Pub Date : 2024-09-17DOI: 10.1016/j.bpj.2024.09.004
Josh E Baker
{"title":"Mixed-scale versus multiscale models of muscle contraction.","authors":"Josh E Baker","doi":"10.1016/j.bpj.2024.09.004","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.09.004","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142246950","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}
Pub Date : 2024-09-17Epub Date: 2024-07-02DOI: 10.1016/j.bpj.2024.07.001
Laura A Carlucci, Keith C Johnson, Wendy E Thomas
The adhesin FimH is expressed by commensal Escherichia coli and is implicated in urinary tract infections, where it mediates adhesion to mannosylated glycoproteins on urinary and intestinal epithelial cells in the presence of a high-shear fluid environment. The FimH-mannose bond exhibits catch behavior in which bond lifetime increases with force, because tensile force induces a transition in FimH from a compact native to an elongated activated conformation with a higher affinity to mannose. However, the lifetime of the activated state of FimH has not been measured under force. Here we apply multiplexed magnetic tweezers to apply a preload force to activate FimH bonds with yeast mannan, then we measure the lifetime of these activated bonds under a wide range of forces above and below the preload force. A higher fraction of FimH-mannan bonds were activated above than below a critical preload force, confirming the FimH catch bond behavior. Once activated, FimH detached from mannose with multi-state kinetics, suggesting the existence of two bound states with a 20-fold difference in dissociation rates. The average lifetime of activated FimH-mannose bonds was 1000 to 10,000 s at forces of 30-70 pN. Structural explanations of the two bound states and the high force resistance provide insights into structural mechanisms for long-lived, force-resistant biomolecular interactions.
{"title":"FimH-mannose noncovalent bonds survive minutes to hours under force.","authors":"Laura A Carlucci, Keith C Johnson, Wendy E Thomas","doi":"10.1016/j.bpj.2024.07.001","DOIUrl":"10.1016/j.bpj.2024.07.001","url":null,"abstract":"<p><p>The adhesin FimH is expressed by commensal Escherichia coli and is implicated in urinary tract infections, where it mediates adhesion to mannosylated glycoproteins on urinary and intestinal epithelial cells in the presence of a high-shear fluid environment. The FimH-mannose bond exhibits catch behavior in which bond lifetime increases with force, because tensile force induces a transition in FimH from a compact native to an elongated activated conformation with a higher affinity to mannose. However, the lifetime of the activated state of FimH has not been measured under force. Here we apply multiplexed magnetic tweezers to apply a preload force to activate FimH bonds with yeast mannan, then we measure the lifetime of these activated bonds under a wide range of forces above and below the preload force. A higher fraction of FimH-mannan bonds were activated above than below a critical preload force, confirming the FimH catch bond behavior. Once activated, FimH detached from mannose with multi-state kinetics, suggesting the existence of two bound states with a 20-fold difference in dissociation rates. The average lifetime of activated FimH-mannose bonds was 1000 to 10,000 s at forces of 30-70 pN. Structural explanations of the two bound states and the high force resistance provide insights into structural mechanisms for long-lived, force-resistant biomolecular interactions.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141496988","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}
Pub Date : 2024-09-17Epub Date: 2024-07-10DOI: 10.1016/j.bpj.2024.07.009
Maxime Kermarrec, Elise Dumont, Natacha Gillet
Guanine radical cations are precursors to oxidatively induced DNA lesions, and the determination of oxidative DNA hot spots beyond oligonucleotides remains a current challenge. In order to rationalize the finetuned ionization properties of the ∼60 guanines in a nucleosome core particle, we report a robust molecular dynamics-then-FO-DFTB/MM (fragment-orbital tight-binding density functional theory/molecular mechanics) simulation protocol spanning 20 μs. Our work allows us to identify several factors governing guanine ionization potential and map oxidative hotspots. Our results highlight the predominant role of the proximity of positively charged histone residues in the modulation of the guanine ionization potential up to 0.6 eV. Consequently, fast, long-range hole transfer in nucleosomal DNA could be tuned by the proximity of histone tails, which differs, from a biological point of view, on the chromatin state.
鸟嘌呤自由基阳离子是氧化诱导 DNA 病变的前体,确定寡核苷酸以外的 DNA 氧化热点仍然是当前的一项挑战。为了合理解释核糖体核心颗粒(NCP)中 60 个鸟嘌呤的微调电离特性,我们报告了一个强大的 MD-then-FO-DFTB/MM 模拟方案,时间跨度为 20 微秒。我们的工作有助于确定鸟嘌呤电离电位的几个影响因素,并绘制氧化热点图。我们的研究结果表明,带正电荷的组蛋白残基在鸟嘌呤电离电位的调节(最高可达 0.6 eV)中起着主导作用。因此,核糖体 DNA 中的快速远距离空穴传输可能因组蛋白尾部的邻近程度而异,因此从生物学角度来看,也可能因染色质状态而异。
{"title":"What tunes guanine ionization potential in a nucleosome? An all-in-one systematic QM/MM assessment.","authors":"Maxime Kermarrec, Elise Dumont, Natacha Gillet","doi":"10.1016/j.bpj.2024.07.009","DOIUrl":"10.1016/j.bpj.2024.07.009","url":null,"abstract":"<p><p>Guanine radical cations are precursors to oxidatively induced DNA lesions, and the determination of oxidative DNA hot spots beyond oligonucleotides remains a current challenge. In order to rationalize the finetuned ionization properties of the ∼60 guanines in a nucleosome core particle, we report a robust molecular dynamics-then-FO-DFTB/MM (fragment-orbital tight-binding density functional theory/molecular mechanics) simulation protocol spanning 20 μs. Our work allows us to identify several factors governing guanine ionization potential and map oxidative hotspots. Our results highlight the predominant role of the proximity of positively charged histone residues in the modulation of the guanine ionization potential up to 0.6 eV. Consequently, fast, long-range hole transfer in nucleosomal DNA could be tuned by the proximity of histone tails, which differs, from a biological point of view, on the chromatin state.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427773/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578929","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}
Pub Date : 2024-09-17Epub Date: 2024-07-06DOI: 10.1016/j.bpj.2024.07.008
Anupam Mondal, Hamid Teimouri, Anatoly B Kolomeisky
Many biological systems exhibit precise timing of events, and one of the most known examples is cell lysis, which is a process of breaking bacterial host cells in the virus infection cycle. However, the underlying microscopic picture of precise timing remains not well understood. We present a novel theoretical approach to explain the molecular mechanisms of effectively deterministic dynamics in biological systems. Our hypothesis is based on the idea of stochastic coupling between relevant underlying biophysical and biochemical processes that lead to noise cancellation. To test this hypothesis, we introduced a minimal discrete-state stochastic model to investigate how holin proteins produced by bacteriophages break the inner membranes of gram-negative bacteria. By explicitly solving this model, the dynamic properties of cell lysis are fully evaluated, and theoretical predictions quantitatively agree with available experimental data for both wild-type and holin mutants. It is found that the observed threshold-like behavior is a result of the balance between holin proteins entering the membrane and leaving the membrane during the lysis. Theoretical analysis suggests that the cell lysis achieves precise timing for wild-type species by maximizing the number of holins in the membrane and narrowing their spatial distribution. In contrast, for mutated species, these conditions are not satisfied. Our theoretical approach presents a possible molecular picture of precise dynamic regulation in intrinsically random biological processes.
{"title":"Molecular mechanisms of precise timing in cell lysis.","authors":"Anupam Mondal, Hamid Teimouri, Anatoly B Kolomeisky","doi":"10.1016/j.bpj.2024.07.008","DOIUrl":"10.1016/j.bpj.2024.07.008","url":null,"abstract":"<p><p>Many biological systems exhibit precise timing of events, and one of the most known examples is cell lysis, which is a process of breaking bacterial host cells in the virus infection cycle. However, the underlying microscopic picture of precise timing remains not well understood. We present a novel theoretical approach to explain the molecular mechanisms of effectively deterministic dynamics in biological systems. Our hypothesis is based on the idea of stochastic coupling between relevant underlying biophysical and biochemical processes that lead to noise cancellation. To test this hypothesis, we introduced a minimal discrete-state stochastic model to investigate how holin proteins produced by bacteriophages break the inner membranes of gram-negative bacteria. By explicitly solving this model, the dynamic properties of cell lysis are fully evaluated, and theoretical predictions quantitatively agree with available experimental data for both wild-type and holin mutants. It is found that the observed threshold-like behavior is a result of the balance between holin proteins entering the membrane and leaving the membrane during the lysis. Theoretical analysis suggests that the cell lysis achieves precise timing for wild-type species by maximizing the number of holins in the membrane and narrowing their spatial distribution. In contrast, for mutated species, these conditions are not satisfied. Our theoretical approach presents a possible molecular picture of precise dynamic regulation in intrinsically random biological processes.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544488","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}
Pub Date : 2024-09-17Epub Date: 2024-07-18DOI: 10.1016/j.bpj.2024.07.019
Pei Qiao, Melanie T Odenkirk, Weiyi Zheng, Yuchen Wang, Jinhui Chen, Wenhao Xu, Erin S Baker
The significant effects of lipid binding on the functionality of potassium channel KcsA have been validated by brilliant studies. However, the specific interactions between lipids and KcsA, such as binding parameters for each binding event, have not been fully elucidated. In this study, we employed native mass spectrometry to investigate the binding of lipids to KcsA and their effects on the channel. The tetrameric structure of KcsA remains intact even in the absence of lipid binding. However, the subunit architecture of the E71A mutant, which is constantly open at low pH, relies on tightly associated copurified lipids. Furthermore, we observed that lipids exhibit weak binding to KcsA at high pH when the channel is at a closed/inactivation state in the absence of permeant cation K+. This feeble interaction potentially facilitates the association of K+ ions, leading to the transition of the channel to a resting closed/open state. Interestingly, both anionic and zwitterionic lipids strongly bind to KcsA at low pH when the channel is in an open/inactivation state. We also investigated the binding patterns of KcsA with natural lipids derived from E. coli and Streptomyces lividans. Interestingly, lipids from E. coli exhibited much stronger binding affinity compared to the lipids from S. lividans. Among the natural lipids from S. lividans, free fatty acids and triacylglycerols demonstrated the tightest binding to KcsA, whereas no detectable binding events were observed with natural phosphatidic acid lipids. These findings suggest that the lipid association pattern in S. lividans, the natural host for KcsA, warrants further investigation. In conclusion, our study sheds light on the role of lipids in stabilizing KcsA and highlights the importance of specific lipid-protein interactions in modulating its conformational states.
脂质结合对钾通道 KcsA 功能的重要影响已通过出色的研究得到验证。然而,脂质与 KcsA 之间的具体相互作用,如每种结合事件的结合参数,尚未完全阐明。在本研究中,我们采用原生质谱法研究了脂质与 KcsA 的结合及其对通道的影响。即使在没有脂质结合的情况下,KcsA 的四聚体结构也保持完好。然而,E71A 突变体的亚单位结构依赖于紧密结合的共聚脂质,该突变体在低 pH 值下持续开放。此外,我们还观察到,当通道在没有渗透阳离子 K+ 的情况下处于关闭/失活状态时,脂质在高 pH 值下与 KcsA 的结合很弱。这种微弱的相互作用可能会促进 K+ 离子的结合,从而使通道过渡到静止的关闭/打开状态。有趣的是,当通道处于打开/失活状态时,阴离子脂质和齐聚物脂质在低 pH 值下都能与 KcsA 紧密结合。我们还研究了 KcsA 与来自大肠杆菌和 S. lividans 的天然脂质的结合模式。有趣的是,与 S. lividans 的脂质相比,大肠杆菌的脂质表现出更强的结合亲和力。在来自 S. lividans 的天然脂质中,游离脂肪酸和三酰甘油与 KcsA 的结合最为紧密,而天然 PA 脂质则未发现任何可检测到的结合事件。这些发现表明,KcsA 的天然宿主 S. lividans 中的脂质结合模式值得进一步研究。总之,我们的研究揭示了脂质在稳定 KcsA 方面的作用,并强调了特定脂质-蛋白质相互作用在调节其构象状态方面的重要性。
{"title":"Elucidating the role of lipid interactions in stabilizing the membrane protein KcsA.","authors":"Pei Qiao, Melanie T Odenkirk, Weiyi Zheng, Yuchen Wang, Jinhui Chen, Wenhao Xu, Erin S Baker","doi":"10.1016/j.bpj.2024.07.019","DOIUrl":"10.1016/j.bpj.2024.07.019","url":null,"abstract":"<p><p>The significant effects of lipid binding on the functionality of potassium channel KcsA have been validated by brilliant studies. However, the specific interactions between lipids and KcsA, such as binding parameters for each binding event, have not been fully elucidated. In this study, we employed native mass spectrometry to investigate the binding of lipids to KcsA and their effects on the channel. The tetrameric structure of KcsA remains intact even in the absence of lipid binding. However, the subunit architecture of the E71A mutant, which is constantly open at low pH, relies on tightly associated copurified lipids. Furthermore, we observed that lipids exhibit weak binding to KcsA at high pH when the channel is at a closed/inactivation state in the absence of permeant cation K<sup>+</sup>. This feeble interaction potentially facilitates the association of K<sup>+</sup> ions, leading to the transition of the channel to a resting closed/open state. Interestingly, both anionic and zwitterionic lipids strongly bind to KcsA at low pH when the channel is in an open/inactivation state. We also investigated the binding patterns of KcsA with natural lipids derived from E. coli and Streptomyces lividans. Interestingly, lipids from E. coli exhibited much stronger binding affinity compared to the lipids from S. lividans. Among the natural lipids from S. lividans, free fatty acids and triacylglycerols demonstrated the tightest binding to KcsA, whereas no detectable binding events were observed with natural phosphatidic acid lipids. These findings suggest that the lipid association pattern in S. lividans, the natural host for KcsA, warrants further investigation. In conclusion, our study sheds light on the role of lipids in stabilizing KcsA and highlights the importance of specific lipid-protein interactions in modulating its conformational states.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141730966","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}
Pub Date : 2024-09-17Epub Date: 2024-07-23DOI: 10.1016/j.bpj.2024.07.023
Marjolein de Jager, Pauline J Kolbeck, Willem Vanderlinden, Jan Lipfert, Laura Filion
Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved in DNA bending, bridging, looping, and compaction (≥1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations a natural approach. Here, we present a simple and generic coarse-grained model for DNA-protein and protein-protein interactions and investigate the role of the latter in the protein-induced compaction of DNA. Our approach models the DNA as a discrete worm-like chain. The proteins are treated in the grand canonical ensemble, and the protein-DNA binding strength is taken from experimental measurements. Protein-DNA interactions are modeled as an isotropic binding potential with an imposed binding valency without specific assumptions about the binding geometry. To systematically and quantitatively classify DNA-protein complexes, we present an unsupervised machine learning pipeline that receives a large set of structural order parameters as input, reduces the dimensionality via principal-component analysis, and groups the results using a Gaussian mixture model. We apply our method to recent data on the compaction of viral genome-length DNA by HIV integrase and find that protein-protein interactions are critical to the formation of looped intermediate structures seen experimentally. Our methodology is broadly applicable to DNA-binding proteins and protein-induced DNA compaction and provides a systematic and semi-quantitative approach for analyzing their mesoscale complexes.
蛋白质与 DNA 的相互作用以及蛋白质介导的 DNA 压实在一系列生物过程中发挥着关键作用。DNA 弯曲、桥接、环绕和压实通常涉及的长度尺度(≥ 1 kbp)是实验或全原子分子动力学模拟所难以解决的,因此粗粒度模拟是一种自然的方法。在此,我们提出了一个简单通用的粗粒度模型,用于描述 DNA 与蛋白质以及蛋白质与蛋白质之间的相互作用,并研究了后者在蛋白质诱导的 DNA 压实中的作用。我们的方法将 DNA 建模为离散的蠕虫链。蛋白质在大规范集合中处理,蛋白质与 DNA 的结合强度来自实验测量。蛋白质与 DNA 的相互作用被模拟为各向同性的结合势,并施加了一个结合价,而不对结合的几何形状做具体假设。为了对 DNA 蛋白复合物进行系统和定量的分类,我们提出了一种无监督机器学习方法,该方法接收大量结构顺序参数作为输入,通过主成分分析降低维度,并使用高斯混合模型对结果进行分组。我们将这一方法应用于 HIV 整合酶压实病毒基因组长 DNA 的最新数据,发现蛋白质与蛋白质之间的相互作用对于形成实验所见的环状中间结构至关重要。我们的方法广泛适用于 DNA 结合蛋白和蛋白质诱导的 DNA 压实,并为分析它们的中尺度复合物提供了一种系统的半定量方法。
{"title":"Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning.","authors":"Marjolein de Jager, Pauline J Kolbeck, Willem Vanderlinden, Jan Lipfert, Laura Filion","doi":"10.1016/j.bpj.2024.07.023","DOIUrl":"10.1016/j.bpj.2024.07.023","url":null,"abstract":"<p><p>Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved in DNA bending, bridging, looping, and compaction (≥1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations a natural approach. Here, we present a simple and generic coarse-grained model for DNA-protein and protein-protein interactions and investigate the role of the latter in the protein-induced compaction of DNA. Our approach models the DNA as a discrete worm-like chain. The proteins are treated in the grand canonical ensemble, and the protein-DNA binding strength is taken from experimental measurements. Protein-DNA interactions are modeled as an isotropic binding potential with an imposed binding valency without specific assumptions about the binding geometry. To systematically and quantitatively classify DNA-protein complexes, we present an unsupervised machine learning pipeline that receives a large set of structural order parameters as input, reduces the dimensionality via principal-component analysis, and groups the results using a Gaussian mixture model. We apply our method to recent data on the compaction of viral genome-length DNA by HIV integrase and find that protein-protein interactions are critical to the formation of looped intermediate structures seen experimentally. Our methodology is broadly applicable to DNA-binding proteins and protein-induced DNA compaction and provides a systematic and semi-quantitative approach for analyzing their mesoscale complexes.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141750994","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}
Pub Date : 2024-09-14DOI: 10.1016/j.bpj.2024.09.012
Benjamin Pfeuty
The transduction of free energy in metabolic networks represents a thermodynamic mechanism by which the free energy derived from nutrients is converted to drive nonspontaneous, energy-requiring metabolic reactions. This transduction is typically observed in processes that generate energy-rich molecules such as ATP and NAD(P)H, which, in turn, power specific reactions, particularly biosynthetic reactions. This property establishes a pivotal connection between the intricate topology of metabolic networks and their ability to reroute energy for functional purposes. The present study proposes a dedicated framework aimed at exploring the relationship between free-energy dissipation, network topology, and metabolic objectives. The starting point is that, regardless of the network topology, nonequilibrium chemostatting conditions impose stringent thermodynamic constraints on the feasible flux steady states to satisfy energy and entropy balance. An analysis of randomly sampled reaction networks shows that the network topology imposes additional constraints that restrict the accessible flux solution space, depending on key structural features such as the reaction’s molecularity, reaction cycles, and conservation laws. Notably, topologies featuring multimolecular reactions that implement free-energy transduction mechanisms tend to extend the accessible flux domains, facilitating the achievement of metabolic objectives such as anabolic flux maximization or flux rerouting capacity. This approach is applied to a coarse-grained model of carbohydrate metabolism, highlighting the structural requirements for optimal biomass yield.
新陈代谢网络中的自由能转换是一种热力学机制,通过这种机制,从营养物质中获得的自由能被转换为非自发的、需要能量的新陈代谢反应的动力。这种转换通常发生在产生 ATP 和 NAD(P)H 等富含能量分子的过程中,而 ATP 和 NAD(P)H 又反过来为特定反应,特别是生物合成反应提供能量。这一特性建立了新陈代谢网络错综复杂的拓扑结构与其为功能目的重新分配能量的能力之间的关键联系。本研究提出了一个专门的框架,旨在探索自由能耗散、网络拓扑结构和代谢目标之间的关系。研究的出发点是,无论网络拓扑结构如何,非平衡化合条件都会对可行的通量稳态施加严格的热力学约束,以满足能量和熵的平衡。对随机取样反应网络的分析表明,网络拓扑结构还施加了额外的约束,限制了可访问的通量解决方案空间,这取决于反应的分子性、反应周期和守恒定律等关键结构特征。值得注意的是,以实施自由能转换机制的多分子反应为特征的拓扑结构往往会扩展可访问的通量域,从而有利于实现同化通量最大化或通量改道能力等代谢目标。这种方法被应用于碳水化合物代谢的粗粒度模型,突出了最佳生物质产量的结构要求。
{"title":"Free-energy transduction mechanisms shape the flux space of metabolic networks","authors":"Benjamin Pfeuty","doi":"10.1016/j.bpj.2024.09.012","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.09.012","url":null,"abstract":"The transduction of free energy in metabolic networks represents a thermodynamic mechanism by which the free energy derived from nutrients is converted to drive nonspontaneous, energy-requiring metabolic reactions. This transduction is typically observed in processes that generate energy-rich molecules such as ATP and NAD(P)H, which, in turn, power specific reactions, particularly biosynthetic reactions. This property establishes a pivotal connection between the intricate topology of metabolic networks and their ability to reroute energy for functional purposes. The present study proposes a dedicated framework aimed at exploring the relationship between free-energy dissipation, network topology, and metabolic objectives. The starting point is that, regardless of the network topology, nonequilibrium chemostatting conditions impose stringent thermodynamic constraints on the feasible flux steady states to satisfy energy and entropy balance. An analysis of randomly sampled reaction networks shows that the network topology imposes additional constraints that restrict the accessible flux solution space, depending on key structural features such as the reaction’s molecularity, reaction cycles, and conservation laws. Notably, topologies featuring multimolecular reactions that implement free-energy transduction mechanisms tend to extend the accessible flux domains, facilitating the achievement of metabolic objectives such as anabolic flux maximization or flux rerouting capacity. This approach is applied to a coarse-grained model of carbohydrate metabolism, highlighting the structural requirements for optimal biomass yield.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142275762","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}
Pub Date : 2024-09-14DOI: 10.1016/j.bpj.2024.09.014
Inayat Ullah Irshad, Ajeet K. Sharma
Protein synthesis regulation primarily occurs at translation initiation, the first step of gene translation. However, the regulation of translation initiation under various conditions is not fully understood. Specifically, the reason why protein production from certain mRNAs remains resistant to stress while others do not show such resilience. Moreover, why is protein production enhanced from a few transcripts under stress conditions, whereas it is decreased in the majority of transcripts? We address them by developing a Monte Carlo simulation model of protein synthesis and ribosome scanning. We find that mRNAs with strong Kozak contexts exhibit minimal reduction in translation initiation rate under stress conditions. Moreover, these transcripts exhibit even greater resilience to stress when the scanning speed of 43S ribosome subunit is slow, albeit at the cost of reduced initiation rate. This implies a trade-off between initiation rate and the ability of mRNA to withstand stress. We also show that mRNAs featuring an upstream ORF can act as a regulatory switch. This switch elevates protein production from the main ORF under stress conditions; however, minimal to no proteins are produced under the normal condition. Because, in stress, a larger fraction of 43S ribosomes bypasses the upstream ORF due to its weak Kozak context. This, in turn, increases the number of scanning ribosomes reaching the main ORF, whose strong Kozak context can convert them into 80S ribosomes, even under stress conditions. This switching allows an efficient use of cellular resources by producing proteins when they are required. Thus, our computational study provides valuable insights into our understanding of stress-responsive translation-initiation.
{"title":"Understanding the regulation of protein synthesis under stress conditions","authors":"Inayat Ullah Irshad, Ajeet K. Sharma","doi":"10.1016/j.bpj.2024.09.014","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.09.014","url":null,"abstract":"Protein synthesis regulation primarily occurs at translation initiation, the first step of gene translation. However, the regulation of translation initiation under various conditions is not fully understood. Specifically, the reason why protein production from certain mRNAs remains resistant to stress while others do not show such resilience. Moreover, why is protein production enhanced from a few transcripts under stress conditions, whereas it is decreased in the majority of transcripts? We address them by developing a Monte Carlo simulation model of protein synthesis and ribosome scanning. We find that mRNAs with strong Kozak contexts exhibit minimal reduction in translation initiation rate under stress conditions. Moreover, these transcripts exhibit even greater resilience to stress when the scanning speed of 43S ribosome subunit is slow, albeit at the cost of reduced initiation rate. This implies a trade-off between initiation rate and the ability of mRNA to withstand stress. We also show that mRNAs featuring an upstream ORF can act as a regulatory switch. This switch elevates protein production from the main ORF under stress conditions; however, minimal to no proteins are produced under the normal condition. Because, in stress, a larger fraction of 43S ribosomes bypasses the upstream ORF due to its weak Kozak context. This, in turn, increases the number of scanning ribosomes reaching the main ORF, whose strong Kozak context can convert them into 80S ribosomes, even under stress conditions. This switching allows an efficient use of cellular resources by producing proteins when they are required. Thus, our computational study provides valuable insights into our understanding of stress-responsive translation-initiation.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142275761","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}
Pub Date : 2024-09-13DOI: 10.1016/j.bpj.2024.09.013
P. Campitelli, D. Ross, L. Swint-Kruse, S.B. Ozkan
In some proteins, a unique class of nonconserved positions is characterized by their ability to generate diverse functional outcomes through single amino acid substitutions. Due to their ability to tune protein function, accurately identifying such “rheostat” positions is crucial for protein design, for understanding the impact of mutations observed in humans, and for predicting the evolution of pathogen drug resistance. However, identifying rheostat positions has been challenging, due—in part—to the absence of a clear structural relationship with binding sites. In this study, experimental data from our previous study of the Escherichia coli lactose repressor protein (LacI) was used to identify rheostat positions for which mutations tune in vivo EC50 for the allosteric ligand “IPTG.” We next used the rheostat assignments to test the hypothesis that rheostat positions have unique dynamic features that will enable their identification. To that end, we integrated all-atom molecular dynamics simulations with perturbation residue response analysis. Results first revealed distinct dynamic behavior in IPTG-bound LacI compared with apo LacI, which was consistent with IPTG’s role as an allosteric inducer. Next, we used a variety of dynamic features to build a classification model that discriminates experimentally characterized rheostat positions in LacI from positions with other types of substitution outcomes. In parallel, we built a second classifier model based on the 3D structural “static” network features of LacI. In comparative studies, the dynamic model better identified rheostat positions that were >8 Å from the binding site. In summary, our study provides insights into the dynamic characteristics of rheostat positions and suggests that models built on dynamic features may be useful for predicting the locations of rheostat positions in a wide range of proteins.
{"title":"Dynamics-based protein network features accurately discriminate neutral and rheostat positions","authors":"P. Campitelli, D. Ross, L. Swint-Kruse, S.B. Ozkan","doi":"10.1016/j.bpj.2024.09.013","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.09.013","url":null,"abstract":"In some proteins, a unique class of nonconserved positions is characterized by their ability to generate diverse functional outcomes through single amino acid substitutions. Due to their ability to tune protein function, accurately identifying such “rheostat” positions is crucial for protein design, for understanding the impact of mutations observed in humans, and for predicting the evolution of pathogen drug resistance. However, identifying rheostat positions has been challenging, due—in part—to the absence of a clear structural relationship with binding sites. In this study, experimental data from our previous study of the <ce:italic>Escherichia coli</ce:italic> lactose repressor protein (LacI) was used to identify rheostat positions for which mutations tune in vivo EC<ce:inf loc=\"post\">50</ce:inf> for the allosteric ligand “IPTG.” We next used the rheostat assignments to test the hypothesis that rheostat positions have unique dynamic features that will enable their identification. To that end, we integrated all-atom molecular dynamics simulations with perturbation residue response analysis. Results first revealed distinct dynamic behavior in IPTG-bound LacI compared with apo LacI, which was consistent with IPTG’s role as an allosteric inducer. Next, we used a variety of dynamic features to build a classification model that discriminates experimentally characterized rheostat positions in LacI from positions with other types of substitution outcomes. In parallel, we built a second classifier model based on the 3D structural “static” network features of LacI. In comparative studies, the dynamic model better identified rheostat positions that were >8 Å from the binding site. In summary, our study provides insights into the dynamic characteristics of rheostat positions and suggests that models built on dynamic features may be useful for predicting the locations of rheostat positions in a wide range of proteins.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142275765","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}