Biochemistry Biochemistry最新文献_第4页

A Distinct Mechanism of RNA Recognition by the Transcription Factor GATA1.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-25 DOI: 10.1021/acs.biochem.4c00818

Daniella A Ugay, Robert T Batey, Deborah S Wuttke

{"title":"A Distinct Mechanism of RNA Recognition by the Transcription Factor GATA1.","authors":"Daniella A Ugay, Robert T Batey, Deborah S Wuttke","doi":"10.1021/acs.biochem.4c00818","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00818","url":null,"abstract":"Several human transcription factors (TFs) have been reported to directly bind RNA through noncanonical RNA-binding domains; however, most of these TFs remain to be further validated as bona fide RNA-binding proteins (RBPs). Our systematic analysis of RBP discovery data sets reveals a varied set of candidate TF-RBPs that encompass most TF families. These candidate RBPs include members of the GATA family that are essential factors in embryonic development. Investigation of the RNA-binding features of GATA1, a major hematopoietic TF, reveals robust sequence independent binding to RNAs in vitro. Moreover, RNA binding by GATA1 is competitive with DNA binding, which occurs through a shared binding surface spanning the DNA-binding domain and arginine-rich motif (ARM)-like domain. We show that the ARM-like domain contributes substantially to high-affinity DNA binding and electrostatically to plastic RNA recognition, suggesting that the separable RNA-binding domain assigned to the ARM-domain in GATA1 is an oversimplification of a more complex recognition network. These biochemical data demonstrate a unified integration of DNA- and RNA-binding surfaces within GATA1, whereby the ARM-like domain provides an electrostatic surface for RNA binding but does not fully dominate GATA1-RNA interactions, which may also apply to other TF-RBPs. This competitive DNA/RNA binding activity using overlapping nucleic acid binding regions points to the possibility of RNA-mediated regulation of the GATA1 function during hematopoiesis. Our study highlights the multifunctionality of DNA-binding domains in RNA recognition and supports the need for robust characterization of predicted noncanonical RNA-binding domains such as ARM-like domains.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497455","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

Presenilin, γ-Secretase, and the Search for Pathogenic Triggers of Alzheimer's Disease.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-25 DOI: 10.1021/acs.biochem.4c00830

Michael S Wolfe

{"title":"Presenilin, γ-Secretase, and the Search for Pathogenic Triggers of Alzheimer's Disease.","authors":"Michael S Wolfe","doi":"10.1021/acs.biochem.4c00830","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00830","url":null,"abstract":"Cerebral plaques of the amyloid β-peptide (Aβ) are a defining pathology in Alzheimer's disease (AD). The amyloid hypothesis of AD pathogenesis has dominated the field for over 30 years, ostensibly validated by rare AD-causing mutations in the substrate and enzyme that produce Aβ. The γ-secretase complex carries out intramembrane proteolysis of the substrate derived from the amyloid precursor protein (APP). Mutations in APP and presenilin, the catalytic component of γ-secretase, typically increase the ratio of aggregation-prone 42-residue Aβ (Aβ42) over the more soluble 40-residue form (Aβ40). Nevertheless, the inability to clarify how Aβ aggregation leads to neurodegeneration, along with poor progress in developing effective AD therapeutics that target Aβ, raises concern about whether Aβ is the primary disease driver. γ-Secretase carries out processive proteolysis on the APP substrate, producing long Aβ peptides that are generally trimmed in tripeptide intervals to shorter secreted peptides. Recent studies on effects of AD-causing mutations on the complicated proteolytic processing of the APP substrate by γ-secretase has led to the discovery that these mutations reduce─but do not abolish─processive proteolysis. Reduced proteolysis is apparently due to stabilization of enzyme-substrate complexes, and these stalled substrate-bound γ-secretase complexes can trigger synaptic degeneration even in the absence of Aβ production. Thus, the stalled process rather than the proteolytic products may be a principal initiator of AD pathogenesis. This new amyloid-independent hypothesis suggests that pharmacological agents that rescue stalled γ-secretase enzyme-substrate complexes might be effective therapeutics for AD prevention and/or treatment.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490281","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

Fine-Tuning of ATF4 DNA Binding Activity by a Secondary Basic Motif Unique to the ATF-X Subfamily of bZip Transcription Factors.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-24 DOI: 10.1021/acs.biochem.4c00640

Steven Siang, Urval Patel, Manuela Chaves-Mejía, Jeffrey A Purslow, Davit Potoyan, Julien Roche

{"title":"Fine-Tuning of ATF4 DNA Binding Activity by a Secondary Basic Motif Unique to the ATF-X Subfamily of bZip Transcription Factors.","authors":"Steven Siang, Urval Patel, Manuela Chaves-Mejía, Jeffrey A Purslow, Davit Potoyan, Julien Roche","doi":"10.1021/acs.biochem.4c00640","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00640","url":null,"abstract":"The fine-tuning of transcription factor DNA-binding activity is often governed by transient intramolecular interactions between the transactivation domain and the DNA-binding domain. An example of such interaction is found in the transcription factor ATF4, a central regulator of the Integrated Stress Response. In ATF4, dynamic coupling between the transactivation domain and the basic-leucine zipper (bZip) domain modulates the phosphorylation levels of the disordered transactivation domain by casein kinase 2. However, the structural and molecular basis of these interdomain interactions remains poorly understood. This study focuses on a secondary basic motif at the C-terminus of ATF4, which is shared exclusively with its closest paralogue, ATF5. Through a combination of solution NMR spectroscopy, fluorescence polarization assays, and long-timescale molecular simulations, we demonstrate that this secondary basic motif is the primary driver of interdomain coupling between the transactivation and bZip domains of ATF4. Moreover, this motif enhances ATF4's DNA-binding specificity via interaction with the transactivation domain while also potentially facilitating rapid DNA scanning. Our findings reveal the pivotal role of a conserved motif in establishing disorder-mediated interactions that critically modulate ATF4's DNA-binding activity.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490277","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

Inhibitors of SAMHD1 Obtained from Chemical Tethering to the Guanine Antiviral Acyclovir

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-24 DOI: 10.1021/acs.biochem.4c0085410.1021/acs.biochem.4c00854

Matthew Egleston, Shridhar Bhat, A. Hasan Howlader, Mario A. Bianchet, Yi Liu, Laura Maria Lopez Rovira, Brandon Smith, Marc M. Greenberg* and James T. Stivers*,

{"title":"Inhibitors of SAMHD1 Obtained from Chemical Tethering to the Guanine Antiviral Acyclovir","authors":"Matthew Egleston, Shridhar Bhat, A. Hasan Howlader, Mario A. Bianchet, Yi Liu, Laura Maria Lopez Rovira, Brandon Smith, Marc M. Greenberg* and James T. Stivers*, ","doi":"10.1021/acs.biochem.4c0085410.1021/acs.biochem.4c00854","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00854https://doi.org/10.1021/acs.biochem.4c00854","url":null,"abstract":"Sterile alpha motif histidine-aspartate domain protein 1 (SAMHD1) is an enzyme with diverse activities. Its dNTPase activity degrades all canonical dNTPs and many anticancer nucleoside drugs, while its single-stranded nucleic acid binding activity promotes DNA repair and RNA homeostasis in cells. These functions require guanine nucleotide binding to a specific allosteric site (A1) on the enzyme. We previously described how the activities of SAMHD1 could be inhibited in vitro with fragment-based inhibitor design, using dGMP as a targeting fragment for the A1 site. However, these dGMP-tethered inhibitors had poor cell permeability due to the charged guanine monophosphate group. Here, we describe a new approach where the amino form of the guanine acyclic nucleoside acyclovir (NH2-ACV) is used as the targeting fragment, allowing facile coupling to activated carboxylic acids (R–COOH), either directly or using linkers. This approach generates a neutral amide instead of charged monophosphate attachment points. High-throughput screening of a ∼375 compound carboxylic acid library identified two compounds (8, 11) with similar micromolar affinities for SAMHD1. Compound 11 was obtained by direct coupling to NH2-ACV, while compound 8 used a five-carbon linker. Both inhibitors had the same dibromonaphthol component from the carboxylic acid library screen. A crystal structure of a complex between SAMHD1 and 8, combined with computational models of bound 11, suggest how the dibromonaphthol promotes binding. The findings establish that guanine-based inhibitors targeting the A1 site do not require nucleotide or cyclic nucleoside structural elements. This guanine site targeting strategy is highly amenable to further chemical optimization.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 5","pages":"1109–1120 1109–1120"},"PeriodicalIF":2.9,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533981","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

Multiple Copper Ions Bind to and Promote the Oligomerization of Huntingtin Protein with Nonpathological Repeat Expansions

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-21 DOI: 10.1021/acs.biochem.5c0001210.1021/acs.biochem.5c00012

Deepa Neupane, Miguel Santos-Fernandez, Francisco Fernandez-Lima and Katlyn K. Meier*,

{"title":"Multiple Copper Ions Bind to and Promote the Oligomerization of Huntingtin Protein with Nonpathological Repeat Expansions","authors":"Deepa Neupane, Miguel Santos-Fernandez, Francisco Fernandez-Lima and Katlyn K. Meier*, ","doi":"10.1021/acs.biochem.5c0001210.1021/acs.biochem.5c00012","DOIUrl":"https://doi.org/10.1021/acs.biochem.5c00012https://doi.org/10.1021/acs.biochem.5c00012","url":null,"abstract":"Huntington’s disease (HD) is a fatal neurodegenerative disease characterized by the expression of huntingtin protein (htt) that has a polyglutamine (CAG; polyQ) repeat domain consisting of 36 or more glutamines (mhtt). Historically, mhtt is more broadly associated with HD severity, as are elevated metal levels observed in HD patients. The depletion of wild-type (WT) htt (fewer than 36Qs) is also recognized as a contributing factor to HD progression; however, many questions remain about the interactions of biorelevant metals with WT htt and the impact of the interactions on protein aggregation. In the present work, we utilize a combination of biochemical assays and spectroscopic techniques to provide insights into the interaction of copper with an in vitro htt model (N171–17Q). Herein, we use sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and dynamic light scattering to show that the addition of equimolar or higher concentrations of Cu(II) to htt induces time- and temperature-dependent protein oligomerization/aggregation. Additionally, chelation assays, trapped ion mobility spectrometry, and mass spectrometry confirm the (i) rapid reduction of Cu(II) in the presence of N171–17Q htt, (ii) direct binding of multiple copper ions per protein, and (iii) complex Cu:htt speciation profile with a preference for three distinct Cu:htt states. These findings contribute to our molecular level understanding of copper’s role in the depletion and oligomerization/aggregation of WT htt while underscoring the physiological significance of our work, its potential relevance to metal binding in mhtt, and its significance for identifying new avenues for biomarker exploration and therapeutic design strategies.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 5","pages":"1121–1135 1121–1135"},"PeriodicalIF":2.9,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533793","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

Regulation of GLP-1 and Glucagon Receptor Function by β-Arrestins in Metabolically Important Cell Types

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-21 DOI: 10.1021/acs.biochem.4c0086710.1021/acs.biochem.4c00867

Liu Liu, Misbah Rashid and Jürgen Wess*,

{"title":"Regulation of GLP-1 and Glucagon Receptor Function by β-Arrestins in Metabolically Important Cell Types","authors":"Liu Liu, Misbah Rashid and Jürgen Wess*, ","doi":"10.1021/acs.biochem.4c0086710.1021/acs.biochem.4c00867","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00867https://doi.org/10.1021/acs.biochem.4c00867","url":null,"abstract":"Glucagon-like peptide-1 (GLP-1) and glucagon (GCG) are polypeptides derived from a common precursor (preproglucagon) that modulates the activity of numerous cell types involved in regulating glucose and energy homeostasis. GLP-1 and GCG exert their biological functions via binding to specific G protein-coupled receptors (GLP-1Rs and GCGRs). Ligand-activated GLP-1Rs and GCGRs preferentially activate the heterotrimeric G protein Gs, resulting in increased cytosolic cAMP levels. However, activation of the two receptors also leads to the recruitment of β-arrestin-1 and -2 (βarr1 and βarr2, respectively) to the intracellular surface of the receptor proteins. The binding of β-arrestins to the activated receptors contributes to the termination of receptor-stimulated G protein coupling. In addition, receptor-β-arrestin complexes can act as signaling nodes in their own right by modulating the activity of many intracellular signaling pathways. In this Review, we will discuss the roles of βarr1 and βarr2 in regulating key metabolic functions mediated by activated GLP-1Rs and GCGRs. During the past decade, GLP-1R agonists have emerged as highly efficacious antidiabetic and antiobesity drugs. Moreover, dual agonists that stimulate both GLP-1Rs and GCGRs are predicted to offer additional therapeutic benefits as compared to GLP-1R agonist monotherapy. We will summarize and try to synthesize a series of studies suggesting that the development of G protein-biased GLP-1R and/or GCGR agonists, which do not lead to the recruitment of β-arrestins, may lead to even more efficacious therapeutic agents.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 5","pages":"978–986 978–986"},"PeriodicalIF":2.9,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533888","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

Interpreting the Histidine-Containing Small Peptides on Tau Protein Tautomerism: A Theoretical Perspective

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-21 DOI: 10.1021/acs.biochem.4c0063310.1021/acs.biochem.4c00633

Yingqi Tang, Nannan Li, Hai Li and Jin Yong Lee*,

{"title":"Interpreting the Histidine-Containing Small Peptides on Tau Protein Tautomerism: A Theoretical Perspective","authors":"Yingqi Tang, Nannan Li, Hai Li and Jin Yong Lee*, ","doi":"10.1021/acs.biochem.4c0063310.1021/acs.biochem.4c00633","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00633https://doi.org/10.1021/acs.biochem.4c00633","url":null,"abstract":"Exploring the nature of histidine residue tautomerization via a systematic conformational study is essential for understanding the pathology and toxicity of several neurodegenerative diseases, as well as for their diagnosis and treatment. Herein, density functional theory (DFT) calculations were used to determine the Tau protein’s histidine-containing dipeptide (Lys-His, His-Gln, and His-Val) and tripeptide (Lys-His-Gln and Lys-His-Val) isomeric conformations via intramolecular hydrogen bond interactions, with particular attention to the influence of N–H group isomeric forms on their properties. The calculated infrared (IR) spectroscopy of the N–H stretch region of each isomer and nuclear magnetic resonance (NMR) shielding of the imidazole ring carbon atoms (13C1, 13C2, and 13C3) were investigated. The results show that both the IR spectrum of the N–H group and the NMR shielding of 13C nuclei on the imidazole ring can be used to identify the histidine-containing dipeptide and tripeptide tautomeric isomers. Systematically analyzing the hydrogen bonding interactions, the atomic charge distribution, the potential energy distribution, and the HOMO–LUMO transitions of each isomer further verified the above conclusions. This study provides theoretical evidence for the conformation identification of the histidine-containing dipeptide and tripeptide isomers on Tau protein.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 5","pages":"1079–1091 1079–1091"},"PeriodicalIF":2.9,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533887","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

Quantitative and Systematic NMR Measurements of Sequence-Dependent A–T Hoogsteen Dynamics in the DNA Double Helix

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-21 DOI: 10.1021/acs.biochem.4c0082010.1021/acs.biochem.4c00820

Akanksha Manghrani, Atul Kaushik Rangadurai, Or Szekely, Bei Liu, Serafima Guseva and Hashim M. Al-Hashimi*,

{"title":"Quantitative and Systematic NMR Measurements of Sequence-Dependent A–T Hoogsteen Dynamics in the DNA Double Helix","authors":"Akanksha Manghrani, Atul Kaushik Rangadurai, Or Szekely, Bei Liu, Serafima Guseva and Hashim M. Al-Hashimi*, ","doi":"10.1021/acs.biochem.4c0082010.1021/acs.biochem.4c00820","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00820https://doi.org/10.1021/acs.biochem.4c00820","url":null,"abstract":"The dynamic properties of DNA depend on the sequence, providing an important source of sequence-specificity in biochemical reactions. However, comprehensively measuring how these dynamics vary with sequence is challenging, especially when they involve lowly populated and short-lived conformational states. Using 1H CEST supplemented by targeted 13C R1ρ NMR experiments, we quantitatively measured Watson–Crick to Hoogsteen dynamics for an A–T base pair in 13 trinucleotide sequence contexts. The Hoogsteen population and exchange rate varied 4-fold and 16-fold, respectively, and were dependent on both the 3′- and 5′-neighbors but only weakly dependent on monovalent ion concentration (25 versus 100 mM NaCl) and pH (6.8 versus 8.0). Flexible TA and CA dinucleotide steps exhibited the highest Hoogsteen populations, and their kinetics rates strongly depended on the 3′-neighbor. In contrast, the stiffer AA and GA steps had the lowest Hoogsteen population, and their kinetics were weakly dependent on the 3′-neighbor. The Hoogsteen lifetime was especially short when G–C neighbors flanked the A–T base pair. Our results uncover a unique conformational basis for sequence-specificity in the DNA double helix and establish the utility of NMR to quantitatively and comprehensively measure sequence-dependent DNA dynamics.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 5","pages":"1042–1054 1042–1054"},"PeriodicalIF":2.9,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533794","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

Dynamics in the Phytophthora capsici Effector AVR3a11 Confirm the Core WY Domain Fold

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-20 DOI: 10.1021/acs.biochem.4c0066010.1021/acs.biochem.4c00660

James Tolchard, Vicki S. Chambers, Laurence S. Boutemy, Mark J. Banfield and Tharin M. A. Blumenschein*,

{"title":"Dynamics in the Phytophthora capsici Effector AVR3a11 Confirm the Core WY Domain Fold","authors":"James Tolchard, Vicki S. Chambers, Laurence S. Boutemy, Mark J. Banfield and Tharin M. A. Blumenschein*, ","doi":"10.1021/acs.biochem.4c0066010.1021/acs.biochem.4c00660","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00660https://doi.org/10.1021/acs.biochem.4c00660","url":null,"abstract":"Oomycete pathogens cause large economic losses in agriculture through diseases such as late blight (Phytophthora infestans), and stem and root rot of soybean (Phytophthora sojae). The effector protein AVR3a, from P. infestans, and its homologue AVR3a11 from Phytophthora capsici, are host-translocated effectors that interact with plant proteins to evade defense mechanisms and enable infection. Both proteins belong to the family of RXLR effectors and contain an N-terminal secretion signal, an RXLR motif for translocation into the host cell, and a C-terminal effector domain. Within this family, many proteins have been predicted to contain one or more WY domains as their effector domain, which is proposed to encompass a conserved minimal core fold containing three helices, further stabilized by additional helices or dimerization. In AVR3a11, a helical N-terminal extension to the core fold forms a four-helix bundle, as determined by X-ray crystallography. For a complete picture of the dynamics of AVR3a11, we have determined the solution structure of AVR3a11, and studied its dynamics in the fast time scale (ns–ps, from NMR relaxation parameters) and in the slow time scale (seconds to minutes, from hydrogen/deuterium exchange experiments). Hydrogen/deuterium exchange showed that the N-terminal helix is less stable than the other three helices, confirming the core fold originally proposed. Relaxation measurements confirm that AVR3a11 undergoes extensive conformational exchange, despite the uniform presence of fast motions in the spectral density function throughout most of its sequence. As functional residues are in the more mobile regions, flexibility in the slow/intermediate time scale may be functionally important.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 5","pages":"1146–1156 1146–1156"},"PeriodicalIF":2.9,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.biochem.4c00660","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533700","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

N-Terminal Protein Binding and Disorder-to-Order Transition by a Synthetic Receptor

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-02-20 DOI: 10.1021/acs.biochem.4c0072910.1021/acs.biochem.4c00729

Niamh M. Mockler, Kiefer O. Ramberg, Ronan J. Flood and Peter B. Crowley*,

{"title":"N-Terminal Protein Binding and Disorder-to-Order Transition by a Synthetic Receptor","authors":"Niamh M. Mockler, Kiefer O. Ramberg, Ronan J. Flood and Peter B. Crowley*, ","doi":"10.1021/acs.biochem.4c0072910.1021/acs.biochem.4c00729","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00729https://doi.org/10.1021/acs.biochem.4c00729","url":null,"abstract":"We describe the capture and structuring of disordered N-terminal regions by the macrocycle sulfonato-calix[4]arene (sclx4). Using the trimeric β-propeller Ralstonia solanacearum lectin (RSL) as a scaffold, we generated a series of mutants with extended and dynamic N-termini. Three of the mutants feature an N-terminal methionine-lysine motif. The fourth mutant contains the disordered 8-residue N-terminus of Histone 3, a component of the nucleosome. X-ray crystallography and NMR spectroscopy provide evidence for sclx4 binding to the flexible N-terminal regions. Three crystal structures reveal that the calixarene recognizes the N-terminal Met-Lys motif, capturing either residue. We provide crystallographic proof for sclx4 encapsulation of N-terminal methionine. Calixarene capture of intrinsically disordered regions may have applications in regulating protein secondary (and tertiary) structure.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 5","pages":"1092–1098 1092–1098"},"PeriodicalIF":2.9,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.biochem.4c00729","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533862","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