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Pouliquen DL. The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research. Front Cell Dev Biol 2024; 12:1403037. [PMID: 38803391 PMCID: PMC11128620 DOI: 10.3389/fcell.2024.1403037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.
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Affiliation(s)
- Daniel L. Pouliquen
- Inserm, CNRS, CRCINA, Nantes Université, University of Angers, Angers, France
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2
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Some Clues about Enzymes from Psychrophilic Microorganisms. Microorganisms 2022; 10:microorganisms10061161. [PMID: 35744679 PMCID: PMC9227589 DOI: 10.3390/microorganisms10061161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 02/04/2023] Open
Abstract
Enzymes purified from psychrophilic microorganisms prove to be efficient catalysts at low temperatures and possess a great potential for biotechnological applications. The low-temperature catalytic activity has to come from specific structural fluctuations involving the active site region, however, the relationship between protein conformational stability and enzymatic activity is subtle. We provide a survey of the thermodynamic stability of globular proteins and their rationalization grounded in a theoretical approach devised by one of us. Furthermore, we provide a link between marginal conformational stability and protein flexibility grounded in the harmonic approximation of the vibrational degrees of freedom, emphasizing the occurrence of long-wavelength and excited vibrations in all globular proteins. Finally, we offer a close view of three enzymes: chloride-dependent α-amylase, citrate synthase, and β-galactosidase.
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3
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Structural Analysis and Construction of a Thermostable Antifungal Chitinase. Appl Environ Microbiol 2022; 88:e0065222. [PMID: 35652665 DOI: 10.1128/aem.00652-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chitin is a biopolymer of N-acetyl-d-glucosamine with β-1,4-bond and is the main component of arthropod exoskeletons and the cell walls of many fungi. Chitinase (EC 3.2.1.14) is an enzyme that hydrolyzes the β-1,4-bond in chitin and degrades chitin into oligomers. It has been found in a wide range of organisms. Chitinase from Gazyumaru (Ficus microcarpa) latex exhibits antifungal activity by degrading chitin in the cell wall of fungi and is expected to be used in medical and agricultural fields. However, the enzyme's thermostability is an important factor; chitinase is not thermostable enough to maintain its activity under the actual application conditions. In addition to the fact that thermostable chitinases exhibiting antifungal activity can be used under various conditions, they have some advantages for the production process and long-term preservation, which are highly demanded in industrial use. We solved the crystal structure of chitinase to explore the target sites to improve its thermostability. We rationally introduced proline residues, a disulfide bond, and salt bridges in the chitinase using protein-engineering methods based on the crystal structure and sequence alignment among other chitinases. As a result, we successfully constructed the thermostable mutant chitinases rationally with high antifungal and specific activities. The results provide a useful strategy to enhance the thermostability of this enzyme family. IMPORTANCE We solved the crystal structure of the chitinase from Gazyumaru (Ficus microcarpa) latex exhibiting antifungal activity. Furthermore, we demonstrated that the thermostable mutant enzyme with a melting temperature (Tm) 6.9°C higher than wild type (WT) and a half-life at 60°C that is 15 times longer than WT was constructed through 10 amino acid substitutions, including 5 proline residues substitutions, making disulfide bonding, and building a salt bridge network in the enzyme. These mutations do not affect its high antifungal activity and chitinase activity, and the principle for the construction of the thermostable chitinase was well explained by its crystal structure. Our results provide a useful strategy to enhance the thermostability of this enzyme family and to use the thermostable mutant as a seed for antifungal agents for practical use.
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Fongaro G, Maia GA, Rogovski P, Cadamuro RD, Lopes JC, Moreira RS, Camargo AF, Scapini T, Stefanski FS, Bonatto C, Marques Souza DS, Stoco PH, Duarte RTD, Cabral da Cruz AC, Wagner G, Treichel H. Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools. Curr Genomics 2020; 21:240-252. [PMID: 33071618 PMCID: PMC7521039 DOI: 10.2174/1389202921999200601144137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/02/2020] [Accepted: 04/20/2020] [Indexed: 12/03/2022] Open
Abstract
Abstract: Genomic and proteomic advances in extremophile microorganism studies are increasingly demonstrating their ability to produce a variety of enzymes capable of converting biomass into bioenergy. Such microorganisms are found in environments with nutritional restrictions, anaerobic environments, high salinity, varying pH conditions and extreme natural environments such as hydrothermal vents, soda lakes, and Antarctic sediments. As extremophile microorganisms and their enzymes are found in widely disparate locations, they generate new possibilities and opportunities to explore biotechnological prospecting, including biofuels (biogas, hydrogen and ethanol) with an aim toward using multi-omics tools that shed light on biotechnological breakthroughs.
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Affiliation(s)
- Gislaine Fongaro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Guilherme Augusto Maia
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Paula Rogovski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rafael Dorighello Cadamuro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Joana Camila Lopes
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Renato Simões Moreira
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Aline Frumi Camargo
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Thamarys Scapini
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Fábio Spitza Stefanski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Charline Bonatto
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Doris Sobral Marques Souza
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Patrícia Hermes Stoco
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Tadeu Delgado Duarte
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Ariadne Cristiane Cabral da Cruz
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Glauber Wagner
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Helen Treichel
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
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5
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Statistical and molecular dynamics (MD) simulation approach to investigate the role of intrinsically disordered regions of shikimate dehydrogenase in microorganisms surviving at different temperatures. Extremophiles 2020; 24:831-842. [PMID: 32975630 DOI: 10.1007/s00792-020-01198-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
Hyperthermophiles, a subset of prokaryotes that thrive in adverse temperatures, potentially utilize the protein molecular biosystem for maintaining thermostability in a wide range of temperatures. Recent studies revealed that these organisms have smaller proportions of intrinsically disordered proteins. In this study, we performed sequence and structural analysis to investigate the maintenance of protein conformation and their stability at different temperatures. The sequence analysis reveals the higher proportion of charged amino acids are responsible for preventing the helix formation and, hence, become disordered regions. For structural analysis, we chose shikimate dehydrogenase from four species, namely Listeria monocytogenes, Escherichia coli, Thermus thermophilus, and Methanopyrus kandleri, and evaluated the protein adaptation at 283 K, 300 K, and 395 K temperatures. From this investigation, we found more residues of shikimate dehydrogenase prefer an order-to-disorder transition at 395 K only for hyperthermophilic species. The solvent-accessible surface area (SASA) and hydrogen-bond analysis revealed that the tertiary conformation and the number of hydrogen bonds for hyperthermophilic shikimate dehydrogenase are highly preserved at 395 K, compared to 300 K. Our simulation results conjointly provide shikimate dehydrogenase of hyperthermophile which resists high temperatures through stronger protein tertiary conformations.
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6
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López-Chávez E, Pérez-Hernández G, Aparicio F, Alas SJ. On the Thermal Stability of O 6-Methylguanine-DNA Methyltransferase from Archaeon Pyrococcus kodakaraensis by Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:2138-2154. [PMID: 32250621 DOI: 10.1021/acs.jcim.0c00012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have employed molecular dynamics simulations to analyze the thermal stability of the O6-methylguanine-DNA methyltransferase (MGMT) protein, both hyperthermophilic archaeon Pyrococcus kodakaraensis (Pk-MGMT) and its mesophilic homologue pair, obtained from enterobacterium Escherichia coli (AdaC). This theoretical study was done at three different temperatures: 302, 371, and 450 K. The molecular dynamics has been performed in explicit aqueous solvent during a period of time of 95 ns, including periodic boundary conditions and constant pressure. The same procedure has been used for both proteins, and each simulation has been carried out by triplicate. Hence, we performed 18 simulations. In this way, we have done different analyses to explore the factors that may affect the thermal stability of Pk-MGMT. The structural behavior was analyzed using indicators such as root-mean-square deviation, radius of gyration, solvent-accessible surface area, hydrogen bonds, native contacts, secondary structure, and salt bridge formation. The results showed that when the temperature increases, the global atomic fluctuations increase too, which suggests that both proteins lose thermal stability, but as expected, this fact is highlighted in AdaC. Moreover, the contacts of the native state in AdaC are considerably lower than those found in Pk-MGMT at 450 K. Also, the structural studies showed that conserved and nonconserved salt bridges kept close contacts with the Pk-MGMT protein at high temperatures. These interaction types act as molecular staples and are mainly responsible to provide thermostability to the hyperthermophilic protein.
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Affiliation(s)
- Erick López-Chávez
- Posgrado en Ciencias Naturales e Ingeniería, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico
| | - Felipe Aparicio
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico
| | - Salomón J Alas
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México 05300, Mexico.,Departamento de Química, Unidad Iztapalapa, Universidad Autónoma Metropolitana, Ciudad de México 09340, Mexico
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7
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Maffucci I, Laage D, Stirnemann G, Sterpone F. Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes. Phys Chem Chem Phys 2020; 22:18361-18373. [DOI: 10.1039/d0cp02738c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The thermal resistance of two homolog enzymes is investigated, with an emphasis on their local stability and flexibility, and on the possible implications regarding their reactivity.
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Affiliation(s)
- Irene Maffucci
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Damien Laage
- PASTEUR
- Département de chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
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8
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Huang Q, Rodgers JM, Hemley RJ, Ichiye T. Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile. Int J Mol Sci 2019; 20:E1452. [PMID: 30909394 PMCID: PMC6470811 DOI: 10.3390/ijms20061452] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/04/2022] Open
Abstract
Determining the effects of extreme conditions on proteins from "extremophilic" and mesophilic microbes is important for understanding how life adapts to living at extremes as well as how extreme conditions can be used for sterilization and food preservation. Previous molecular dynamics simulations of dihydrofolate reductase (DHFR) from a psychropiezophile (cold- and pressure-loving), Moritella profunda (Mp), and a mesophile, Escherichia coli (Ec), at various pressures and temperatures indicate that atomic fluctuations, which are important for enzyme function, increase with both temperature and pressure. Here, the factors that cause increases in atomic fluctuations in the simulations are examined. The fluctuations increase with temperature not only because of greater thermal energy and thermal expansion of the protein but also because hydrogen bonds between protein atoms are weakened. However, the increase in fluctuations with pressure cannot be due to thermal energy, which remains constant, nor the compressive effects of pressure, but instead, the hydrogen bonds are also weakened. In addition, increased temperature causes larger increases in fluctuations of the loop regions of MpDHFR than EcDHFR, and increased pressure causes both increases and decreases in fluctuations of the loops, which differ between the two.
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Affiliation(s)
- Qi Huang
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
| | - Jocelyn M Rodgers
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
| | - Russell J Hemley
- Department of Civil and Environmental Engineering, George Washington University, Washington, DC 20052, USA.
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
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Huang Q, Rodgers JM, Hemley RJ, Ichiye T. Adaptations for Pressure and Temperature Effects on Loop Motion in Escherichia coli and Moritella profunda Dihydrofolate Reductase. HIGH PRESSURE RESEARCH 2019; 39:225-237. [PMID: 31359910 PMCID: PMC6662930 DOI: 10.1080/08957959.2019.1584799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/13/2019] [Indexed: 06/10/2023]
Abstract
Determining how enzymes in piezophilic microbes function at high pressure can give insights into how life adapts to living at high pressure. Here, the effects of pressure and temperature on loop motions are compared Escherichia coli (Ec) and Moritella profunda (Mp) dihydrofolate reductase (DHFR) via molecular dynamics simulations at combinations of the growth temperature and pressure of the two organisms. Analysis indicates that a flexible CD loop in MpDHFR is an adaptation for cold because it makes the adenosine binding subdomain more flexible. Also, analysis indicates that the Thr113-Glu27 hydrogen bond in MpDHFR is an adaptation for high pressure because it provides flexibility within the loop subdomain compared to the very strong Thr113-Asp27 hydrogen bond in EcDHFR, and affects the correlation of the Met20 and GH loops. In addition, the results suggest that temperature might affect external loops more strongly while pressure might affect motion between elements within the protein.
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Affiliation(s)
- Qi Huang
- Department of Chemistry, Georgetown University, Washington, DC 20057
| | | | - Russell J. Hemley
- Department of Civil and Environmental Engineering and Institute for Materials Science, George Washington University, Washington, DC 20052
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057
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Nakabayashi M, Kamachi S, Malle D, Yanamoto T, Kishishita S, Fujii T, Inoue H, Ishikawa K. Construction of thermostable cellobiohydrolase I from the fungus Talaromyces cellulolyticus by protein engineering. Protein Eng Des Sel 2019; 32:33-40. [DOI: 10.1093/protein/gzz001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/09/2018] [Accepted: 01/07/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Fungus-derived GH-7 family cellobiohydrolase I (CBHI, EC 3.2.1.91) is one of the most important industrial enzymes for cellulosic biomass saccharification. Talaromyces cellulolyticus is well known as a mesophilic fungus producing a high amount of CBHI. Thermostability enhances the economic value of enzymes by making them more robust. However, CBHI has proven difficult to engineer, a fact that stems in part from its low expression in heterozygous hosts and its complex structure. Here, we report the successful improvement of the thermostability of CBHI from T. cellulolyticus using our homologous expression system and protein engineering method. We examined the key structures that seem to contribute to its thermostability using the 3D structural information of CBHI. Some parts of the structure of the Talaromyces emersonii CBHI were grafted into T. cellulolyticus CBHI and thermostable mutant CBHIs were constructed. The thermostability was primarily because of the improvement in the loop structures, and the positive effects of the mutations for thermostability were additive. By combing the mutations, the constructed thermophilic CBHI exhibits high hydrolytic activity toward crystalline cellulose with an optimum temperature at over 70°C. In addition, the strategy can be applied to the construction of the other thermostable CBHIs.
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Affiliation(s)
- Makoto Nakabayashi
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Saori Kamachi
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Dominggus Malle
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
- Faculty of Agriculture, Pattimura University, Jl. Ir. M. Putuhena, Kampus Poka, Ambon, Maluku, Indonesia
| | - Toshiaki Yanamoto
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Seiichiro Kishishita
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Tatsuya Fujii
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Hiroyuki Inoue
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Kazuhiko Ishikawa
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
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11
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Lin KC, Jagannath B, Muthukumar S, Prasad S. Sub-picomolar label-free detection of thrombin using electrochemical impedance spectroscopy of aptamer-functionalized MoS 2. Analyst 2018. [PMID: 28650005 DOI: 10.1039/c7an00548b] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An ultrasensitive aptasensor for the label free non-faradaic detection of thrombin has been demonstrated on molybdenum disulphide (MoS2) nanosheets. These nanosheets were physiochemically immobilized onto a silicon micro-electrode platform. Thrombin detection was achieved through the charge modulation of the electrical double layer due to the specific and dose dependent binding of thrombin to the surface of thiol terminated ssDNA aptamer functionalized MoS2 nanosheets. Electrical double layer charge modulation associated with thrombin binding was characterized using electrochemical impedance spectroscopy. Dynamic light scattering was also used to confirm the dose dependent behavior. ATR-FTIR spectroscopy and XPS analysis were independently used to validate the functionalization of the ssDNA aptamer onto MoS2 nanosheets. ssDNA aptamer functionalized molybdenum disulfide (MoS2) for selective and specific capture of thrombin was demonstrated both in phosphate buffered saline (PBS) and human serum. The optimized immunoassay enabled the detection of thrombin ranging from 267 fM to 267 pM in phosphate buffer. The limit of detection of 53 pM and the linear dynamic range of detection of thrombin ranged from 53 to 854 pM in human serum. The rapid response time for the electrochemical impedance spectroscopy signal makes it an attractive option for the real-time detection of thrombin based point-of-care diagnostic devices.
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Affiliation(s)
- Kai-Chun Lin
- Department of Bioengineering, University of Texas, Dallas, Richardson, TX 75080, USA.
| | - Badrinath Jagannath
- Department of Bioengineering, University of Texas, Dallas, Richardson, TX 75080, USA.
| | | | - Shalini Prasad
- Department of Bioengineering, University of Texas, Dallas, Richardson, TX 75080, USA.
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12
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Abstract
The discovery of microbial communities in extreme conditions that would seem hostile to life leads to the question of how the molecules making up these microbes can maintain their structure and function. While microbes that live under extremes of temperature have been heavily studied, those that live under extremes of pressure, or "piezophiles", are now increasingly being studied because of advances in sample collection and high-pressure cells for biochemical and biophysical measurements. Here, adaptations of enzymes in piezophiles against the effects of pressure are discussed in light of recent experimental and computational studies. However, while concepts from studies of enzymes from temperature extremophiles can provide frameworks for understanding adaptations by piezophile enzymes, the effects of temperature and pressure on proteins differ in significant ways. Thus, the state of the knowledge of adaptation in piezophile enzymes is still in its infancy and many more experiments and computational studies on different enzymes from a variety of piezophiles are needed.
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Affiliation(s)
- Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC, 20057, United States
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13
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Huang Q, Rodgers JM, Hemley RJ, Ichiye T. Quasiharmonic Analysis of the Energy Landscapes of Dihydrofolate Reductase from Piezophiles and Mesophiles. J Phys Chem B 2018; 122:5527-5533. [PMID: 29370701 PMCID: PMC6287743 DOI: 10.1021/acs.jpcb.7b11838] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A quasiharmonic analysis (QHA) method is used to compare the potential energy landscapes of dihydrofolate reductase (DHFR) from a piezophile (pressure-loving organism), Moritella profunda (Mp), and a mesophile, Escherichia coli (Ec). The QHA method considers atomic fluctuations of the protein as motions of an atom in a local effective potential created by neighboring atoms and quantitates it in terms of effective force constants, isothermal compressibilities, and thermal expansivities. The analysis indicates that the underlying potential energy surface of MpDHFR is inherently softer than that of EcDHFR. In addition, on picosecond time scales, the energy surfaces become more similar under the growth conditions of Mp and Ec. On these time scales, DHFR behaves as expected; namely, increasing temperature makes the effective energy minimum less steep because thermal fluctuations increase the available volume, whereas increasing pressure steepens it because compression reduces the available volume. Our longer simulations show that, on nanosecond time scales, increasing temperature has a similar effect as on picosecond time scales because thermal fluctuations increase the volume even more on a longer time scale. However, these simulations also indicate that, on nanosecond time scales, pressure makes the local potential less steep, contrary to picosecond time scales. Further examination of the QHA indicates the nanosecond pressure response may originate at picosecond time scales at the exterior of the protein, which suggests that protein-water interactions may be involved. The results may lead to understanding adaptations in enzymes made by piezophiles that enable them to function at higher pressures.
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Affiliation(s)
- Qi Huang
- Department of Chemistry, Georgetown University, Washington, DC 20057
| | | | - Russell J. Hemley
- Institute of Materials Science and Department of Civil and Environmental Engineering, The George Washington University, Washington, DC 20052
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057
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14
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Zhang X, Zheng QC. Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation. Biopolymers 2017; 109. [DOI: 10.1002/bip.23068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/27/2017] [Accepted: 09/15/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Xue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University; Changchun 130023 People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University; Changchun 130023 People's Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education; Jilin University; Changchun 130023 People's Republic of China
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15
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Jeyalatha MV, Qu Y, Liu Z, Ou S, He X, Bu J, Li S, Reinach PS, Liu Z, Li W. Function of meibomian gland: Contribution of proteins. Exp Eye Res 2017; 163:29-36. [DOI: 10.1016/j.exer.2017.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/04/2017] [Accepted: 06/12/2017] [Indexed: 10/18/2022]
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16
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Song JG, Lee SH, Han HK. The stabilization of biopharmaceuticals: current understanding and future perspectives. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2017. [DOI: 10.1007/s40005-017-0341-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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Miller SR. An appraisal of the enzyme stability‐activity trade‐off. Evolution 2017; 71:1876-1887. [DOI: 10.1111/evo.13275] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/09/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Scott R. Miller
- Division of Biological SciencesThe University of Montana Missoula Montana 59812
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18
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Pica A, Graziano G. Shedding light on the extra thermal stability of thermophilic proteins. Biopolymers 2017; 105:856-63. [PMID: 27449333 DOI: 10.1002/bip.22923] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 07/12/2016] [Accepted: 07/20/2016] [Indexed: 11/08/2022]
Abstract
An entropic stabilization mechanism has recently gained attention and credibility as the physical ground for the extra thermal stability of globular proteins from thermophilic microorganisms. An empirical result, obtained from the analysis of thermodynamic data for a large set of proteins, strengthens the general reliability of the theoretical approach originally devised to rationalize the occurrence of cold denaturation [Graziano, PCCP 2014, 16, 21755-21767]. It is shown that this theoretical approach can readily account for the entropic stabilization mechanism. On decreasing the conformational entropy gain associated with denaturation, the thermal stability of a model globular protein increases markedly.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, Napoli, 80126, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11, Benevento, 82100, Italy.
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19
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Extraction and purification of a highly thermostable alkaline caseinolytic protease from wastes Penaeus vannamei suitable for food and detergent industries. Food Chem 2016; 202:110-5. [DOI: 10.1016/j.foodchem.2016.01.104] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 01/14/2016] [Accepted: 01/25/2016] [Indexed: 11/21/2022]
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20
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Závodszky P, Hajdú I. Evolution of the concept of conformational dynamics of enzyme functions over half of a century: A personal view. Biopolymers 2016; 99:263-9. [PMID: 23348674 DOI: 10.1002/bip.22159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/07/2012] [Indexed: 01/01/2023]
Abstract
To most physicists, it was always evident that conformational fluctuation is an inherent property of all molecules. Its existence in proteins was mentioned first by Linderström-Lang and Schellman in 1959 based on their hydrogen-deuterium exchange experiments. The "induced fit" mechanism to explain ligand-induced conformational changes was suggested by Koshland in 1958. Straub combined these two concepts in his "fluctuation fit" theory in 1964. The era of protein X-ray crystallography imposed a static view of protein structures. With proteins becoming accessible to NMR analysis, conformational dynamics could be mapped, and a new wave of dynamic interpretation of enzymatic catalysis and molecular recognition appeared. Energy landscapes, energy funnels, conformational selection, conformational distribution shifts are now frequent terms in interpreting biomolecular recognition and enzymatic catalysis. All these interpretations are based on the concept that evolution uses the conformational fluctuations of enzymes to develop efficient and dynamic catalytic machines. In a resurrection of the original "fluctuation fit" concept, it is generally recognized now that spatial and temporal events of catalysis are equally important to describe its mechanism. This special issue, dedicated to the memory of Henryk Eisenberg, prompted us to look back at the last 50 years of development of a concept that-like other important concepts-appeared, evolved and became accepted during the period covered by the scientific lifespan of Henryk.
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Affiliation(s)
- Péter Závodszky
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1113, Budapest, Hungary.
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21
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Karshikoff A, Nilsson L, Ladenstein R. Rigidity versus flexibility: the dilemma of understanding protein thermal stability. FEBS J 2015; 282:3899-917. [PMID: 26074325 DOI: 10.1111/febs.13343] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/17/2015] [Accepted: 06/09/2015] [Indexed: 01/19/2023]
Abstract
The role of fluctuations in protein thermostability has recently received considerable attention. In the current literature a dualistic picture can be found: thermostability seems to be associated with enhanced rigidity of the protein scaffold in parallel with the reduction of flexible parts of the structure. In contradiction to such arguments it has been shown by experimental studies and computer simulation that thermal tolerance of a protein is not necessarily correlated with the suppression of internal fluctuations and mobility. Both concepts, rigidity and flexibility, are derived from mechanical engineering and represent temporally insensitive features describing static properties, neglecting that relative motion at certain time scales is possible in structurally stable regions of a protein. This suggests that a strict separation of rigid and flexible parts of a protein molecule does not describe the reality correctly. In this work the concepts of mobility/flexibility versus rigidity will be critically reconsidered by taking into account molecular dynamics calculations of heat capacity and conformational entropy, salt bridge networks, electrostatic interactions in folded and unfolded states, and the emerging picture of protein thermostability in view of recently developed network theories. Last, but not least, the influence of high temperature on the active site and activity of enzymes will be considered.
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Affiliation(s)
- Andrey Karshikoff
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Rudolf Ladenstein
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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22
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Spir LG, Ataide JA, De Lencastre Novaes LC, Moriel P, Mazzola PG, De Borba Gurpilhares D, Silveira E, Pessoa A, Tambourgi EB. Application of an aqueous two-phase micellar system to extract bromelain from pineapple (Ananas comosus) peel waste and analysis of bromelain stability in cosmetic formulations. Biotechnol Prog 2015; 31:937-45. [PMID: 25919128 DOI: 10.1002/btpr.2098] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/11/2015] [Indexed: 11/09/2022]
Abstract
Bromelain is a set of proteolytic enzymes found in pineapple (Ananas comosus) tissues such as stem, fruit and leaves. Because of its proteolytic activity, bromelain has potential applications in the cosmetic, pharmaceutical, and food industries. The present study focused on the recovery of bromelain from pineapple peel by liquid-liquid extraction in aqueous two-phase micellar systems (ATPMS), using Triton X-114 (TX-114) and McIlvaine buffer, in the absence and presence of electrolytes CaCl2 and KI; the cloud points of the generated extraction systems were studied by plotting binodal curves. Based on the cloud points, three temperatures were selected for extraction: 30, 33, and 36°C for systems in the absence of salts; 40, 43, and 46°C in the presence of KI; 24, 27, and 30°C in the presence of CaCl2 . Total protein and enzymatic activities were analyzed to monitor bromelain. Employing the ATPMS chosen for extraction (0.5 M KI with 3% TX-114, at pH 6.0, at 40°C), the bromelain extract stability was assessed after incorporation into three cosmetic bases: an anhydrous gel, a cream, and a cream-gel formulation. The cream-gel formulation presented as the most appropriate base to convey bromelain, and its optimal storage conditions were found to be 4.0 ± 0.5°C. The selected ATPMS enabled the extraction of a biomolecule with high added value from waste lined-up in a cosmetic formulation, allowing for exploration of further cosmetic potential.
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Affiliation(s)
- Lívia Genovez Spir
- Dept. of Clinical Pathology, Faculty of Medical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil.,Faculty of Pharmaceutical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Janaína Artem Ataide
- Dept. of Clinical Pathology, Faculty of Medical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil.,Faculty of Pharmaceutical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Letícia Celia De Lencastre Novaes
- Dept. of Clinical Pathology, Faculty of Medical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil.,Faculty of Pharmaceutical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Patrícia Moriel
- Dept. of Clinical Pathology, Faculty of Medical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil.,Faculty of Pharmaceutical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Priscila Gava Mazzola
- Dept. of Clinical Pathology, Faculty of Medical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil.,Faculty of Pharmaceutical Sciences, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | | | - Edgar Silveira
- Genetics and Biochemistry Institute, Federal University of Uberlândia (UFU), Uberlândia, Minas Gerais, Brazil
| | - Adalberto Pessoa
- Dept. of Biochemical and Pharmaceutical Technology, Faculty of Pharmaceutical Science, University of São Paulo (USP), São Paulo, Brazil
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23
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Li H, Voutilainen S, Ojamo H, Turunen O. Stability and activity of Dictyoglomus thermophilum GH11 xylanase and its disulphide mutant at high pressure and temperature. Enzyme Microb Technol 2015; 70:66-71. [DOI: 10.1016/j.enzmictec.2014.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/20/2014] [Indexed: 01/16/2023]
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24
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Frappier V, Najmanovich R. Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering. Protein Sci 2014; 24:474-83. [PMID: 25367089 DOI: 10.1002/pro.2592] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/16/2014] [Accepted: 10/17/2014] [Indexed: 11/10/2022]
Abstract
We recently introduced ENCoM, an elastic network atomic contact model, as the first coarse-grained normal mode analysis method that accounts for the nature of amino acids and can predict the effect of mutations on thermostability based on changes vibrational entropy. In this proof-of-concept article, we use pairs of mesophile and thermophile homolog proteins with identical structures to determine if a measure of vibrational entropy based on normal mode analysis can discriminate thermophile from mesophile proteins. We observe that in around 60% of cases, thermophile proteins are more rigid at equivalent temperatures than their mesophile counterpart and this difference can guide the design of proteins to increase their thermostability through series of mutations. We observe that mutations separating thermophile proteins from their mesophile orthologs contribute independently to a decrease in vibrational entropy and discuss the application and implications of this methodology to protein engineering.
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Affiliation(s)
- Vincent Frappier
- Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, J1H 5N4, Quebec, Canada
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25
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Li T, Tracka MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR. Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle. PLoS One 2014; 9:e92870. [PMID: 24671209 PMCID: PMC3966838 DOI: 10.1371/journal.pone.0092870] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 02/26/2014] [Indexed: 11/18/2022] Open
Abstract
Le Châtelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier's principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect.
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Affiliation(s)
- Tong Li
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | | | - Shahid Uddin
- Department of Formulation Sciences, MedImmune Ltd., Cambridge, United Kingdom
| | - Jose Casas-Finet
- Analytical Biochemistry Department, MedImmune LLC, Gaithersburg, Maryland, United States of America
| | - Donald J. Jacobs
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Dennis R. Livesay
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
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26
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Liu M, He H, Su J. Is it possible to stabilize a thermophilic protein further using sequences and structures of mesophilic proteins: a theoretical case study concerning DgAS. Theor Biol Med Model 2013; 10:26. [PMID: 23575217 PMCID: PMC3639903 DOI: 10.1186/1742-4682-10-26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 03/29/2013] [Indexed: 11/13/2022] Open
Abstract
Incorporating structural elements of thermostable homologs can greatly improve the thermostability of a mesophilic protein. Despite the effectiveness of this method, applying it is often hampered. First, it requires alignment of the target mesophilic protein sequence with those of thermophilic homologs, but not every mesophilic protein has a thermophilic homolog. Second, not all favorable features of a thermophilic protein can be incorporated into the structure of a mesophilic protein. Furthermore, even the most stable native protein is not sufficiently stable for industrial applications. Therefore, creating an industrially applicable protein on the basis of the thermophilic protein could prove advantageous. Amylosucrase (AS) can catalyze the synthesis of an amylose-like polysaccharide composed of only α-1,4-linkages using sucrose as the lone energy source. However, industrial development of AS has been hampered owing to its low thermostability. To facilitate potential industrial applications, the aim of the current study was to improve the thermostability of Deinococcus geothermalis amylosucrase (DgAS) further; this is the most stable AS discovered to date. By integrating ideas from mesophilic AS with well-established protein design protocols, three useful design protocols are proposed, and several promising substitutions were identified using these protocols. The successful application of this hybrid design method indicates that it is possible to stabilize a thermostable protein further by incorporating structural elements of less-stable homologs.
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Affiliation(s)
- Ming Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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27
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Lloret N, Frederiksen RS, Møller TC, Rieben NI, Upadhyay S, De Vico L, Jensen JH, Nygård J, Martinez KL. Effects of buffer composition and dilution on nanowire field-effect biosensors. NANOTECHNOLOGY 2013; 24:035501. [PMID: 23263553 DOI: 10.1088/0957-4484/24/3/035501] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Nanowire-based field-effect transistors (FETs) can be used as ultra-sensitive and label-free biosensors for detecting protein-protein interactions. A way to increase the performance of such sensors is to dilute the sensing buffer drastically. However, we show here that this can have an important effect on the function of the proteins. Moreover, it is demonstrated that this dilution significantly affects the pH stability of the sensing buffer, which consequently impacts the charge of the protein and thus the response and signal-to-noise ratio in the sensing experiments. Three model systems are investigated experimentally to illustrate the impact on ligand-protein and protein-protein interactions. Simulations are performed to illustrate the effect on the performance of the sensors. Combining various parameters, the current study provides a means for evaluating and selecting the most appropriate buffer composition for bioFET measurements.
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Affiliation(s)
- Noémie Lloret
- Bio-Nanotechnology and Nanomedicine Laboratory, Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
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28
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Jiang CJ, Chen G, Huang J, Huang Q, Jin K, Shen PH, Li JF, Wu B. A novel β-glucosidase with lipolytic activity from a soil metagenome. Folia Microbiol (Praha) 2011; 56:563-70. [PMID: 22116645 DOI: 10.1007/s12223-011-0083-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 10/25/2011] [Indexed: 11/25/2022]
Abstract
Moonlighting proteins have two different functions within a single polypeptide chain. Exploring moonlighting enzymes from the environment using the metagenomic approach is interesting. In the present study, a novel β-glucosidase gene, designated as bgl1D, with lipolytic activity (renamed Lip1C) was cloned through function-based screening of a metagenomic library from uncultured soil microorganisms. The deduced amino acid sequence comparison and phylogenetic analysis also indicated that Lip1C and other putative lipases are closely related. Biochemical characterization demonstrated that the maximum activity of the recombinant Lip1C protein occurs at pH 8.0 and 30°C using 4-nitrophenyl butyrate as substrate. The putative lipase had an apparent K(m) value of 0.88 mmol/L, a k(cat) value of 212/min, and a k(cat)/K(m) value of 241 L/mmol/min. Lip1C exhibited habitat-specific characteristics with 5 mmol/L AlCl(3), CuCl(2), and LiCl. The characterization of the biochemical properties of Lip1C enhances our understanding of this novel moonlighting enzyme isolated from a soil metagenome.
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Affiliation(s)
- Cheng-Jian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, Guangxi 530004, People's Republic of China
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29
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Daily MD, Phillips GN, Cui Q. Interconversion of functional motions between mesophilic and thermophilic adenylate kinases. PLoS Comput Biol 2011; 7:e1002103. [PMID: 21779157 PMCID: PMC3136430 DOI: 10.1371/journal.pcbi.1002103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 05/12/2011] [Indexed: 11/21/2022] Open
Abstract
Dynamic properties are functionally important in many proteins, including the enzyme adenylate kinase (AK), for which the open/closed transition limits the rate of catalytic turnover. Here, we compare our previously published coarse-grained (double-well Gō) simulation of mesophilic AK from E. coli (AKmeso) to simulations of thermophilic AK from Aquifex aeolicus (AKthermo). In AKthermo, as with AKmeso, the LID domain prefers to close before the NMP domain in the presence of ligand, but LID rigid-body flexibility in the open (O) ensemble decreases significantly. Backbone foldedness in O and/or transition state (TS) ensembles increases significantly relative to AKmeso in some interdomain backbone hinges and within LID. In contact space, the TS of AKthermo has fewer contacts at the CORE-LID interface but a stronger contact network surrounding the CORE-NMP interface than the TS of AKmeso. A “heated” simulation of AKthermo at 375K slightly increases LID rigid-body flexibility in accordance with the “corresponding states” hypothesis. Furthermore, while computational mutation of 7 prolines in AKthermo to their AKmeso counterparts produces similar small perturbations, mutation of these sites, especially positions 8 and 155, to glycine is required to achieve LID rigid-body flexibility and hinge flexibilities comparable to AKmeso. Mutating the 7 sites to proline in AKmeso reduces some hinges' flexibilities, especially hinge 2, but does not reduce LID rigid-body flexibility, suggesting that these two types of motion are decoupled in AKmeso. In conclusion, our results suggest that hinge flexibility and global functional motions alike are correlated with but not exclusively determined by the hinge residues. This mutational framework can inform the rational design of functionally important flexibility and allostery in other proteins toward engineering novel biochemical pathways. Dynamic properties are functionally important in many proteins, including the enzyme adenylate kinase (AK), which undergoes chemically rate-limiting domain motions coupled to substrate binding. Since mesophiles and thermophiles often differ in functionally important motions, we compare coarse-grained simulations of AKmeso and AKthermo as well as several proline and glycine mutational variants designed to interconvert the dynamics. As might be expected, both domain motions and local unfolding motions are reduced in AKthermo relative to AKmeso. In AKthermo, both of these types of motions can be partially shifted toward more flexible AKmeso by heating or by mutating hinge prolines. However, only mutation to highly flexible glycine produces motions like those of AKmeso. Thus, the rate-limiting global transition likely depends on a combination of hinge flexibility and stability within the LID and NMP domains. Finally, this mutagenic framework can inform the rational design of flexibility and allostery in other proteins toward engineering novel biological control systems.
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Affiliation(s)
- Michael D. Daily
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Computation and Informatics in Biology and Medicine Training Program, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - George N. Phillips
- Departments of Biochemistry and Computer Sciences, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Theoretical Chemical Institute, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- * E-mail:
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30
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Fiorentino G, Del Giudice I, Bartolucci S, Durante L, Martino L, Del Vecchio P. Identification and Physicochemical Characterization of BldR2 from Sulfolobus solfataricus, a Novel Archaeal Member of the MarR Transcription Factor Family. Biochemistry 2011; 50:6607-21. [DOI: 10.1021/bi200187j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriella Fiorentino
- Department of Structural and Functional Biology, University of Naples Federico II, Edificio 7, via Cinthia, 80126 Naples, Italy
| | - Immacolata Del Giudice
- Department of Structural and Functional Biology, University of Naples Federico II, Edificio 7, via Cinthia, 80126 Naples, Italy
| | - Simonetta Bartolucci
- Department of Structural and Functional Biology, University of Naples Federico II, Edificio 7, via Cinthia, 80126 Naples, Italy
| | - Lorenzo Durante
- Department of Chemistry “Paolo Corradini”, University of Naples Federico II, via Cinthia, 80126 Naples, Italy
| | - Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, U.K
| | - Pompea Del Vecchio
- Department of Chemistry “Paolo Corradini”, University of Naples Federico II, via Cinthia, 80126 Naples, Italy
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31
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Lemos GSD, Márquez-Bernardes LF, Arvelos LR, Paraíso LF, Penha-Silva N. Influence of Glucose Concentration on the Membrane Stability of Human Erythrocytes. Cell Biochem Biophys 2011; 61:531-7. [DOI: 10.1007/s12013-011-9235-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Allosteric response is both conserved and variable across three CheY orthologs. Biophys J 2011; 99:2245-54. [PMID: 20923659 DOI: 10.1016/j.bpj.2010.07.043] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 07/16/2010] [Accepted: 07/22/2010] [Indexed: 11/22/2022] Open
Abstract
A computational method to identify residues likely to initiate allosteric signals has been developed. The method is based on differences within stability and flexibility profiles between wild-type and perturbed structures as computed by a distance constraint model. Application of the approach to three bacterial chemotaxis protein Y (CheY) orthologs provides a comparison of allosteric response across protein family divergence. Interestingly, we observe a rich mixture of both conservation and variability within the identified allosteric sites. While similarity within the overall response parallels the evolutionary relationships, >50% of the best scoring putative sites are only identified in a single ortholog. These results suggest that detailed descriptions of intraprotein communication are substantially more variable than structure and function, yet do maintain some evolutionary relationships. Finally, structural clusters of large response identify four allosteric hotspots, including the β4/α4 loop known to be critical to relaying the CheY phosphorylation signal.
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33
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Kumar R, Mauk AG. Atypical Effects of Salts on the Stability and Iron Release Kinetics of Human Transferrin. J Phys Chem B 2009; 113:12400-9. [DOI: 10.1021/jp903257c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Rajesh Kumar
- Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, B.C. V6T 1Z3 Canada
| | - A. Grant Mauk
- Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, B.C. V6T 1Z3 Canada
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34
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Almog O, González A, Godin N, de Leeuw M, Mekel MJ, Klein D, Braun S, Shoham G, Walter RL. The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state. Proteins 2009; 74:489-96. [PMID: 18655058 DOI: 10.1002/prot.22175] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We determine and compare the crystal structure of two proteases belonging to the subtilisin superfamily: S41, a cold-adapted serine protease produced by Antarctic bacilli, at 1.4 A resolution and Sph, a mesophilic serine protease produced by Bacillus sphaericus, at 0.8 A resolution. The purpose of this comparison was to find out whether multiple calcium ion binding is a molecular factor responsible for the adaptation of S41 to extreme low temperatures. We find that these two subtilisins have the same subtilisin fold with a root mean square between the two structures of 0.54 A. The final models for S41 and Sph include a calcium-loaded state of five ions bound to each of these two subtilisin molecules. None of these calcium-binding sites correlate with the high affinity known binding site (site A) found for other subtilisins. Structural analysis of the five calcium-binding sites found in these two crystal structures indicate that three of the binding sites have two side chains of an acidic residue coordinating the calcium ion, whereas the other two binding sites have either a main-chain carbonyl, or only one acidic residue side chain coordinating the calcium ion. Thus, we conclude that three of the sites are of high affinity toward calcium ions, whereas the other two are of low affinity. Because Sph is a mesophilic subtilisin and S41 is a psychrophilic subtilisin, but both crystal structures were found to bind five calcium ions, we suggest that multiple calcium ion binding is not responsible for the adaptation of S41 to low temperatures.
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Affiliation(s)
- Orna Almog
- Department of Clinical Biochemistry, Faculty of Health Sciences, Ben-Gurion University, Beer Sheva 84105, Israel.
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35
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Popp SL, Reinstein J. Functional characterization of the DnaK chaperone system from the archaeon Methanothermobacter thermautotrophicus DeltaH. FEBS Lett 2009; 583:573-8. [PMID: 19162025 DOI: 10.1016/j.febslet.2008.12.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 12/19/2008] [Accepted: 12/30/2008] [Indexed: 11/15/2022]
Abstract
We characterized the biochemical and functional properties of the DnaK system from the archaeon Methanothermobacter thermautotrophicus DeltaH. In contrast to the eubacterial chaperone components the archaeal Hsp70 system shows thermal transitions only slightly above the optimal environmental temperature (65 degrees C). Nevertheless, it prevents aggregation of luciferase in the physiological temperature range of the organism, but is also fully functional at 30 degrees C in luciferase refolding. Additionally, GrpE(M.th.) and DnaJ(M.th.) substitute their eubacterial counterparts whereas DnaK(M.th.) is only functional with its native cochaperones which could be attributed to a functional specialization of the eubacterial chaperones during evolution.
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Affiliation(s)
- Simone L Popp
- Max-Planck-Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
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36
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Vazquez-Figueroa E, Yeh V, Broering JM, Chaparro-Riggers JF, Bommarius AS. Thermostable variants constructed via the structure-guided consensus method also show increased stability in salts solutions and homogeneous aqueous-organic media. Protein Eng Des Sel 2008; 21:673-80. [PMID: 18799474 DOI: 10.1093/protein/gzn048] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Enzyme instability is a major factor preventing widespread adoption of enzymes for catalysis. Stability at high temperatures and in the presence of high salt concentrations and organic solvents would allow enzymes to be employed for transformations of compounds not readily soluble in low temperature or in purely aqueous systems. Furthermore, many redox enzymes require costly cofactors for function and consequently a robust cofactor regeneration system. In this work, we demonstrate how thermostable variants developed via an amino acid sequence-based consensus method also showed improved stability in solutions with high concentrations of kosmotropic and chaotropic salts and water-miscible organic solvents. This is invaluable to protein engineers since deactivation in salt solutions and organic solvents is not well understood, rendering a priori design of enzyme stability in these media difficult. Variants of glucose 1-dehydrogenase (GDH) were studied in solutions of different salts along the Hofmeister series and in the presence of varying amounts of miscible organic solvent. Only the most stable variants showed little deactivation dependence on salt-type and salt concentration. Kinetic stability, expressed by the deactivation rate constant k(d,obs), did not always correlate with thermodynamic stability of variants, as measured by melting temperature T(m). However, a strong correlation (R(2) > 0.95) between temperature stability and organic solvent stability was found when plotting T(50)(60) versus C(50)(60) values. All GDH variants retained stability in homogeneous aqueous-organic solvents with >80% v/v of organic solvent.
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Affiliation(s)
- E Vazquez-Figueroa
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, Atlanta, GA 30332-0363, USA
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37
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Almog O, Kogan A, Leeuw MD, Gdalevsky GY, Cohen-Luria R, Parola AH. Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41. Biopolymers 2008; 89:354-9. [PMID: 17937401 DOI: 10.1002/bip.20866] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A wide variety of enzymes can undergo a reversible loss of activity at low temperature, a process that is termed cold inactivation. This phenomenon is found in oligomeric enzymes such as tryptophanase (Trpase) and other pyridoxal phosphate dependent enzymes. On the other hand, cold-adapted, or psychrophilic enzymes, isolated from organisms able to thrive in permanently cold environments, have optimal activity at low temperature, which is associated with low thermal stability. Since cold inactivation may be considered "contradictory" to cold adaptation, we have looked into the amino acid sequences and the crystal structures of two families of enzymes, subtilisin and tryptophanase. Two cold adapted subtilisins, S41 and subtilisin-like protease from Vibrio, were compared to a mesophilic and a thermophilic subtilisins, as well as to four PLP-dependent enzymes in order to understand the specific surface residues, specific interactions, or any other molecular features that may be responsible for the differences in their tolerance to cold temperatures. The comparison between the psychrophilic and the mesophilic subtilisins revealed that the cold adapted subtilisins have a high content of acidic residues mainly found on their surface, making it charged. The analysis of the Trpases showed that they have a high content of hydrophobic residues on their surface. Thus, we suggest that the negatively charged residues on the surface of the subtilisins may be responsible for their cold adaptation, whereas the hydrophobic residues on the surface of monomeric Trpase molecules are responsible for the tetrameric assembly, and may account for their cold inactivation and dissociation.
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Affiliation(s)
- Orna Almog
- Department of Clinical Biochemistry, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel.
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38
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Adjustment of conformational flexibility of glyceraldehyde-3-phosphate dehydrogenase as a means of thermal adaptation and allosteric regulation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:1139-44. [PMID: 18449535 DOI: 10.1007/s00249-008-0332-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 04/09/2008] [Accepted: 04/11/2008] [Indexed: 10/22/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Thermotoga maritima (TmGAPDH) is a thermostable enzyme (Tm = 102 degrees C), which is fully active at temperatures near 80 degrees C but has very low activity at room temperature. In search for an explanation of this behavior, we measured the conformational flexibility of the protein by hydrogen-deuterium exchange and compared the results with those obtained with GAPDH from rabbit muscle (RmGAPDH). At room temperature, the conformational flexibility of TmGAPDH is much less than that of RmGAPDH, but increases with increasing temperature and becomes comparable to that of RmGAPDH near the physiological temperature of Thermotoga maritima. Using the available three-dimensional structures of the two enzymes, we compared the B factors that reflect the local mobility of protein atoms. The largest differences in B factors are seen in the coenzyme and NAD binding regions. The likely reason for the low activity of TmGAPDH at room temperature is that the motions required for enzyme functions are restricted. The findings support the idea of "corresponding states" which claims that over the time span of evolution, the overall conformational flexibility of proteins has been preserved at their corresponding physiological temperatures.
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39
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Goldstein RA. Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: insights from the quasi-chemical approximation. Protein Sci 2007; 16:1887-95. [PMID: 17766385 PMCID: PMC2206978 DOI: 10.1110/ps.072947007] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We investigate the mechanisms used by proteins to maintain thermostability throughout a wide range of temperatures. We use the quasi-chemical approximation to estimate interaction strengths for psychrophiles, mesophiles, thermophiles, and hyperthermophiles. Our results highlight the importance of core packing in thermophilic stability. Although we observed an increase in the number of charged residues, the contribution of salt bridges appears to be relatively modest by comparison. We observed results consistent with a gradual loosening of structure in psychrophiles, including a weakening of almost all types of interactions.
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Affiliation(s)
- Richard A Goldstein
- Mathematical Biology, National Institute of Medical Research, Mill Hill, London NW7 1AA, United Kingdom.
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40
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41
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Adaptation of model proteins from cold to hot environments involves continuous and small adjustments of average parameters related to amino acid composition. J Theor Biol 2007; 250:156-71. [PMID: 17950361 DOI: 10.1016/j.jtbi.2007.09.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 08/29/2007] [Accepted: 09/01/2007] [Indexed: 10/22/2022]
Abstract
The growth temperature adaptation of six model proteins has been studied in 42 microorganisms belonging to eubacterial and archaeal kingdoms, covering optimum growth temperatures from 7 to 103 degrees C. The selected proteins include three elongation factors involved in translation, the enzymes glyceraldehyde-3-phosphate dehydrogenase and superoxide dismutase, the cell division protein FtsZ. The common strategy of protein adaptation from cold to hot environments implies the occurrence of small changes in the amino acid composition, without altering the overall structure of the macromolecule. These continuous adjustments were investigated through parameters related to the amino acid composition of each protein. The average value per residue of mass, volume and accessible surface area allowed an evaluation of the usage of bulky residues, whereas the average hydrophobicity reflected that of hydrophobic residues. The specific proportion of bulky and hydrophobic residues in each protein almost linearly increased with the temperature of the host microorganism. This finding agrees with the structural and functional properties exhibited by proteins in differently adapted sources, thus explaining the great compactness or the high flexibility exhibited by (hyper)thermophilic or psychrophilic proteins, respectively. Indeed, heat-adapted proteins incline toward the usage of heavier-size and more hydrophobic residues with respect to mesophiles, whereas the cold-adapted macromolecules show the opposite behavior with a certain preference for smaller-size and less hydrophobic residues. An investigation on the different increase of bulky residues along with the growth temperature observed in the six model proteins suggests the relevance of the possible different role and/or structure organization played by protein domains. The significance of the linear correlations between growth temperature and parameters related to the amino acid composition improved when the analysis was collectively carried out on all model proteins.
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42
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Ruggiero I, Raimo G, Palma M, Arcari P, Masullo M. Molecular and functional properties of the psychrophilic elongation factor G from the Antarctic Eubacterium Pseudoalteromonas haloplanktis TAC 125. Extremophiles 2007; 11:699-709. [PMID: 17541754 DOI: 10.1007/s00792-007-0088-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 04/17/2007] [Indexed: 11/25/2022]
Abstract
The molecular and functional properties of the elongation factor (EF) G from the psychrophilic Antarctic eubacterium Pseudoalteromonas haloplanktis (Ph) were studied. PhEF-G catalyzed protein synthesis in vitro that was inhibited by fusidic acid, an antibiotic specifically acting on EF-G. The EF interacted with GDP only in the presence of P. haloplanktis ribosome and fusidic acid with an affinity similar to that displayed by Escherichia coli EF-G. The psychrophilic translocase elicited a ribosome-dependent GTPase that was competitively inhibited by GDP, the slowly hydrolyzable GTP analog GppNHp, and the protein synthesis inhibitor ppGDP. The temperature dependence of the activity of PhEF-G reached its maximum at least 26 degrees C beyond the growth temperature of P. haloplanktis (4-20 degrees C). The heat inactivation profile of the ribosome-dependent GTPase of PhEF-G gave a temperature for half inactivation (46 degrees C), significantly lower than that for half denaturation measured by either UV- (57 degrees C) or fluorescence-melting (62 degrees C). This finding was attributed to a different effect of the temperature on the catalytic domain with respect to that elicited on the other domains constituting the EF, thus confirming the differential molecular flexibility present in psychrophilic enzymes. A molecular model, based on the 3D coordinates of a thermophilic EF-G, showed differences only in connecting loops.
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Affiliation(s)
- Immacolata Ruggiero
- Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Via S. Pansini 5, 80131, Naples, Italy
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43
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de Noo ME, Tollenaar RAEM, Ozalp A, Kuppen PJK, Bladergroen MR, Eilers PHC, Deelder AM. Reliability of human serum protein profiles generated with C8 magnetic beads assisted MALDI-TOF mass spectrometry. Anal Chem 2007; 77:7232-41. [PMID: 16285670 DOI: 10.1021/ac050571f] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein profiling with mass spectrometry is a promising approach for classification and identification of biomarkers; however, there is debate about measurement quality and reliability. Here, we present a pipeline for preprocessing, statistical data analysis and presentation. Serum samples of 16 healthy individuals are used to generate protein profiles with high-resolution MALDI-TOF after isolation of peptides with C8 magnetic beads. Analysis of variance was performed after binning, baseline correction and normalization of the mean spectra. Relative variations in the spectra are expressed as coefficient of variation, which depending on the respective preanalytical variation parameter investigated, was found to range between 0.15 and 0.67 in this study. With this novel method, the reproducibility of our protein profiling procedure could be quantified. We showed that circadian rhythm and the number of freeze-thaw cycles had relatively limited influence on serum protein profiles, whereas the period between collection and serum centrifugation had a more pronounced effect.
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Affiliation(s)
- Mirre E de Noo
- Department of Surgery, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, The Netherlands.
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44
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Abstract
Studies that compare proteins from thermophilic and mesophilic organisms can provide insights into ability of thermophiles to function at their high habitat temperatures and may provide clues that enable us to better define the forces that stabilize all proteins. Most of the comparative studies have focused on thermal stability and show, as expected, that thermophilic proteins have higher Tm values than their mesophilic counterparts. Although these comparisons are useful, more detailed thermodynamic analyses are required to reach a more complete understanding of the mechanisms thermophilic protein employ to remain folded over a wider range of temperatures. This complete thermodynamic description allows one to generate a stability curve for a protein that defines how the conformational stability (DeltaG) varies with temperature. Here we compare stability curves for many pairs of homologous proteins from thermophilic and mesophilc organisms. Of the basic methods that can be employed to achieve enhanced thermostability, we find that most thermophilic proteins use the simple method that raises the DeltaG at all temperatures as the principal way to increase their Tm. We discuss and compare this thermodynamic method with the possible alternatives. In addition we propose ways that structural alterations and changes to the amino acid sequences might give rise to varied methods used to obtain thermostability.
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Affiliation(s)
- Abbas Razvi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843-1114, USA
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45
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Sánchez IE, Tejero J, Gómez-Moreno C, Medina M, Serrano L. Point mutations in protein globular domains: contributions from function, stability and misfolding. J Mol Biol 2006; 363:422-32. [PMID: 16978645 DOI: 10.1016/j.jmb.2006.08.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 07/25/2006] [Accepted: 08/08/2006] [Indexed: 11/25/2022]
Abstract
Several contrasting hypotheses have been formulated about the influence of functional and conformational properties, like stability and avoidance of misfolding, on the evolution of protein globular domains. Selection at functional sites has been suggested to be detrimental to stability or coupled to it. Avoidance of misfolding may be achieved by discarding misfolding-prone sequences or by maintaining a stable native state and thus destabilizing partially or fully unfolded states from which misfolding can take place. We have performed a hierarchical analysis of a large database of point mutations to dissect the relative contributions of function, stability and misfolding in the evolution of natural sequences. We show that at catalytic sites, selection for function overrules selection for stability but find no evidence for an anticorrelation between function and stability. Selection for stability plays a secondary role at binding sites, but is not fully coupled to selection for function. Remarkably, we did not find a selective pressure against misfolding-prone sequences in globular proteins at the level of individual positions. We suggest that such a selection would compromise native-state stability due to a correlation between the stabilities of native and misfolded states. Stabilization of the native state is the most frequent way in which natural proteins avoid misfolding.
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Affiliation(s)
- I E Sánchez
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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46
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Ghosh Dastidar K, Maitra S, Goswami L, Roy D, Das KP, Majumder AL. An insight into the molecular basis of salt tolerance of L-myo-inositol 1-P synthase (PcINO1) from Porteresia coarctata (Roxb.) Tateoka, a halophytic wild rice. PLANT PHYSIOLOGY 2006; 140:1279-96. [PMID: 16500989 PMCID: PMC1435794 DOI: 10.1104/pp.105.075150] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 01/05/2006] [Accepted: 01/05/2006] [Indexed: 05/06/2023]
Abstract
The molecular basis of salt tolerance of L-myo-inositol 1-P synthase (MIPS; EC 5.5.1.4) from Porteresia coarctata (Roxb.) Tateoka (PcINO1, AF412340) earlier reported from this laboratory, has been analyzed by in vitro mutant and hybrid generation and subsequent biochemical and biophysical studies of the recombinant proteins. A 37-amino acid stretch between Trp-174 and Ser-210 has been confirmed as the salt-tolerance determinant domain in PcINO1 both by loss or gain of salt tolerance by either deletion or by addition to salt-sensitive MIPS(s) of Oryza (OsINO1) and Brassica juncea (BjINO1). This was further verified by growth analysis under salt environment of Schizosaccharomyces pombe transformed with the various gene constructs and studies on the differential behavior of mutant and wild proteins by Trp fluorescence, aggregation, and circular dichroism spectra in the presence of salt. 4,4'-Dianilino-1,1'-binaphthyl-5,5-disulfonic acid binding experiments revealed a lower hydrophobic surface on PcINO1 than OsINO1, contributed by this 37-amino acid stretch explaining the differential behavior of OsINO1 and PcINO1 both with respect to their enzymatic functions and thermodynamic stability in high salt environment. Detailed amino acid sequence comparison and modeling studies revealed the interposition of polar and charged residues and a well-connected hydrogen-bonding network formed by Ser and Thr in this stretch of PcINO1. On the contrary, hydrophobic residues clustered in two continuous stretches in the corresponding region of OsINO1 form a strong hydrophobic patch on the surface. It is conceivable that salt-tolerant MIPS proteins may be designed out of the salt-sensitive plant MIPS proteins by replacement of the corresponding amino acid stretch by the designated 37-amino acid stretch of PcINO1.
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Affiliation(s)
- Krishnarup Ghosh Dastidar
- Plant Molecular and Cellular Genetics, Bose Institute, Calcutta Improvement Trust Scheme-VIIM, Calcutta 700 054, India
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47
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Solá RJ, Griebenow K. Chemical glycosylation: New insights on the interrelation between protein structural mobility, thermodynamic stability, and catalysis. FEBS Lett 2006; 580:1685-90. [PMID: 16494868 DOI: 10.1016/j.febslet.2006.02.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 01/19/2006] [Accepted: 02/05/2006] [Indexed: 11/22/2022]
Abstract
Chemical protein glycosylation was employed to sequentially modulate the structural dynamics of the serine protease alpha-chymotrypsin as evidenced from amide H/D exchange kinetics. The reduction in alpha-CT's structural dynamics at increasing glycan molar contents statistically correlated with the increased thermodynamic stability (T(m)) and reduced rate of enzyme catalysis (k(cat)) exhibited by the enzyme upon chemical glycosylation. Temperature-dependent experiments revealed that native-like structural dynamics and function could be restored for the glycosylated conjugates at temperature values close to their thermodynamic stability suggesting that the concept of "corresponding states" can be extended to glycoproteins. These results demonstrate the value of chemical glycosylation as a tool for studying the role of protein structural dynamics on protein biophysical properties; e.g. enzyme stability and function.
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Affiliation(s)
- Ricardo J Solá
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Facundo Bueso Bldg Lab-215, San Juan 23346, PR 00931-3346
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48
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Lindman S, Xue WF, Szczepankiewicz O, Bauer MC, Nilsson H, Linse S. Salting the charged surface: pH and salt dependence of protein G B1 stability. Biophys J 2006; 90:2911-21. [PMID: 16443658 PMCID: PMC1414578 DOI: 10.1529/biophysj.105.071050] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study shows significant effects of protein surface charges on stability and these effects are not eliminated by salt screening. The stability for a variant of protein G B1 domain was studied in the pH-range of 1.5-11 at low, 0.15 M, and 2 M salt. The variant has three mutations, T2Q, N8D, and N37D, to guarantee an intact covalent chain at all pH values. The stability of the protein shows distinct pH dependence with the highest stability close to the isoelectric point. The stability is pH-dependent at all three NaCl concentrations, indicating that interactions involving charged residues are important at all three conditions. We find that 2 M salt stabilizes the protein at low pH (protein net charge is +6 and total number of charges is 6) but not at high pH (net charge is <or=-6 and total number of charges is >or=18). Furthermore, 0.15 M salt slightly decreases the stability of the protein over the pH range. The results show that a net charge of the protein is destabilizing and indicate that proteins contain charges for reasons other than improved stability. Salt seems to reduce the electrostatic contributions to stability under conditions with few total charges, but cannot eliminate electrostatic effects in highly charged systems.
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Affiliation(s)
- Stina Lindman
- Department of Biophysical Chemistry, Lund University, Lund, Sweden
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49
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LeMaster DM, Tang J, Paredes DI, Hernández G. Enhanced thermal stability achieved without increased conformational rigidity at physiological temperatures: Spatial propagation of differential flexibility in rubredoxin hybrids. Proteins 2005; 61:608-16. [PMID: 16130131 DOI: 10.1002/prot.20594] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The extreme thermal stability of proteins from hyperthermophilic organisms is widely believed to arise from an increased conformational rigidity in the native state. In apparent contrast to this paradigm, both Pyrococcus furiosus (Pf) rubredoxin, the most thermostable protein characterized to date, and its Clostridium pasteurianum (Cp) mesophile homolog undergo a transient conformational opening of their multi-turn segments, which is more favorable in hyperthermophile proteins below room temperature. Substitution of the hyperthermophile multi-turn sequence into the mesophile protein sequence yields a hybrid, (14-33(Pf)) Cp, that exhibits a 12 degrees increase in its reversible thermal unfolding transition midpoint. Nuclear magnetic resonance (NMR) magnetization transfer-based hydrogen exchange was used to monitor backbone conformational dynamics in the subsecond time regime. Despite the substantially increased thermostability, flexibility throughout the entire main chain of the more thermostable hybrid is equal to or greater than that of the wild type mesophile rubredoxin near its normal growth temperature. In comparison to the identical core residues of the (14-33(Pf)) Cp rubredoxin hybrid, six spatially clustered residues in the parental mesophile protein exhibit a substantially larger temperature dependence of exchange. The exchange behavior of these six residues closely matches that observed in the multi-turn segment, consistent with a more extensive conformational process. These six core residues exhibit a much weaker temperature dependence of exchange in the (14-33(Pf)) Cp hybrid, similar to that observed for the multi-turn segment in its parental Pf rubredoxin. These results suggest that differential temperature dependence of flexibility can underlie variations in thermostability observed for mesophile versus hyperthermophile homologs.
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Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany- SUNY, 12201-0509, USA
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Bhatnagar BS, Nehm SJ, Pikal MJ, Bogner RH. Post-Thaw Aging Affects Activity of Lactate Dehydrogenase. J Pharm Sci 2005; 94:1382-8. [PMID: 15858849 DOI: 10.1002/jps.20345] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Freeze-thawing is routinely used to study freezing-induced irreversible protein denaturation in the formulation characterization and development of lyophilized proteins. In most cases, the temperature profiles of the samples are not fully monitored during freeze-thawing and therefore, the sample thermal histories are largely unknown. The objective of this study was to develop experimental protocols for the study of isothermal protein degradation using a temperature-step apparatus. Freeze-thaw experiments were performed at a freezing rate of 10 degrees C/min and various thawing rates (0.5-3.3 degrees C/min) using a temperature-step apparatus. In our efforts to design validation studies, we encountered anomalies in the recovered enzyme activity data of an enzyme, lactate dehydrogenase at the end of freeze-thawing. The effect of thawing rate was studied to explain the variability in the data. In addition, post-thaw "aging" of freshly frozen and thawed samples was performed at 5 degrees C to reduce the variability in the recovered enzyme activity. Results from these experiments implicate the use of aging of dilute multimeric enzymes at the end of freeze-thawing to control the variability in enzyme assays.
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Affiliation(s)
- Bakul S Bhatnagar
- School of Pharmacy, U2092, University of Connecticut, Storrs, CN 06269, USA
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