LMx(Sp > Ca)I – Kinetic Mechanisms of Enzyme Inhibition and Activation

Linear mixed, predominantly specific inhibition

**Fingerprints of LMx(Sp>Ca)I: Dependence of the parameters on [X]**

**Fingerprints of LMx(Sp>Ca)I: Specific velocity plot and replot**

Featured examples

#	Enzyme Species	EC no.	Modifier	Substrate⁽¹⁾	Name given by authors⁽²⁾	Reference ⁽³⁾
1	Peroxiredoxin Homo sapiens	1.11.1.15	Catechol	H₂O₂	Partial mixed type noncompetitive inhibition α = 2.2, K_X = 1.8 mM	Chow (2016)
2	Alpha,alpha trehalase Chironomus riparius	3.2.1.28	Compound 7	Trehalose	Linear mixed type inhibition α = 5.8, K_X = 34 mM	D'Adamio (2015)
3	Aminopeptidase N Homo sapiens	3.4.11.2	Cholic acid	Leu-Met	Competitive-noncompetitive linear mixed type inhibition α = 9.0, K_X = 0.91 mM	Nakanishi (1989)
4	Aminopeptidase N Homo sapiens	3.4.11.2	Deoxycholic acid	Leu-Met	Competitive-noncompetitive linear mixed type inhibition α = 21, K_X = 0.42 mM	Nakanishi (1989)
5	Aminopeptidase N Homo sapiens	3.4.11.2	Chenodeoxycholic acid	Leu-Met	Competitive-noncompetitive linear mixed type inhibition α = 7.0, K_X = 0.24 mM	Nakanishi (1989)
6	Aminopeptidase N Homo sapiens	3.4.11.2	Deoxycholic acid	Leu-Gly	Competitive-noncompetitive linear mixed type inhibition α = 11, K_X = 0.51 mM	Nakanishi (1989)
7	Acetylcholinesterase Electrophorus electricus	3.1.1.7	Pararosaniline	Acetylthiocholine	Linear mixed inhibition α = 3.9, K_X = 3.0 μM	Küçükkilinç (2007)
8	Cholinesterase Homo sapiens	3.1.1.8	Pararosaniline	Butyrylthiocholine	Linear mixed inhibition α = 13, K_X = 1.9 μM	Küçükkilinç (2005)
9	Cholinesterase Homo sapiens	3.1.1.8	Malachite green	Butyrylthiocholine	Linear mixed inhibition α = 23, K_X = 0.28 μM	Küçükkilinç (2005)
10	Cholinesterase Homo sapiens	3.1.1.8	Ethopropazine	Butyrylthiocholine	Linear mixed inhibition α = 8.4, K_X = 0.037 μM	Küçükkilinç (2007)
11	Acetylcholinesterase Electrophorus electricus	3.1.1.7	Malachite green	Acetylthiocholine	Linear mixed inhibition α = 4.8, K_X = 1.9 μM	Küçükkilinç (2008)
12	Coagulation factor XIa Homo sapiens	3.4.21.27	Aprotinin	Coagulation factor IX	Non-competitive inhibition α = 6.3, K_X = 0.89 μM	Ogawa (2005)
13	Memapsin 2 ⁽⁴⁾ Homo sapiens	3.4.23.46	Pepstatin A methylester pH = 6.5, 22°C	C100 ⁽⁵⁾	Linear non-competitive inhibition ⁽⁶⁾ α = 2.1±1.8, K_X = 0.15 μM	Tian (2002)
14	Memapsin 2 ⁽⁴⁾ Homo sapiens	3.4.23.46	Pepstatin A methylester pH = 6.5, 37°C	C100 ⁽⁵⁾	Linear non-competitive inhibition ⁽⁶⁾ α = 2.0±0.5, K_X = 0.71 μM	Tian (2002)
15	Aldehyde oxidase Homo sapiens	1.2.3.1	Domperidone	Phtalazine	Mixed, predominantly competitive inhibition α = 2.6, K_X = 5.3 μM	Barr (2011)
16	Aldehyde oxidase Homo sapiens	1.2.3.1	Chlorpromazine	Phtalazine	Mixed, predominantly competitive inhibition α = 5.3, K_X = 0.62 μM	Barr (2011)
17	Aldehyde oxidase Homo sapiens	1.2.3.1	Clozapine	Phtalazine	Mixed, predominantly competitive inhibition α = 15, K_X = 3.9 μM	Barr (2011)
18	Spermine synthase Bos taurus	2.5.1.22	Spermine (reaction product)	Spermidine	Mixed, predominantly competitive inhibition α = 4, K_X = 10 μM	Pajula (1983) ⁽⁷⁾
19	Spermine synthase Bos taurus	2.5.1.22	5'-methylthioadenosine (reaction product)	Decarboxylated adenosylmethionine	Mixed, predominantly competitive inhibition α = 10, K_X = 0.2 μM	Pajula (1983) ⁽⁷⁾
20	Tyrosinase ⁽⁸⁾ Homo sapiens	1.14.18.1	Kojic acid	L-Dopa	Mixed, predominantly competitive inhibition α = 3.9, K_X = 145 μM	Sun (2014) ⁽⁹⁾
21	Butane-utilizing bacterial cultures ⁽¹⁰⁾	—	Butane	1,1-dichloroethylene	Mixed inhibition α = 20, K_X = 0.23 μM	Kim (2002)
22	Butane-utilizing bacterial cultures ⁽¹⁰⁾	—	Butane	1,1-dichloroethane	Mixed inhibition α = 1.8, K_X = 1.8 μM	Kim (2002)
23	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Lys2-Tat(1-9) MKPVDPNIE	Ala-Pro-p-nitroanilide	Linear mixed type inhibition α = 10, K_X = 42.7 μM	Lorey (2003) ⁽¹¹⁾
24	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Trp2-Tat(1–9) MWPVDPNIE	Ala-Pro-p-nitroanilide	Linear mixed type inhibition α = 16, K_X = 2.12 μM	Lorey (2003) ⁽¹¹⁾
25	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Met-Trp1-G-CSF(1–8) MWPLGPASS	Ala-Pro-p-nitroanilide	Linear mixed type inhibition α = 16, K_X = 12.4 μM	Lorey (2003) ⁽¹¹⁾
26	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Met-IL-2(1–12) MAPTSSSTKKTQL	Ala-Pro-p-nitroanilide	Linear mixed type inhibition α = 9.4, K_X = 269 μM	Lorey (2003) ⁽¹¹⁾
27	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Met-Trp-Val MWV	Ala-Pro-p-nitroanilide	Linear mixed type inhibition α = 15, K_X = 200 μM	Lorey (2003) ⁽¹¹⁾
28	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Tat(1–9) MDPVDPNIE	Ala-Pro-p-nitroanilide	Parabolic mixed-type inhibition α = 8.9, γ = 0.3, δ =6.5 K_X = 267 μM	Lorey (2003) ⁽¹¹⁾⁽¹²⁾
29	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Tat(1–9) MDPVDPNIE	Gly-Pro-R110-CO-(CH₂)₄Cl ⁽¹³⁾	Parabolic mixed-type inhibition α = 0.8, γ = 0.8, δ =2.2 K_X = 230 μM	Lorey (2003) ⁽¹¹⁾⁽¹²⁾
30	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Trp1-Tat(1–9) WDPVDPNIE	Ala-Pro-p-nitroanilide	Parabolic mixed-type inhibition α = 46, γ = 1.5, δ =15 K_X = 150 μM	Lorey (2003) ⁽¹¹⁾⁽¹²⁾
31	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Gly3-Tat(1–9) MDGVDPNIE	Ala-Pro-p-nitroanilide	Parabolic mixed-type inhibition α = 3.7, γ = 0.3, δ =2.2 K_X = 487 μM	Lorey (2003) ⁽¹¹⁾⁽¹²⁾
32	Dipeptidyl-peptidase IV Homo sapiens	3.4.14.5	Ile3-Tat(1–9) MDIVDPNIE	Ala-Pro-p-nitroanilide	Parabolic mixed-type inhibition α = 1.7, γ = 9.2, δ =0.01 K_X = 1.75 mM	Lorey (2003) ⁽¹¹⁾⁽¹²⁾
33	β-Lactamase Bacillus cereus 5B6	3.5.2.6	Compound 6a	Nitrocefin	Mixed type inhibition α = 3.8, K_X = 6.6 μM	Siemann (2002)
34	β-Lactamase Bacillus cereus 5B6	3.5.2.6	Compound 11c	Nitrocefin	Mixed type inhibition α = 3.1, K_X = 0.7 μM	Siemann (2002)
35	Catechol 1,2-dioxygenase Acinetobacter baylyi	1.13.11.1 ⁽¹³⁾	4-Chloroaniline	3,4-Dichloroaniline	Mixed inhibition α = 1.14, K_X = 101 μM	Hongsawat (2011)
36	Cruzipain Tripanosoma cruzi	3.4.22.51	Fukugetin	Cbz-Phe-Arg-7-amino-4-methyl coumarylamide	Partial competitive inhibition α = 4.5, K_X = 1.0 μM	Assis (2013)
37	S-(hydroxymethyl)gluta- thione dehydrogenase Homo sapiens	1.1.1.284	Resveratrol	Doxorubicin	Mixed type inhibition α = 2.98, K_X = 55.8 μM	Ito (2013)
38	Linoleate 13S-lipoxygenase Glycine max	1.13.11.12	(Z)-9-palmitoleyl sulfate	Linoleic acid	Linear mixed inhibition α = 10.2, K_X = 13.7 μM	Ruddat (2003)
39	NADH:ubiquinone reductase (H⁺-translocating) Escherichia coli	1.6.5.3	Zn²⁺	NAD_red	Linear mixed inhibition α = 1.7, K_X = 50 μM	Schulte (2014)
40	Neurolysin Rattus norvegicus	3.4.24.16	R2	Internally quenched peptide containing the neurotensin sequence	Mixed inhibition, noncompetitive and competitive components α = 6.1, K_X = 18 μM	Hines (2014)
41	Adenylate cyclase Homo sapiens	4.6.1.1	Bithionol	ATP	Mixed type inhibition α = 1.7, K_X = 2.3 μM	Kleinboelting (2016)
42	Acetylcholinesterase Torpedo californica	3.1.1.7	Edrophonium	Acetylthiocholine	Linear mixed inhibition α = 7.1, K_X = 0.15 μM	Berman (1990)
43	Acetylcholinesterase Torpedo californica	3.1.1.7	Phenyltrimethylammonium	Acetylthiocholine	Linear mixed inhibition α = 5.9, K_X = 20 μM	Berman (1990)
44	Acetylcholinesterase Torpedo californica	3.1.1.7	N-Methylacridinium	Acetylthiocholine	Linear mixed inhibition α = 1.9, K_X = 46 μM	Berman (1990)
45	Acetylcholinesterase Torpedo californica	3.1.1.7	Decamethonium	Acetylthiocholine	Linear mixed inhibition α = 3.2, K_X = 0.56 μM	Pietsch (2005)
46	Acetylcholinesterase Torpedo californica	3.1.1.7	Hexamethonium	Acetylthiocholine	Linear mixed inhibition α = 4.2, K_X = 13 μM	Pietsch (2005)
47	Acetylcholinesterase Torpedo californica	3.1.1.7	Decyltrimethylammonium	Acetylthiocholine	Linear mixed inhibition α = 8.4, K_X = 34 μM	Pietsch (2005)
48	Acetylcholinesterase Torpedo californica	3.1.1.7	Hexyltrimethylammonium	Acetylthiocholine	Linear mixed inhibition α = 3.3, K_X = 142 μM	Pietsch (2005)
49	Acetylcholinesterase Torpedo californica	3.1.1.7	Propidium	Acetylthiocholine	Linear mixed inhibition α = 1.6, K_X = 1.1 μM	Pietsch (2005)
50	Acetylcholinesterase Torpedo californica	3.1.1.7	d-Tubocurarine	Acetylthiocholine	Linear mixed inhibition α = 3.4, K_X = 40 μM	Pietsch (2005)
51	Acetylcholinesterase Electrophorus electricus	3.1.1.7	Tacrine	Acetylthiocholine	Linear mixed type inhibition α = 1.48, K_X = 25 μM	Pietsch (2005)
52	Acetylcholinesterase Electrophorus electricus	3.1.1.7	Galanthamine	Acetylthiocholine	Linear mixed type inhibition α = 2.0, K_X = 37 μM	Pietsch (2005)
53	Protein-glutamine gamma-glutamyl- transferase ⁽¹⁴⁾ Homo sapiens	2.3.2.13	Compound 5c	Compound 5b	Linear mixed, predominantly specific inhibition α = 2.0, K_X = 585 μM	Wodtke (2016) ⁽¹⁵⁾
54	Tyrosinase Agaricus bisporus	1.14.18.1	Kojic acid	L-Dopa	Competitive-noncompetitive inhibition α = 2.0, K_X = 37 μM	Liu (2017)
55	ABC-type quaternary amine transporter Homo sapiens	7.6.2.9	Compound 9	γ-Aminobutyric acid	Competitive inhibition	Al-Khawaja (2014)
56	Proton-translocating NAD(P)⁺ transhydrogenase Escherichia coli	7.1.1.1	5'-AMP	NADP_red (at fixed 3-acetylpyridine adenine dinucleotide)	Noncompetitive inhibition α = 2.7, K_X = 3.7 μM	Hanson (1979)
57	Pyridoxal 5'-phosphate synthase (wild type) Escherichia coli	1.4.3.5	Pyridoxal 5'-phosphate (reaction product)	Pyridoxine 5'-phosphate	Mixed-type inhibition α = 12-14, K_X = 7.1 μM	Barile ⁽¹⁶⁾ (2019)
58	beta-Galactosidase Escherichia coli	3.2.1.23	Glycofullerene 10 ⁽¹⁷⁾	p-Nitrophenyl β-D-Galactopyranoside	Mixed-type inhibition α = 6.1, K_X = 1.8 μM	Abellán Flos (2016)

⁽¹⁾ Always the varied substrate. In two- or more-substrate reactions the concentration(s) of the non varied substrate(s) is/are kept constant.

⁽²⁾ Name of the mechanism given by the authors in the quoted reference. α, β and the inhibition/activation constants for the modifier (X), uniformly denoted K_X, are the values specified by the authors. In some cases, missing parameters have been calculated from graphical or tabular data provided in the papers. In two- or more-substrate reactions, K_X represents an apparent constant at given concentrations of the fixed substrates and no calculations of the intrinsic values have been attempted.

⁽³⁾ Full references at the end of the page provide also the digital object identifier (doi), if available. Clicking the authors (highlighted) opens the reference in PubMed.

⁽⁴⁾ Memapsin 2 is the recommended name of an enzyme with 82 synonyms (BRENDA, July 2016), including β-secretase and γ-secretase. It is part of a complex membrane-bound macromolecular complex that involves presenilins 1 and 2.

⁽⁵⁾ C100 = Recombinant protein with amino acid sequence identical to the C-terminal fragment of presenilin (cleaved by memapsin 2 from the amyloid precursor protein) bearing an extra methionine residue at the N-terminus.

⁽⁶⁾ In this study Tian et al. (2002) paid particular attention to accurate determinations of K_is and K_ii, the specific and the catalytic components of the mechanisms, respectively, providing errors and graphical representations. The linearity of inhibition was ascertained experimentally. Taking into account error propagation, these data have been used in this table to calculate α as K_ii/K_is with its associated error that, together with graphics, was useful to identify the mechanism. The authors called all mechanisms ‘linear non-competitive inhibition’, which belong however to LMx(Sp>Ca)I, LMx(Sp<Ca)I and LMx(Sp=Ca)I. See also the tables of LMx(Sp<Ca)I and LMx(Sp=Ca)I.

⁽⁷⁾ A study dedicated to inhibition of spermine synthase (two substrates-two products reaction) by reaction products that suggests a compulsory-order mechanism in which both substrates bind the enzyme before release of products. See also the pages of LMx(Sp<Ca)I and LSpI.

⁽⁸⁾ In this study a truncated, His-tagged form of tyrosinase, which includes the catalytic domain, was used.

⁽⁹⁾ This paper by Sun and coworkers is a recommended reading because it is a useful tutorial in the management of enzyme-inhibition kinetic data. The authors fit the general modifier mechanism of Botts and Morales to an entire ensemble of data with a large number of experimental points. The analysis of inhibition mechanism is based on graphical representation of data and on statistical test that include the Akaike information criterion. See also other results from this study under LSpI and LMx(Sp<Ca)I.

⁽¹⁰⁾ Aerobic cometabolism cultures of Gram-positive and Gram-negative bacteria aimed at decontaminating groundwater from chlorinated hydrocarbons. Despite the enzymes responsible for the decontaminating reactions could not be identified, the inhibition results are clear and support the optimization of bacterial growth conditions in plants of water decontamination.

⁽¹¹⁾ The study by Lorey et al. (2003) is centered on the inhibition of human dipeptidyl-peptidase IV by the peptide MDPVDPNIE, Tat(1-9), corresponding to the N-terminus of the human immunodeficiency virus-1 transactivator Tat (HIV-1 Tat, which consists of 86 amino acids), and derived peptides. See also cases of linear specific inhibition at the page LSpI.

⁽¹²⁾ The entries with colored background represent a mechanism, called by the authors parabolic mixed-type inhibition, which has its roots in linear mixed, predominantly specific inhibition, LMx(Sp>Ca)I. The term parabolic refers to the curved-up slope replot of double-reciprocal plots but the inhibitory nature is still linear since the reaction rate approaches zero at saturating inhibitor concentrations. Further details HERE.

⁽¹³⁾ And possibly similar activities in the bacterial culture.

⁽¹⁴⁾ Synonyms: Tissue transglutaminase 2, Transglutaminase 2.

⁽¹⁵⁾ This is the first publication in which the systematics of enzyme-modifier interactions proposed by Baici, including the nomenclature, has been adopted.

⁽¹⁶⁾ A significant example of allosteric product inhibition. This paper is a recommended reading for accurate experimental design, data analysis and discussion that strongly support the results. The mechanism was unequivocally assigned on the basis of all dependencies of the apparent kinetic parameters on modifier concentration.

⁽¹⁷⁾ Complex structure: see Abellán Flos et al. (2016), Supplementary Information, p. 19.

References

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