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Toward Predictive Models of Biased Agonists of the Mu Opioid Receptor. 阿片受体偏向性激动剂的预测模型研究。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 Epub Date: 2025-04-10 DOI: 10.1021/acs.biochem.4c00885
Fernando J Tun-Rosado, Elier E Abreu-Martínez, Axel Magdaleno-Rodriguez, Karina Martinez-Mayorga
{"title":"Toward Predictive Models of Biased Agonists of the Mu Opioid Receptor.","authors":"Fernando J Tun-Rosado, Elier E Abreu-Martínez, Axel Magdaleno-Rodriguez, Karina Martinez-Mayorga","doi":"10.1021/acs.biochem.4c00885","DOIUrl":"10.1021/acs.biochem.4c00885","url":null,"abstract":"<p><p>The mu-opioid receptor (MOR), a member of the G-protein-coupled receptor superfamily, is pivotal in pain modulation and analgesia. Biased agonism at MOR offers a promising avenue for developing safer opioid therapeutics by selectively engaging specific signaling pathways. This study presents a comprehensive analysis of biased agonists using a newly curated database, BiasMOR, comprising 166 unique molecules with annotated activity data for GTPγS, cAMP, and β-arrestin assays. Advanced structure-activity relationship (SAR) analyses, including network similarity graphs, maximum common substructures, and activity cliff identification, reveal critical molecular features underlying bias signaling. Modelability assessments indicate high suitability for predictive modeling, with RMODI indices exceeding 0.96 and SARI indices highlighting moderately continuous SAR landscapes for cAMP and β-arrestin assays. Interaction patterns for biased agonists are discussed, including key residues such as D<sup>3.32</sup>, Y<sup>7.43</sup>, and Y<sup>3.33</sup>. Comparative studies of enantiomer-specific interactions further underscore the role of ligand-induced conformational states in modulating signaling pathways. This work underscores the potential of combining computational and experimental approaches to advance the understanding of MOR-biased signaling, paving the way for safer opioid therapies. The database provided here will serve as a starting point for designing biased mu opioid receptor ligands and will be updated as new data become available. Increasing the repertoire of biased ligands and analyzing molecules collectively, as the database described here, contributes to pinpointing structural features responsible for biased agonism that can be associated with biological effects still under debate.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 9","pages":"1943-1949"},"PeriodicalIF":2.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042718","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}
引用次数: 0
How Omecamtiv Modulates Myosin Motion Omecamtiv如何调节肌球蛋白运动
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 DOI: 10.1021/acs.biochem.4c0080710.1021/acs.biochem.4c00807
Ritaban Halder,  and , Arieh Warshel*, 
{"title":"How Omecamtiv Modulates Myosin Motion","authors":"Ritaban Halder,&nbsp; and ,&nbsp;Arieh Warshel*,&nbsp;","doi":"10.1021/acs.biochem.4c0080710.1021/acs.biochem.4c00807","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00807https://doi.org/10.1021/acs.biochem.4c00807","url":null,"abstract":"<p >Myosin VI is a unique reverse-directed motor protein in the myosin family. The D179Y mutation in Myosin VI is associated with deafness in mammals. This mutation destroys the processive motion of myosin and inhibits its functional activity due to an elevated phosphate release rate. The current work explores the way by which this mutation affects the phosphate release rate and changes the action of Myosin VI. Our study involves a wide range of approaches comprising free energy-based simulations, contact map analysis, binding energy investigation, structural inspection, renormalization simulation, multiple sequence alignment, and bioinformatics analysis. It is found that when the evolutionary conserved aspartic acid (D179) of Myosin VI is mutated to tyrosine (Y179), it leads to premature phosphate release from Myosin VI. Most importantly, the drug omecamtiv rescues the processivity of the mutant by slowing down the actin-independent phosphate release from Myosin VI. Thus, we also explore the molecular mechanism behind the premature phosphate release of the D179Y mutant of Myosin VI and the actin-independent slowing down of the phosphate release in the presence of omecamtiv. This phosphate release modulation is related to Myosin VI’s processivity as found experimentally. Overall, our proposed model indicates that omecamtiv significantly alters the interaction between the P-loop of Myosin VI and the interfacial residues, which is the driving force behind the slowing down of the phosphate release of the D179Y mutant in the presence of omecamtiv. Finally, our study provides additional support to our proposal that the directionality of myosins is determined by the highest barrier along the cycle and not by any dynamical effect.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 10","pages":"2318–2331 2318–2331"},"PeriodicalIF":2.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144088422","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
Biochemical, Structural, and Conformational Characterization of a Fungal Ethylene-Forming Enzyme. 一种真菌乙烯生成酶的生化、结构和构象特征。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 Epub Date: 2025-03-07 DOI: 10.1021/acs.biochem.5c00038
Shramana Chatterjee, Joel A Rankin, Mark A Farrugia, Simahudeen Bathir J S Rifayee, Christo Z Christov, Jian Hu, Robert P Hausinger
{"title":"Biochemical, Structural, and Conformational Characterization of a Fungal Ethylene-Forming Enzyme.","authors":"Shramana Chatterjee, Joel A Rankin, Mark A Farrugia, Simahudeen Bathir J S Rifayee, Christo Z Christov, Jian Hu, Robert P Hausinger","doi":"10.1021/acs.biochem.5c00038","DOIUrl":"10.1021/acs.biochem.5c00038","url":null,"abstract":"<p><p>The ethylene-forming enzyme (EFE) from the fungus <i>Penicillium digitatum</i> strain Pd1 was heterologously produced in <i>Escherichia coli</i> and its properties were compared to the extensively characterized bacterial enzyme from <i>Pseudomonas savastanoi</i> strain PK2. Both enzymes catalyze four reactions: the conversion of 2-oxoglutarate (2OG) to ethylene and CO<sub>2</sub>, oxidative decarboxylation of 2OG coupled to l-arginine (l-Arg) hydroxylation, uncoupled oxidative decarboxylation of 2OG, and the production of 3-hydroxypropionate (3-HP) from 2OG. The strain Pd1 enzyme exhibited a greater ratio of ethylene production over l-Arg hydroxylation than the PK2 strain EFE. The uncoupled decarboxylation of 2OG and 3-HP production are minor reactions in both cases, but they occur to a greater extent using the fungal enzyme. Additional distinctions of the fungal versus bacterial enzyme are noted in the absorbance maxima and l-Arg dependence of their anaerobic electronic spectra. The structures of the Pd1 EFE apoprotein and the EFE·Mn(II)·2OG complex resembled the corresponding structures of the PK2 enzyme, but notable structural differences were observed in the computationally predicted Pd1 EFE·Fe(II)·2OG·l-Arg complex versus the PK2 EFE·Mn(II)·2OG·l-Arg crystal structure. These studies extend our biochemical understanding and represent the first structural and conformational characterization of a eukaryotic EFE.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"2054-2067"},"PeriodicalIF":2.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571550","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}
引用次数: 0
MIPAR and ImageJ FIJI as Tools for Electron Microscopy Quantification of Amyloid Fibrils. MIPAR和ImageJ FIJI作为电子显微镜定量淀粉样蛋白原纤维的工具。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 Epub Date: 2025-04-08 DOI: 10.1021/acs.biochem.5c00031
Charles A Garcia, Veena Prasad, Truman C Gamblin
{"title":"MIPAR and ImageJ FIJI as Tools for Electron Microscopy Quantification of Amyloid Fibrils.","authors":"Charles A Garcia, Veena Prasad, Truman C Gamblin","doi":"10.1021/acs.biochem.5c00031","DOIUrl":"10.1021/acs.biochem.5c00031","url":null,"abstract":"<p><p>Measuring of tau filaments is an important method that can provide useful information in the study of tau <i>in vitro</i>. However, methods such as right-angle laser light scattering and Thioflavin T fluorescence assay only provide bulk information on the amount of tau aggregation that is occurring. Electron microscopy (EM) can be used to provide a semiquantitative method on the lengths of individual filaments and provide a length distribution of tau aggregates. The issue with quantifying tau aggregation through EM is that it can be time costly if done manually. Here we explore two different programs, MIPAR and ImageJ FIJI, as methods to automate the quantification of EM grids. Using both programs to measure filaments produced from inducing 2N4R tau with the fatty acid arachidonic acid (ARA), we are able to reliably measure filaments producing similar results from MIPAR and ImageJ, with these methods applicable to other filamentous biological structures.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1907-1915"},"PeriodicalIF":2.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143801945","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
A Balancing Act: Thymine DNA Glycosylase Combines Sequence and Rotational Preferences To Define Lesion Excision in the Nucleosome Core Particle. 平衡行为:胸腺嘧啶DNA糖基化酶结合序列和旋转偏好来定义核小体核心颗粒中的病变切除。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 Epub Date: 2025-04-14 DOI: 10.1021/acs.biochem.5c00090
Julia C Ferrara, Sarah Delaney
{"title":"A Balancing Act: Thymine DNA Glycosylase Combines Sequence and Rotational Preferences To Define Lesion Excision in the Nucleosome Core Particle.","authors":"Julia C Ferrara, Sarah Delaney","doi":"10.1021/acs.biochem.5c00090","DOIUrl":"10.1021/acs.biochem.5c00090","url":null,"abstract":"<p><p>Thymine DNA glycosylase (TDG) is a DNA glycosylase involved in base excision repair (BER) with a specialized role in the regulation of transcription through the maintenance of 5'-CpG-3' sites via active demethylation. In this work, we investigate the ability of TDG to excise modified nucleobases from the simplest unit of compacted DNA, the nucleosome core particle (NCP). We measure TDG activity on a population of NCPs with uracil (U) at various geometric positions and report that <i>k</i><sub>obs</sub> for U excision from the NCP depends on positioning and dinucleotide sequence context. Specifically, TDG prefers solution accessible 5'-UpG-3' and 5'-UpA-3' sites. By coupling our findings with previous studies, we suggest that TDG's stringent substrate preferences facilitate its epigenetic role through the extensive contacts made with its DNA substrate.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 9","pages":"2068-2076"},"PeriodicalIF":2.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951187","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
L-Type Voltage-Gated Ca2+ Channel C-Terminal Proximal and Distal Domains (PCRD and DCRD) Bind to the IQ-Motif and May Modulate Channel Function. l型电压门控Ca2+通道c端近端和远端结构域(PCRD和DCRD)结合IQ-Motif并可能调节通道功能。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 Epub Date: 2025-04-16 DOI: 10.1021/acs.biochem.4c00880
Deepak Kumar Yadav, Effibe O Ahoulou, David E Anderson, Aritra Bej, Johannes W Hell, James B Ames
{"title":"L-Type Voltage-Gated Ca<sup>2+</sup> Channel C-Terminal Proximal and Distal Domains (PCRD and DCRD) Bind to the IQ-Motif and May Modulate Channel Function.","authors":"Deepak Kumar Yadav, Effibe O Ahoulou, David E Anderson, Aritra Bej, Johannes W Hell, James B Ames","doi":"10.1021/acs.biochem.4c00880","DOIUrl":"10.1021/acs.biochem.4c00880","url":null,"abstract":"<p><p>The L-type voltage-gated Ca<sup>2+</sup> channel (Ca<sub>V</sub>1.2) controls gene expression, cardiac contraction, and neuronal activity. The C-terminal cytosolic region of the Ca<sub>V</sub>1.2 alpha subunit (α1C) contains two domains known as proximal and distal C-terminal regulatory domains (PCRD and DCRD), which have been suggested to control Ca<sup>2+</sup>-dependent channel inactivation (CDI). Previous studies identified a salt bridge interaction between PCRD and DCRD that might be central to channel function. In this study, we expressed and purified recombinant constructs of PCRD (residues 1680-1750) and DCRD (residues 2035-2089) in <i><i>E. coli</i></i> for NMR structural analysis. PCRD and DCRD each exhibit backbone NMR chemical shifts consistent with a random coil and lack of tertiary structure. A disordered random coil structure may explain the absence of electron density for these domains in recent cryo-EM structures of Ca<sub>V</sub>1.2. Despite this lack of structure, fluorescence polarization binding assays reveal PCRD and DCRD each bind to the Ca<sub>V</sub>1.2 IQ-motif (residues 1644-1668) with dissociation constants of 1.5 ± 1 and 14 ± 5 μM, respectively. Both PCRD and DCRD also become insoluble in the presence of high micromolar levels of the IQ peptide, consistent with each domain forming an insoluble complex with the IQ peptide. AlphaFold3 predicts that DCRD adopts a 3-helix bundle that binds to the helical IQ-motif, while PCRD was previously suggested to form a 4-helix bundle. We propose that the PCRD and DCRD bind to opposite sides of the helical IQ-motif, which may oppose calmodulin (CaM) binding to Ca<sub>V</sub>1.2 and thus modulate channel CDI.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 9","pages":"1933-1942"},"PeriodicalIF":2.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955514","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
Beyond the β-α-β Fold: Characterization of a SnoaL Domain in the Tautomerase Superfamily. 超越β-α-β折叠:互变异构酶超家族中SnoaL结构域的表征。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 Epub Date: 2025-04-15 DOI: 10.1021/acs.biochem.5c00051
Trevor R Melkonian, Nemanja Vuksanovic, Maria D Person, Tzu-Yu Chen, Wei-Chen Chang, Karen N Allen, Christian P Whitman
{"title":"Beyond the β-α-β Fold: Characterization of a SnoaL Domain in the Tautomerase Superfamily.","authors":"Trevor R Melkonian, Nemanja Vuksanovic, Maria D Person, Tzu-Yu Chen, Wei-Chen Chang, Karen N Allen, Christian P Whitman","doi":"10.1021/acs.biochem.5c00051","DOIUrl":"10.1021/acs.biochem.5c00051","url":null,"abstract":"<p><p>Tautomerase superfamily (TSF) members are constructed from a single β-α-β unit or two consecutively joined β-α-β units, and most have a catalytic Pro1. This pattern prevails throughout the superfamily consisting of more than 11,000 members where homo- or heterohexamers are localized in the 4-oxalocrotonate tautomerase (4OT)-like subgroup and trimers are found in the other four subgroups except for a small subset of 4OT trimers, symmetric and asymmetric, that are found in the 4OT-like subgroup. During a sequence similarity network (SSN) update, a small cluster of sequences (117 sequences) was discovered in the 4OT-like subgroup that begins with Pro1. These sequences consist of a 4OT-like domain fused to a SnoaL domain at the C-terminus (except for one), as annotated in the UniProt database. The <i>Pseudooceanicola atlanticus</i> one (designated \"4OT-SnoaL\") was chosen for kinetic, mechanistic, and crystallographic analysis. 4OT-SnoaL did not display detectable activity with known TSF substrates, suggesting a new activity. A genome neighborhood diagram (GND) places 4OT-SnoaL in an operon for a hydantoin degradation/utilization pathway. Treatment of 4OT-SnoaL with 3-bromopropiolate results in covalent modification of Pro1 by a 3-oxopropanoate adduct. Crystallographic analysis of the apo and modified enzymes shows that the 4OT domain is a hexamer of six identical subunits (a trimer of dimers), where each dimer consists of two β-α-β building blocks. Each C-terminus is attached to a SnoaL-like domain that displays a distorted α + β-barrel. The motif is a new one in the TSF and adds structural diversity to the TSF by using a SnoaL-like domain.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 9","pages":"1950-1962"},"PeriodicalIF":2.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955582","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
Insights into the Sequence and Structural Diversity of the Nucleotidases Belonging to the Haloacid Dehalogenase Superfamily. 卤酸脱卤酶超家族核苷酸酶的序列和结构多样性研究。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 Epub Date: 2025-04-18 DOI: 10.1021/acs.biochem.4c00801
Sai Krishna Avs, Hemalatha Balaram
{"title":"Insights into the Sequence and Structural Diversity of the Nucleotidases Belonging to the Haloacid Dehalogenase Superfamily.","authors":"Sai Krishna Avs, Hemalatha Balaram","doi":"10.1021/acs.biochem.4c00801","DOIUrl":"10.1021/acs.biochem.4c00801","url":null,"abstract":"<p><p>The haloacid dehalogenase (HAD) superfamily (HADSF) of enzymes includes nucleotidases, which catalyze the hydrolysis of sugar phosphate bonds in 5'(3') nucleoside monophosphates with specificity for purines and pyrimidines. These enzymes have varied physiological roles and clinical implications. Despite binding of similar substrates and the chemistry of catalysis being the same, the sequences and structures of HADSF nucleotidases show dramatic variability. Despite the availability of structures of many nucleotidases, a comprehensive analysis of similarities and differences is lacking. In this study, we have adopted a bioinformatic approach focusing on HADSF nucleotidases' sequence and structural diversity. The sequence analysis clustered HADSF nucleotidases into functional classes, indicating that sequence-based features are associated with substrate specificities. A common structural feature across the HADSF nucleotidases is the presence of the Rossmannoid core domain with 4 HAD catalytic motifs and a cap domain with varied tertiary structures. Through analysis of these domain structures, we show that the insertion of additional secondary structural elements in the core does not disrupt the architecture of the active site, whereas no such conservation is seen in the cap domain. Finally, a structural phylogeny of the core domains constructed using DALI shows the prokaryotic and eukaryotic nucleotidases grouping into distinct branches. The diversity of the tertiary folds of the cap domain prevented a similar DALI analysis. Interestingly, the cap and core domains of IMP-specific nucleotidase 1, a member of HADSF nucleotidases, have a close structural relationship with certain sugar phosphatases, suggesting a common lineage. This is the first comprehensive study of the structural relationships of HADSF nucleotidases.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 9","pages":"2010-2024"},"PeriodicalIF":2.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955141","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
De Novo Design of Parallel and Antiparallel A3B3 Heterohexameric α-Helical Barrels. 平行和反平行A3B3异质六聚体α-螺旋管的从头设计。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 Epub Date: 2025-04-14 DOI: 10.1021/acs.biochem.4c00584
Joel J Chubb, Katherine I Albanese, Alison Rodger, Derek N Woolfson
{"title":"De Novo Design of Parallel and Antiparallel A<sub>3</sub>B<sub>3</sub> Heterohexameric α-Helical Barrels.","authors":"Joel J Chubb, Katherine I Albanese, Alison Rodger, Derek N Woolfson","doi":"10.1021/acs.biochem.4c00584","DOIUrl":"10.1021/acs.biochem.4c00584","url":null,"abstract":"<p><p>The de novo design of α-helical coiled-coil peptides is advanced. Using established sequence-to-structure relationships, it is possible to generate various coiled-coil assemblies with predictable numbers and orientations of helices. Here, we target new assemblies, namely, A<sub>3</sub>B<sub>3</sub> heterohexamer α-helical barrels. These designs are based on pairs of sequences with three heptad repeats (<b><i>abcdefg</i></b>), programmed with <b><i>a</i></b> = Leu, <b><i>d</i></b> = Ile, <b><i>e</i></b> = Ala, and <b><i>g</i></b> = Ser, and <b><i>b</i></b> = <b><i>c</i></b> = Glu to make the acidic (A) chains and <b><i>b</i></b> = <b><i>c</i></b> = Lys in the basic (B) chains. These design rules ensure that the desired oligomeric state and stoichiometry are readily achieved. However, controlling the orientation of neighboring helices (parallel or antiparallel) is less straightforward. Surprisingly, we find that assembly and helix orientation are sensitive to the length of the overhang between helices. To study this, cyclically permutated peptide sequences with three heptad repeats (the register) in the peptide sequences were analyzed. Peptides starting at <b><i>g</i></b> (<b><i>g</i></b>-register) form a parallel 6-helix barrel in solution and in an X-ray crystal structure, whereas the <b><i>b</i></b>- and <b><i>c</i></b>-register peptides form an antiparallel complex. In lieu of experimental X-ray structures for <b><i>b</i></b>- and <b><i>c</i></b>-register peptides, AlphaFold-Multimer is used to predict atomistic models. However, considerably more sampling than the default value is required to match the models and the experimental data, as many confidently predicted and plausible models are generated with incorrect helix orientations. This work reveals the previously unknown influence of the heptad register on helical overhang and the orientation of α-helical coiled-coil peptides and provides insights for the modeling of oligopeptide coiled-coil complexes with AlphaFold.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 9","pages":"1973-1982"},"PeriodicalIF":2.9,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951303","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}
引用次数: 0
Protonation State Insights into the Influence of Biocatalytic Function for Acetylcholinesterase Mediated by Neonicotinoids. 质子化状态对新烟碱类介导乙酰胆碱酯酶生物催化功能影响的研究。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2025-05-06 Epub Date: 2025-04-19 DOI: 10.1021/acs.biochem.5c00024
Zhi-Cong He, Tao Zhang, Wei Peng, Fei Ding
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