Biochemistry Biochemistry最新文献_第4页

Zinc and RNA Binding Is Linked to the Conformational Flexibility of ZRANB2: A CCCC-Type Zinc Finger Protein.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-16 DOI: 10.1021/acs.biochem.4c00470

Matthew S Hursey, Abigail D Reitz, Kyle C Kihn, Daniel J Deredge, Sarah L J Michel

{"title":"Zinc and RNA Binding Is Linked to the Conformational Flexibility of ZRANB2: A CCCC-Type Zinc Finger Protein.","authors":"Matthew S Hursey, Abigail D Reitz, Kyle C Kihn, Daniel J Deredge, Sarah L J Michel","doi":"10.1021/acs.biochem.4c00470","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00470","url":null,"abstract":"Ran-binding domain-containing protein 2 (ZRANB2) is a zinc finger (ZF) protein that plays a key role in alternative splicing. ZRANB2 is composed of two ZF domains that contain four invariant cysteine residues per domain. ZRANB2 binds RNA targets that contain AGGUAA sequence motifs. Three constructs of ZRANB2, ZRANB2-ZF1 (first ZF domain), ZRANB2-ZF2 (second ZF domain), and ZRANB2-2D (both ZF domains), were isolated in the apo form and shown to bind Zn(II) via UV-visible-monitored competitive titrations with Co(II) as a spectroscopic probe. Zn binding to each construct led to the adoption of a limited secondary structure of each domain, as measured by circular dichroism (CD). Hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) of the two-domain construct, ZRANB2-2D, revealed that both ZF domains adopt a more rigid structure upon Zn binding. Zn binding to the first ZF domain resulted in a greater decrease in the conformational dynamics than Zn binding to the second ZF domain. RNA binding to TRA2B pre-mRNA, a physiological splicing target, was measured by fluorescence anisotropy (FA), and high-affinity RNA binding was found to require Zn coordination to both domains. HDX-MS of ZRANB2-2D with TRA2B RNA as well as two optimized RNA sequences that contain a single and double AGGUAA hexamer revealed additional protection from H/D exchange for ZRANB2 in the presence of RNA. Here, greater protection was observed for the second ZF of ZRANB2-2D, suggesting a larger effect on conformational dynamics. A model for zinc-mediated RNA binding of ZRANB2 is proposed.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Discovery of the Cytocapsular Membrane as Hallmark of Malignant Tumors. 发现作为恶性肿瘤标志的胞囊膜

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-16 DOI: 10.1021/acs.biochem.4c00576

Tingfang Yi, Gerhard Wagner

{"title":"Discovery of the Cytocapsular Membrane as Hallmark of Malignant Tumors.","authors":"Tingfang Yi, Gerhard Wagner","doi":"10.1021/acs.biochem.4c00576","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00576","url":null,"abstract":"While optimizing cancer cell growth conditions, we discovered that cancer stem cells can generate second membranes outside the plasma membranes forming compartments separated from the extracellular matrix. The encapsulating membranes can extend and generate long cytocapsular tubes, wherein multiple cells can migrate. SILAC proteomics of the second cytocapsular membranes identified 400 membrane proteins, and a small subset of them are highly upregulated in cytocapsular cancers compared to normal tissues. The ATP-dependent calcium pump PMCA2 is one of the highest upregulated factors of the cytocapsular membrane, and antibodies serve as biomarkers for malignant tumors, as checked for 293 subtypes of cancers. Cytocapsular tumors have not been described before, possibly because the CC membranes do not exhibit epitopes targeted by conventional methods, and no efforts have been made to search for new cancer specific organelles. Antibodies against PMCA2 can now be used to map cancer evolution pathways in human bodies by comparisons of more than 12 000 annotated specimens from tissue banks worldwide. The current research reveals that the native malignant cancer cell is enclosed in a cytocapsular membrane. With the PMCA2 cancer biomarker available, the development of human cancers can be studied from cancer tissue banks and clinical cancer biopsies with a previously unknown diversity. The emerging knowledge on cancer-driving biomarkers opens doors for new routes in cancer diagnosis, surgery, therapy, and treatments.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation. 利用加速量子力学分子机械自由能模拟探索 CRISPR-Cas9 HNH-Domain 催化的 DNA 裂解。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-16 DOI: 10.1021/acs.biochem.4c00651

Richard Van, Xiaoliang Pan, Saadi Rostami, Jin Liu, Pratul K Agarwal, Bernard Brooks, Rakhi Rajan, Yihan Shao

{"title":"Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation.","authors":"Richard Van, Xiaoliang Pan, Saadi Rostami, Jin Liu, Pratul K Agarwal, Bernard Brooks, Rakhi Rajan, Yihan Shao","doi":"10.1021/acs.biochem.4c00651","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00651","url":null,"abstract":"The target DNA (tDNA) cleavage catalyzed by the CRISPR Cas9 enzyme is a critical step in the Cas9-based genome editing technologies. Previously, the tDNA cleavage from an active SpyCas9 enzyme conformation was modeled by Palermo and co-workers (Nierzwicki et al., Nat. Catal. 2022 5, 912) using ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulations, where the free energy barrier was found to be more favorable than that from a pseudoactive enzyme conformation. In this work, we performed ai-QM/MM simulations based on another catalytically active conformation (PDB 7Z4J) of the Cas9 HNH domain from cryo-electron microscopy experiments. For the wildtype enzyme, we acquired a free energy profile for the tDNA cleavage that is largely consistent with the previous report. Furthermore, we explored the role of the active-site K866 residue on the catalytic efficiency by modeling the K866A mutant and found that the K866A mutation increased the reaction free energy barrier, which is consistent with the experimentally observed reduction in the enzyme activity.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cryo-EM Structure of Recombinantly Expressed hUGDH Unveils a Hidden, Alternative Allosteric Inhibitor.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-16 DOI: 10.1021/acs.biochem.4c00555

John H O'Brien, Renuka Kadirvelraj, Po-Sen Tseng, Nolan Ross-Kemppinen, David Crich, Richard M Walsh, Zachary A Wood

{"title":"Cryo-EM Structure of Recombinantly Expressed hUGDH Unveils a Hidden, Alternative Allosteric Inhibitor.","authors":"John H O'Brien, Renuka Kadirvelraj, Po-Sen Tseng, Nolan Ross-Kemppinen, David Crich, Richard M Walsh, Zachary A Wood","doi":"10.1021/acs.biochem.4c00555","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00555","url":null,"abstract":"Human UDP-glucose dehydrogenase (hUGDH) catalyzes the oxidation of UDP-glucose into UDP-glucuronic acid, an essential substrate in the Phase II metabolism of drugs. hUGDH is a hexamer that exists in an equilibrium between an active (E) state and an inactive (EΩ) state, with the latter being stabilized by the binding of the allosteric inhibitor UDP-xylose (UDP-Xyl). The allosteric transition between EΩ and E is slow and can be observed as a lag in progress curves. Previous analysis of the lag suggested that unliganded hUGDH exists mainly as EΩ, but two unique crystal forms suggest that the enzyme favors the E state. Resolving this discrepancy is necessary to fully understand the allosteric mechanism of hUGDH. Here, we used cryo-EM to show that recombinant hUGDH expressed in Escherichia coli copurifies with UDP-4-keto-xylose (UX4O), which mimics the UDP-Xyl inhibitor and favors the EΩ state. Cryo-EM studies show that removing UX4O from hUGDH shifts the ensemble to favor the E state. This shift is consistent with progress curve analysis, which shows the absence of a lag for unliganded hUGDH. Inhibition studies show that hUGDH has similar affinities for UDP-Xyl and UX4O. The discovery that UX4O inhibits allosteric hUGDH suggests that UX4O may be the physiologically relevant inhibitor of allosteric UGDHs in bacteria that do not make UDP-Xyl.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Thermal-Stable LH1-RC Complex of a Hot Spring Purple Bacterium Powers Photosynthesis with Extremely Low-Energy Near-Infrared Light.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-16 DOI: 10.1021/acs.biochem.4c00506

Yukihiro Kimura, Ryo Kanno, Kaisei Mori, Yoshiki Matsuda, Ryuta Seto, Shinji Takenaka, Hiroyuki Mino, Tatsunari Ohkubo, Mai Honda, Yuji C Sasaki, Jun-Ichi Kishikawa, Kaoru Mitsuoka, Kazuhiro Mio, Malgorzata Hall, Endang R Purba, Toshiaki Mochizuki, Akira Mizoguchi, Bruno M Humbel, Michael T Madigan, Zheng-Yu Wang-Otomo, Kazutoshi Tani

{"title":"The Thermal-Stable LH1-RC Complex of a Hot Spring Purple Bacterium Powers Photosynthesis with Extremely Low-Energy Near-Infrared Light.","authors":"Yukihiro Kimura, Ryo Kanno, Kaisei Mori, Yoshiki Matsuda, Ryuta Seto, Shinji Takenaka, Hiroyuki Mino, Tatsunari Ohkubo, Mai Honda, Yuji C Sasaki, Jun-Ichi Kishikawa, Kaoru Mitsuoka, Kazuhiro Mio, Malgorzata Hall, Endang R Purba, Toshiaki Mochizuki, Akira Mizoguchi, Bruno M Humbel, Michael T Madigan, Zheng-Yu Wang-Otomo, Kazutoshi Tani","doi":"10.1021/acs.biochem.4c00506","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00506","url":null,"abstract":"Blastochloris (Blc.) tepida is a hot spring purple nonsulfur phototrophic bacterium that contains bacteriochlorophyll (BChl) b. Here, we present a 2.21 Å cryo-EM structure of the thermostable light-harvesting 1-reaction center (LH1-RC) complex from Blc. tepida. The LH1 ring comprises 16 circularly arranged αβγ-subunits plus one αβ-subunit that surround the RC complex composed of C-, H-, L-, and M-subunits. In a comparative study, the Blc. tepida LH1-RC showed numerous electrostatic and hydrophobic interactions both within the LH1 complex itself and between the LH1 and the RC complexes that are absent from the LH1-RC complex of its mesophilic counterpart, Blc. viridis. These additional interactions result in a tightly packed LH1-RC architecture with a reduced accessible surface area per volume that enhances the thermal stability of the Blc. tepida complex and allows the light reactions of photosynthesis to proceed at hot spring temperatures. Moreover, based on high-resolution structural information combined with spectroscopic evidence, the unique photosynthetic property of the Blc. tepida LH1-RC─absorption of energy-poor near-infrared light beyond 1000 nm─can be attributed to strong hydrogen-bonding interactions between the C3-acetyl C═O of the LH1 BChl b and two LH1 α-Trp residues, structural rigidity of the LH1, and the enhanced exciton coupling of the LH1 BChls of this thermophile.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of Amino Acid Residues Critical for the Interaction of Fibrin with N-Cadherin.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-13 DOI: 10.1021/acs.biochem.4c00510

Sergiy Yakovlev, David A Nyenhuis, Nico Tjandra, Dudley K Strickland, Leonid Medved

{"title":"Identification of Amino Acid Residues Critical for the Interaction of Fibrin with N-Cadherin.","authors":"Sergiy Yakovlev, David A Nyenhuis, Nico Tjandra, Dudley K Strickland, Leonid Medved","doi":"10.1021/acs.biochem.4c00510","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00510","url":null,"abstract":"We recently identified N-cadherin as a novel receptor for fibrin and localized complementary binding sites within the fibrin βN-domains and the third and fifth extracellular domains (EC3 and EC5) of N-cadherin. We also hypothesized that the His16 and Arg17 residues of the βN-domains and the (Asp/Glu)-X-(Asp/Glu) motifs present in the EC3 and EC5 domains may play roles in the interaction between fibrin and N-cadherin. The primary objectives of this study were to test these hypotheses and to further clarify the structural basis for this interaction. To test our hypotheses, we first mutated His16 and Arg17 in the recombinant (β15-66)2 fragment, which mimics the dimeric arrangement of the βN-domains in fibrin, using site-directed mutagenesis. The results revealed that the mutations of both His16 and Arg17 are critical for the interaction. Next, we mutated Asp/Glu residues in the three (Asp/Glu)-X-(Asp/Glu) motifs, M1 (Asp-Phe-Glu), M2 (Glu-Ala-Glu), and M3 (Asp-Tyr-Asp), of the fibrin-binding N-cad(3-5) fragment of N-cadherin. The results showed that Asp292 and Glu294 of M1, and Asp468 and Asp470 of M3, are critical for the interaction. Our molecular modeling of the 3D structure of the EC3-EC4-EC5 domains revealed that these residues are located at the interfaces of EC3-EC4 and EC4-EC5 and that some may also be involved in calcium binding. In conclusion, our study identified amino acid residues in the fibrin βN-domains and the EC3 and EC5 domains of N-cadherin that are critical for the interaction of fibrin with N-cadherin and localized the fibrin-binding residues in the 3D structure of N-cadherin.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of an In Silico Platform (TRIPinRNA) for the Identification of Novel RNA Intramolecular Triple Helices and Their Validation Using Biophysical Techniques.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-12 DOI: 10.1021/acs.biochem.4c00334

Isha Rakheja, Vishal Bharti, S Sahana, Prosad Kumar Das, Gyan Ranjan, Ajit Kumar, Niyati Jain, Souvik Maiti

{"title":"Development of an In Silico Platform (TRIPinRNA) for the Identification of Novel RNA Intramolecular Triple Helices and Their Validation Using Biophysical Techniques.","authors":"Isha Rakheja, Vishal Bharti, S Sahana, Prosad Kumar Das, Gyan Ranjan, Ajit Kumar, Niyati Jain, Souvik Maiti","doi":"10.1021/acs.biochem.4c00334","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00334","url":null,"abstract":"There are surprisingly few RNA intramolecular triple helices known in the human transcriptome. The structure has been most well-studied as a stability-element at the 3' end of lncRNAs such as MALAT1 and NEAT1, but the intrigue remains whether it is indeed as rare as it is understood to be or just waiting for a closer look from a new vantage point. TRIPinRNA, our Python-based in silico platform, allows for a comprehensive sequence-pattern search for potential triplex formation in the human transcriptome─noncoding as well as coding. Using this tool, we report the putative occurrence of homopyrimidine type (canonical) triple helices as well as heteropurine-pyrimidine strand type (noncanonical) triple helices in the human transcriptome and validate the formation of both types of triplexes using biophysical approaches. We find that the occurrence of triplex structures has a strong correlation with local GC content, which might be influencing their formation. By employing a search that encompasses both canonical and noncanonical triplex structures across the human transcriptome, this study enriches the understanding of RNA biology. Lastly, TRIPinRNA can be utilized in finding triplex structures for any organism with an annotated transcriptome.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Activation of Dithiolopyrrolone Antibiotics by Cellular Reductants.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-12 DOI: 10.1021/acs.biochem.4c00533

Olivia M Steiner, Rachel A Johnson, Xiaoyan Chen, William C Simke, Bo Li

引用次数: 0

Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-11 DOI: 10.1021/acs.biochem.4c00519

Lilith A Schwartz, Jordan O Norman, Sharika Hasan, Olive E Adamek, Elisa Dzuong, Jasmine C Lowenstein, Olivia G Yost, Banumathi Sankaran, Krystle J McLaughlin

{"title":"Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure.","authors":"Lilith A Schwartz, Jordan O Norman, Sharika Hasan, Olive E Adamek, Elisa Dzuong, Jasmine C Lowenstein, Olivia G Yost, Banumathi Sankaran, Krystle J McLaughlin","doi":"10.1021/acs.biochem.4c00519","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00519","url":null,"abstract":"Bacteroides are often the most abundant, commensal species in the gut microbiome of industrialized human populations. One of the most commonly detected species is Bacteroides ovatus. It has been linked to benefits like the suppression of intestinal inflammation but is also correlated with some autoimmune disorders, for example irritable bowel disorder (IBD). Bacterial cell surface carbohydrates, like capsular polysaccharides (CPS), may play a role in modulating these varied host interactions. Recent studies have begun to explore the diversity of CPS loci in Bacteroides; however, there is still much unknown. Here, we present structural and functional characterization of a putative polysaccharide deacetylase from Bacteroides ovatus (BoPDA) encoded in a CPS biosynthetic locus. We solved four high resolution crystal structures (1.36-1.56 Å) of the enzyme bound to divalent cations Co2+, Ni2+, Cu2+, or Zn2+ and performed carbohydrate binding and deacetylase activity assays. Structural analysis of BoPDA revealed an atypical domain architecture that is unique to this enzyme, with a carbohydrate esterase 4 (CE4) superfamily catalytic domain inserted into a carbohydrate binding module (CBM). Additionally, BoPDA lacks the canonical CE4 His-His-Asp metal binding motif and our structures show it utilizes a noncanonical His-Asp dyad to bind metal ions. BoPDA is the first protein involved in CPS biosynthesis from B. ovatus to be characterized, furthering our understanding of significant biosynthetic processes in this medically relevant gut microbe.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluation and Comparison of Candida albicans vs Mammalian 6-O-Phospho-Kinases: Substrate Specificity and Applications.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-11 DOI: 10.1021/acs.biochem.4c00525

Min Liu, Caroline Williams, Stephen N Hyland, Marina P Vasconcelos, Bella R Carnahan, Rachel Putnik, Sushanta Ratna, Catherine L Grimes

{"title":"Evaluation and Comparison of Candida albicans vs Mammalian 6-O-Phospho-Kinases: Substrate Specificity and Applications.","authors":"Min Liu, Caroline Williams, Stephen N Hyland, Marina P Vasconcelos, Bella R Carnahan, Rachel Putnik, Sushanta Ratna, Catherine L Grimes","doi":"10.1021/acs.biochem.4c00525","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00525","url":null,"abstract":"Sensing of peptidoglycan fragments is essential for inducing downstream signaling in both mammalian and fungal systems. The hexokinases NagK and Hxk1 are crucial enzymes for the phosphorylation of peptidoglycan molecules in order to activate specific cellular responses; however, biochemical characterization of their enzymatic specificity and efficiency has yet to be investigated in depth. Here a mass spectrometry enzymatic screen was implemented to assess substrate specificity, and an ATP coupled assay provided the quantitative kinetic profiles of these two homologous, eukaryotic enzymes. The data show, that while homologous, NagK and Hxk1 have vastly different substrate profiles. NagK accepts a variety of different peptidoglycan-based substrates albeit with reduced efficiency but are still valuable as a tool in large scale chemoenzymatic settings. Conversely, Hxk1 has a smaller substrate scope but can turnover these alternative substrates at similar levels to its natural substrate. These results allow for deeper understanding into the biosynthetic machinery responsible for essential cellular processes including UDP-GlcNAc regulation and immune recognition events in the cell.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0