title: A Networks Approach to Modeling Enzymatic Reactions.
abstract: Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes.
authors: Institute of Theoretical Physics, Free University Berlin, Berlin, Germany. Electronic address: petra.imhof@fu-berlin.de.
authors: P
authors: P
authors: Imhof
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry*; D055162:Biocatalysis; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry*; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology; D006801:Humans; D007700:Kinetics; D053858:Metabolic Networks and Pathways; D056004:Molecular Dynamics Simulation; D009218:Myosins / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry*; D044502:Thymine DNA Glycosylase / Q000737:chemistry*
chemical_list: D000255:Adenosine Triphosphate; D015252:Deoxyribonucleases, Type II Site-Specific; C027440:GATATC-specific type II deoxyribonucleases; D044502:Thymine DNA Glycosylase; D009218:Myosins; D013941:Thymine
keywords: Energy landscape; Hydrolysis; Path sampling; QM/MM; Transition network