H3K14Cr) were unsuccessful. In addition, recent cryoEM and modeled structures failed to define the Req domain of BAF45D, which is responsible for reading lysine modifications. Thus, the precise mechanism of crotonyl group recognition and binding by BAF45D within the BAF complex remains unclear. We turned to protein footprinting mass spectrometry to map the binding interface between H3K14Cr and BAF45D. This technique is able to demarcate protein-binding interfaces by modifying surface-accessible residues and is not limited by protein size or composition. Experiments performed in the isolated DPF domain of BAF45D (BAF45D_DPF)-delineated H3K14Cr peptide binding across the PHD1 and PHD2 pockets. We observed markedly similar effects on the BAF45D subunit when assessing H3K14Cr binding in the purified full BAF complex. The ATPase motor, BRM, also displayed H3K14Cr-protected peptides in two separate domains that were subsequently evaluated in direct binding assays. These data confirm the BAF45D–crotonylamide interaction within its obligate complex and are the first to demonstrate H3K14Cr direct binding to BRM.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"4 4","pages":"204–213 204–213"},"PeriodicalIF":3.8,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsbiomedchemau.4c00009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142011107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mass Spectrometry-Based Protein Footprinting Defines the Binding Pocket of Crotonylated H3K14 in the PHD1 Domain of BAF45D within the BAF Chromatin Remodeling Complex","authors":"Marissa R. Martinez, Janna Kiselar, Benlian Wang, Dipti Sadalge, Laura Zawadzke, Asad Taherbhoy, Derek Musser, Yunji Davenport, Jeremy Setser, Mark R. Chance, Steve Bellon","doi":"10.1021/acsbiomedchemau.4c00009","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00009","url":null,"abstract":"The BRG-/BRM-associated factor (BAF) chromatin remodeling complex is a central actor in transcription. One mechanism by which BAF affects gene expression is via its various histone mark readers, including double plant homeodomains (DPF), located in the BAF45D subunit. DPF domains recognize lysine acetyl and acylations, including crotonylation, localized at promoters and enhancers. Despite a significant degree of conservation between DPF domains, attempts to crystallize BAF45D with a crotonylated histone 3 peptide (H3K14Cr) were unsuccessful. In addition, recent cryoEM and modeled structures failed to define the Req domain of BAF45D, which is responsible for reading lysine modifications. Thus, the precise mechanism of crotonyl group recognition and binding by BAF45D within the BAF complex remains unclear. We turned to protein footprinting mass spectrometry to map the binding interface between H3K14Cr and BAF45D. This technique is able to demarcate protein-binding interfaces by modifying surface-accessible residues and is not limited by protein size or composition. Experiments performed in the isolated DPF domain of BAF45D (BAF45D_DPF)-delineated H3K14Cr peptide binding across the PHD1 and PHD2 pockets. We observed markedly similar effects on the BAF45D subunit when assessing H3K14Cr binding in the purified full BAF complex. The ATPase motor, BRM, also displayed H3K14Cr-protected peptides in two separate domains that were subsequently evaluated in direct binding assays. These data confirm the BAF45D–crotonylamide interaction within its obligate complex and are the first to demonstrate H3K14Cr direct binding to BRM.","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141530091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}