无分支代谢途径中的最佳酶谱。

IF 3.6 3区 生物学 Q1 BIOLOGY Interface Focus Pub Date : 2024-02-09 eCollection Date: 2024-02-15 DOI:10.1098/rsfs.2023.0029
Elad Noor, Wolfram Liebermeister
{"title":"无分支代谢途径中的最佳酶谱。","authors":"Elad Noor, Wolfram Liebermeister","doi":"10.1098/rsfs.2023.0029","DOIUrl":null,"url":null,"abstract":"<p><p>How to optimize the allocation of enzymes in metabolic pathways has been a topic of study for many decades. Although the general problem is complex and nonlinear, we have previously shown that it can be solved by convex optimization. In this paper, we focus on unbranched metabolic pathways with simplified enzymatic rate laws and derive analytic solutions to the optimization problem. We revisit existing solutions based on the limit of mass-action rate laws and present new solutions for other rate laws. Furthermore, we revisit a known relationship between flux control coefficients and enzyme abundances in optimal metabolic states. We generalize this relationship to models with density constraints on enzymes and metabolites, and present a new local relationship between optimal reaction elasticities and enzyme amounts. Finally, we apply our theory to derive simple kinetics-based formulae for protein allocation during bacterial growth.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"14 1","pages":"20230029"},"PeriodicalIF":3.6000,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10853694/pdf/","citationCount":"0","resultStr":"{\"title\":\"Optimal enzyme profiles in unbranched metabolic pathways.\",\"authors\":\"Elad Noor, Wolfram Liebermeister\",\"doi\":\"10.1098/rsfs.2023.0029\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>How to optimize the allocation of enzymes in metabolic pathways has been a topic of study for many decades. Although the general problem is complex and nonlinear, we have previously shown that it can be solved by convex optimization. In this paper, we focus on unbranched metabolic pathways with simplified enzymatic rate laws and derive analytic solutions to the optimization problem. We revisit existing solutions based on the limit of mass-action rate laws and present new solutions for other rate laws. Furthermore, we revisit a known relationship between flux control coefficients and enzyme abundances in optimal metabolic states. We generalize this relationship to models with density constraints on enzymes and metabolites, and present a new local relationship between optimal reaction elasticities and enzyme amounts. Finally, we apply our theory to derive simple kinetics-based formulae for protein allocation during bacterial growth.</p>\",\"PeriodicalId\":13795,\"journal\":{\"name\":\"Interface Focus\",\"volume\":\"14 1\",\"pages\":\"20230029\"},\"PeriodicalIF\":3.6000,\"publicationDate\":\"2024-02-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10853694/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Interface Focus\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1098/rsfs.2023.0029\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/2/15 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q1\",\"JCRName\":\"BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Interface Focus","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1098/rsfs.2023.0029","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/2/15 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

几十年来,如何优化代谢途径中酶的分配一直是一个研究课题。虽然一般问题是复杂的非线性问题,但我们之前已经证明,它可以通过凸优化来解决。在本文中,我们将重点放在具有简化酶速率定律的无分支代谢途径上,并推导出优化问题的解析解。我们重新审视了基于质量作用速率定律极限的现有解法,并针对其他速率定律提出了新的解法。此外,我们还重新审视了最佳代谢状态下通量控制系数与酶丰度之间的已知关系。我们将这一关系推广到对酶和代谢物有密度限制的模型,并提出了最佳反应弹性与酶数量之间的新局部关系。最后,我们应用我们的理论推导出细菌生长过程中蛋白质分配的简单动力学公式。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Optimal enzyme profiles in unbranched metabolic pathways.

How to optimize the allocation of enzymes in metabolic pathways has been a topic of study for many decades. Although the general problem is complex and nonlinear, we have previously shown that it can be solved by convex optimization. In this paper, we focus on unbranched metabolic pathways with simplified enzymatic rate laws and derive analytic solutions to the optimization problem. We revisit existing solutions based on the limit of mass-action rate laws and present new solutions for other rate laws. Furthermore, we revisit a known relationship between flux control coefficients and enzyme abundances in optimal metabolic states. We generalize this relationship to models with density constraints on enzymes and metabolites, and present a new local relationship between optimal reaction elasticities and enzyme amounts. Finally, we apply our theory to derive simple kinetics-based formulae for protein allocation during bacterial growth.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Interface Focus
Interface Focus BIOLOGY-
CiteScore
9.20
自引率
0.00%
发文量
44
审稿时长
6-12 weeks
期刊介绍: Each Interface Focus themed issue is devoted to a particular subject at the interface of the physical and life sciences. Formed of high-quality articles, they aim to facilitate cross-disciplinary research across this traditional divide by acting as a forum accessible to all. Topics may be newly emerging areas of research or dynamic aspects of more established fields. Organisers of each Interface Focus are strongly encouraged to contextualise the journal within their chosen subject.
期刊最新文献
Fundamental constraints to the logic of living systems. The legacy and evolvability of Pere Alberch's ideas. The logic of monsters: development and morphological diversity in stem-cell-based embryo models. Capacity building in porous materials research for sustainable energy applications. Chem4Energy: a consortium of the Royal Society Africa Capacity-Building Initiative.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1