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Computational model of excitable cell indicates ATP free energy dynamics in response to calcium oscillations are undampened by cytosolic ATP buffers. 可兴奋细胞的计算模型表明，响应钙振荡的ATP自由能动力学不受细胞质ATP缓冲液的抑制。
Systems biology Pub Date : 2006-09-01 DOI: 10.1049/ip-syb:20060017
R G P M van Stiphout, N A W van Riel, P J Verhoog, P A J Hilbers, K Nicolay, J A L Jeneson
{"title":"Computational model of excitable cell indicates ATP free energy dynamics in response to calcium oscillations are undampened by cytosolic ATP buffers.","authors":"R G P M van Stiphout,&nbsp;N A W van Riel,&nbsp;P J Verhoog,&nbsp;P A J Hilbers,&nbsp;K Nicolay,&nbsp;J A L Jeneson","doi":"10.1049/ip-syb:20060017","DOIUrl":"https://doi.org/10.1049/ip-syb:20060017","url":null,"abstract":"<p><p>Mitochondria in excitable cells are recurrently exposed to pulsatile calcium gradients that activate cell function. Rapid calcium uptake by the mitochondria has previously been shown to cause uncoupling of oxidative phosphorylation. To test (i) if periodic nerve firing may cause oscillation of the cytosolic thermodynamic potential of ATP hydrolysis and (ii) if cytosolic adenylate (AK) and creatine kinase (CK) ATP buffering reactions dampen such oscillations, a lumped kinetic model of an excitable cell capturing major aspects of the physiology has been developed. Activation of ATP metabolism by low-frequency calcium pulses caused large oscillation of the cytosolic, but not mitochondrial ATP/ADP, ratio. This outcome was independent of net ATP synthesis or hydrolysis during mitochondrial calcium uptake. The AK/CK ATP buffering reactions dampened the amplitude and rate of cytosolic ATP/ADP changes on a timescale of seconds, but not milliseconds. These model predictions suggest that alternative sources of capacitance in neurons and striated muscles should be considered to protect ATP-free energy-driven cell functions.</p>","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"405-8"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/ip-syb:20060017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26262547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 13
Molecular modelling of K(ATP) channel blockers-ADP/ ATP carrier interactions. K(ATP)通道阻滞剂- adp / ATP载体相互作用的分子模拟。
Systems biology Pub Date : 2006-09-01 DOI: 10.1049/ip-syb:20060007
A Ziemys, A Toleikis, D M Kopustinskiene
{"title":"Molecular modelling of K(ATP) channel blockers-ADP/ ATP carrier interactions.","authors":"A Ziemys,&nbsp;A Toleikis,&nbsp;D M Kopustinskiene","doi":"10.1049/ip-syb:20060007","DOIUrl":"https://doi.org/10.1049/ip-syb:20060007","url":null,"abstract":"<p><p>The modelling of molecule-molecule interactions has been widely accepted as a tool for drug discovery and development studies. However, this powerful technique is unappreciated in physiological and biochemical studies, where it could be extremely useful for understanding the mechanisms of action of various compounds in cases when experimental data are controversial due to complexity of the investigated systems. In this study, based on the biochemical data suggesting involvement of mitochondrial ADP/ATP carrier in K+ and H+ transport to mitochondrial matrix molecular modelling is applied to elucidate the possible interactions between the ADP/ATP carrier and its putative ligands--K(ATP) channel blockers glybenclamide, tolbutamide and 5-hydroxydecanoate. Results revealed that K(ATP) channel blockers could bind to the specific location proximal to H1, H4, H5 and H6 transmembrane helices within the cavity of the ADP/ ATP carrier. Analysis of the predicted binding site suggests that K(ATP) channel blockers could interfere with both the ADP/ATP translocation and possible cation flux through the ADP/ATP carrier, and supports the hypothesis that the ADP/ATP carrier is a target of K(ATP) channel modulators.</p>","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"390-3"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/ip-syb:20060007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26320437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Summation theorems for flux and concentration control coefficients of dynamic systems. 动态系统通量和浓度控制系数的求和定理。
Systems biology Pub Date : 2006-09-01 DOI: 10.1049/ip-syb:20060024
R Conradie, H V Westerhoff, J M Rohwer, J H S Hofmeyr, J L Snoep
{"title":"Summation theorems for flux and concentration control coefficients of dynamic systems.","authors":"R Conradie,&nbsp;H V Westerhoff,&nbsp;J M Rohwer,&nbsp;J H S Hofmeyr,&nbsp;J L Snoep","doi":"10.1049/ip-syb:20060024","DOIUrl":"https://doi.org/10.1049/ip-syb:20060024","url":null,"abstract":"<p><p>Metabolic control analysis (MCA) was developed to quantify how system variables are affected by parameter variations in a system. In addition, MCA can express the global properties of a system in terms of the individual catalytic steps, using connectivity and summation theorems to link the control coefficients to the elasticity coefficients. MCA was originally developed for steady-state analysis and not all summation theorems have been derived for dynamic systems. A method to determine time-dependent flux and concentration control coefficients for dynamic systems by expressing the time domain as a function of percentage progression through any arbitrary fixed interval of time is reported. Time-dependent flux and concentration control coefficients of dynamic systems, provided that they are evaluated in this novel way, obey the same summation theorems as steady-state flux and concentration control coefficients, respectively.</p>","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"314-7"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/ip-syb:20060024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26262199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
Time-dependent hierarchical regulation analysis: deciphering cellular adaptation. 时变层次调控分析:解读细胞适应性。
Systems biology Pub Date : 2006-09-01 DOI: 10.1049/ip-syb:20060027
F J Bruggeman, J de Haan, H Hardin, J Bouwman, S Rossell, K van Eunen, B M Bakker, H V Westerhoff
{"title":"Time-dependent hierarchical regulation analysis: deciphering cellular adaptation.","authors":"F J Bruggeman,&nbsp;J de Haan,&nbsp;H Hardin,&nbsp;J Bouwman,&nbsp;S Rossell,&nbsp;K van Eunen,&nbsp;B M Bakker,&nbsp;H V Westerhoff","doi":"10.1049/ip-syb:20060027","DOIUrl":"https://doi.org/10.1049/ip-syb:20060027","url":null,"abstract":"<p><p>Cells adapt to changes in their environment by the concerted action of many different regulatory mechanisms. Examples of such mechanisms are feedback inhibition by intermediates of metabolism, covalent modification of enzymes and changes in the abundance of mRNAs and proteins. These mechanisms act in parallel at different levels in the cellular hierarchy while regulating a single process. Existing hierarchical regulation analysis determines the relative importance of these mechanisms when the cell regulates a transition from one steady-state to another. Here, the analysis is extended to the regulation of time-dependent phenomena, for which two methods are introduced and illustrated with a kinetic model incorporating transcription and translation of metabolic enzymes.</p>","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"318-22"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/ip-syb:20060027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26262200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 30
Systems biology: redefining biothermokinetics. Proceedings of the 12th BioThermoKinetics (BKT) International Study Group for Systems Biology Meeting. Trakai, Lithuania. 系统生物学:重新定义生物热动力学。第12届BioThermoKinetics (BKT)国际研究小组系统生物学会议记录。Trakai,立陶宛。
Systems biology Pub Date : 2006-09-01
{"title":"Systems biology: redefining biothermokinetics. Proceedings of the 12th BioThermoKinetics (BKT) International Study Group for Systems Biology Meeting. Trakai, Lithuania.","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"312-408"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26329425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Is there an optimal ribosome concentration for maximal protein production? 是否有一个最佳的核糖体浓度，以最大限度地产生蛋白质?
Systems biology Pub Date : 2006-09-01 DOI: 10.1049/ip-syb:20060023
J L Snoep, H V Westerhoff, J M Rohwer, J H S Hofmeyr
{"title":"Is there an optimal ribosome concentration for maximal protein production?","authors":"J L Snoep,&nbsp;H V Westerhoff,&nbsp;J M Rohwer,&nbsp;J H S Hofmeyr","doi":"10.1049/ip-syb:20060023","DOIUrl":"https://doi.org/10.1049/ip-syb:20060023","url":null,"abstract":"<p><p>A core model is presented for protein production in Escherichia coli to address the question whether there is an optimal ribosomal concentration for non-ribosome protein production. Analysing the steady-state solution of the model over a range of mRNA concentrations, indicates that such an optimum ribosomal content exists, and that the optimum shifts to higher ribosomal contents at higher specific growth rates.</p>","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"398-400"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/ip-syb:20060023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26320439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Challenges to be faced in the reconstruction of metabolic networks from public databases. 从公共数据库重建代谢网络面临的挑战。
Systems biology Pub Date : 2006-09-01 DOI: 10.1049/ip-syb:20060012
M G Poolman, B K Bonde, A Gevorgyan, H H Patel, D A Fell
{"title":"Challenges to be faced in the reconstruction of metabolic networks from public databases.","authors":"M G Poolman,&nbsp;B K Bonde,&nbsp;A Gevorgyan,&nbsp;H H Patel,&nbsp;D A Fell","doi":"10.1049/ip-syb:20060012","DOIUrl":"https://doi.org/10.1049/ip-syb:20060012","url":null,"abstract":"<p><p>In the post-genomic era, the biochemical information for individual compounds, enzymes, reactions to be found within named organisms has become readily available. The well-known KEGG and BioCyc databases provide a comprehensive catalogue for this information and have thereby substantially aided the scientific community. Using these databases, the complement of enzymes present in a given organism can be determined and, in principle, used to reconstruct the metabolic network. However, such reconstructed networks contain numerous properties contradicting biological expectation. The metabolic networks for a number of organisms are reconstructed from KEGG and BioCyc databases, and features of these networks are related to properties of their originating database.</p>","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"379-84"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/ip-syb:20060012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26320435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 67
Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism. 生物网络分析的连通性矩阵方法及其在碳水化合物代谢模型网络原子水平分析中的应用。
Systems biology Pub Date : 2006-09-01 DOI: 10.1049/ip-syb:20060018
J Ohta
{"title":"Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism.","authors":"J Ohta","doi":"10.1049/ip-syb:20060018","DOIUrl":"https://doi.org/10.1049/ip-syb:20060018","url":null,"abstract":"<p><p>An approach for analysis of biological networks is proposed. In this approach, named the connectivity matrix (CM) method, all the connectivities of interest are expressed in a matrix. Then, a variety of analyses are performed on GNU Octave or Matlab. Each node in the network is expressed as a row vector or numeral that carries information defining or characterising the node itself. Information about connectivity itself is also expressed as a row vector or numeral. Thus, connection of node n1 to node n2 through edge e is expressed as [n1, n2, e], a row vector formed by the combination of three row vectors or numerals, where n1, n2 and e indicate two different nodes and one connectivity, respectively. All the connectivities in any given network are expressed as a matrix, CM, each row of which corresponds to one connectivity. Using this CM method, intermetabolite atom-level connectivity is investigated in a model metabolic network composed of the reactions for glycolysis, oxidative decarboxylation of pyruvate, citric acid cycle, pentose phosphate pathway and gluconeogenesis.</p>","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"372-4"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/ip-syb:20060018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26320433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Brownian dynamic model of the glycine receptor chloride channel: effect of the position of charged amino acids on ion membrane currents. 甘氨酸受体氯离子通道的布朗动力学模型:带电氨基酸位置对离子膜电流的影响。
Systems biology Pub Date : 2006-09-01 DOI: 10.1049/ip-syb:20060008
S E Boronovsky, I P Seraya, Ya R Nartsissov
{"title":"Brownian dynamic model of the glycine receptor chloride channel: effect of the position of charged amino acids on ion membrane currents.","authors":"S E Boronovsky,&nbsp;I P Seraya,&nbsp;Ya R Nartsissov","doi":"10.1049/ip-syb:20060008","DOIUrl":"https://doi.org/10.1049/ip-syb:20060008","url":null,"abstract":"<p><p>Glycine is the major inhibitory neurotransmitter in the brainstem and spinal cord, where it participates in a variety of motor and sensory functions. It activates a special type of ligand-gated membrane receptor, which provides for Cl- ion conductance of the neuronal membrane. Computer simulations of a single-channel current through this receptor have been carried out on the basis of Brownian (Langevin) dynamics. The dependence of the currents on pore diameter and the location of the charged amino acid residues have been obtained. It has been shown that the presence and the symmetry of the filter-forming residues determined not only the ion-selectivity of the channel but also increased transmembrane anion current.</p>","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"394-7"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/ip-syb:20060008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26320438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Evaluation of a simplified generic bi-substrate rate equation for computational systems biology. 计算系统生物学中简化的双底物速率方程的评价。
Systems biology Pub Date : 2006-09-01 DOI: 10.1049/ip-syb:20060026
J M Rohwer, A J Hanekom, C Crous, J L Snoep, J H S Hofmeyr
{"title":"Evaluation of a simplified generic bi-substrate rate equation for computational systems biology.","authors":"J M Rohwer,&nbsp;A J Hanekom,&nbsp;C Crous,&nbsp;J L Snoep,&nbsp;J H S Hofmeyr","doi":"10.1049/ip-syb:20060026","DOIUrl":"https://doi.org/10.1049/ip-syb:20060026","url":null,"abstract":"<p><p>The evaluation of a generic simplified bi-substrate enzyme kinetic equation, whose derivation is based on the assumption of equilibrium binding of substrates and products in random order, is described. This equation is much simpler than the mechanistic (ordered and ping-pong) models, in that it contains fewer parameters (that is, no K(i) values for the substrates and products). The generic equation fits data from both the ordered and the ping-pong models well over a wide range of substrate and product concentrations. In the cases where the fit is not perfect, an improved fit can be obtained by considering the rate equation for only a single set of product concentrations. Due to its relative simplicity in comparison to the mechanistic models, this equation will be useful for modelling bi-substrate reactions in computational systems biology.</p>","PeriodicalId":87457,"journal":{"name":"Systems biology","volume":"153 5","pages":"338-41"},"PeriodicalIF":0.0,"publicationDate":"2006-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/ip-syb:20060026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26320029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 35
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