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Transcription Attenuation in Synthetic Promoters in Nonoverlapping Tandem Formation. 非重叠串联合成启动子的转录衰减
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-12 DOI: 10.1021/acs.biochem.4c00012
Vatsala Chauhan, Ines S C Baptista, Amir M Arsh, Rahul Jagadeesan, Suchintak Dash, Andre S Ribeiro
{"title":"Transcription Attenuation in Synthetic Promoters in Nonoverlapping Tandem Formation.","authors":"Vatsala Chauhan, Ines S C Baptista, Amir M Arsh, Rahul Jagadeesan, Suchintak Dash, Andre S Ribeiro","doi":"10.1021/acs.biochem.4c00012","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00012","url":null,"abstract":"<p><p>Closely spaced promoters are ubiquitous in prokaryotic and eukaryotic genomes. How their structure and dynamics relate remains unclear, particularly for tandem formations. To study their transcriptional interference, we engineered two pairs and one trio of synthetic promoters in nonoverlapping, tandem formation, in single-copy plasmids transformed into <i>Escherichia coli</i> cells. From in vivo measurements, we found that these promoters in tandem formation can have attenuated transcription rates. The attenuation strength can be widely fine-tuned by the promoters' positioning, natural regulatory mechanisms, and other factors, including the antibiotic rifampicin, which is known to hamper RNAP promoter escape. From this, and supported by in silico models, we concluded that the attenuation in these constructs emerges from premature terminations generated by collisions between RNAPs elongating from upstream promoters and RNAPs occupying downstream promoters. Moreover, we found that these collisions can cause one or both RNAPs to falloff. Finally, the broad spectrum of possible, externally regulated, attenuation strengths observed in our synthetic tandem promoters suggests that they could become useful as externally controllable regulators of future synthetic circuits.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141597878","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
Novel DNA-Binding Activity Exhibited by Poly(aspartic acid) Hydrolase-1 Inhibits Poly(aspartic acid) Hydrolase Activity. 聚(天冬氨酸)水解酶-1 显示的新型 DNA 结合活性抑制了聚(天冬氨酸)水解酶的活性。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-12 DOI: 10.1021/acs.biochem.4c00127
Joshua Couch, Justin D Marsee, Waylan W Callaway, Thi Ho, Kathryn E Glorioso, Michael Mercante, Britney Williams, Connor Coughran, Mitch H Weiland, Justin M Miller
{"title":"Novel DNA-Binding Activity Exhibited by Poly(aspartic acid) Hydrolase-1 Inhibits Poly(aspartic acid) Hydrolase Activity.","authors":"Joshua Couch, Justin D Marsee, Waylan W Callaway, Thi Ho, Kathryn E Glorioso, Michael Mercante, Britney Williams, Connor Coughran, Mitch H Weiland, Justin M Miller","doi":"10.1021/acs.biochem.4c00127","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00127","url":null,"abstract":"<p><p>Significant attention has been shifted toward the use and development of biodegradable polymeric materials to mitigate environmental accumulation and potential health impacts. One such material, poly(aspartic acid) (PAA), is a biodegradable alternative to superabsorbent poly(carboxylates), like poly(acrylate). Three enzymes are known to hydrolyze PAA: PahZ1<sub>KT-1</sub> and PahZ2<sub>KT-1</sub> from <i>Sphingomonas</i> sp. KT-1 and PahZ1<sub>KP-2</sub> from <i>Pedobacter</i> sp. KP-2. We previously reported the X-ray crystal structure for PahZ1<sub>KT-1</sub>, which revealed a homodimer complex with a strongly cationic surface spanning one side of each monomer. Here, we report the first characterization of any polymer hydrolase binding to DNA, where modeling data predict binding of the polyanionic DNA near the cationic substrate binding surface. Our data reveal that PahZ1 homologues from <i>Sphingomonas</i> sp. KT-1 and <i>Pedobacter</i> sp. KP-2 bind ssDNA and dsDNA with nanomolar binding affinities. PahZ1<sub>KT-1</sub> binds ssDNA and dsDNA with an apparent dissociation constant, <i>K</i><sub>D,app</sub> = 81 ± 14 and 19 ± 1 nM, respectively, and these estimates are similar to the same behaviors exhibited by PahZ1<sub>KP-2</sub>. Gel permeation chromatography data reveal that dsDNA binding promotes inhibition of PahZ1-catalyzed PAA biodegradation for each homologue. We propose a working model wherein binding of PahZ1 to extracellular biofilm DNA aids in the localization of the hydrolase to the environment in which PAA would first be encountered, thereby providing a mechanism to degrade extracellular PAA and potentially harvest aspartic acid for nutritional uptake.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141588913","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
Theoretical Insights into MutY Glycosylase DNA Repair Mechanism. MutY 糖基化酶 DNA 修复机制的理论启示
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-11 DOI: 10.1021/acs.biochem.4c00153
Alessio Olivieri, Alessandro Nicola Nardi, Marco D'Abramo
{"title":"Theoretical Insights into MutY Glycosylase DNA Repair Mechanism.","authors":"Alessio Olivieri, Alessandro Nicola Nardi, Marco D'Abramo","doi":"10.1021/acs.biochem.4c00153","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00153","url":null,"abstract":"<p><p>Maintaining the integrity of the genome is fundamental to living organisms. To this end, nature developed several mechanisms to find and promptly repair DNA lesions. Among them, base excision repair (BER) enzymes evolved to efficiently carry out this task. Notably, the mechanisms allowing these proteins to search for, detect, and fix DNA damage on a biologically relevant time scale still remain partially unclear. By taking MutY, a BER enzyme implied in the repair of the 8-oxoguanine-adenine mismatches, as a model system, we shed some light on the repair mechanism through a theoretical-computational approach. First, we estimated the effect of the oxidation state of the MutY iron-sulfur cluster on the protein-DNA binding. Then, the redox thermodynamics of both the protein cluster and DNA nucleobases are calculated. Finally, the charge migration kinetics along the double strand bound to the enzyme has been evaluated. The rationalization of our results indicates that the search for DNA lesions is essentially dictated by the redox chemistry of the species involved, i.e., the iron-sulfur redox cofactor and the DNA bound to the enzyme.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141588914","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 Facile LC-MS Method for Profiling Cholesterol and Cholesteryl Esters in Mammalian Cells and Tissues. 分析哺乳动物细胞和组织中胆固醇和胆固醇酯的简便 LC-MS 方法。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-10 DOI: 10.1021/acs.biochem.4c00160
Aakash Chandramouli, Siddhesh S Kamat
{"title":"A Facile LC-MS Method for Profiling Cholesterol and Cholesteryl Esters in Mammalian Cells and Tissues.","authors":"Aakash Chandramouli, Siddhesh S Kamat","doi":"10.1021/acs.biochem.4c00160","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00160","url":null,"abstract":"<p><p>Cholesterol is central to mammalian lipid metabolism and serves many critical functions in the regulation of diverse physiological processes. Dysregulation in cholesterol metabolism is causally linked to numerous human diseases, and therefore, in vivo, the concentrations and flux of cholesterol and cholesteryl esters (fatty acid esters of cholesterol) are tightly regulated. While mass spectrometry has been an analytical method of choice for detecting cholesterol and cholesteryl esters in biological samples, the hydrophobicity, chemically inert nature, and poor ionization of these neutral lipids have often proved a challenge in developing lipidomics compatible liquid chromatography-mass spectrometry (LC-MS) methods to study them. To overcome this problem, here, we report a reverse-phase LC-MS method that is compatible with existing high-throughput lipidomics strategies and capable of identifying and quantifying cholesterol and cholesteryl esters from mammalian cells and tissues. Using this sensitive yet robust LC-MS method, we profiled different mammalian cell lines and tissues and provide a comprehensive picture of cholesterol and cholesteryl esters content in them. Specifically, among cholesteryl esters, we find that mammalian cells and tissues largely possess monounsaturated and polyunsaturated variants. Taken together, our lipidomics compatible LC-MS method to study this lipid class opens new avenues in understanding systemic and tissue-level cholesterol metabolism under various physiological conditions.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578227","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 and Biochemical Analysis of the Human Chemokine Receptor CCR8. 人类趋化因子受体 CCR8 的低温电子显微镜结构和生化分析。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-10 DOI: 10.1021/acs.biochem.4c00121
Qi Peng, Haihai Jiang, Xinyu Cheng, Na Wang, Sili Zhou, Yuting Zhang, Tingting Yang, Yixiang Chen, Wei Zhang, Sijia Lv, Weiwei Nan, JianFei Wang, Guo-Huang Fan, Jian Li, Jin Zhang
{"title":"Cryo-EM Structure and Biochemical Analysis of the Human Chemokine Receptor CCR8.","authors":"Qi Peng, Haihai Jiang, Xinyu Cheng, Na Wang, Sili Zhou, Yuting Zhang, Tingting Yang, Yixiang Chen, Wei Zhang, Sijia Lv, Weiwei Nan, JianFei Wang, Guo-Huang Fan, Jian Li, Jin Zhang","doi":"10.1021/acs.biochem.4c00121","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00121","url":null,"abstract":"<p><p>The C-C motif chemokine receptor 8 (CCR8) is a class A G-protein-coupled receptor that has emerged as a promising therapeutic target in cancer and autoimmune diseases. In the present study, we solved the cryo-electron microscopy (cryo-EM) structure of the human CCR8-G<sub>i</sub> complex in the absence of a ligand at 2.58 Å. Structural analysis and comparison revealed that our apo CCR8 structure undergoes some conformational changes and is similar to that in the CCL1-CCR8 complex structure, indicating an active state. In addition, the key residues of CCR8 involved in the recognition of LMD-009, a potent nonpeptide agonist, were investigated by mutating CCR8 and testing the calcium flux induced by LMD-009-CCR8 interaction. Three mutants of CCR8, Y113<sup>3.32</sup>A, Y172<sup>4.64</sup>A, and E286<sup>7.39</sup>A, showed a dramatically decreased ability in mediating calcium mobilization, indicating their key interaction with LMD-009 and key roles in activation. These structural and biochemical analyses enrich molecular insights into the agonism and activation of CCR8 and will facilitate CCR8-targeted therapy.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578228","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
Antimalarial Delivery with a Ferritin-Based Protein Cage: A Step toward Developing Smart Therapeutics against Malaria. 基于铁蛋白的蛋白笼抗疟输送:向开发抗疟疾智能疗法迈出的一步。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-08 DOI: 10.1021/acs.biochem.3c00692
Shruti Bhatt, Subrata Dasgupta, Chiging Tupe, Cherish Prashar, Utpal Adhikari, Kailash C Pandey, Suman Kundu, Soumyananda Chakraborti
{"title":"Antimalarial Delivery with a Ferritin-Based Protein Cage: A Step toward Developing Smart Therapeutics against Malaria.","authors":"Shruti Bhatt, Subrata Dasgupta, Chiging Tupe, Cherish Prashar, Utpal Adhikari, Kailash C Pandey, Suman Kundu, Soumyananda Chakraborti","doi":"10.1021/acs.biochem.3c00692","DOIUrl":"https://doi.org/10.1021/acs.biochem.3c00692","url":null,"abstract":"<p><p>Over the past two decades, the utilization of protein cages has witnessed exponential growth driven by their extensive applications in biotechnology and therapeutics. In the context of the recent Covid-19 pandemic, protein-cage-based scaffolds played a pivotal role in vaccine development. Beyond vaccines, these protein cages have proven valuable in diverse drug delivery applications thanks to their distinctive architecture and structural stability. Among the various types of protein cages, ferritin-based cages have taken the lead in drug delivery applications. This is primarily attributed to their ease of production, exceptional thermal stability, and nontoxic nature. While ferritin-based cages are commonly employed in anticancer drug delivery and contrast agent delivery, their efficacy in malarial drug delivery had not been explored until this study. In this investigation, several antimalarial drugs were encapsulated within horse spleen ferritin, and the binding and loading processes were validated through both experimental and computational techniques. The data unequivocally demonstrate the facile incorporation of antimalarial drugs into ferritin without disrupting its three-dimensional structure. Computational docking and molecular dynamics simulations were employed to pinpoint the precise location of the drug binding site within ferritin. Subsequent efficacy testing on <i>Plasmodium</i> revealed that the developed nanoconjugate, comprising the drug-ferritin conjugate, exhibited significant effectiveness in eradicating the parasite. In conclusion, the findings strongly indicate that ferritin-based carrier systems hold tremendous promise for the future of antimalarial drug delivery, offering high selectivity and limited side effects.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141553605","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 Divalent Metal Cation-Metabolite Interaction Model Reveals Cation Buffering and Speciation. 二价金属阳离子-代谢物相互作用模型揭示了阳离子缓冲作用和种类。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-08 DOI: 10.1021/acs.biochem.4c00125
Jacob P Sieg
{"title":"A Divalent Metal Cation-Metabolite Interaction Model Reveals Cation Buffering and Speciation.","authors":"Jacob P Sieg","doi":"10.1021/acs.biochem.4c00125","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00125","url":null,"abstract":"<p><p>I present the perspective that the divalent metalome and the metabolome can be modeled as a network of chelating interactions instead of separate entities. I review progress in understanding the complex cellular environment, in particular recent contributions to modeling metabolite-Mg<sup>2+</sup> interactions. I then demonstrate a simple extension of these strategies based approximately on intracellular <i>Escherichia coli</i> concentrations. This model is composed of four divalent metal cations with a range of cellular concentrations and physical properties (Mg<sup>2+</sup>, Ca<sup>2+</sup>, Mn<sup>2+</sup>, and Zn<sup>2+</sup>), eight representative metabolites, and interaction constants. I applied this model to predict the speciation of divalent metal cations between free and metabolite-chelated species. This approach reveals potentially beneficial properties, including maintenance of free divalent metal cations at biologically relevant concentrations, buffering of free divalent metal cations, and enrichment of functional metabolite-chelated species. While currently limited by available interaction coefficients, this modeling strategy can be generalized to more complex systems. In summary, biochemists should consider the potential of cellular metabolites to form chelating interactions with divalent metal cations.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141553604","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
Probing the Electrostatic Effects of H-Ras Tyrosine 32 Mutations on Intrinsic GTP Hydrolysis Using Vibrational Stark Effect Spectroscopy of a Thiocyanate Probe. 利用硫氰酸盐探针的振动斯塔克效应光谱探测 H-Ras 酪氨酸 32 突变对内在 GTP水解的静电效应
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-05 DOI: 10.1021/acs.biochem.4c00075
Jackson C Fink, Danielle Landry, Lauren J Webb
{"title":"Probing the Electrostatic Effects of H-Ras Tyrosine 32 Mutations on Intrinsic GTP Hydrolysis Using Vibrational Stark Effect Spectroscopy of a Thiocyanate Probe.","authors":"Jackson C Fink, Danielle Landry, Lauren J Webb","doi":"10.1021/acs.biochem.4c00075","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00075","url":null,"abstract":"<p><p>The wildtype H-Ras protein functions as a molecular switch in a variety of cell signaling pathways, and mutations to key residues result in a constitutively active oncoprotein. However, there is some debate regarding the mechanism of the intrinsic GTPase activity of H-Ras. It has been hypothesized that ordered water molecules are coordinated at the active site by Q61, a highly transforming amino acid site, and Y32, a position that has not previously been investigated. Here, we examine the electrostatic contribution of the Y32 position to GTP hydrolysis by comparing the rate of GTP hydrolysis of Y32X mutants to the vibrational energy shift of each mutation measured by a nearby thiocyanate vibrational probe to estimate changes in the electrostatic environment caused by changes at the Y32 position. We further compared vibrational energy shifts for each mutation to the hydration potential of the respective side chain and demonstrated that Y32 is less critical for recruiting water molecules into the active site to promote hydrolysis than Q61. Our results show a clear interplay between a steric contribution from Y32 and an electrostatic contribution from Q61 that are both critical for intrinsic GTP hydrolysis.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141532879","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
Structural and Functional Characterization of New Lipid Transfer Proteins with Chitin-Binding Properties: Insights from Protein Structure Prediction, Molecular Docking, and Antifungal Activity. 具有几丁质结合特性的新型脂质转移蛋白的结构和功能特征:从蛋白质结构预测、分子对接和抗真菌活性中获得的启示
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-05 DOI: 10.1021/acs.biochem.4c00124
Gabriella Rodrigues Gonçalves, Marciele Souza da Silva, Layrana Azevedo Dos Santos, Thomas Zacarone Afonso Guimarães, Gabriel Bonan Taveira, Felipe Astolpho Almeida, Sarah Rodrigues Ferreira, Antonia Elenir Amancio Oliveira, Celso Shiniti Nagano, Renata Pinheiro Chaves, Vanildo Silveira, André de Oliveira Carvalho, Rosana Rodrigues, Valdirene Moreira Gomes
{"title":"Structural and Functional Characterization of New Lipid Transfer Proteins with Chitin-Binding Properties: Insights from Protein Structure Prediction, Molecular Docking, and Antifungal Activity.","authors":"Gabriella Rodrigues Gonçalves, Marciele Souza da Silva, Layrana Azevedo Dos Santos, Thomas Zacarone Afonso Guimarães, Gabriel Bonan Taveira, Felipe Astolpho Almeida, Sarah Rodrigues Ferreira, Antonia Elenir Amancio Oliveira, Celso Shiniti Nagano, Renata Pinheiro Chaves, Vanildo Silveira, André de Oliveira Carvalho, Rosana Rodrigues, Valdirene Moreira Gomes","doi":"10.1021/acs.biochem.4c00124","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00124","url":null,"abstract":"<p><p>Faced with the emergence of multiresistant microorganisms that affect human health, microbial agents have become a serious global threat, affecting human health and plant crops. Antimicrobial peptides have attracted significant attention in research for the development of new microbial control agents. This work's goal was the structural characterization and analysis of antifungal activity of chitin-binding peptides from <i>Capsicum baccatum</i> and <i>Capsicum frutescens</i> seeds on the growth of <i>Candida</i> and <i>Fusarium</i> species. Proteins were initially submitted to extraction in phosphate buffer pH 5.4 and subjected to chitin column chromatography. Posteriorly, two fractions were obtained for each species, <i>Cb</i>-F1 and <i>Cf</i>-F1 and <i>Cb</i>-F2 and <i>Cf</i>-F2, respectively. The <i>Cb</i>-F1 (<i>C. baccatum</i>) and <i>Cf</i>-F1 (<i>C. frutescens</i>) fractions did not bind to the chitin column. The electrophoresis results obtained after chromatography showed two major protein bands between 3.4 and 14.2 kDa for <i>Cb</i>-F2. For <i>Cf</i>-F2, three major bands were identified between 6.5 and 14.2 kDa. One band from each species was subjected to mass spectrometry, and both bands showed similarity to nonspecific lipid transfer protein. <i>Candida albicans</i> and <i>Candida tropicalis</i> had their growth inhibited by <i>Cb</i>-F2. <i>Cf</i>-F2 inhibited the development of <i>C. albicans</i> but did not inhibit the growth of <i>C. tropicalis</i>. Both fractions were unable to inhibit the growth of <i>Fusarium</i> species. The toxicity of the fractions was tested in vivo on <i>Galleria mellonella</i> larvae, and both showed a low toxicity rate at high concentrations. As a result, the fractions have enormous promise for the creation of novel antifungal compounds.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141537144","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
Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1. Zn(II)-Dependent Matrix Metalloproteinase-1 对胶原蛋白溶解催化机制的新见解。
IF 2.9 3区 生物学
Biochemistry Biochemistry Pub Date : 2024-07-04 DOI: 10.1021/acs.biochem.4c00076
Koteswara Rao Gorantla, Anandhu Krishnan, Sodiq O Waheed, Ann Varghese, Isabella DiCastri, Ciara LaRouche, Meredith Paik, Gregg B Fields, Tatyana G Karabencheva-Christova
{"title":"Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1.","authors":"Koteswara Rao Gorantla, Anandhu Krishnan, Sodiq O Waheed, Ann Varghese, Isabella DiCastri, Ciara LaRouche, Meredith Paik, Gregg B Fields, Tatyana G Karabencheva-Christova","doi":"10.1021/acs.biochem.4c00076","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00076","url":null,"abstract":"<p><p>Collagen hydrolysis, catalyzed by Zn(II)-dependent matrix metalloproteinases (MMPs), is a critical physiological process. Despite previous computational investigations into the catalytic mechanisms of MMP-mediated collagenolysis, a significant knowledge gap in understanding remains regarding the influence of conformational sampling and entropic contributions at physiological temperature on enzymatic collagenolysis. In our comprehensive multilevel computational study, employing quantum mechanics/molecular mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge this gap and provide valuable insights into the catalytic mechanism of MMP-1. Specifically, we compared the full enzyme-substrate complex in solution, clusters in solution, and gas-phase to elucidate insights into MMP-1-catalyzed collagenolysis. Our findings reveal significant differences in the catalytic mechanism when considering thermal effects and the dynamic evolution of the system, contrasting with conventional static potential energy surface QM/MM reaction path studies. Notably, we observed a significant stabilization of the critical tetrahedral intermediate, attributed to contributions from conformational flexibility and entropy. Moreover, we found that protonation of the scissile bond nitrogen occurs via proton transfer from a Zn(II)-coordinated hydroxide rather than from a solvent water molecule. Following C-N bond cleavage, the C-terminus remains coordinated to the catalytic Zn(II), while the N-terminus forms a hydrogen bond with a solvent water molecule. Subsequently, the release of the C-terminus is facilitated by the coordination of a water molecule. Our study underscores the pivotal role of protein conformational dynamics at physiological temperature in stabilizing the transition state of the rate-limiting step and key intermediates, compared to the corresponding reaction in solution. These fundamental insights into the mechanism of collagen degradation provide valuable guidance for the development of MMP-1-specific inhibitors.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141496312","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
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