Yan Xie, Shelley D. Minteer, Scott Banta and Scott Calabrese Barton*,
{"title":"三羧酸循环超配合物静电通道的马尔可夫状态研究","authors":"Yan Xie, Shelley D. Minteer, Scott Banta and Scott Calabrese Barton*, ","doi":"10.1021/acsnanoscienceau.2c00011","DOIUrl":null,"url":null,"abstract":"<p >The high efficiency of cascade reactions in supramolecular enzyme nanoassemblies, known as metabolons, has attracted substantial attention in various fields ranging from fundamental biochemistry and molecular biology to recent applications in biofuel cells, biosensors, and chemical synthesis. One reason for the high efficiency of metabolons is the structures formed by sequential enzymes that allow the direct transport of intermediates between consecutive active sites. The supercomplex of malate dehydrogenase (MDH) and citrate synthase (CS) is an ideal example of the controlled transport of intermediates via electrostatic channeling. Here, using a combination of molecular dynamics (MD) simulations and a Markov state model (MSM), we examined the transport process of the intermediate oxaloacetate (OAA) from MDH to CS. The MSM enables the identification of the dominant transport pathways of OAA from MDH to CS. Analysis of all pathways using a hub score approach reveals a small set of residues that control OAA transport. This set includes an arginine residue previously identified experimentally. MSM analysis of a mutated complex, where the identified arginine is replaced by alanine, led to a 2-fold decrease in transfer efficiency, also consistent with experimental results. This work provides a molecular-level understanding of the electrostatic channeling mechanism and will enable the further design of catalytic nanostructures utilizing electrostatic channeling.</p>","PeriodicalId":29799,"journal":{"name":"ACS Nanoscience Au","volume":null,"pages":null},"PeriodicalIF":4.8000,"publicationDate":"2022-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/77/b8/ng2c00011.PMC10125334.pdf","citationCount":"0","resultStr":"{\"title\":\"Markov State Study of Electrostatic Channeling within the Tricarboxylic Acid Cycle Supercomplex\",\"authors\":\"Yan Xie, Shelley D. Minteer, Scott Banta and Scott Calabrese Barton*, \",\"doi\":\"10.1021/acsnanoscienceau.2c00011\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p >The high efficiency of cascade reactions in supramolecular enzyme nanoassemblies, known as metabolons, has attracted substantial attention in various fields ranging from fundamental biochemistry and molecular biology to recent applications in biofuel cells, biosensors, and chemical synthesis. One reason for the high efficiency of metabolons is the structures formed by sequential enzymes that allow the direct transport of intermediates between consecutive active sites. The supercomplex of malate dehydrogenase (MDH) and citrate synthase (CS) is an ideal example of the controlled transport of intermediates via electrostatic channeling. Here, using a combination of molecular dynamics (MD) simulations and a Markov state model (MSM), we examined the transport process of the intermediate oxaloacetate (OAA) from MDH to CS. The MSM enables the identification of the dominant transport pathways of OAA from MDH to CS. Analysis of all pathways using a hub score approach reveals a small set of residues that control OAA transport. This set includes an arginine residue previously identified experimentally. MSM analysis of a mutated complex, where the identified arginine is replaced by alanine, led to a 2-fold decrease in transfer efficiency, also consistent with experimental results. This work provides a molecular-level understanding of the electrostatic channeling mechanism and will enable the further design of catalytic nanostructures utilizing electrostatic channeling.</p>\",\"PeriodicalId\":29799,\"journal\":{\"name\":\"ACS Nanoscience Au\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.8000,\"publicationDate\":\"2022-06-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/77/b8/ng2c00011.PMC10125334.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ACS Nanoscience Au\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://pubs.acs.org/doi/10.1021/acsnanoscienceau.2c00011\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"NANOSCIENCE & NANOTECHNOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Nanoscience Au","FirstCategoryId":"1085","ListUrlMain":"https://pubs.acs.org/doi/10.1021/acsnanoscienceau.2c00011","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"NANOSCIENCE & NANOTECHNOLOGY","Score":null,"Total":0}
Markov State Study of Electrostatic Channeling within the Tricarboxylic Acid Cycle Supercomplex
The high efficiency of cascade reactions in supramolecular enzyme nanoassemblies, known as metabolons, has attracted substantial attention in various fields ranging from fundamental biochemistry and molecular biology to recent applications in biofuel cells, biosensors, and chemical synthesis. One reason for the high efficiency of metabolons is the structures formed by sequential enzymes that allow the direct transport of intermediates between consecutive active sites. The supercomplex of malate dehydrogenase (MDH) and citrate synthase (CS) is an ideal example of the controlled transport of intermediates via electrostatic channeling. Here, using a combination of molecular dynamics (MD) simulations and a Markov state model (MSM), we examined the transport process of the intermediate oxaloacetate (OAA) from MDH to CS. The MSM enables the identification of the dominant transport pathways of OAA from MDH to CS. Analysis of all pathways using a hub score approach reveals a small set of residues that control OAA transport. This set includes an arginine residue previously identified experimentally. MSM analysis of a mutated complex, where the identified arginine is replaced by alanine, led to a 2-fold decrease in transfer efficiency, also consistent with experimental results. This work provides a molecular-level understanding of the electrostatic channeling mechanism and will enable the further design of catalytic nanostructures utilizing electrostatic channeling.
期刊介绍:
ACS Nanoscience Au is an open access journal that publishes original fundamental and applied research on nanoscience and nanotechnology research at the interfaces of chemistry biology medicine materials science physics and engineering.The journal publishes short letters comprehensive articles reviews and perspectives on all aspects of nanoscience and nanotechnology:synthesis assembly characterization theory modeling and simulation of nanostructures nanomaterials and nanoscale devicesdesign fabrication and applications of organic inorganic polymer hybrid and biological nanostructuresexperimental and theoretical studies of nanoscale chemical physical and biological phenomenamethods and tools for nanoscience and nanotechnologyself- and directed-assemblyzero- one- and two-dimensional materialsnanostructures and nano-engineered devices with advanced performancenanobiotechnologynanomedicine and nanotoxicologyACS Nanoscience Au also publishes original experimental and theoretical research of an applied nature that integrates knowledge in the areas of materials engineering physics bioscience and chemistry into important applications of nanomaterials.