“Graph theory in enzymatic kinetics”的意思、由来-开放百科全书

The first paper introducing the graph theory in enzyme kinetics was published in 1979. In that paper, three graphical rules based on graph theory were presented for deriving kinetic equations in steady-state enzyme-catalyzed systems. Shortly afterwards, two more effective graphical rules were proposed.^[2] In 1985, these graphic rules had been implemented by David Myers and Graham Plamer^[4] as microcomputer tools for finding numeric solutions for extremely complicated enzyme kinetics systems.

Using graphical rules to deal with kinetic systems is an elegant approach that combines graph representation and rigorous mathematical derivation. It has the following advantages: (1) providing an intuitive picture or illuminative insights; (2) helping grasp the key points from complicated details; (3) greatly simplifying many tedious, laborious, and error-prone calculations; and (4) able to double-check the final results. In 1989, a set of four graphic rules were summarized by Kuo-Chen Chou,^[5] where rules 1-3 are for steady state enzyme-catalyzed systems, while Rule 4 is for non-steady state enzyme-catalyzed systems. Subsequently, these graphic rules were extended to deal with protein folding kinetics as well.^[6]

Special applications in biology and drug development

These graphical rules can significantly simplify the derivation of enzyme kinetic equations^[7] and help mechanism analysis.^[8] They may be utilized to investigate kinetic mechanisms of drugs inhibiting HIV reverse transcriptase,^[9]^[10] and inhibition kinetics of processive nucleic acid polymerases and nucleases.^[11]

In 2008, based on Chou’s graphic rules,^[5] John Andraos^[13] developed two fast methods for determining product ratios for kinetic schemes leading to multiple products without rate laws. In 2010, the non-steady state graphic rule was extended to deal with drug metabolism systems.^[14]

References

1. ^¹{{cite journal |pmid=7188428 |year=1980 |last1=Chou |first1=Kuo-Chen |last2=Forsén |first2=Sture |title=Graphical Rules for Enzyme-Catalysed Rate Laws |volume=187 |issue=3 |pages=829–35 |pmc=1162468 |journal=The Biochemical Journal}}
2. ^¹²{{cite journal |pmid=2745429 |year=1989 |last1=Chou |first1=Kuo-Chen |title=Graphic Rules in Steady and Non-steady State Enzyme Kinetics |url=http://www.jbc.org/cgi/pmidlookup?view=long&pmid=2745429 |volume=264 |issue=20 |pages=12074–9 |journal=The Journal of Biological Chemistry}}
3. ^¹{{cite journal |doi=10.1016/0301-4622(90)80056-D |title=Applications of graph theory to enzyme kinetics and protein folding kinetics |year=1990 |last1=Chou |first1=Kuo-Chen |journal=Biophysical Chemistry |volume=35 |pages=1–24 |pmid=2183882 |issue=1}}
4. ^¹{{cite journal |pmid=6477507 |year=1984 |last1=Zhou |first1=Guo-Ping |last2=Deng |first2=Mei-Hua |title=An extension of Chou's graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways |volume=222 |issue=1 |pages=169–76 |pmc=1144157 |journal=The Biochemical Journal}}
5. ^¹{{cite journal |pmid=2351663 |year=1990 |last1=Lin |first1=Sheng-Xiang |last2=Neet |first2=Kenneth E. |title=Demonstration of a Slow Conformational Change in Liver Glucokinase by Fluorescence Spectroscopy |url=http://www.jbc.org/cgi/pmidlookup?view=long&pmid=2351663 |volume=265 |issue=17 |pages=9670–5 |journal=The Journal of Biological Chemistry}}
6. ^¹{{cite journal |pmid=7681060 |year=1993 |last1=Althaus |first1=Irene W. |last2=Chou |first2=James J. |last3=Gonzales |first3=Andrea J. |last4=Deibel |first4=Martin R. |last5=Chou |first5=Kuo-Chen |last6=Kezdy |first6=Ferenc J. |last7=Romero |first7=Donna L. |last8=Aristoff |first8=Paul A. |last9=Tarpley |first9=W. Gary |last10=Reusser |first10=F |title=Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E |url=http://www.jbc.org/cgi/pmidlookup?view=long&pmid=7681060 |volume=268 |issue=9 |pages=6119–24 |journal=The Journal of Biological Chemistry|display-authors=8 }}
7. ^¹{{cite journal |pmid=7687145 |year=1993 |last1=Althaus |first1=IW |last2=Chou |first2=JJ |last3=Gonzales |first3=AJ |last4=Deibel |first4=MR |last5=Chou |first5=KC |last6=Kezdy |first6=FJ |last7=Romero |first7=DL |last8=Palmer |first8=JR |last9=Thomas |first9=RC |last10=Aristoff |first10=P. A. |title=Kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-88204E |volume=32 |issue=26 |pages=6548–54 |journal=Biochemistry |doi=10.1021/bi00077a008|display-authors=8 }}
8. ^¹{{cite journal |doi=10.1006/abio.1994.1405 |title=Kinetics of Processive Nucleic Acid Polymerases and Nucleases |year=1994 |last1=Chou |first1=K.C. |last2=Kezdy |first2=F.J. |last3=Reusser |first3=F. |journal=Analytical Biochemistry |volume=221 |issue=2 |pages=217–30 |pmid=7529005}}
9. ^¹{{cite journal |doi=10.1093/bioinformatics/1.2.105 |pmid=3880330 |year=1985 |last1=Myers |first1=David |last2=Palmer |first2=Graham |title=Microcomputer tools for steady–state enzyme kinetics |volume=1 |issue=2 |pages=105–10 |journal=Computer Applications in the Biosciences}}
10. ^¹{{cite journal |doi=10.1139/V08-020 |title=Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws — New methods based on directed graphs |year=2008 |last1=Andraos |first1=John |journal=Canadian Journal of Chemistry |volume=86 |issue=4 |pages=342–57}}
11. ^¹{{cite journal |doi=10.2174/138920010791514261 |title=Graphic Rule for Drug Metabolism Systems |year=2010 |last1=Chou |first1=Kuo-Chen |journal=Current Drug Metabolism |volume=11 |issue=4 |pages=369–78 |pmid=20446902}}