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Aune K, Lee J, Prakash V, Bhat R, Andreu J, Monasterio O, Perez-Ramirez B, Shearwin K, Arakawa T, Carpenter J, Crowe J, Crowe L, Somero G, Gagnon P, Charles MT. A tribute to Dr. Serge N. Timasheff, our mentor. Biophys Rev 2021; 13:459-484. [PMID: 34471434 PMCID: PMC8355303 DOI: 10.1007/s12551-021-00814-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/17/2021] [Indexed: 10/20/2022] Open
Abstract
Dr. Serge N. Timasheff, our mentor and friend, passed away in 2019. This article is a collection of tributes from his postdoctoral fellows, friends, and daughter, who all have been associated with or influenced by him or his research. Dr. Timasheff is a pioneer of research on thermodynamic linkage between ligand interaction and macromolecular reaction. We all learned a great deal from Dr. Timasheff, not only about science but also about life.
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Affiliation(s)
- Kirk Aune
- 7647 Cortana Drive, Granger, IN 46530 USA
| | - James Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77059 USA
| | - V. Prakash
- Nutraceuticals and Nutritional Research Center, Ramaiah University of Applied Sciences, Bangalore, India
| | - Rajiv Bhat
- School of Biotechnology, Jawaharalal Nehru University, New Delhi, 110067 India
| | - Jose Andreu
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Octavio Monasterio
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Bernardo Perez-Ramirez
- CMC-Drug Device Integration, DP-Due Diligence, Biologics Drug Product Development & Manufacturing, Sanofi, 1 the Mountain Road, Framingham, MA 01701 USA
| | - Keith Shearwin
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, 5005 Australia
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Road, San Diego, CA 92130 USA
| | - John Carpenter
- Department of Pharmaceutical Sciences, Center for Pharmaceutical Biotechnology, University of Colorado Anshutz Medical Campus, Auroa, CO 80045 USA
| | - John Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616 USA
| | - Lois Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616 USA
| | - George Somero
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950 USA
| | - Pete Gagnon
- BIA Separations, Mirce 21, 5270, Ajdovscina, Slovenia
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Purification of lactoperoxidase from bovine milk by integrating the technique of salting-out extraction with cation exchange chromatographic separation. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2019. [DOI: 10.1007/s11694-019-00056-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Arakawa T, Gagnon P. Excluded Cosolvent in Chromatography. J Pharm Sci 2018; 107:2297-2305. [DOI: 10.1016/j.xphs.2018.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/02/2018] [Indexed: 10/14/2022]
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Arakawa T, Tsumoto K, Ejima D. Alternative downstream processes for production of antibodies and antibody fragments. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2032-2040. [PMID: 24859179 DOI: 10.1016/j.bbapap.2014.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/24/2014] [Accepted: 05/15/2014] [Indexed: 01/26/2023]
Abstract
Protein-A or Protein-L affinity chromatography and virus inactivation are key processes for the manufacturing of therapeutic antibodies and antibody fragments. These two processes often involve exposure of therapeutic proteins to denaturing low pH conditions. Antibodies have been shown to undergo conformational changes at low pH, which can lead to irreversible damages on the final product. Here, we review alternative downstream approaches that can reduce the degree of low pH exposure and consequently damaged product. We and others have been developing technologies that minimize or eliminate such low pH processes. We here cover facilitated elution of antibodies using arginine in Protein-A and Protein-G affinity chromatography, a more positively charged amidated Protein-A, two Protein-A mimetics (MEP and Mabsorbent), mixed-mode and steric exclusion chromatography, and finally enhanced virus inactivation by solvents containing arginine. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, 6042 Cornerstone Court West, Suite A, San Diego, CA 9212, USA.
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering and Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Japan
| | - Daisuke Ejima
- Institute of Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
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Grover PK, Ryall RL. Critical Appraisal of Salting-Out and Its Implications for Chemical and Biological Sciences. Chem Rev 2004; 105:1-10. [PMID: 15720150 DOI: 10.1021/cr030454p] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Phulwinder K Grover
- Division of Urology, Department of Surgery, Flinders University School of Medicine, Flinders Medical Centre, Bedford Park, South Australia 5042, Australia.
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Sellek GA, Chaudhuri JB. Biocatalysis in organic media using enzymes from extremophiles. Enzyme Microb Technol 1999. [DOI: 10.1016/s0141-0229(99)00075-7] [Citation(s) in RCA: 172] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Steinert K, Wagner V, Kroth-Pancic PG, Bickel-Sandkötter S. Characterization and subunit structure of the ATP synthase of the halophilic archaeon Haloferax volcanii and organization of the ATP synthase genes. J Biol Chem 1997; 272:6261-9. [PMID: 9045643 DOI: 10.1074/jbc.272.10.6261] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The archaeal ATPase of the halophile Haloferax volcanii synthesizes ATP at the expense of a proton gradient, as shown by sensitivity to the uncoupler carboxyl cyanide p-trifluoromethoxyphenylhydrazone, to the ionophore nigericin, and to the proton channel-modifying reagent N,N'-dicyclohexylcarbodiimide. The conditions for an optimally active ATP synthase have been determined. We were able to purify the enzyme complex and to identify the larger subunits with antisera raised against synthetic peptides. To identify additional subunits of this enzyme complex, we cloned and sequenced a gene cluster encoding five hydrophilic subunits of the A1 part of the proton-translocating archaeal ATP synthase. Initiation, termination, and ribosome-binding sequences as well as the result of a single transcript suggest that the ATPase genes are organized in an operon. The calculated molecular masses of the deduced gene products are 22. 0 kDa (subunit D), 38.7 kDa (subunit C), 11.6 kDa (subunit E), 52.0 kDa (subunit B), and 64.5 kDa (subunit A). The described operon contains genes in the order D, C, E, B, and A; it contains no gene for the hydrophobic, so-called proteolipid (subunit c, the proton-conducting subunit of the A0 part). This subunit has been isolated and purified; its molecular mass as deduced by SDS-polyacrylamide gel electrophoresis is 9.7 kDa.
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Affiliation(s)
- K Steinert
- Institut für Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Federal Republic of Germany
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Continuous buffer exchange of column chromatographic eluates using a hollow-fibre membrane module. J Chromatogr A 1993. [DOI: 10.1016/0021-9673(93)83085-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Golovchenko NP, Kataeva IA, Akimenko VK. Analysis of pH-dependent protein interactions with gel filtration medium. J Chromatogr A 1992; 591:121-8. [PMID: 1613047 DOI: 10.1016/0021-9673(92)80229-n] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A prepacked Superose 12 HR 10/30 column was used to study the effects of elution ionic strength and pH on the chromatographic behaviour of a strong hydrophobic Clostridium thermocellum endoglucanase (1) and two weak hydrophobic proteins, Clostridium thermocellum endoglucanase C and egg white lysozyme. Ion-exclusion or ion-exchange interactions between weakly hydrophobic proteins and the gel matrix were observed at low ionic strength, depending on whether the pH of the elution buffer was higher or lower than the pI values of the proteins. These interactions were due to the presence of negatively charged groups on the surface of Superose and could be eliminated at any pH by adding electrolyte at a concentration determined by its chemical identity. The optimum results were observed with sodium sulphate at a concentration of 100 mM. The chromatographic behaviour of strong hydrophobic endoglucanase (1) on a Superose column as a function of pH was much more complex because of two interplaying effects, electrostatic and hydrophobic. Ideal size-exclusion chromatography could be achieved only in a narrow range of the conditions: first, the mobile phase must contain a weak salting-out electrolyte such as NaCl, and second, the mobile phase pH must be high enough that hydrophobic interactions between the solute and support are balanced by their electrostatic repulsion. At pH greater than pI, the retardation of endoglucanase (1) gradually increased with decreasing pH as a result of lowering of repulsive electrostatic interactions whether or not the buffer ionic strength was high. At pH less than pI a drastic increase in the capacity factor k' was observed owing to the additivity of hydrophobic and ion-exchange effects.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- N P Golovchenko
- Department of Anaerobic Processes, Institute of Biochemistry and Physiology of Microorganisms, Puschino, Moscow Region
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Eisenberg H, Mevarech M, Zaccai G. Biochemical, structural, and molecular genetic aspects of halophilism. ADVANCES IN PROTEIN CHEMISTRY 1992; 43:1-62. [PMID: 1442321 DOI: 10.1016/s0065-3233(08)60553-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- H Eisenberg
- Structural Biology Department, Weizmann Institute of Science, Rehovot, Israel
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Monstadt GM, Holldorf AW. Arginine deiminase from Halobacterium salinarium. Purification and properties. Biochem J 1991; 273 ( Pt 3):739-45. [PMID: 1847623 PMCID: PMC1149825 DOI: 10.1042/bj2730739] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Arginine deiminase from the extreme halophilic archaebacterium Halobacterium salinarium was purified to homogeneity in a four-step procedure with a 310-fold enrichment. The enzyme consists of two identical subunits of 55 kDa; its native molecular mass is 105 kDa. The pI of 4.7 indicates that acidic nature of the protein, which is evidenced by its amino acid composition, which shows an excess of more than 15% of acidic amino acids. The N-terminal amino acid of the enzyme is lysine. Arginine deiminase from Halobacterium salinarium exhibits its highest catalytic activity in the presence of 3.5 M-NaCl, pH 7.6, and at 40 degrees C. The half-activity constant, Ks, for arginine is 3.1 mM. The enzyme is inhibited by ornithine.
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Affiliation(s)
- G M Monstadt
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, Germany
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12
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Schmitt W, Rdest U, Goebel W. Efficient high-performance liquid chromatographic system for the purification of a halobacterial serine protease. J Chromatogr A 1990. [DOI: 10.1016/0021-9673(90)85045-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Sundquist AR, Fahey RC. The novel disulfide reductase bis-gamma-glutamylcystine reductase and dihydrolipoamide dehydrogenase from Halobacterium halobium: purification by immobilized-metal-ion affinity chromatography and properties of the enzymes. J Bacteriol 1988; 170:3459-67. [PMID: 3136140 PMCID: PMC211315 DOI: 10.1128/jb.170.8.3459-3467.1988] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
An NADPH-specific disulfide reductase that is active with bis-gamma-glutamylcystine has been purified 1,900-fold from Halobacterium halobium to yield a homogeneous preparation of the enzyme. Purification of this novel reductase, designated bis-gamma-glutamylcystine reductase (GCR), and purification of halobacterial dihydrolipoamide dehydrogenase (DLD) were accomplished with the aid of immobilized-metal-ion affinity chromatography in high-salt buffers. Chromatography of GCR on immobilized Cu2+ resin in buffer containing 1.23 M (NH4)2SO4 and on immobilized Ni2+ resin in buffer containing 4.0 M NaCl together effected a 120-fold increase in purity. Native GCR was found to be a dimeric flavoprotein of Mr 122,000 and to be more stable to heat when in buffer of very high ionic strength. DLD was chromatographed on columns of immobilized Cu2+ resin in buffer containing NaCl and in buffer containing (NH4)2SO4, the elution of DLD differing markedly in the two buffers. Purified DLD was found to be a heat-stable, dimeric flavoprotein of Mr 120,000 and to be very specific for NAD. The utility of immobilized-metal-ion affinity chromatography for the purification of halobacterial enzymes and the likely cellular function of GCR are discussed.
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Affiliation(s)
- A R Sundquist
- Department of Chemistry, University of California-San Diego, La Jolla 92093-0506
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May BP, Dennis PP. Superoxide dismutase from the extremely halophilic archaebacterium Halobacterium cutirubrum. J Bacteriol 1987; 169:1417-22. [PMID: 3104309 PMCID: PMC211962 DOI: 10.1128/jb.169.4.1417-1422.1987] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Halobacterium cutirubrum, a member of the archaebacteria, contains one superoxide dismutase (EC 1.15.1.1). This enzyme functions in the high-ionic-strength intracellular environment and protects the organism against the toxic effects of the superoxide anion. The enzyme has been purified to about 90% homogeneity by a four-step procedure which never removes it from conditions of high ionic strength. The subunits of the purified enzyme have a molecular weight of 25,000 and are possibly in tetrameric association. The enzyme shows anomalously high resistance to azide inhibition and sensitivity to inactivation by hydrogen peroxide. Metal analysis indicates 0.2 atom of Mn, less than 0.03 atom of Cu, and less than 0.001 atom of Fe per subunit. The low content of Mn may explain the low specific activity found for this enzyme compared with that of eubacterial enzymes. Optimum activity occurs in 2 M KCl; KCl gives about twice as much activity as NaCl over the range of 2 to 4 M. The enzyme appears to be related to those isolated from other archaebacteria but also exhibits several novel features.
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15
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Werber MM, Sussman J, Eisenberg H. Molecular basis for the special properties of proteins and enzymes fromHalobacterium marismortui. FEMS Microbiol Lett 1986. [DOI: 10.1111/j.1574-6968.1986.tb01853.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Arakawa T. Thermodynamic analysis of the effect of concentrated salts on protein interaction with hydrophobic and polysaccharide columns. Arch Biochem Biophys 1986; 248:101-5. [PMID: 3729409 DOI: 10.1016/0003-9861(86)90405-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An attempt was made to explain the effect of concentrated salts on protein interaction with hydrophobic columns. From the previously observed results of preferential interactions for salting-out salts with proteins, it was shown that the free energy of the protein is increased by addition of the salts and this unfavorable free energy is smaller for the proteins bound to the columns because of their smaller surface area exposed to solvent; i.e., the bound form of the proteins is thermodynamically more stable. This explains the protein binding to the hydrophobic columns at high salt concentrations and the elution by decreasing the salt concentration. The unfavorable interaction free energy was greater for Na2SO4 or (NH4)2SO4 than for NaCl, which explains the stronger effect of the former salts on the protein binding to the columns. The observed favorable interaction between KSCN or guanidine hydrochloride and the proteins explains the decreasing effect of these salts on the protein binding to the hydrophobic columns.
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Carrea G, Pasta P, Antonini E. Purification of glucagon by subunit exchange chromatography. Biotechnol Bioeng 1985; 27:704-10. [DOI: 10.1002/bit.260270520] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kroviarski Y, Cochet S, Boivin P, Bertrand O. Automated purification of human erythrocytic 6-phosphogluconate dehydrogenase. J Chromatogr A 1982; 243:111-21. [PMID: 7107799 DOI: 10.1016/s0021-9673(00)88169-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Human 6-phosphogluconate dehydrogenase (6PGD) was purified from hemolyzate by group affinity chromatography on 2',5'-ADP-Sepharose, followed by buffer exchange chromatography on Sephadex G-25 and finally salting-out chromatography on Sepharose 6B. An apparatus was assembled from commercially available elements, in which the purification procedure can proceed and be completed unattended and under fully automatic control. The weekly production of the set-up is at present 10 mg of pure 6PGD. The choice of the purification of procedure and the advantages of automation are discussed.
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