chemart / conrad-enzymatic

{"species": [{"id": "MDH", "structure": "malate dehydrogenase; locks coenzyme=001011 substrate=010101 modulator=000111; modulator site free"}, {"id": "MDH_NAD", "structure": "malate dehydrogenase; locks coenzyme=001011 substrate=010101 modulator=000111; modulator site free; coenzyme site: NAD key=110100 (6/6)"}, {"id": "MDH_NAD_MAL", "structure": "malate dehydrogenase; locks coenzyme=001011 substrate=010101 modulator=000111; modulator site free; coenzyme site: NAD key=110100; substrate site: MAL key=101010 (6/6)"}, {"id": "MDH_Mg", "structure": "malate dehydrogenase; locks coenzyme=001011 substrate=010101 modulator=000111; modulator site: Mg key=111000 (6/6)"}, {"id": "MDH_Mg_NAD", "structure": "malate dehydrogenase; locks coenzyme=001011 substrate=010101 modulator=000111; modulator site: Mg key=111000 (6/6); coenzyme site: NAD key=110100 (6/6)"}, {"id": "MDH_Mg_NAD_MAL", "structure": "malate dehydrogenase; locks coenzyme=001011 substrate=010101 modulator=000111; modulator site: Mg key=111000 (6/6); coenzyme site: NAD key=110100; substrate site: MAL key=101010 (6/6)"}, {"id": "NAD", "structure": "NAD+ coenzyme; key=110100"}, {"id": "MAL", "structure": "L-malate substrate; key=101010"}, {"id": "OAA", "structure": "oxaloacetate; key=011010"}, {"id": "NADH", "structure": "NADH, read at 339 nm; key=110111"}, {"id": "H", "structure": "proton released on turnover (glycine/NaOH buffer, pH 10)"}, {"id": "Mg", "structure": "Mg2+ signal carrier; key=111000"}], "reactions": [{"reactants": {"MDH": 1, "NAD": 1}, "products": {"MDH_NAD": 1}, "rate": null, "count": null}, {"reactants": {"MDH_NAD": 1}, "products": {"MDH": 1, "NAD": 1}, "rate": null, "count": null}, {"reactants": {"MDH_NAD": 1, "MAL": 1}, "products": {"MDH_NAD_MAL": 1}, "rate": null, "count": null}, {"reactants": {"MDH_NAD_MAL": 1}, "products": {"MDH_NAD": 1, "MAL": 1}, "rate": null, "count": null}, {"reactants": {"MDH_NAD_MAL": 1}, "products": {"MDH": 1, "OAA": 1, "NADH": 1, "H": 1}, "rate": null, "count": null}, {"reactants": {"MDH_Mg": 1, "NAD": 1}, "products": {"MDH_Mg_NAD": 1}, "rate": null, "count": null}, {"reactants": {"MDH_Mg_NAD": 1}, "products": {"MDH_Mg": 1, "NAD": 1}, "rate": null, "count": null}, {"reactants": {"MDH_Mg_NAD": 1, "MAL": 1}, "products": {"MDH_Mg_NAD_MAL": 1}, "rate": null, "count": null}, {"reactants": {"MDH_Mg_NAD_MAL": 1}, "products": {"MDH_Mg_NAD": 1, "MAL": 1}, "rate": null, "count": null}, {"reactants": {"MDH_Mg_NAD_MAL": 1}, "products": {"MDH_Mg": 1, "OAA": 1, "NADH": 1, "H": 1}, "rate": null, "count": null}, {"reactants": {"MDH": 1, "Mg": 1}, "products": {"MDH_Mg": 1}, "rate": null, "count": null}, {"reactants": {"MDH_Mg": 1}, "products": {"MDH": 1, "Mg": 1}, "rate": null, "count": null}], "status": "complete", "initial_state": {"NAD": 1.29, "MAL": 5.41, "Mg": 144.76}, "inflow": null, "outflow": null, "extras": {"interaction_law": {"recognition": "lock and key: a ligand binds a site when at least match_bits of the shape_bits positions are complementary (bit-inverted)", "shape_bits": 6, "match_bits": 5, "keys": {"Mg": "111000", "Ca": "011000", "NAD": "110100", "MAL": "101010", "NADH": "110111", "OAA": "011010"}, "locks": {"coenzyme": "001011", "substrate": "010101", "modulator": "000111"}, "match_scores": {"coenzyme/NAD": 6, "coenzyme/MAL": 2, "coenzyme/Mg": 4, "coenzyme/Ca": 3, "coenzyme/NADH": 4, "coenzyme/OAA": 2, "substrate/NAD": 2, "substrate/MAL": 6, "substrate/Mg": 4, "substrate/Ca": 3, "substrate/NADH": 2, "substrate/OAA": 4, "modulator/NAD": 4, "modulator/MAL": 4, "modulator/Mg": 6, "modulator/Ca": 5, "modulator/NADH": 2, "modulator/OAA": 4}, "conformational_fusion": "Mg2+ and Ca2+ bind the modulator site and select a conformer; the conformational dynamics fuses the milieu signals nonlinearly, so the catalytic activity is a nonmonotonic function of each signal concentration", "response": "r = NADH absorbance at 339 nm at a fixed time after initiation; measured to rise to a maximum and then fall along both ion axes", "signal_coding": "a 1-signal is the presence of one encoding unit of the carrier ions, a 0-signal their absence; two input lines give milieu states a (00), b (01 or 10) and c (11)", "signal_strength": "Delta s = min(r over the milieu states that must be active) - max(r over the rest); the operation is realisable iff Delta s > 0", "output": "threshold the response; above threshold is an active output"}, "analysis": {"operation": "XOR", "truth_table": {"00": 0, "01": 1, "10": 1, "11": 0}, "active_milieu_states": ["b"], "signal_strength": "r(b) - max(r(a), r(c))", "inputs": "11", "milieu_state": "c", "encoding_mM": {"Mg": 72.38}, "milieu_mM": {"Mg": {"a": 0.0, "b": 72.38, "c": 144.76}}, "linearly_separable": false, "implementable_on_the_published_response_surface": true, "not_implementable": ["NXOR"], "published_classification": {"operation": "XOR", "signalling_substance": "MgCl2", "presentations": 135, "by_pattern": {"00": 45, "01/10": 46, "11": 44}, "correct": 135, "accuracy": 1.0, "readout_time_s": 10.0, "figure": "Figure 9"}, "published_encodings": [{"operation": "OR", "encoding_mM": {"Mg": 20.0}}, {"operation": "XOR", "encoding_mM": {"Mg": 20.0, "Ca": 40.0}}]}, "conservation": [{"name": "enzyme", "vector": {"MDH": 1, "MDH_NAD": 1, "MDH_NAD_MAL": 1, "MDH_Mg": 1, "MDH_Mg_NAD": 1, "MDH_Mg_NAD_MAL": 1}}, {"name": "nicotinamide dinucleotide", "vector": {"MDH_NAD": 1, "MDH_NAD_MAL": 1, "MDH_Mg_NAD": 1, "MDH_Mg_NAD_MAL": 1, "NAD": 1, "NADH": 1}}, {"name": "C4 dicarboxylate", "vector": {"MDH_NAD_MAL": 1, "MDH_Mg_NAD_MAL": 1, "MAL": 1, "OAA": 1}}, {"name": "Mg (free and bound)", "vector": {"MDH_Mg": 1, "MDH_Mg_NAD": 1, "MDH_Mg_NAD_MAL": 1, "Mg": 1}}], "buffered": ["H"], "experiment": {"source": "K.-P. Zauner and M. Conrad, Enzymatic Computing, Biotechnol. Prog. 17(3):553-559, 2001 (doi:10.1021/bp010004n)", "enzyme": "mitochondrial malate dehydrogenase, pig heart (ICN Biomedicals); 6 uL/mL of the suspension in the enzyme solution - its molar concentration is not published", "overall_reaction": "L-malate + NAD+ -> oxaloacetate + NADH + H+", "readout": "NADH absorbance at 339 nm, 1 cm light path", "response_surface": {"assays": 36, "design": "6 x 6 MgCl2 x CaCl2 factor levels, run as 7 blocks of 6 cuvettes", "ion_levels_uL": "0; 25 of 2 M; 25, 50, 75, 100 of 4 M, made up to 300 uL", "assay_volume_mL": 3.0, "readout_time_s": 300.0, "buffer": "0.12 M glycine/NaOH, pH 10", "temperature_C": 29.0, "shape": "rises to a maximum and then falls along both ion axes ('convex', i.e. strictly nonmonotonic)"}, "signal_processor": {"signal_volume_mL": 0.8, "enzyme_volume_mL": 0.5, "malate_in_signal_mM": 7.1, "nad_in_enzyme_solution_mM": 5.4, "mgcl2_in_1_signal_mM": 190.0, "readout_time_s": 10.0}}}, "chemistry": "conrad-enzymatic", "params": {"operation": "XOR", "inputs": "11", "encoding_mM": {"Mg": 72.38}, "match_bits": 5, "malate_mM": 5.41, "nad_mM": 1.29}, "seed": 1}