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Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions. Molecules 2022; 27:molecules27206861. [PMID: 36296453 PMCID: PMC9610776 DOI: 10.3390/molecules27206861] [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: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.
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Norgate EL, Upton R, Hansen K, Bellina B, Brookes C, Politis A, Barran PE. Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage. Angew Chem Int Ed Engl 2022; 61:e202115047. [PMID: 35313047 PMCID: PMC9325448 DOI: 10.1002/anie.202115047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 12/12/2022]
Abstract
The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.
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Affiliation(s)
- Emma L Norgate
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - Rosie Upton
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
| | - C Brookes
- Bristol-Myers Squibb, Moreton, Wirral, CH46 1QW, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Perdita E Barran
- Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester, M1 7DN, UK
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3
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Norgate EL, Upton R, Hansen K, Bellina B, Brookes C, Politis A, Barran PE. Cold Denaturation of Proteins in the Absence of Solvent: Implications for Protein Storage. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202115047. [PMID: 38505418 PMCID: PMC10947158 DOI: 10.1002/ange.202115047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/07/2022]
Abstract
The effect of temperature on the stability of proteins is well explored above 298 K, but harder to track experimentally below 273 K. Variable-temperature ion mobility mass spectrometry (VT IM-MS) allows us to measure the structure of molecules at sub-ambient temperatures. Here we monitor conformational changes that occur to two isotypes of monoclonal antibodies (mAbs) on cooling by measuring their collision cross sections (CCS) at discrete drift gas temperatures from 295 to 160 K. The CCS at 250 K is larger than predicted from collisional theory and experimental data at 295 K. This restructure is attributed to change in the strength of stabilizing intermolecular interactions. Below 250 K the CCS of the mAbs increases in line with prediction implying no rearrangement. Comparing data from isotypes suggest disulfide bridging influences thermal structural rearrangement. These findings indicate that in vacuo deep-freezing minimizes denaturation and maintains the native fold and VT IM-MS measurements at sub ambient temperatures provide new insights to the phenomenon of cold denaturation.
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Affiliation(s)
- Emma L. Norgate
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Rosie Upton
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Kjetil Hansen
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Bruno Bellina
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - C. Brookes
- Bristol-Myers SquibbMoretonWirralCH46 1QWUK
| | - Argyris Politis
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Perdita E. Barran
- Manchester Institute of BiotechnologyUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
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Pulavarti SVSRK, Maguire JB, Yuen S, Harrison JS, Griffin J, Premkumar L, Esposito EA, Makhatadze GI, Garcia AE, Weiss TM, Snell EH, Kuhlman B, Szyperski T. From Protein Design to the Energy Landscape of a Cold Unfolding Protein. J Phys Chem B 2022; 126:1212-1231. [PMID: 35128921 PMCID: PMC9281400 DOI: 10.1021/acs.jpcb.1c10750] [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] [Indexed: 11/28/2022]
Abstract
Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein-water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ∼0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.
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Affiliation(s)
- Surya V S R K Pulavarti
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jack B Maguire
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shirley Yuen
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jermel Griffin
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edward A Esposito
- Malvern Panalytical Inc, Northhampton, Massachsetts 01060, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 08544, United States
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center, Stanford University, Menlo Park, California 94025, United States
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Materials Design and Innovation, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas Szyperski
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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5
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Durell SR, Ben-Naim A. Temperature Dependence of Hydrophobic and Hydrophilic Forces and Interactions. J Phys Chem B 2021; 125:13137-13146. [PMID: 34850632 DOI: 10.1021/acs.jpcb.1c07802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations are used to compare the forces and Gibbs free energies associated with bringing small hydrophobic and hydrophilic solutes together in an aqueous solution at different temperatures between 280 and 360 °K. For the hydrophilic solutes, different relative orientations are used to distinguish between direct, intersolute hydrogen bonds (Hbond) and solutes simultaneously hydrogen bonding to a solvent water bridge. Interestingly, the temperature dependence of the hydrophobic and directly hydrogen bonding solutes turns out to be opposite to that of the bridged hydrophilic solutes, with the ΔG becoming more negative for the former and less negative for the latter with increasing temperature. Dissection of the free energy curves into enthalpy and entropy contributions, and further separation of the enthalpy term into solute-solute, solute-solvent, and solvent-solvent components provides insight into the physical molecular causes for the distinctive thermodynamic results. Finally, it is reasoned how the opposite temperature dependencies of the two types of hydrophilic interactions provide a rationale for the cold denaturation of proteins.
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Affiliation(s)
- Stewart R Durell
- Laboratory of Cell Biology, National Cancer Institute; National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Arieh Ben-Naim
- Department of Physical Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat Ram, Jerusalem 91904, Israel
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6
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Parui S, Jana B. Cold denaturation induced helix-to-helix transition and its implication to activity of helical antifreeze protein. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Yang C, Jang S, Pak Y. Computational Probing of Temperature-Dependent Unfolding of a Small Globular Protein: From Cold to Heat Denaturation. J Chem Theory Comput 2020; 17:515-524. [DOI: 10.1021/acs.jctc.0c01046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Changwon Yang
- Department of Chemistry, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, South Korea
| | - Soonmin Jang
- Department of Chemistry, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, South Korea
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8
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Tomar DS, Paulaitis ME, Pratt LR, Asthagiri DN. Hydrophilic Interactions Dominate the Inverse Temperature Dependence of Polypeptide Hydration Free Energies Attributed to Hydrophobicity. J Phys Chem Lett 2020; 11:9965-9970. [PMID: 33170720 DOI: 10.1021/acs.jpclett.0c02972] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We address the association of the hydrophobic driving forces in protein folding with the inverse temperature dependence of protein hydration, wherein stabilizing hydration effects strengthen with increasing temperature in a physiological range. All-atom calculations of the free energy of hydration of aqueous deca-alanine conformers, holistically including backbone and side-chain interactions together, show that attractive peptide-solvent interactions and the thermal expansion of the solvent dominate the inverse temperature signatures that have been interpreted traditionally as the hydrophobic stabilization of proteins in aqueous solution. Equivalent calculations on a methane solute are also presented as a benchmark for comparison. The present study calls for a reassessment of the forces that stabilize folded protein conformations in aqueous solutions and of the additivity of hydrophobic/hydrophilic contributions.
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Affiliation(s)
- Dheeraj S Tomar
- Xilio Therapeutics Inc., Waltham, Massachusetts 02451, United States
| | - Michael E Paulaitis
- Center for Nanomedicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21231, United States
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Dilipkumar N Asthagiri
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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9
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Spadiut O, Gundinger T, Pittermann B, Slouka C. Spatially Resolved Effects of Protein Freeze-Thawing in a Small-Scale Model Using Monoclonal Antibodies. Pharmaceutics 2020; 12:E382. [PMID: 32326286 PMCID: PMC7238022 DOI: 10.3390/pharmaceutics12040382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/02/2020] [Accepted: 04/18/2020] [Indexed: 11/26/2022] Open
Abstract
Protein freeze-thawing is frequently used to stabilize and store recombinantly produced proteins after different unit operations in upstream and downstream processing. However, freeze-thawing is often accompanied by product damage and, hence, loss of product. Different effects are responsible, including cold denaturation, aggregation effects, which are caused by inhomogeneities in protein concentration, as well as pH and buffer ingredients, especially during the freeze cycle. In this study, we tested a commercially available small-scale protein freezing unit using immunoglobin G (IgG) as monoclonal antibody in a typical formulation buffer containing sodium phosphate, sodium chloride, and Tween 80. Different freezing rates were used respectively, and the product quality was tested in the frozen sample. Spatially resolved tests for protein concentration, pH, conductivity, and aggregation revealed high spatial differences in the frozen sample. Usage of slow freezing rates revealed high inhomogeneities in terms of buffer salt and protein distribution, while fast rates led to far lower spatial differences. These protein and buffer salt inhomogeneities can be reliably monitored using straight forward analytics, like conductivity and photometric total protein concentration measurements, reducing the need for HPLC analytics in screening experiments. Summarizing, fast freezing using steep rates shows promising results concerning homogeneity of the final frozen product and inhibits increased product aggregation.
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Affiliation(s)
- Oliver Spadiut
- Research Division Biochemical Engineering, Group for Integrated Bioprocess Development, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, 1060 Vienna, Austria; (O.S.); (T.G.)
| | - Thomas Gundinger
- Research Division Biochemical Engineering, Group for Integrated Bioprocess Development, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, 1060 Vienna, Austria; (O.S.); (T.G.)
| | - Birgit Pittermann
- Head of R&D, ZETA GmbH, Zetaplatz 1, A-8501 Lieboch, 8501 Graz, Austria;
| | - Christoph Slouka
- Research Division Biochemical Engineering, Group for Integrated Bioprocess Development, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, 1060 Vienna, Austria; (O.S.); (T.G.)
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10
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Uralcan B, Debenedetti PG. Computational Investigation of the Effect of Pressure on Protein Stability. J Phys Chem Lett 2019; 10:1894-1899. [PMID: 30939023 DOI: 10.1021/acs.jpclett.9b00545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Previous studies show parabolic or elliptical regions of protein stability in the pressure-temperature ( P, T) plane. The construction of stability diagrams requires accessing a sufficiently broad ( P, T) range, which is often frustrated by ice formation in experiments and sampling challenges in simulations. We perform a fully atomistic computational study of the miniprotein Trp-cage over the range of temperatures 210 ≤ T ≤ 420 K and pressures P ≤ 5 kbar and construct the corresponding stability diagram. At ambient temperature, pressure shifts the conformational states toward unfolding. Below 250 K, the native fold's stability depends nonmonotonically on pressure. While cold unfolding and thermal denaturation differ significantly at ambient pressure, they exhibit progressive similarity at elevated pressures. At ambient pressure, cold denaturation is an enthalpically driven process that preserves significant elements of Trp-cage's secondary structure. In contrast, cold unfolding at elevated pressures involves a more substantial loss of secondary and tertiary structure, similar to thermal denaturation.
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Affiliation(s)
- Betul Uralcan
- Department of Chemical and Biological Engineering , Princeton University , Princeton , New Jersey 08544 , United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering , Princeton University , Princeton , New Jersey 08544 , United States
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11
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Taricska N, Bokor M, Menyhárd DK, Tompa K, Perczel A. Hydration shell differentiates folded and disordered states of a Trp-cage miniprotein, allowing characterization of structural heterogeneity by wide-line NMR measurements. Sci Rep 2019; 9:2947. [PMID: 30814556 PMCID: PMC6393587 DOI: 10.1038/s41598-019-39121-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 12/10/2018] [Indexed: 12/12/2022] Open
Abstract
Hydration properties of folded and unfolded/disordered miniproteins were monitored in frozen solutions by wide-line 1H-NMR. The amount of mobile water as function of T (-80 °C < T < 0 °C) was found characteristically different for folded (TC5b), semi-folded (pH < 3, TCb5(H+)) and disordered (TC5b_N1R) variants. Comparing results of wide-line 1H-NMR and molecular dynamics simulations we found that both the amount of mobile water surrounding proteins in ice, as well as their thaw profiles differs significantly as function of the compactness and conformational heterogeneity of their structure. We found that (i) at around -50 °C ~50 H2Os/protein melt (ii) if the protein is well-folded then this amount of mobile water remains quasi-constant up to -20 °C, (iii) if disordered then the quantity of the lubricating mobile water increases with T in a constant manner up to ~200 H2Os/protein by reaching -20 °C. Especially in the -55 °C ↔ -15 °C temperature range, wide-line 1H-NMR detects the heterogeneity of protein fold, providing the size of the hydration shell surrounding the accessible conformers at a given temperature. Results indicate that freezing of protein solutions proceeds by the gradual selection of the enthalpically most favored states that also minimize the number of bridging waters.
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Affiliation(s)
- Nóra Taricska
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Mónika Bokor
- Institute for Solid State Physics and Optics, Wigner RCP of the HAS, 1121, Budapest, Hungary
| | - Dóra K Menyhárd
- MTA-ELTE Protein Modelling Research Group, Pázmány Péter st. 1A, 1117, Budapest, Hungary
| | - Kálmán Tompa
- Institute for Solid State Physics and Optics, Wigner RCP of the HAS, 1121, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, 1117, Hungary.
- MTA-ELTE Protein Modelling Research Group, Pázmány Péter st. 1A, 1117, Budapest, Hungary.
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12
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Hernández-Sánchez IE, Maruri-López I, Molphe-Balch EP, Becerra-Flora A, Jaimes-Miranda F, Jiménez-Bremont JF. Evidence for in vivo interactions between dehydrins and the aquaporin AtPIP2B. Biochem Biophys Res Commun 2019; 510:545-550. [PMID: 30738581 DOI: 10.1016/j.bbrc.2019.01.095] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 11/29/2022]
Abstract
Plants have developed mechanisms that allow them to tolerate different abiotic stresses. Among these mechanisms, the accumulation of specific proteins such as dehydrins (DHNs) and aquaporins (AQPs) can protect other proteins from damage during dehydration and may allow the control of water loss, respectively. Although both types of proteins are involved in plant protection against dehydration stress, a direct interaction between them has not been explored. A previous screen to identify potential OpsDHN1 protein interactions revealed an aquaporin as a possible candidate. Here, we used the Bimolecular Fluorescence Complementation (BiFC) approach to investigate the direct interaction of the cactus OpsDHN1 protein with the Arabidopsis plasma membrane PIP family aquaporin AtPIP2B (At2G37170). Since AtPIP2B is a membrane protein and OpsDHN1 is a cytosolic protein that may be peripherally associated with membranes, we propose that OpsDHN1/AtPIP2B interaction takes place at cellular membranes. Furthermore, we also demonstrate the interaction of AtPIP2B with the three Arabidopsis dehydrins COR47 (AT1G20440), ERD10 (At1g20450), and RAB18 (At5g66400).
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Affiliation(s)
- Itzell Eurídice Hernández-Sánchez
- Laboratorio de Biología Molecular de Hongos y Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica AC, San Luis Potosí, SLP, Mexico
| | - Israel Maruri-López
- Laboratorio de Biología Molecular de Hongos y Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica AC, San Luis Potosí, SLP, Mexico
| | - Eugenio Pérez Molphe-Balch
- Unidad de Biotecnología Vegetal, Departamento de Química, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags, Mexico
| | - Alicia Becerra-Flora
- Laboratorio de Biología Molecular de Hongos y Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica AC, San Luis Potosí, SLP, Mexico
| | - Fabiola Jaimes-Miranda
- CONACyT-Instituto Potosino de Investigación Científica y Tecnológica AC, División de Biología Molecular, San Luis Potosí, SLP, Mexico.
| | - Juan F Jiménez-Bremont
- Laboratorio de Biología Molecular de Hongos y Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica AC, San Luis Potosí, SLP, Mexico.
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13
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Dubey V, Daschakraborty S. Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins’ stabilization at low temperature. Phys Chem Chem Phys 2019; 21:800-812. [DOI: 10.1039/c8cp06513f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Glycerol reduces the cooling effect of pair hydrophobicity (reduction of hydrophobicity with decreasing temperature) in water.
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Affiliation(s)
- Vikas Dubey
- Department of Chemistry
- Indian Institute of Technology Patna
- Bihar 801106
- India
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14
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Daschakraborty S. How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction. J Chem Phys 2018; 148:134501. [PMID: 29626866 DOI: 10.1063/1.5019239] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.
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15
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Assaf JC, El Khoury A, Atoui A, Louka N, Chokr A. A novel technique for aflatoxin M1 detoxification using chitin or treated shrimp shells: in vitro effect of physical and kinetic parameters on the binding stability. Appl Microbiol Biotechnol 2018; 102:6687-6697. [DOI: 10.1007/s00253-018-9124-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 11/28/2022]
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16
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van der Vegt NFA, Nayar D. The Hydrophobic Effect and the Role of Cosolvents. J Phys Chem B 2017; 121:9986-9998. [DOI: 10.1021/acs.jpcb.7b06453] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nico F. A. van der Vegt
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Divya Nayar
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
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Parui S, Jana B. Pairwise Hydrophobicity at Low Temperature: Appearance of a Stable Second Solvent-Separated Minimum with Possible Implication in Cold Denaturation. J Phys Chem B 2017; 121:7016-7026. [DOI: 10.1021/acs.jpcb.7b02676] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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18
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Rational Engineering of a Cold-Adapted α-Amylase from the Antarctic Ciliate Euplotes focardii for Simultaneous Improvement of Thermostability and Catalytic Activity. Appl Environ Microbiol 2017; 83:AEM.00449-17. [PMID: 28455329 PMCID: PMC5478988 DOI: 10.1128/aem.00449-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/18/2017] [Indexed: 12/04/2022] Open
Abstract
The α-amylases are endo-acting enzymes that hydrolyze starch by randomly cleaving the 1,4-α-d-glucosidic linkages between the adjacent glucose units in a linear amylose chain. They have significant advantages in a wide range of applications, particularly in the food industry. The eukaryotic α-amylase isolated from the Antarctic ciliated protozoon Euplotes focardii (EfAmy) is an alkaline enzyme, different from most of the α-amylases characterized so far. Furthermore, EfAmy has the characteristics of a psychrophilic α-amylase, such as the highest hydrolytic activity at a low temperature and high thermolability, which is the major drawback of cold-active enzymes in industrial applications. In this work, we applied site-directed mutagenesis combined with rational design to generate a cold-active EfAmy with improved thermostability and catalytic efficiency at low temperatures. We engineered two EfAmy mutants. In one mutant, we introduced Pro residues on the A and B domains in surface loops. In the second mutant, we changed Val residues to Thr close to the catalytic site. The aim of these substitutions was to rigidify the molecular structure of the enzyme. Furthermore, we also analyzed mutants containing these combined substitutions. Biochemical enzymatic assays of engineered versions of EfAmy revealed that the combination of mutations at the surface loops increased the thermostability and catalytic efficiency of the enzyme. The possible mechanisms responsible for the changes in the biochemical properties are discussed by analyzing the three-dimensional structural model. IMPORTANCE Cold-adapted enzymes have high specific activity at low and moderate temperatures, a property that can be extremely useful in various applications as it implies a reduction in energy consumption during the catalyzed reaction. However, the concurrent high thermolability of cold-adapted enzymes often limits their applications in industrial processes. The α-amylase from the psychrophilic Antarctic ciliate Euplotes focardii (named EfAmy) is a cold-adapted enzyme with optimal catalytic activity in an alkaline environment. These unique features distinguish it from most α-amylases characterized so far. In this work, we engineered a novel EfAmy with improved thermostability, substrate binding affinity, and catalytic efficiency to various extents, without impacting its pH preference. These characteristics can be considered important properties for use in the food, detergent, and textile industries and in other industrial applications. The enzyme engineering strategy developed in this study may also provide useful knowledge for future optimization of molecules to be used in particular industrial applications.
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van der Vegt NFA, Rodríguez-Ropero F. Comment on "Relating side chain organization of PNIPAm with its conformation in aqueous methanol" by D. Mukherji, M. Wagner, M. D. Watson, S. Winzen, T. E. de Oliveira, C. M. Marques and K. Kremer, Soft Matter, 2016, 12, 7995. SOFT MATTER 2017; 13:2289-2291. [PMID: 28262864 DOI: 10.1039/c6sm02139e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In a recent paper, Mukherji et al. describe the collapse of poly(N-isopropyl acrylamide) in methanol-water mixtures based on experiments and molecular dynamics simulations. The conclusion of their work is that chain collapse is dominated by enthalpic bridging interactions while entropic effects play no major role. Here we show that this claim arises from an improper interpretation of preferential binding and the corresponding thermodynamic data presented. When interpreted correctly, the data instead provide evidence for repulsive enthalpic interactions of methanol with the polymer, supporting the emerging view of entropic chain collapse.
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Affiliation(s)
- Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Germany.
| | - Francisco Rodríguez-Ropero
- Department of Physics and Center of Molecular Study of Soft Condensed Matter, Illinois Institute of Technology, Chicago, Illinois 60160, USA
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20
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Thakare S, Stachelek P, Mula S, More AB, Chattopadhyay S, Ray AK, Sekar N, Ziessel R, Harriman A. Solvent-Driven Conformational Exchange for Amide-Linked Bichromophoric BODIPY Derivatives. Chemistry 2016; 22:14356-66. [DOI: 10.1002/chem.201602354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Shrikant Thakare
- Department of Dyestuff Technology; Institute of Chemical Technology; Mumbai 400019 India
| | - Patrycja Stachelek
- Molecular Photonics Laboratory; School of Chemistry; Newcastle University; Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Soumyaditya Mula
- Bio-Organic Division; Bhabha Atomic Research Centre; Mumbai 400085 India
| | - Ankush B. More
- Department of Dyestuff Technology; Institute of Chemical Technology; Mumbai 400019 India
| | | | - Alok K. Ray
- Laser and Plasma Technology Division; Bhabha Atomic Research Centre; Mumbai 400085 India
| | - Nagaiyan Sekar
- Department of Dyestuff Technology; Institute of Chemical Technology; Mumbai 400019 India
| | - Raymond Ziessel
- Laboratoire de Chimie Organique et Spectroscopies Avancées (LCOSA); Ecole Européenne de Chimie; Polymères et Matériaux; Université de Strasbourg; 25 rue Becquerel 67087 Strasbourg Cedex 02 France
| | - Anthony Harriman
- Molecular Photonics Laboratory; School of Chemistry; Newcastle University; Bedson Building Newcastle upon Tyne NE1 7RU UK
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21
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Kim SB, Palmer JC, Debenedetti PG. Computational investigation of cold denaturation in the Trp-cage miniprotein. Proc Natl Acad Sci U S A 2016; 113:8991-6. [PMID: 27457961 PMCID: PMC4987839 DOI: 10.1073/pnas.1607500113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The functional native states of globular proteins become unstable at low temperatures, resulting in cold unfolding and impairment of normal biological function. Fundamental understanding of this phenomenon is essential to rationalizing the evolution of freeze-tolerant organisms and developing improved strategies for long-term preservation of biological materials. We present fully atomistic simulations of cold denaturation of an α-helical protein, the widely studied Trp-cage miniprotein. In contrast to the significant destabilization of the folded structure at high temperatures, Trp-cage cold denatures at 210 K into a compact, partially folded state; major elements of the secondary structure, including the α-helix, are conserved, but the salt bridge between aspartic acid and arginine is lost. The stability of Trp-cage's α-helix at low temperatures suggests a possible evolutionary explanation for the prevalence of such structures in antifreeze peptides produced by cold-weather species, such as Arctic char. Although the 310-helix is observed at cold conditions, its position is shifted toward Trp-cage's C-terminus. This shift is accompanied by intrusion of water into Trp-cage's interior and the hydration of buried hydrophobic residues. However, our calculations also show that the dominant contribution to the favorable energetics of low-temperature unfolding of Trp-cage comes from the hydration of hydrophilic residues.
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Affiliation(s)
- Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Jeremy C Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544;
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22
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Camilloni C, Bonetti D, Morrone A, Giri R, Dobson CM, Brunori M, Gianni S, Vendruscolo M. Towards a structural biology of the hydrophobic effect in protein folding. Sci Rep 2016; 6:28285. [PMID: 27461719 PMCID: PMC4962056 DOI: 10.1038/srep28285] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/03/2016] [Indexed: 11/09/2022] Open
Abstract
The hydrophobic effect is a major driving force in protein folding. A complete understanding of this effect requires the description of the conformational states of water and protein molecules at different temperatures. Towards this goal, we characterise the cold and hot denatured states of a protein by modelling NMR chemical shifts using restrained molecular dynamics simulations. A detailed analysis of the resulting structures reveals that water molecules in the bulk and at the protein interface form on average the same number of hydrogen bonds. Thus, even if proteins are 'large' particles (in terms of the hydrophobic effect, i.e. larger than 1 nm), because of the presence of complex surface patterns of polar and non-polar residues their behaviour can be compared to that of 'small' particles (i.e. smaller than 1 nm). We thus find that the hot denatured state is more compact and richer in secondary structure than the cold denatured state, since water at lower temperatures can form more hydrogen bonds than at high temperatures. Then, using Φ-value analysis we show that the structural differences between the hot and cold denatured states result in two alternative folding mechanisms. These findings thus illustrate how the analysis of water-protein hydrogen bonds can reveal the molecular origins of protein behaviours associated with the hydrophobic effect.
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Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Daniela Bonetti
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Angela Morrone
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Rajanish Giri
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
| | | | - Maurizio Brunori
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" Università di Roma "La Sapienza", 00185 Rome, Italy
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23
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Ben-Naim A. Theoretical aspects of self-assembly of proteins: A Kirkwood-Buff-theory approach. J Chem Phys 2013; 138:224906. [DOI: 10.1063/1.4810806] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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