John J Tanner, Juan Ji, Alexandra N Bogner, Gary K Scott, Sagar M Patel, Javier Seravalli, Kent S Gates, Christopher C Benz, Donald F Becker
{"title":"Noncovalent Inhibition and Covalent Inactivation of Proline Dehydrogenase by Analogs of <i>N</i>-Propargylglycine.","authors":"John J Tanner, Juan Ji, Alexandra N Bogner, Gary K Scott, Sagar M Patel, Javier Seravalli, Kent S Gates, Christopher C Benz, Donald F Becker","doi":"10.1021/acs.biochem.4c00429","DOIUrl":"10.1021/acs.biochem.4c00429","url":null,"abstract":"<p><p>The flavoenzyme proline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the oxidation of l-proline to Δ<sup>1</sup>-pyrroline-5-carboxylate. The enzyme is a target for chemical probe discovery because of its role in the metabolism of certain cancer cells. <i>N</i>-propargylglycine is the first and best characterized mechanism-based covalent inactivator of PRODH. This compound consists of a recognition module (glycine) that directs the inactivator to the active site and an alkyne warhead that reacts with the FAD after oxidative activation, leading to covalent modification of the FAD N5 atom. Here we report structural and kinetic data on analogs of <i>N</i>-propargylglycine with the goals of understanding the initial docking step of the inactivation mechanism and to test the allyl group as a warhead. The crystal structures of PRODH complexed with unreactive analogs in which N is replaced by S show how the recognition module mimics the substrate proline by forming ion pairs with conserved arginine and lysine residues. Further, the C atom adjacent to the alkyne warhead is optimally positioned for hydride transfer to the FAD, providing the structural basis for the first bond-breaking step of the inactivation mechanism. The structures also suggest new strategies for designing improved <i>N</i>-propargylglycine analogs. <i>N</i>-allylglycine, which consists of a glycine recognition module and allyl warhead, is shown to be a covalent inactivator; however, it is less efficient than <i>N</i>-propargylglycine in both enzyme inactivation and cellular assays. Crystal structures of the <i>N</i>-allylglycine-inactivated enzyme are consistent with covalent modification of the N5 by propanal.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491085","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}
{"title":"Biochemical Analysis of the Regulatory Role of Gα<sub>o</sub> in the Conformational Transitions of <i>Drosophila</i> Pins.","authors":"Yuxuan Song, Jie Ji, Chunhua Liu, Wenning Wang","doi":"10.1021/acs.biochem.4c00404","DOIUrl":"10.1021/acs.biochem.4c00404","url":null,"abstract":"<p><p><i>Drosophila</i> Pins (and its mammalian homologue LGN) play a crucial role in the process of asymmetric cell division (ACD). Extensive research has established that Pins/LGN functions as a conformational switch primarily through intramolecular interactions involving the N-terminal TPR repeats and the C-terminal GoLoco (GL) motifs. The GL motifs served as binding sites for the α subunit of the trimeric G protein (Gα), which facilitates the release of the autoinhibited conformation of Pins/LGN. While LGN has been observed to specifically bind to Gα<sub>i</sub>·GDP, Pins has been found to associate with both <i>Drosophila</i> Gα<sub>i</sub> (<i>d</i>Gα<sub>i</sub>) and Gα<sub>o</sub> (<i>d</i>Gα<sub>o</sub>) isoforms. Moreover, <i>d</i>Gα<sub>o</sub> was reported to be able to bind Pins in both the GDP- and GTP-bound forms. However, the precise mechanism underlying the influence of <i>d</i>Gα<sub>o</sub> on the conformational states of Pins remains unclear, despite extensive investigations into the Gα<sub>i</sub>·GDP-mediated regulatory conformational changes in LGN/Pins. In this study, we conducted a comprehensive characterization of the interactions between Pins-GL motifs and <i>d</i>Gα<sub>o</sub> in both GDP- and GTP-loaded forms. Our findings reveal that Pins-GL specifically binds to GDP-loaded <i>d</i>Gα<sub>o</sub>. Through biochemical characterization, we determined that the intramolecular interactions of Pins primarily involve the entire TPR domain and the GL23 motifs. Additionally, we observed that Pins can simultaneously bind three molecules of <i>d</i>Gα<sub>o</sub>·GDP, leading to a partial opening of the autoinhibited conformation. Furthermore, our study presents evidence contrasting with previous observations indicating the absence of binding between <i>d</i>Gα<sub>i</sub> and Pins-GLs, thus implying the pivotal role of <i>d</i>Gα<sub>o</sub> as the principal participant in the ACD pathway associated with Pins.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491081","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}
{"title":"Atomistic Insights into Sequence-Mediated Spontaneous Association of Short RNA Chains.","authors":"Manas Mondal, Yi Qin Gao","doi":"10.1021/acs.biochem.4c00293","DOIUrl":"10.1021/acs.biochem.4c00293","url":null,"abstract":"<p><p>RNA-RNA association and phase separation appear to be essential for the assembly of stress granules and underlie RNA foci formation in repeat expansion disorders. RNA molecules are found to play a significant role in gene-regulatory functions via condensate formation among themselves or with RNA-binding proteins. The interplay between driven versus spontaneous processes is likely to be an important factor for controlling the formation of RNA-mediated biomolecular condensate. However, the sequence-specific interactions and molecular mechanisms that drive the spontaneous RNA-RNA association and help to form RNA-mediated phase-separated condensate remain unclear. With microseconds-long atomistic molecular simulations here, we report how essential aspects of RNA chains, namely, base composition, metal ion binding, and hydration properties, contribute to the association of the series of simplest biologically relevant homopolymeric and heteropolymeric short RNA chains. We show that spontaneous processes make the key contributions governed by the sequence-intrinsic properties of RNA chains, where the definite roles of base-specific hydrogen bonding and stacking interactions are prominent in the association of the RNA chains. Purine versus pyrimidine contents of RNA chains can directly influence the association properties of RNA chains by modulating hydrogen bonding and base stacking interactions. This study determines the impact of ionic environment in sequence-specific spontaneous association of short RNA chains, hydration features, and base-specific interactions of Na<sup>+</sup>, K<sup>+</sup>, and Mg<sup>2+</sup> ions with RNA chains.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386372","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}
Nishant Kumar Choudhary, Shalini Gupta, Gourav Das, Avijit Sahoo, S Harikrishna, Surajit Sinha, Kiran R Gore
{"title":"Selective Recognition of the Dimeric NG16 Parallel G-Quadruplex Structure Using Synthetic Turn-On Red Fluorescent Protein Chromophore.","authors":"Nishant Kumar Choudhary, Shalini Gupta, Gourav Das, Avijit Sahoo, S Harikrishna, Surajit Sinha, Kiran R Gore","doi":"10.1021/acs.biochem.4c00407","DOIUrl":"10.1021/acs.biochem.4c00407","url":null,"abstract":"<p><p>Red fluorescent protein (RFP)-based fluorescent probes that can selectively interact with specific nucleic acids are of great importance for therapeutic and bioimaging applications. Herein, we have reported the synthesis of RFP chromophores for selective recognition of G-quadruplex nucleic acids in vitro and ex vivo. We identified <b>DFHBI-DM</b> as a fluorescent turn-on probe that binds to the dimeric NG16 parallel quadruplex with superior selectivity and sensitivity over various parallel, antiparallel, and hybrid topologies. The binding of <b>DFHBI-DM</b> to NG16 exhibited excellent photophysical properties, including high binding affinity, large Stokes shift, high photostability, and quantum yield. The MD simulation study supports the 1:1 binding stoichiometry. It confirms the planar conformation of <b>DFHBI-DM</b>, which makes strong binding interactions with a flat quartet of NG16 compared to other antiparallel and hybrid topologies. The cell imaging and MTT assays revealed that <b>DFHBI-DM</b> is a biocompatible and efficient fluorescent probe for intracellular imaging of NG16. Overall, these results demonstrated that <b>DFHBI-DM</b> could be an effective fluorescent G4-stabilizing agent for the dimeric NG16 parallel quadruplex, and it could be a promising candidate for further exploration of bioimaging and therapeutic applications.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453399","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}
{"title":"Insights into the Structure and Dynamics of Proteins from <sup>19</sup>F Solution NMR Spectroscopy.","authors":"Ishita Sengupta","doi":"10.1021/acs.biochem.4c00534","DOIUrl":"10.1021/acs.biochem.4c00534","url":null,"abstract":"<p><p><sup>19</sup>F NMR spectroscopy has recently witnessed a resurgence as an attractive analytical tool for the study of the structure and dynamics of biomolecules in vitro and in cells, despite reports of its applications in biomolecular NMR since the 1970s. The high gyromagnetic ratio, large chemical shift dispersion, and complete absence of the spin 1/2 <sup>19</sup>F nucleus from biomolecules results in background-free, high-resolution <sup>19</sup>F NMR spectra. The introduction of <sup>19</sup>F probes in a few selected locations in biomolecules reduces spectral crowding despite its increased line width in comparison to typical <sup>1</sup>H NMR line widths and allows rapid site-specific measurements from simple 1D spectra alone. The design and synthesis of novel <sup>19</sup>F probes with reduced line widths and increased chemical shift sensitivity to the surrounding environment, together with advances in labeling techniques, NMR methodology, and hardware, have overcome several drawbacks of <sup>19</sup>F NMR spectroscopy. The increased interest and widespread use of <sup>19</sup>F NMR spectroscopy of biomolecules is gradually establishing it as a sensitive and high-resolution probe of biomolecular structure and dynamics, supplementing traditional <sup>13</sup>C/<sup>15</sup>N-based methods. This Review focuses on the advances in <sup>19</sup>F solution NMR spectroscopy of proteins in the past 5 years, with an emphasis on novel <sup>19</sup>F tags and labeling techniques, NMR experiments to probe protein structure and conformational dynamics in vitro, and in-cell NMR applications.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574831","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}
Zhi Yue, Jiangbo Wu, Da Teng, Zhi Wang, Gregory A Voth
{"title":"Activation of the Influenza B M2 Proton Channel (BM2).","authors":"Zhi Yue, Jiangbo Wu, Da Teng, Zhi Wang, Gregory A Voth","doi":"10.1021/acs.biochem.4c00607","DOIUrl":"10.1021/acs.biochem.4c00607","url":null,"abstract":"<p><p>Influenza B viruses have cocirculated during most seasonal flu epidemics and can cause significant human morbidity and mortality due to their rapid mutation, emerging drug resistance, and severe impact on vulnerable populations. The influenza B M2 proton channel (BM2) plays an essential role in viral replication, but the mechanisms behind its symmetric proton conductance and the involvement of a second histidine (His27) cluster remain unclear. Here we performed membrane-enabled continuous constant-pH molecular dynamics simulations on wildtype BM2 and a key H27A mutant channel to explore its pH-dependent conformational switch. Simulations captured the activation as the first histidine (His19) protonates and revealed the transition at lower pH values compared to AM2 is a result of electrostatic repulsions between His19 and preprotonated His27. Crucially, we provided an atomic-level understanding of the symmetric proton conduction by identifying preactivating channel hydration in the C-terminal portion. This research advances our understanding of the function of BM2 function and lays the groundwork for further chemically reactive modeling of the explicit proton transport process as well as possible antiflu drug design efforts.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566659","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}
{"title":"Sugar Highs: Recent Notable Breakthroughs in Glycobiology.","authors":"Jimin Hu, Duc T Huynh, Michael Boyce","doi":"10.1021/acs.biochem.4c00418","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00418","url":null,"abstract":"<p><p>Glycosylation is biochemically complex and functionally critical to a wide range of processes and disease states, making it a vibrant area of contemporary research. Here, we highlight a selection of notable recent advances in the glycobiology of SARS-CoV-2 infection and immunity, cancer biology and immunotherapy, and newly discovered glycosylated RNAs. Together, these studies illustrate the significance of glycosylation in normal biology and the great promise of manipulating glycosylation for therapeutic benefit in disease.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542850","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}
{"title":"Crystal Structure and Mutagenesis of an XYP Subfamily Cyclodipeptide Synthase Reveal Key Determinants of Enzyme Activity and Substrate Specificity.","authors":"Jun-Bin He, Yichen Ren, Peifeng Li, Yi-Pei Liu, Hai-Xue Pan, Lin-Juan Huang, Jiayuan Wang, Pengfei Fang, Gong-Li Tang","doi":"10.1021/acs.biochem.4c00505","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00505","url":null,"abstract":"<p><p>Cyclodipeptide synthases (CDPSs) catalyze the synthesis of diverse cyclodipeptides (CDPs) by utilizing two aminoacyl-tRNA (aa-tRNA) substrates in a sequential ping-pong reaction mechanism. Numerous CDPSs have been characterized to provide precursors for diketopiperazines (DKPs) with diverse structural characteristics and biological activities. BcmA, belonging to the XYP subfamily, is a cyclo(l-Ile-l-Leu)-synthesizing CDPS involved in the biosynthesis of the antibiotic bicyclomycin. The structural basis and determinants influencing BcmA enzyme activity and substrate selectivity are not well understood. Here, we report the crystal structure of <i>Ss</i>BcmA from <i>Streptomyces sapporonensis</i>. Through structural comparison and systematic site-directed mutagenesis, we highlight the significance of key residues located in the aminoacyl-binding pocket for enzyme activity and substrate specificity. In particular, the nonconserved residues D161 and K165 in pocket P2 are essential for the activity of <i>Ss</i>BcmA without significant alteration of the substrate specificity, while the conserved residues F158 as well as F210 and S211 in P2 are responsible for determining substrate selectivity. These findings facilitate the understanding of how CDPSs selectively accept hydrophobic substrates and provide additional clues for the engineering of these enzymes for synthetic biology applications.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542849","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}
Han N Phan, Paul D Swartz, Medha Gangopadhyay, Yisong Guo, Alex I Smirnov, Thomas M Makris
{"title":"Assembly of a Heterobimetallic Fe/Mn Cofactor in the <i>para</i>-Aminobenzoate Synthase Chlamydia Protein Associating with Death Domains (CADD) Initiates Long-Range Radical Hole-Hopping.","authors":"Han N Phan, Paul D Swartz, Medha Gangopadhyay, Yisong Guo, Alex I Smirnov, Thomas M Makris","doi":"10.1021/acs.biochem.4c00326","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00326","url":null,"abstract":"<p><p>Chlamydia protein associating with death domains (<i>Ct</i>CADD) is involved in the biosynthesis of <i>p</i>-aminobenzoic acid (pABA) for integration into folate, a critical cofactor that is required for pathogenic survival. CADD activates dioxygen and utilizes its own tyrosine and lysine as synthons to furnish the carboxylate, carbon backbone, and amine group of pABA in a complex multistep mechanism. Unlike other members of the heme oxygenase-like dimetal oxidase (HDO) superfamily that typically house an Fe<sub>2</sub> cofactor, previous activity studies have shown that <i>Ct</i>CADD likely uses a heterobimetallic Fe/Mn center. The structure of the Fe<sup>2+</sup>/Mn<sup>2+</sup> cofactor and how the conserved HDO scaffold mediates metal selectivity have remained enigmatic. Adopting an <i>in crystallo</i> metalation approach, <i>Ct</i>CADD was solved in the apo, Fe<sup>2+</sup><sub>2</sub>, Mn<sup>2+</sup><sub>2</sub>, and catalytically active Fe<sup>2+</sup>/Mn<sup>2+</sup> forms to identify the probable site for Mn binding. The analysis of <i>Ct</i>CADD active-site variants further reinforces the importance of the secondary coordination sphere on cofactor preference for competent pABA formation. Rapid kinetic optical and electron paramagnetic resonance (EPR) studies show that the heterobimetallic cofactor selectively reacts with dioxygen and likely initiates pABA assembly through the formation of a transient tyrosine radical intermediate and a resultant heterobimetallic Mn<sup>3+</sup>/Fe<sup>3+</sup> cluster.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542848","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}
{"title":"How Salt and Temperature Drive Reentrant Condensation of Aβ40.","authors":"Susmita Sarkar, Jagannath Mondal","doi":"10.1021/acs.biochem.4c00412","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00412","url":null,"abstract":"<p><p>Within the framework of liquid-liquid phase separation (LLPS), biomolecular condensation orchestrates vital cellular processes, and its dysregulation is implicated in severe pathological conditions. Recent studies highlight the role of intrinsically disordered proteins (IDPs) in LLPS, yet the influence of microenvironmental factors has remained a puzzling factor. Here, via computational simulation of the impact of solution conditions on LLPS behavior of neurologically pathogenic IDP Aβ40, we chanced upon a salt-driven reentrant condensation phenomenon, wherein Aβ40 aggregation increases with low salt concentrations (25-50 mM), followed by a decline with further salt increments. An exploration of the thermodynamic and kinetic signatures of reentrant condensation unveils a nuanced interplay between protein electrostatics and ionic strength as potential drivers. Notably, the charged residues of the N-terminus exhibit a nonmonotonic response to salt screening, intricately linked to the recurrence of reentrant behavior in hydrophobic core-induced condensation. Intriguingly, our findings also unveil the reappearance of similar reentrant condensation phenomena under varying temperature conditions. Collectively, our study illuminates the profoundly context-dependent nature of Aβ40s liquid-liquid phase separation behavior, extending beyond its intrinsic molecular framework, where microenvironmental cues wield significant influence over its aberrant functionality.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491084","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}