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Kayrav A, Mumcu H, Durmus N, Karaguler NG. Revealing the role of the X25 domains through the characterization of truncated variants of amylopullulanase enzyme from Thermoanaerobacter brockii brockii. Int J Biol Macromol 2024; 270:132404. [PMID: 38754672 DOI: 10.1016/j.ijbiomac.2024.132404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
To understand the role of the X25 domains of the amylopullulanase enzyme from Thermoanaerobacter brockii brockii (T. brockii brockii), four truncated variants that are TbbApuΔX25-1-SH3 (S130-A1484), TbbApuΔX25-2-SH3 (T235-A1484), TbbApuΔX25-1-CBM20 (S130-P1254), and TbbApuΔX25-2-CBM20 (T235-P1254) were constructed, expressed and characterized together with the SH3 and CBM20 domain truncated variants (TbbApuΔSH3 (V1-A1484) and TbbApuΔCBM20 (V1-P1254). TbbApuΔSH3 showed improved affinity and specificity for both pullulan and soluble starch than full-length TbbApu with lower Km and higher kcat/Km values. It indicates that SH3 is a disposable domain without any effect on the activity and stability of the enzyme. However, TbbApuΔX25-1-SH3, TbbApuΔX25-2-SH3, TbbApuΔX25-1-CBM20, TbbApuΔX25-2-CBM20 (T235-P1254) and TbbApuΔCBM20 showed higher Km and lower kcat/Km values than TbbApuΔSH3 to both soluble starch and pullulan. It specifies that the X25 domains and CBM20 play an important role in both α-amylase and pullulanase activity. Also, it is revealed that while truncation of the CBM20 domain as starch binding domain (SBD) did not affect on raw starch binding ability of the enzyme, truncation of both X25 domains caused almost complete loss of the raw starch binding ability of the enzyme. All these results enlightened the function of the X25 domains that play a more crucial role than CBM20 in the enzyme's binding to raw starch and also play a crucial role in its activity.
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Affiliation(s)
- Aycan Kayrav
- Istanbul Technical University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 34469 Istanbul, Türkiye; Istanbul Technical University, Dr. Orhan Öcalgiray Molecular Biology-Biotechnology and Genetics Research Center, Istanbul, Türkiye
| | - Hande Mumcu
- Istanbul Technical University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 34469 Istanbul, Türkiye; Istanbul Technical University, Dr. Orhan Öcalgiray Molecular Biology-Biotechnology and Genetics Research Center, Istanbul, Türkiye
| | - Naciye Durmus
- Istanbul Technical University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 34469 Istanbul, Türkiye; Istanbul Technical University, Dr. Orhan Öcalgiray Molecular Biology-Biotechnology and Genetics Research Center, Istanbul, Türkiye
| | - Nevin Gul Karaguler
- Istanbul Technical University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, 34469 Istanbul, Türkiye; Istanbul Technical University, Dr. Orhan Öcalgiray Molecular Biology-Biotechnology and Genetics Research Center, Istanbul, Türkiye.
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Helmick H, Hartanto C, Ettestad S, Liceaga A, Bhunia AK, Kokini JL. Quantitative structure-property relationships of thermoset pea protein gels with ethanol, shear, and sub-zero temperature pretreatments. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tiwari P, Kaila P, Guptasarma P. Understanding anomalous mobility of proteins on SDS‐PAGE with special reference to the highly acidic extracellular domains of human E‐ and N‐cadherins. Electrophoresis 2019; 40:1273-1281. [DOI: 10.1002/elps.201800219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 12/21/2018] [Accepted: 01/14/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Prince Tiwari
- Centre for Protein ScienceDesign and EngineeringDepartment of Biological SciencesIndian Institute of Science Education and Research (IISER) Mohali Punjab India
| | - Pallavi Kaila
- Centre for Protein ScienceDesign and EngineeringDepartment of Biological SciencesIndian Institute of Science Education and Research (IISER) Mohali Punjab India
| | - Purnananda Guptasarma
- Centre for Protein ScienceDesign and EngineeringDepartment of Biological SciencesIndian Institute of Science Education and Research (IISER) Mohali Punjab India
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Multiple thermostable enzyme hydrolases on magnetic nanoparticles: An immobilized enzyme-mediated approach to saccharification through simultaneous xylanase, cellulase and amylolytic glucanotransferase action. Int J Biol Macromol 2018; 120:1650-1658. [DOI: 10.1016/j.ijbiomac.2018.09.106] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022]
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Sharma P, Guptasarma P. Endoglucanase activity at a second site in Pyrococcus furiosus triosephosphate isomerase-Promiscuity or compensation for a metabolic handicap? FEBS Open Bio 2017; 7:1126-1143. [PMID: 28781953 PMCID: PMC5537068 DOI: 10.1002/2211-5463.12249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/05/2017] [Accepted: 05/23/2017] [Indexed: 01/16/2023] Open
Abstract
The eight‐stranded (β/α)8 barrel fold known as the Triosephosphate isomerase (TIM) barrel is the most commonly observed fold in enzymes, displaying an eightfold structural symmetry. The sequences and structures of different TIM barrel enzymes suggest that nature exploits the modularity inherent in the eightfold symmetry to generate enzymes with diverse enzymatic activities and, in certain cases, more than one catalytic activity per enzyme. Here, we report the discovery, verification, and characterization of such an additional activity, a novel endoglucanase/cellulase activity in what is otherwise a triosephosphate isomerase from the hyperthermophile archaeon Pyrococcus furiosus (PfuTIM). The activity is seen in two different ranges of temperatures, with one maximum at 40 °C and a second maximum close to 100 °C. The endoglucanase/cellulase activity is inhibited by norharman, a TIM inhibitor, which is suspected to bind at a site different to that of the regular substrate, glyceraldehyde‐3‐phosphate (G3P). However, endoglucanase/cellulose activity is not inhibited either by G3P analogs or by glycine‐scanning mutations involving residues in loops 1, 4, and 6 of PfuTIM, which are known to be important for TIM activity. It appears, therefore, that two different sites on PfuTIM are responsible for the observed TIM and endoglucanase activities. We discuss possible correlations between this discovery and certain unusual features of the glycolytic pathway in P. furiosus. Enzyme Pyrococcus furiosus Triosephosphate isomerase (EC:5.3.1.1)
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Affiliation(s)
- Prerna Sharma
- Department of Biological Sciences Centre for Protein Science Design and Engineering (CPSDE) Indian Institute of Science Education and Research (IISER) Mohali Punjab.,Division of Protein Science and Engineering CSIR- Institute of Microbial Technology Chandigarh India
| | - Purnananda Guptasarma
- Department of Biological Sciences Centre for Protein Science Design and Engineering (CPSDE) Indian Institute of Science Education and Research (IISER) Mohali Punjab.,Division of Protein Science and Engineering CSIR- Institute of Microbial Technology Chandigarh India
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‘Super-perfect’ enzymes: Structural stabilities and activities of recombinant triose phosphate isomerases from Pyrococcus furiosus and Thermococcus onnurineus produced in Escherichia coli. Biochem Biophys Res Commun 2015; 460:753-8. [DOI: 10.1016/j.bbrc.2015.03.102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/19/2015] [Indexed: 11/20/2022]
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Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev 2014; 78:89-175. [PMID: 24600042 DOI: 10.1128/mmbr.00041-13] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of "new," unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.
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Chandrayan SK, Prakash S, Ahmed S, Guptasarma P. Hyperthermophile protein behavior: partially-structured conformations of Pyrococcus furiosus rubredoxin monomers generated through forced cold-denaturation and refolding. PLoS One 2014; 9:e80014. [PMID: 24603413 PMCID: PMC3945965 DOI: 10.1371/journal.pone.0080014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 09/27/2013] [Indexed: 11/21/2022] Open
Abstract
Some years ago, we showed that thermo-chemically denatured, partially-unfolded forms of Pyrococcus furiosus triosephosphateisomerase (PfuTIM) display cold-denaturation upon cooling, and heat-renaturation upon reheating, in proportion with the extent of initial partial unfolding achieved. This was the first time that cold-denaturation was demonstrated for a hyperthermophile protein, following unlocking of surface salt bridges. Here, we describe the behavior of another hyperthermophile protein, the small, monomeric, 53 residues-long rubredoxin from Pyrococcus furiosus (PfRd), which is one of the most thermostable proteins known to man. Like PfuTIM, PfRd too displays cold-denaturation after initial thermo-chemical perturbation, however, with two differences: (i) PfRd requires considerably higher temperatures as well as higher concentrations of guanidium hydrochloride (Gdm.HCl) than PfuTIM; (ii) PfRd's cold-denaturation behavior during cooling after thermo-chemical perturbation is incompletely reversible, unlike PfuTIM's, which was clearly reversible (from each different conformation generated). Differential cold-denaturation treatments allow PfRd to access multiple partially-unfolded states, each of which is clearly highly kinetically-stable. We refer to these as ‘Trishanku’ unfolding intermediates (or TUIs). Fascinatingly, refolding of TUIs through removal of Gdm.HCl generates multiple partially-refolded, monomeric, kinetically-trapped, non-native ‘Trishanku’ refolding intermediates (or TRIs), which differ from each other and from native PfRd and TUIs, in structural content and susceptibility to proteolysis. We find that the occurrence of cold denaturation and observations of TUI and TRI states is contingent on the oxidation status of iron, with redox agents managing to modulate the molecule's behavior upon gaining access to PfRd's iron atom. Mass spectrometric examination provides no evidence of the formation of disulfide bonds, but other experiments suggest that the oxidation status of iron (and its extent of burial) together determine whether or not PfRd shows cold denaturation, and also whether redox agents are able to modulate its behavior.
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Affiliation(s)
- Sanjeev Kumar Chandrayan
- Protein Science & Engineering Division, Institute of Microbial Technology, (IMTECH), Council of Scientific & Industrial Research (CSIR), Chandigarh, India
| | - Satya Prakash
- Department of Biological Sciences, Indian Institute of Science Education & Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar (Mohali), Punjab, India; Protein Science & Engineering Division, Institute of Microbial Technology, (IMTECH), Council of Scientific & Industrial Research (CSIR), Chandigarh, India
| | - Shubbir Ahmed
- Protein Science & Engineering Division, Institute of Microbial Technology, (IMTECH), Council of Scientific & Industrial Research (CSIR), Chandigarh, India
| | - Purnananda Guptasarma
- Department of Biological Sciences, Indian Institute of Science Education & Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar (Mohali), Punjab, India; Protein Science & Engineering Division, Institute of Microbial Technology, (IMTECH), Council of Scientific & Industrial Research (CSIR), Chandigarh, India
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Dhaunta N, Arora K, Chandrayan SK, Guptasarma P. Introduction of a thermophile-sourced ion pair network in the fourth beta/alpha unit of a psychophile-derived triosephosphate isomerase from Methanococcoides burtonii significantly increases its kinetic thermal stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1023-33. [DOI: 10.1016/j.bbapap.2013.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 12/07/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
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Dias CL, Ala-Nissila T, Wong-ekkabut J, Vattulainen I, Grant M, Karttunen M. The hydrophobic effect and its role in cold denaturation. Cryobiology 2009; 60:91-9. [PMID: 19616532 DOI: 10.1016/j.cryobiol.2009.07.005] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 07/14/2009] [Accepted: 07/14/2009] [Indexed: 11/19/2022]
Abstract
The hydrophobic effect is considered the main driving force for protein folding and plays an important role in the stability of those biomolecules. Cold denaturation, where the native state of the protein loses its stability upon cooling, is also attributed to this effect. It is therefore not surprising that a lot of effort has been spent in understanding this phenomenon. Despite these efforts, many unresolved fundamental aspects remain. In this paper we review and summarize the thermodynamics of proteins, the hydrophobic effect and cold denaturation. We start by accounting for these phenomena macroscopically then move to their atomic-level description. We hope this review will help the reader gain insights into the role played by the hydrophobic effect in cold denaturation.
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Affiliation(s)
- Cristiano L Dias
- Department of Applied Mathematics, The University of Western Ontario, Middlesex College, 1151 Richmond St. N., London, Ont., Canada N6A 5B7.
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Chandrayan SK, Guptasarma P. Attenuation of ionic interactions profoundly lowers the kinetic thermal stability of Pyrococcus furiosus triosephosphate isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:905-12. [DOI: 10.1016/j.bbapap.2009.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 02/08/2009] [Accepted: 03/05/2009] [Indexed: 10/21/2022]
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Catalysis by isolated beta-subunits of the ATP Synthase/ATPase from Thermophilic bacillus PS3. Hydrolysis of pyrophosphate. J Bioenerg Biomembr 2009; 40:561-8. [PMID: 19139978 DOI: 10.1007/s10863-008-9192-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 12/12/2008] [Indexed: 10/21/2022]
Abstract
Although the capacity of isolated beta-subunits of the ATP synthase/ATPase to perform catalysis has been extensively studied, the results have not conclusively shown that the subunits are catalytically active. Since soluble F(1) of mitochondrial H(+)-ATPase can bind inorganic pyrophosphate (PP(i)) and synthesize PP(i) from medium phosphate, we examined if purified His-tagged beta-subunits from Thermophilic bacillus PS3 can hydrolyze PP(i). The difference spectra in the near UV CD of beta-subunits with and without PP(i) show that PP(i) binds to the subunits. Other studies show that beta-subunits hydrolyze [(32)P] PP(i) through a Mg(2+)-dependent process with an optimal pH of 8.3. Free Mg(2+) is required for maximal hydrolytic rates. The Km for PP(i) is 75 microM and the Vmax is 800 pmol/min/mg. ATP is a weak inhibitor of the reaction, it diminishes the Vmax and increases the Km for PP(i). Thus, isolated beta-subunits are catalytically competent with PP(i) as substrate; apparently, the assembly of beta-subunits into the ATPase complex changes substrate specificity, and leads to an increase in catalytic rates.
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Cold stability of intrinsically disordered proteins. FEBS Lett 2008; 583:465-9. [PMID: 19121309 DOI: 10.1016/j.febslet.2008.12.054] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 01/27/2023]
Abstract
Contrary to globular proteins, intrinsically disordered proteins (IDPs) lack a folded structure and they do not lose solubility at elevated temperatures. Although this should also be true at low temperatures, cold stability of IDPs has not been addressed in any scientific work so far. As direct characterization of cold-denaturation is difficult, we approached the problem through a freezing-induced loss-of-function model of globular-disordered functional protein pairs (m-calpain-calpastatin, tubulin-Map2c, Hsp90-ERD14). Our results affirm that in contrast with globular proteins IDPs are resistant to cold treatment. The theoretical and functional aspects of this observation are discussed.
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