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7 protocols using amicon stirred cell concentrators

1

Enzyme Substrate Library Characterization

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Chemicals, biochemicals, and buffers were purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO), Fisher Scientific, Inc. (Pittsburgh, PA), EMD Millipore, Inc. (Billerica, MA) or Bio-Rad Laboratories, Inc. (Hercules, CA), unless otherwise noted below. Phenylenolpyruvate (PP) was purchased from Fluka Chemical Corp. (Milwaukee, WI) as the crystalline free acid, which exists in the enol form. 2-Oxo-3-pentynoate (2-OP) was synthesized, as described elsewhere.21 (link) The compounds in the substrate library were obtained from sources reported elsewhere.23 The DEAE-Sepharose fast flow resin and the PD-10 Sephadex G-25M buffer-exchange columns were obtained from GE Healthcare Bio-Sciences (Pittsburgh, PA). The Econo-Column chromatography columns (used for the DEAE-Sepharose columns) were obtained from Bio-Rad Laboratories, Inc. (Hercules, CA). The Amicon stirred cell concentrators and the ultrafiltration membranes (10000 Da, MW cutoff) were purchased from EMD Millipore Inc. (Billerica, MA). InstantBlue for staining sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels was obtained from C.B.S. Scientific Company, Inc. (Del Mar, CA).
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2

Purification of Malonate Semialdehyde Decarboxylase

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Chemicals, biochemicals, buffers, and solvents were purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO), Fisher Scientific Inc. (Pittsburgh, PA), Fluka Chemical Corp. (Milwaukee, WI), or EMD Millipore, Inc. (Billerica, MA). Sodium phosphate buffer salts were at least 99.99% pure or greater, as indicated by the manufacturer. Propiolic acid (98%, 8) and 2-butynoate (10) were purchased from Sigma- Aldrich. Both were purified further prior to use by distillation (8) or recrystallization (10). 2,3-Butadienoate (9) was synthesized according to published methods.14 The DEAE- Sepharose and Phenyl-Sepharose 6 Fast Flow resins used for protein purification were obtained from Sigma-Aldrich Chemical Co. (St Louis, MO). The Econo-Column chroma- tography columns were obtained from BioRad (Hercules, CA). The Amicon stirred cell concentrators and the ultrafiltration membranes (10000 Da, MW cutoff) were purchased from EMD Millipore Inc. Malonate semialdehyde decarboxylase (MSAD) was purified as described previously.10 (link)
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3

Purification and Analysis of Compound 10

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Chemicals, biochemicals, buffers, and solvents were purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO), Fisher Scientific Inc. (Pittsburgh, PA), Fluka Chemical Corp. (Milwaukee, WI), or EMD Millipore, Inc. (Billerica, MA). 2-Carboxybenzaldehyde (10) was obtained from Sigma-Aldrich Chemical Co. Phenyl-Sepharose 6 Fast Flow resin was obtained from GE Healthcare Bio-sciences (Pittsburgh, PA). The Econo-Column® chromatography columns were obtained from BioRad (Hercules, CA). The Amicon stirred cell concentrators and the ultrafiltration membranes (10,000 Da, MW cutoff) were purchased from EMD Millipore Inc. Oligonucleotide primers were synthesized by Sigma-Aldrich.
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4

Purification and Characterization of N2 Enzyme

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Chemicals, biochemicals, buffers, and solvents were purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO), Fisher Scientific Inc. (Pittsburgh, PA), Fluka Chemical Corp. (Milwaukee, WI), or EMD Millipore, Inc. (Billerica, MA). 2-Hydroxymuconate (2-HM)11 and 3-bromopropiolate (3-BP)12 were synthesized by the indicated references. Phenylenolpyruvate (PP) was purchased from Fluka Chemical Corp. (Milwaukee, WI) as the crystalline free acid, which exists exclusively in the enol form. Propiolic acid (98%) was purchased from Sigma-Aldrich, and purified further prior to use by distillation. N2 was purified by a literature procedure.13 (link) N2 is an enzyme from Gammaproteobacteria bacterium SG8_31 (UniProt accession A0A0S8FF56) and is in the 4-oxalocrotonate tautomerase (4-OT) subgroup, as described elsewhere.13 (link) The DEAE Sephadex, Phenyl-Sepharose 6 Fast Flow, and Sephadex G-75 resins were obtained from GE Healthcare Bio-sciences (Pittsburgh, PA). The Econo-Column® chromatography columns were obtained from BioRad (Hercules, CA). The Amicon stirred cell concentrators and the ultrafiltration membranes (3,000 or 5,000 Da, MW cutoff) were purchased from EMD Millipore Inc.
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5

Synthesis and Purification of 2-Oxo-3-pentynoate

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All chemicals, biochemical, and enzyme substrates were obtained from sources described elsewhere.19 (link),20 2-Oxo-3-pentynoate (2-OP) was synthesized as reported.21 (link) Chromatographic resins (DEAE Sepharose fast flow and Bio-Gel P60 gel beads) and columns (PD-10 Sephadex G-25M, Econo-Column, and Spectra/Chrom LC) were acquired from sources described elsewhere.19 (link) The Amicon stirred cell concentrators and the ultrafiltration membranes (10,000 Da, MW cutoff) were purchased from EMD Millipore Inc. (Billerica, MA). InstantBlue for staining SDS-PAGE gels was obtained from C.B.S. Scientific Company, Inc. (Del Mar, CA).
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6

Protein Purification Techniques

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All chemicals, biochemical, and enzyme substrates were obtained from sources described elsewhere.7 ,8 (link),1 (link),13 (link),14 (link) Chromatographic resins (DEAE Sepharose fast flow and Phenyl-Sepharose 6 fast flow) and columns (PD-10 Sephadex G-25M, Econo-Column, and Spectra/Chrom LC) were purchased from commercial vendors, as described.7 The Amicon stirred cell concentrators and the ultrafiltration membranes (10,000 Da, MW cutoff) were purchased from EMD Millipore Inc. (Billerica, MA). Coomassie Blue R-250 dye for staining sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels was adapted from a literature source.15
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7

Purification and Characterization of Enzymes

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Chemicals, biochemicals, buffers, and solvents were purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO), Fisher Scientific Inc. (Pittsburgh, PA), Fluka Chemical Corp. (Milwaukee, WI), or EMD Millipore, Inc. (Billerica, MA). Reagents for molecular biology manipulations were obtained from sources listed in the text. trans-o-Hydroxybenzylidenepyruvate was synthesized as described elsewhere.5 (link) The prepacked PD-10 Sephadex G-25 columns were obtained from GE Healthcare (Piscataway, NJ). The Econo-Column® chromatography columns were obtained from BioRad (Hercules, CA). The Ni-NTA resin was purchased from Fisher Scientific (Pittsburgh, PA). The Amicon stirred cell concentrators and the ultrafiltration membranes (10,000 Da, MW cutoff) were purchased from EMD Millipore Inc. Oligonucleotide primers were synthesized by Sigma-Aldrich.
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