用于扰动热力学上不可行的代谢网络的算法。

Algorithm for perturbing thermodynamically infeasible metabolic networks.

作者信息

Nigam R, Liang S

机构信息

W.W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305-4085, USA.

出版信息

Comput Biol Med. 2007 Feb;37(2):126-33. doi: 10.1016/j.compbiomed.2006.01.002. Epub 2006 Apr 17.

DOI:10.1016/j.compbiomed.2006.01.002

PMID:16616911

Abstract

Networks of reactions inside the cell are constrained by the laws of mass and energy balance. The second law of thermodynamics further constrains the topology of the metabolic network, by disallowing interactions that can sustain themselves when they are isolated from the rest of the network. We present an algorithm that identifies such subnetworks and makes them feasible by deleting reactions. This perturbs the network topology, but preserves the optimality of the mass balance solutions. This method has been applied to a full network of Escherichia coli.

摘要

细胞内的反应网络受到质量和能量平衡定律的限制。热力学第二定律进一步限制了代谢网络的拓扑结构，它不允许那些从网络其余部分分离出来时仍能自我维持的相互作用。我们提出了一种算法，该算法可识别此类子网络，并通过删除反应使其可行。这会扰乱网络拓扑结构，但能保持质量平衡解的最优性。此方法已应用于大肠杆菌的完整网络。