1
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Brochier-Armanet C, Madern D. Phylogenetics and biochemistry elucidate the evolutionary link between l-malate and l-lactate dehydrogenases and disclose an intermediate group of sequences with mix functional properties. Biochimie 2021; 191:140-153. [PMID: 34418486 DOI: 10.1016/j.biochi.2021.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/19/2021] [Accepted: 08/15/2021] [Indexed: 01/23/2023]
Abstract
The NAD(P)-dependent malate dehydrogenases (MDH) (EC 1.1.1.37) and NAD-dependent lactate dehydrogenases (LDH) (EC. 1.1.1.27) form a large superfamily that has been characterized in organisms belonging to the three Domains of Life. MDH catalyzes the reversible conversion of the oxaloacetate into malate, while LDH operates at the late stage of glycolysis by converting pyruvate into lactate. Phylogenetic studies proposed that the LDH/MDH superfamily encompasses five main groups of enzymes. Here, starting from 16,052 reference proteomes, we reinvestigated the relationships between MDH and LDH. We showed that the LDH/MDH superfamily encompasses three main families: MDH1, MDH2, and a large family encompassing MDH3, LDH, and L-2-hydroxyisocaproate dehydrogenases (HicDH) sequences. An in-depth analysis of the phylogeny of the MDH3/LDH/HicDH family and of the nature of three important amino acids, located within the catalytic site and involved in binding and substrate discrimination, revealed a large group of sequences displaying unexpected combinations of amino acids at these three critical positions. This group branched in-between canonical MDH3 and LDH sequences. The functional characterization of several enzymes from this intermediate group disclosed a mix of functional properties, indicating that the MDH3/LDH/HicDH family is much more diverse than previously thought, and blurred the frontier between MDH3 and LDH enzymes. Present-days enzymes of the intermediate group are a valuable material to study the evolutionary steps that led to functional diversity and emergence of allosteric regulation within the LDH/MDH superfamily.
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Affiliation(s)
- Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622, Villeurbanne, France.
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2
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Boonstra E, Hatano H, Miyahara Y, Uchida S, Goda T, Cabral H. A proton/macromolecule-sensing approach distinguishes changes in biological membrane permeability during polymer/lipid-based nucleic acid delivery. J Mater Chem B 2021; 9:4298-4302. [PMID: 34018540 DOI: 10.1039/d1tb00645b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Endosomal escape is crucial for the delivery of nucleic acids. However, the understanding of the underlying mechanisms is still deficient. In this work, we explored the effects of lipid- and polymer-based transfection reagents on the permeability of cellular membranes through an innovative method combining a proton-sensing transistor and a cytosolic LDH leakage assay, which allows us to distinguish between modes of molecule permeation that may occur during endosomal escape. By testing the commercial reagents lipofectin and in vivo JetPEI under physiological and endosomal pH conditions, we found that both lipid- and polymer-based transfection reagents have pH-dependent pore-forming activity, with the former creating smaller pores than the latter. This versatile approach of assessing carrier-membrane interactions is expected to contribute to the development of next-generation nucleic acid delivery systems.
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Affiliation(s)
- Eger Boonstra
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan.
| | - Hiroaki Hatano
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan
| | - Satoshi Uchida
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo, Kyoto 602-8566, Japan.
| | - Tatsuro Goda
- Department of Biomedical Engineering, Faculty of Science and Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan.
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656, Japan.
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3
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Liu L, Courtney KC, Huth SW, Rank LA, Weisblum B, Chapman ER, Gellman SH. Beyond Amphiphilic Balance: Changing Subunit Stereochemistry Alters the Pore-Forming Activity of Nylon-3 Polymers. J Am Chem Soc 2021; 143:3219-3230. [PMID: 33611913 PMCID: PMC7944571 DOI: 10.1021/jacs.0c12731] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 12/16/2022]
Abstract
Amphiphilic nylon-3 polymers have been reported to mimic the biological activities of natural antimicrobial peptides, with high potency against bacteria and minimal toxicity toward eukaryotic cells. Amphiphilic balance, determined by the proportions of hydrophilic and lipophilic subunits, is considered one of the most important features for achieving this activity profile for nylon-3 polymers and many other antimicrobial polymers. Insufficient hydrophobicity often correlates with weak activities against bacteria, whereas excessive hydrophobicity correlates with high toxicity toward eukaryotic cells. To ask whether factors beyond amphiphilic balance influence polymer activities, we synthesized and evaluated new nylon-3 polymers with two stereoisomeric subunits, each bearing an ethyl side chain and an aminomethyl side chain. Subunits that differ only in stereochemistry are predicted to contribute equally to amphiphilic balance, but we observed that the stereochemical difference correlates with significant changes in biological activity profile. Antibacterial activities were not strongly affected by subunit stereochemistry, but the ability to disrupt eukaryotic cell membranes varied considerably. Experiments with planar lipid bilayers and synthetic liposomes suggested that eukaryotic membrane disruption results from polymer-mediated formation of large pores. Collectively, our results suggest that factors other than amphiphilic balance influence the membrane activity profile of synthetic polymers. Subunits that differ in stereochemistry are likely to have distinct conformational propensities, which could potentially lead to differences in the average shapes of polymer chains, even when the subunits are heterochiral. These findings highlight a dimension of polymer design that should be considered more broadly in efforts to improve specificity and efficacy of antimicrobial polymers.
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Affiliation(s)
- Lei Liu
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Kevin C. Courtney
- Department
of Neuroscience, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Howard
Hughes Medical Institute, University of
Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Sean W. Huth
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Leslie A. Rank
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Bernard Weisblum
- Department
of Pharmacology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Edwin R. Chapman
- Department
of Neuroscience, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Howard
Hughes Medical Institute, University of
Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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4
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Banach M, Wiśniowski Z, Ptak M, Roterman I. Aggregation-promoting conditions necessary to create the complexes by acylphosphatase from the hyperthermophile Sulfolobus solfataricus. BIO-ALGORITHMS AND MED-SYSTEMS 2019. [DOI: 10.1515/bams-2019-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The structural transition from the globular to the amyloid form of proteins requires aggregation-promoting conditions. The protein example of this category is acylphosphatase from the hyperthermophile Sulfolobus solfataricus. This protein represents a structure with a well-defined hydrophobic core. This is why the complexation (including oligomerization) of this protein is of low probability. The chain fragment participating in aggregation in comparison to the status with respect to the fuzzy oil drop model is discussed in this paper.
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5
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Yoo NG, Dogra S, Meinen BA, Tse E, Haefliger J, Southworth DR, Gray MJ, Dahl JU, Jakob U. Polyphosphate Stabilizes Protein Unfolding Intermediates as Soluble Amyloid-like Oligomers. J Mol Biol 2018; 430:4195-4208. [PMID: 30130556 DOI: 10.1016/j.jmb.2018.08.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/06/2018] [Accepted: 08/14/2018] [Indexed: 02/03/2023]
Abstract
Inorganic polyphosphate (polyP) constitutes one of the most conserved and ubiquitous molecules in biology. Recent work in bacteria demonstrated that polyP increases oxidative stress resistance by preventing stress-induced protein aggregation and promotes biofilm formation by stimulating functional amyloid formation. To gain insights into these two seemingly contradictory functions of polyP, we investigated the effects of polyP on the folding model lactate dehydrogenase. We discovered that the presence of polyP during the thermal unfolding process stabilizes folding intermediates of lactate dehydrogenase as soluble micro-β-aggregates with amyloid-like properties. Size and heterogeneity of the oligomers formed in this process were dependent on the polyP chain length, with longer chains forming smaller, more homogenous complexes. This ability of polyP to stabilize thermally unfolded proteins even upon exposure to extreme temperatures appears to contribute to the observed resistance of uropathogenic Escherichia coli toward severe heat shock treatment. These results suggest that the working mechanism of polyP is the same for both soluble and amyloidogenic proteins, with the ultimate outcome likely being determined by a combination of polyP chain length and the client protein itself. They help to explain how polyP can simultaneously function as general stress-protective chaperone and instigator of amyloidogenic processes in vivo.
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Affiliation(s)
- Nicholas G Yoo
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Siddhant Dogra
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Ben A Meinen
- Howard Hughes Medical Institute, University of Michigan, 2256 Biological Sciences Science Building, 1105 North University Ave, Ann Arbor, MI 48109, United States
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158, United States
| | - Janine Haefliger
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158, United States
| | - Michael J Gray
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Jan-Ulrik Dahl
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States.
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6
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Joyce MA, Hayakawa K, Wolodko WT, Fraser ME. Biochemical and structural characterization of the GTP-preferring succinyl-CoA synthetase from Thermus aquaticus. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:751-62. [PMID: 22751660 PMCID: PMC3388811 DOI: 10.1107/s0907444912010852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/12/2012] [Indexed: 11/11/2022]
Abstract
Succinyl-CoA synthetase (SCS) from Thermus aquaticus was characterized biochemically via measurements of the activity of the enzyme and determination of its quaternary structure as well as its stability and refolding properties. The enzyme is most active between pH 8.0 and 8.4 and its activity increases with temperature to about 339 K. Gel-filtration chromatography and sedimentation equilibrium under native conditions demonstrated that the enzyme is a heterotetramer of two α-subunits and two β-subunits. The activity assays showed that the enzyme uses either ADP/ATP or GDP/GTP, but prefers GDP/GTP. This contrasts with Escherichia coli SCS, which uses GDP/GTP but prefers ADP/ATP. To understand the nucleotide preference, T. aquaticus SCS was crystallized in the presence of GDP, leading to the determination of the structure in complex with GDP-Mn(2+). A water molecule and Pro20β in T. aquaticus take the place of Gln20β in pig GTP-specific SCS, interacting well with the guanine base and other residues of the nucleotide-binding site. This leads to the preference for GDP/GTP, but does not hinder the binding of ADP/ATP.
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Affiliation(s)
- Michael A. Joyce
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Koto Hayakawa
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - William T. Wolodko
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marie E. Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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7
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Engstrom JD, Simpson DT, Cloonan C, Lai ES, Williams RO, Barrie Kitto G, Johnston KP. Stable high surface area lactate dehydrogenase particles produced by spray freezing into liquid nitrogen. Eur J Pharm Biopharm 2007; 65:163-74. [PMID: 17027245 DOI: 10.1016/j.ejpb.2006.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Revised: 07/19/2006] [Accepted: 08/04/2006] [Indexed: 11/18/2022]
Abstract
Enzyme activities were determined for lactate dehydrogenase (LDH) powder produced by lyophilization, and two fast freezing processes, spray freeze-drying (SFD) and spray freezing into liquid (SFL) nitrogen. The 0.25 mg/mL LDH aqueous feed solutions included either 30 or 100 mg/mL trehalose. The SFL process produced powders with very high enzyme activities upon reconstitution, similar to lyophilization. However, the specific surface area of 13 m(2)/g for SFL was an order of magnitude larger than for lyophilization. In SFD activities were reduced in the spraying step by the long exposure to the gas-liquid interface for 0.1-1s, versus only 2 ms in SFL. The ability to produce stable high surface area submicron particles of fragile proteins such as LDH by SFL is of practical interest in protein storage and in various applications in controlled release including encapsulation into bioerodible polymers. The SFL process has been scaled down for solution volumes <1 mL to facilitate studies of therapeutic proteins.
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Affiliation(s)
- Josh D Engstrom
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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8
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Tian R, Li SJ, Wang DL, Zhao Z, Liu Y, He RQ. The acidic C-terminal domain stabilizes the chaperone function of protein disulfide isomerase. J Biol Chem 2004; 279:48830-5. [PMID: 15358778 DOI: 10.1074/jbc.m407076200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Protein disulfide isomerase (PDI, EC 5.3.4.1) is a chaperone and catalyzes the formation and rearrangement of disulfide bonds in proteins. Domain c-(463-491), containing 18 acidic residues, is an interesting and important C-terminal extension of PDI. In this study, the PDI mutant abb'a', in which domain c is truncated, was used to investigate the relationship between the C-terminal structure and chaperone function. Reactivation and light-scattering experiments show that both wild-type PDI and abb'a' interact with lactate dehydrogenase (LDH, EC 1.1.1.27), which tends to self-aggregate during reactivation. The interaction enhances reactivation of LDH and reduces aggregation. According to these results, it seems as if domain c might be dispensable to the chaperone function of PDI. However, abb'a' is prone to self-aggregation and causes increased aggregation of LDH during thermal denaturation. In contrast, wild-type PDI remains active as a chaperone under these conditions and prevents self-aggregation of LDH. Furthermore, measurements of intrinsic fluorescence and difference absorbance during denaturation show that abb'a' is much more labile to heat or guanidine hydrochloride denaturation than wild-type PDI. This suggests that domain c is required for the stabilization and maintenance of the chaperone function of PDI under extreme conditions.
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Affiliation(s)
- Rui Tian
- Laboratory of Visual Information Processing, Chinese Academy of Sciences, Beijing, China
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9
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Ogasahara K, Ishida M, Yutani K. Stimulated interaction between and subunits of tryptophan synthase from hyperthermophile enhances its thermal stability. J Biol Chem 2003; 278:8922-8. [PMID: 12643278 DOI: 10.1074/jbc.m210893200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Tryptophan synthase from hyperthermophile, Pyrococcus furiosus, was found to be a tetrameric form (22) composed of and 2 subunits. To elucidate the relationship between the features of the subunit association and the thermal stability of the tryptophan synthase, the subunit association and thermal stability were examined by isothermal titration calorimetry and differential scanning calorimetry, respectively, in comparison with those of the counterpart from Escherichia coli. The association constants between the and subunits in the hyperthermophile protein were of the order of 108 M1, which were higher by two orders of magnitude than those in the mesophile one. The negative values of the heat capacity change and enthalpy change upon the subunit association were much lower in the hyperthermophile protein than in the mesophile one, indicating that the conformational change of the hyperthermophile protein coupled to the subunit association is slight. The denaturation temperature of the subunit from the hyperthermophile was enhanced by 17 degrees C due to the formation of the 22 complex. This increment in denaturation temperature due to complex formation could be quantitatively estimated by the increase in the association constant compared with that of the counterpart from E. coli.
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Affiliation(s)
- Kyoko Ogasahara
- Institute for Protein Research, Osaka University, Suita City, Osaka 565-0871, Japan
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10
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Flores H, Ellington AD. Increasing the thermal stability of an oligomeric protein, beta-glucuronidase. J Mol Biol 2002; 315:325-37. [PMID: 11786015 DOI: 10.1006/jmbi.2001.5223] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The reporter enzyme beta-glucuronidase was mutagenized and evolved for thermostability. After four cycles of screening the best variant was more active than the wild-type enzyme, and retained function at 70 degrees C, whereas the wild-type enzyme lost function at 65 degrees C. Variants derived from sequential mutagenesis were shuffled together, and re-screened for thermostability. The best variants retained activities at even higher temperatures (80 degrees C), but had specific activities that were now less than that of the wild-type enzyme. The mutations clustered near the tetramer interface of the enzyme, and many of the evolved variants showed much greater resistance to quaternary structure disruption at high temperatures, which is also a characteristic of naturally thermostable enzymes. Together, these results suggest a pathway for the evolution of thermostability in which enzymes initially become stable at high temperatures without loss of activity at low temperatures, while further evolution leads to enzymes that have kinetic parameters that are optimized for high temperatures.
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Affiliation(s)
- Humberto Flores
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology ICMB a4800/MBB 3.424, University of Texas at Austin, 26th and Speedway, Austin, TX 78712, USA
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11
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Rochet JC, Brownie ER, Oikawa K, Hicks LD, Fraser ME, James MN, Kay CM, Bridger WA, Wolodko WT. Pig heart CoA transferase exists as two oligomeric forms separated by a large kinetic barrier. Biochemistry 2000; 39:11291-302. [PMID: 10985774 DOI: 10.1021/bi0003184] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Pig heart CoA transferase (EC 2.8.3.5) has been shown previously to adopt a homodimeric structure, in which each subunit has a molecular weight of 52 197 and consists of N- and C-domains linked by a hydrophilic linker or "hinge". Here we identify and characterize a second oligomeric form constituent in purified enzyme preparations, albeit at low concentrations. Both species catalyze the transfer of CoA with similar values for k(cat) and K(M). This second form sediments more rapidly than the homodimer under the conditions of conventional sedimentation velocity and active enzyme centrifugation. Apparent molecular weight values determined by sedimentation equilibrium and gel filtration chromatography are 4-fold greater than the subunit molecular weight, confirming that this form is a homotetramer. The subunits of both oligomeric forms are indistinguishable with respect to molecular mass, far-UV CD, intrinsic tryptophan fluorescence, and equilibrium unfolding. Dissociation of the homotetramer to the homodimer occurs very slowly in benign solutions containing high salt concentrations (0.25-2.0 M KCl). The homotetramer is fully converted to homodimer during refolding from denaturant at low protein concentrations. Disruption of the hydrophilic linker between the N- and C-domains by mutagenesis or mild proteolysis causes a decrease in the relative amount of the larger conformer. The homotetramer is stabilized by interactions involving the helical hinge region, and a substantial kinetic barrier hinders interconversion of the two oligomeric species under nondenaturing conditions.
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Affiliation(s)
- J C Rochet
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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12
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Jaenicke R, Lilie H. Folding and association of oligomeric and multimeric proteins. ADVANCES IN PROTEIN CHEMISTRY 2000; 53:329-401. [PMID: 10751948 DOI: 10.1016/s0065-3233(00)53007-1] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- R Jaenicke
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Germany
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13
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Andersson MM, Hatti-Kaul R, Brown W. Dynamic and Static Light Scattering and Fluorescence Studies of the Interactions between Lactate Dehydrogenase and Poly(ethyleneimine). J Phys Chem B 2000. [DOI: 10.1021/jp993506g] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria M. Andersson
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, S-221 00 Lund, Sweden
| | - Rajni Hatti-Kaul
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, S-221 00 Lund, Sweden
| | - Wyn Brown
- Department of Physical Chemistry, University of Uppsala, P.O. Box 532, S-751 21 Uppsala, Sweden
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14
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Dams T, Jaenicke R. Stability and folding of dihydrofolate reductase from the hyperthermophilic bacterium Thermotoga maritima. Biochemistry 1999; 38:9169-78. [PMID: 10413491 DOI: 10.1021/bi990635e] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Dihydrofolate reductase (DHFR) has been a well-established model system for protein folding. The enzyme DHFR from the hyperthermophilic bacterium Thermotoga maritima (TmDHFR) displays distinct adaptations toward high temperatures at the level of both structure and stability. The enzyme represents an extremely stable dimer; no isolated structured monomers could be detected in equilibrium or during unfolding. The equilibrium unfolding strictly follows the two-state model for a dimer (N(2) right harpoon over left harpoon 2U), with a free energy of stabilization of DeltaG = -142 +/- 10 kJ/mol at 15 degrees C. The two-state model is applicable over the whole temperature range (5-70 degrees C), yielding a DeltaG vs T profile with maximum stability at around 35 degrees C. There is no flattening of the stability profile. Instead, the enhanced thermostability is characterized by shifts toward higher overall stability and higher temperature of maximum stability. TmDHFR unfolds in a highly cooperative manner via a nativelike transition state without intermediates. The unfolding reaction is much slower (ca. 10(8) times) compared to DHFR from Escherichia coli (EcDHFR). In contrast to EcDHFR, no evidence for heterogeneity of the native state is detectable. Refolding proceeds via at least two intermediates and a burst-phase of rather low amplitude. Reassociation of monomeric intermediates is not rate-limiting on the folding pathway due to the high association constant of the dimer.
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Affiliation(s)
- T Dams
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
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15
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Abstract
Three complete genome sequences of thermophilic bacteria provide a wealth of information challenging current ideas concerning phylogeny and evolution, as well as the determinants of protein stability. Considering known protein structures from extremophiles, it becomes clear that no general conclusions can be drawn regarding adaptive mechanisms to extremes of physical conditions. Proteins are individuals that accumulate increments of stabilization; in thermophiles these come from charge clusters, networks of hydrogen bonds, optimization of packing and hydrophobic interactions, each in its own way. Recent examples indicate ways for the rational design of ultrastable proteins.
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Affiliation(s)
- R Jaenicke
- Institute of Biophysics and Physical Biochemistry University of Regensburg D-93040 Regensburg Germany. rainer.jaenicke@biologie. uni-regensburg.de
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16
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Hess JM, Tchernajenko V, Vieille C, Zeikus JG, Kelly RM. Thermotoga neapolitana homotetrameric xylose isomerase is expressed as a catalytically active and thermostable dimer in Escherichia coli. Appl Environ Microbiol 1998; 64:2357-60. [PMID: 9647799 PMCID: PMC106395 DOI: 10.1128/aem.64.7.2357-2360.1998] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The xylA gene from Thermotoga neapolitana 5068 was expressed in Escherichia coli. Gel filtration chromatography showed that the recombinant enzyme was both a homodimer and a homotetramer, with the dimer being the more abundant form. The purified native enzyme, however, has been shown to be exclusively tetrameric. The two enzyme forms had comparable stabilities when they were thermoinactivated at 95 degrees C. Differential scanning calorimetry revealed thermal transitions at 99 and 109.5 degrees C for both forms, with an additional shoulder at 91 degrees C for the tetramer. These results suggest that the association of the subunits into the tetrameric form may have little impact on the stability and biocatalytic properties of the enzyme.
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Affiliation(s)
- J M Hess
- Department of Chemical Engineering, North Carolina State University, Raleigh 27695-7905, USA
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17
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Auerbach G, Ostendorp R, Prade L, Korndörfer I, Dams T, Huber R, Jaenicke R. Lactate dehydrogenase from the hyperthermophilic bacterium thermotoga maritima: the crystal structure at 2.1 A resolution reveals strategies for intrinsic protein stabilization. Structure 1998; 6:769-81. [PMID: 9655830 DOI: 10.1016/s0969-2126(98)00078-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND L(+)-Lactate dehydrogenase (LDH) catalyzes the last step in anaerobic glycolysis, the conversion of pyruvate to lactate, with the concomitant oxidation of NADH. Extensive physicochemical and structural investigations of LDHs from both mesophilic and thermophilic organisms have been undertaken in order to study the temperature adaptation of proteins. In this study we aimed to determine the high-resolution structure of LDH from the hyperthermophilic bacterium Thermotoga maritima (TmLDH), the most thermostable LDH to be isolated so far. It was hoped that the structure of TmLDH would serve as a model system to reveal strategies of protein stabilization at temperatures near the boiling point of water. RESULTS The crystal structure of the extremely thermostable TmLDH has been determined at 2.1 A resolution as a quaternary complex with the cofactor NADH, the allosteric activator fructose-1,6-bisphosphate, and the substrate analog oxamate. The structure of TmLDH was solved by Patterson search methods using a homology-based model as a search probe. The native tetramer shows perfect 222 symmetry. Structural comparisons with five LDHs from mesophilic and moderately thermophilic organisms and with other ultrastable enzymes from T. maritima reveal possible strategies of protein thermostabilization. CONCLUSIONS Structural analysis of TmLDH and comparison of the enzyme to moderately thermophilic and mesophilic homologs reveals a strong conservation of both the three-dimensional fold and the catalytic mechanism. Going from lower to higher physiological temperatures a variety of structural differences can be observed: an increased number of intrasubunit ion pairs; a decrease of the ratio of hydrophobic to charged surface area, mainly caused by an increased number of arginine and glutamate sidechains on the protein surface; an increased secondary structure content including an additional unique 'thermohelix' (alphaT) in TmLDH; more tightly bound intersubunit contacts mainly based on hydrophobic interactions; and a decrease in both the number and the total volume of internal cavities. Similar strategies for thermal adaptation can be observed in other enzymes from T. maritima.
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Affiliation(s)
- G Auerbach
- Max-Planck-Institut für Biochemie Abt. Strukturforschung, 82152, Martinsried, Germany.
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A Kinetic Analysis of the Endogenous Lactate Dehydrogenase Activity of Duck Lens ε-Crystallin in Reverse Micelles. J Colloid Interface Sci 1998. [DOI: 10.1006/jcis.1997.5325] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Symmetry in the 2.25 MDa homomultimeric phosphoenolpyruvate synthase fromStaphylothermus marinus: Analyses of negatively stained preparations. Micron 1998. [DOI: 10.1016/s0968-4328(97)00069-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Scholz C, Scherer G, Mayr LM, Schindler T, Fischer G, Schmid FX. Prolyl isomerases do not catalyze isomerization of non-prolyl peptide bonds. Biol Chem 1998; 379:361-5. [PMID: 9563833 DOI: 10.1515/bchm.1998.379.3.361] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Prolyl isomerases accelerate the cis <--> trans isomerization of prolyl peptide bonds during protein folding and probably also in folded proteins. We asked whether this catalytic function is in fact restricted to prolyl bonds or whether the isomerizations of 'normal' non-prolyl peptide bonds are catalyzed as well. By using the P39A variant of ribonuclease T1 as a substrate we find that the trans --> cis isomerization of the Tyr38-Ala39 bond in the refolding of this protein is not catalyzed by prolyl isomerases of the cyclophilin, FKBP and parvulin families. These enzymes are neither able to catalyze amide bond isomerizations in the proline-free model peptide Ala-Ala-Tyr-Ala-Ala.
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Affiliation(s)
- C Scholz
- Laboratorium für Biochemie, Universität Bayreuth, Germany
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