1
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Sucharski F, Gallo G, Coelho C, Hardy L, Würtele M. Modeling the role of charged residues in thermophilic proteins by rotamer and dynamic cross correlation analysis. J Mol Model 2023; 29:132. [PMID: 37036538 DOI: 10.1007/s00894-023-05490-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/24/2023] [Indexed: 04/11/2023]
Abstract
Discerning the determinants of protein thermostability is very important both from the theoretical and applied perspective. Different lines of evidence seem to indicate that a dynamical network of salt bridges/charged residues plays a fundamental role in the thermostability of enzymes. In this work, we applied measures of dynamic variance, like the Gini coefficients, Kullback-Leibler (KL) divergence and dynamic cross correlation (DCC) coefficients to compare the behavior of 3 pairs of homologous proteins from the thermophilic bacterium Thermus thermophilus and mesophilic Escherichia coli. Molecular dynamic (MD) simulations of these proteins were performed at 303 K and 363 K. In the characterization of their side chain rotamer distributions, the corresponding Gini coefficients and KL-divergence both revealed significant correlations with temperature. Similarly, a DCC analysis revealed a higher trend to de-correlate the movement of charged residues at higher temperatures in the thermophilic proteins, when compared with their mesophilic homologues. These results highlight the importance of dynamic electrostatic network interactions for the thermostability of enzymes.
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Affiliation(s)
- Fernanda Sucharski
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil
| | - Gloria Gallo
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil
| | - Camila Coelho
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil
| | - Leon Hardy
- Department of Physics, University of South Florida, Tampa, USA
| | - Martin Würtele
- Department of Science and Technology, Federal University of São Paulo, Talim 330, São José Dos Campos, São Paulo, 12231-280, Brazil.
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2
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Lotfi-Sousefi Z, Mehrnejad F, Khanmohammadi S, Kaboli SF. Insight into the Microcosm of the Human Growth Hormone and Its Interactions with Polymers and Copolymers: A Molecular Dynamics Perspective. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:90-104. [PMID: 33356301 DOI: 10.1021/acs.langmuir.0c02441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Therapeutic proteins nowadays have increasingly been applied for their considerable potential in treating a wide variety of diseases. The effectiveness and potency of native therapeutic proteins are limited by various factors (e.g., stability, blood circulation time, specificity). Over the past years, a great deal of effort has been devoted to developing safe and efficient protein delivery systems. Entrapment of protein into polymeric and copolymeric matrices is common among the different types of protein-based drug formulation. However, despite the massive efforts toward developing therapeutic protein delivery in experimental studies and industrial applications, there is relatively little data on the influence of polymers and copolymers on therapeutic proteins at the atomic and molecular levels. Herein, molecular dynamics (MD) simulations are used to study the effects of biocompatible synthetic polymers including methoxy poly(ethylene glycol) (MPEG), poly(lactic acid) (PLA), and poly(lactic acid) copolymers (poly(lactic-co-glycolic acid)) PLGA and MPEG-PLA(PELA)) on the structure and dynamics of the human growth hormone (hGH), and the results are compared with previous experimental findings. Our results indicate that the hGH conformation remains stable both in pure water and in the presence of polymers, and these results are in good agreement with previous experimental data. It is shown that the MPEG chains are self-assembled and folded into a semicrystalline structure; therefore, only a small portion of the protein interacts with the polymer. The other three polymers, however, interact well with the protein and partially cover its surface. Our findings suggest that the use of these polymers for protein encapsulation has the advantage of reducing protein aggregation and thus increasing drug serum half-life. Eventually, we anticipate that the research results will expand the current knowledge about encapsulation mechanisms and the molecular interactions between hGH and the polymers.
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Affiliation(s)
- Zahra Lotfi-Sousefi
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Somayeh Khanmohammadi
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - S Fatemeh Kaboli
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
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3
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Ghasriani H, Frahm GE, Johnston MJW, Aubin Y. Effects of Excipients on the Structure and Dynamics of Filgrastim Monitored by Thermal Unfolding Studies by CD and NMR Spectroscopy. ACS OMEGA 2020; 5:31845-31857. [PMID: 33344838 PMCID: PMC7745408 DOI: 10.1021/acsomega.0c04692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/24/2020] [Indexed: 06/02/2023]
Abstract
Product excipients are used to confer a number of desirable properties on the drug substance to maintain or improve stability and facilitate drug delivery. This is especially important for products where the active pharmaceutical ingredient (API) is a recombinant protein. In this study, we aimed to determine if excipients and formulation conditions affect the structure and/or modulate the dynamics of the protein API of filgrastim products. Samples of uniformly labeled 15N-Met-granulocyte-colony stimulating factor (GCSF) were prepared at 100 μM (near formulation concentration) with various concentrations of individual components (polysorbate-20 and -80, sorbitol) and three pH values. Nuclear magnetic resonance (NMR) spectroscopy techniques were applied to measure chemical shift perturbation (CSP) to detect structural changes, and relaxation parameters (T 1, T 2, and heteronuclear Overhauser effect) were measured to probe the effects on protein backbone motions. In parallel, the same solution conditions were subjected to protein thermal unfolding studies monitored by circular dichroism spectropolarimetry (CD). Detergents (polysorbate-20 and 80) do not induce any observable changes on the protein structure and do not modify its dynamics at formulation concentration. Lowering pH to 4.0, a condition known to stabilize the conformation of filgrastim, as well as the addition of sorbitol produced changes of the fast motion dynamics in the nanosecond and picosecond timescale. NMR-derived order parameters, which measure the local conformational entropy of the protein backbone, show that lowering pH leads to a compaction of the four-helix bundle while the addition of sorbitol relaxes helices B and C, thereby reducing the mobility of loop CD. CSPs and measurements of protein dynamics via NMR-derived order parameters provide a description in structural and motional terms at an atomic resolution on how formulation components contribute to the stabilization of filgrastim products.
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Affiliation(s)
| | | | | | - Yves Aubin
- . Phone: 613-791-1500. Fax: 613-941-8933. 251 Sir Frederick Banting Driveway, Tunney’s Pasture, A/L
2201E, Ottawa, Ontario, Canada K1A 0K9
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4
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Zhang X, Cheng B, Liu X, Li Y, Hou J, Chen S, Chen J, Li S. Screening of α‐Glucosidase Inhibitors from
Houttuynia cordata
and Evaluation of the Binding Mechanisms. ChemistrySelect 2020. [DOI: 10.1002/slct.202001657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xueli Zhang
- Key Laboratory of Edible Wild Plants Conservation and UtilizationHubei Normal University Huangshi 435002 China
| | - Bingjie Cheng
- Key Laboratory of Edible Wild Plants Conservation and UtilizationHubei Normal University Huangshi 435002 China
| | - Xixia Liu
- Key Laboratory of Edible Wild Plants Conservation and UtilizationHubei Normal University Huangshi 435002 China
- Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologyHubei Normal University Huangshi 435002 China
| | - Yani Li
- Key Laboratory of Edible Wild Plants Conservation and UtilizationHubei Normal University Huangshi 435002 China
- Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologyHubei Normal University Huangshi 435002 China
| | - Jianjun Hou
- Key Laboratory of Edible Wild Plants Conservation and UtilizationHubei Normal University Huangshi 435002 China
- Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologyHubei Normal University Huangshi 435002 China
| | - Sirui Chen
- Key Laboratory of Edible Wild Plants Conservation and UtilizationHubei Normal University Huangshi 435002 China
- Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologyHubei Normal University Huangshi 435002 China
| | - Jiamin Chen
- Key Laboratory of Edible Wild Plants Conservation and UtilizationHubei Normal University Huangshi 435002 China
| | - Shuyue Li
- Key Laboratory of Edible Wild Plants Conservation and UtilizationHubei Normal University Huangshi 435002 China
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5
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Wei CC, Fabry E, Hay E, Lloyd L, Kaufman N, Yang YP, Stuehr DJ. Metal binding and conformational studies of the calcium binding domain of NADPH oxidase 5 reveal its similarity and difference to calmodulin. J Biomol Struct Dyn 2019; 38:2352-2368. [DOI: 10.1080/07391102.2019.1633409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Chin-Chuan Wei
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Emily Fabry
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Evan Hay
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Laura Lloyd
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Nichole Kaufman
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Ya-Ping Yang
- Department of Pathobiology, the Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Dennis J. Stuehr
- Department of Pathobiology, the Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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6
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Kocaman S, Serpersu EH. The Thermodynamics of Ligand Binding to the Aminoglycoside O-Nucleotidyltransferase(4′) and Variants Yields Clues about Thermophilic Properties. Biochemistry 2019; 58:1579-1586. [DOI: 10.1021/acs.biochem.8b01201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seda Kocaman
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Engin H. Serpersu
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Graduate School of Genome Science and Technology, The University of Tennessee and Oak Ridge National Laboratories, Knoxville, Tennessee 37996, United States
- National Science Foundation, 2415 Eisenhower Avenue, Alexandria, Virginia 22314, United States
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7
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Shakeel T, Gupta M, Fatma Z, Kumar R, Kumar R, Singh R, Sharma M, Jade D, Gupta D, Fatma T, Yazdani SS. A consensus-guided approach yields a heat-stable alkane-producing enzyme and identifies residues promoting thermostability. J Biol Chem 2018; 293:9148-9161. [PMID: 29632075 PMCID: PMC6005442 DOI: 10.1074/jbc.ra117.000639] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/06/2018] [Indexed: 01/02/2023] Open
Abstract
Aldehyde-deformylating oxygenase (ADO) is an essential enzyme for production of long-chain alkanes as drop-in biofuels, which are compatible with existing fuel systems. The most active ADOs are present in mesophilic cyanobacteria, especially Nostoc punctiforme Given the potential applications of thermostable enzymes in biorefineries, here we generated a thermostable (Cts)-ADO based on a consensus of ADO sequences from several thermophilic cyanobacterial strains. Using an in silico design pipeline and a metagenome library containing 41 hot-spring microbial communities, we created Cts-ADO. Cts-ADO displayed a 3.8-fold increase in pentadecane production on raising the temperature from 30 to 42 °C, whereas ADO from N. punctiforme (Np-ADO) exhibited a 1.7-fold decline. 3D structure modeling and molecular dynamics simulations of Cts- and Np-ADO at different temperatures revealed differences between the two enzymes in residues clustered on exposed loops of these variants, which affected the conformation of helices involved in forming the ADO catalytic core. In Cts-ADO, this conformational change promoted ligand binding to its preferred iron, Fe2, in the di-iron cluster at higher temperature, but the reverse was observed in Np-ADO. Detailed mapping of residues conferring Cts-ADO thermostability identified four amino acids, which we substituted individually and together in Np-ADO. Among these substitution variants, A161E was remarkably similar to Cts-ADO in terms of activity optima, kinetic parameters, and structure at higher temperature. A161E was located in loop L6, which connects helices H5 and H6, and supported ligand binding to Fe2 at higher temperatures, thereby promoting optimal activity at these temperatures and explaining the increased thermostability of Cts-ADO.
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Affiliation(s)
- Tabinda Shakeel
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | - Mayank Gupta
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | - Zia Fatma
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | | | | | - Rahul Singh
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | - Medha Sharma
- From the Microbial Engineering Group.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
| | | | | | - Tasneem Fatma
- the Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Syed Shams Yazdani
- From the Microbial Engineering Group, .,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067 and
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8
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Jing X, Evangelista Falcon W, Baudry J, Serpersu EH. Thermophilic Enzyme or Mesophilic Enzyme with Enhanced Thermostability: Can We Draw a Line? J Phys Chem B 2017; 121:7086-7094. [DOI: 10.1021/acs.jpcb.7b04519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Wilfredo Evangelista Falcon
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Jerome Baudry
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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9
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Smith LJ, Athill R, van Gunsteren WF, Hansen N. Interpretation of Seemingly Contradictory Data: Low NMR S 2 Order Parameters Observed in Helices and High NMR S 2 Order Parameters in Disordered Loops of the Protein hGH at Low pH. Chemistry 2017; 23:9585-9591. [PMID: 28503764 DOI: 10.1002/chem.201700896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Indexed: 12/16/2022]
Abstract
At low pH, human growth hormone (hGH) adopts a partially folded state, in which the native helices are maintained, but the long loop regions and side-chain packing become disordered. Some of the S2 order parameters for backbone N-H vectors derived from NMR relaxation measurements on hGH at low pH initially seem contradictory. Three isolated residues (15, 20, and 171) in helices A and D exhibit low order parameter values (<0.5) indicating flexibility, whereas residue 143 in the centre of a long flexible loop region has a high order parameter (0.82). Using S2 order parameter restraining MD simulations, this paradox has been resolved. Low S2 values in helices are due to the presence of a mixture of 310 -helical and α-helical hydrogen bonds. High S2 values in relatively disordered parts of a protein may be due to fluctuating networks of hydrogen bonds between the backbone and the side chains, which restrict the motion of N-H bond vectors.
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Affiliation(s)
- Lorna J Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | - Roya Athill
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK
| | | | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, 70569, Stuttgart, Germany
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10
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Unveiling the basis of alkaline stability of an evolved versatile peroxidase. Biochem J 2016; 473:1917-28. [DOI: 10.1042/bcj20160248] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022]
Abstract
A variant of high biotechnological interest (called 2-1B) was obtained by directed evolution of the Pleurotus eryngii VP (versatile peroxidase) expressed in Saccharomyces cerevisiae [García-Ruiz, González-Pérez, Ruiz-Dueñas, Martínez and Alcalde (2012) Biochem. J. 441, 487–498]. 2-1B shows seven mutations in the mature protein that resulted in improved functional expression, activity and thermostability, along with a remarkable stronger alkaline stability (it retains 60% of the initial activity after 120 h of incubation at pH 9 compared with complete inactivation of the native enzyme after only 1 h). The latter is highly demanded for biorefinery applications. In the present study we investigate the structural basis behind the enhanced alkaline stabilization of this evolved enzyme. In order to do this, several VP variants containing one or several of the mutations present in 2-1B were expressed in Escherichia coli, and their alkaline stability and biochemical properties were determined. In addition, the crystal structures of 2-1B and one of the intermediate variants were solved and carefully analysed, and molecular dynamics simulations were carried out. We concluded that the introduction of three basic residues in VP (Lys-37, Arg-39 and Arg-330) led to new connections between haem and helix B (where the distal histidine residue is located), and formation of new electrostatic interactions, that avoided the hexa-co-ordination of the haem iron. These new structural determinants stabilized the haem and its environment, helping to maintain the structural enzyme integrity (with penta-co-ordinated haem iron) under alkaline conditions. Moreover, the reinforcement of the solvent-exposed area around Gln-305 in the proximal side, prompted by the Q202L mutation, further enhanced the stability.
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11
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Jiang X, Chen G, Wang L. Structural and dynamic evolution of the amphipathic N-terminus diversifies enzyme thermostability in the glycoside hydrolase family 12. Phys Chem Chem Phys 2016; 18:21340-50. [DOI: 10.1039/c6cp02998a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The N-terminus diversifies enzyme thermostability in the GH12 family, which was investigated by MD simulations, and provides potential applications in protein engineering.
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Affiliation(s)
- Xukai Jiang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
- State Key Laboratory of Biochemical Engineering
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12
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Wang CK, Swedberg JE, Northfield SE, Craik DJ. Effects of Cyclization on Peptide Backbone Dynamics. J Phys Chem B 2015; 119:15821-30. [DOI: 10.1021/acs.jpcb.5b11085] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Conan K. Wang
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joakim E. Swedberg
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susan E. Northfield
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J. Craik
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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13
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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: 176] [Impact Index Per Article: 19.6] [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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14
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Horváth G, Egyed O, Toke O. Temperature Dependence of Backbone Dynamics in Human Ileal Bile Acid-Binding Protein: Implications for the Mechanism of Ligand Binding. Biochemistry 2014; 53:5186-98. [DOI: 10.1021/bi500553f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Gergő Horváth
- Institute of Organic Chemistry,
Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, H-1117 Budapest, Hungary
| | - Orsolya Egyed
- Institute of Organic Chemistry,
Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, H-1117 Budapest, Hungary
| | - Orsolya Toke
- Institute of Organic Chemistry,
Research Centre for Natural Sciences, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, H-1117 Budapest, Hungary
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15
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Johansson H, Jensen MR, Gesmar H, Meier S, Vinther JM, Keeler C, Hodsdon ME, Led JJ. Specific and nonspecific interactions in ultraweak protein-protein associations revealed by solvent paramagnetic relaxation enhancements. J Am Chem Soc 2014; 136:10277-86. [PMID: 24969589 PMCID: PMC4111215 DOI: 10.1021/ja503546j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Weak
and transient protein–protein interactions underlie
numerous biological processes. However, the location of the interaction
sites of the specific complexes and the effect of transient, nonspecific
protein–protein interactions often remain elusive. We have
investigated the weak self-association of human growth hormone (hGH, KD = 0.90 ± 0.03 mM) at neutral pH by the
paramagnetic relaxation enhancement (PRE) of the amide protons induced
by the soluble paramagnetic relaxation agent, gadodiamide (Gd(DTPA-BMA)).
Primarily, it was found that the PREs are in agreement with the general
Hwang-Freed model for relaxation by translational diffusion (J. Chem. Phys.1975, 63, 4017–4025),
only if crowding effects on the diffusion in the protein solution
are taken into account. Second, by measuring the PREs of the amide
protons at increasing hGH concentrations and a constant concentration
of the relaxation agent, it is shown that a distinction can be made
between residues that are affected only by transient, nonspecific
protein–protein interactions and residues that are involved
in specific protein–protein associations. Thus, the PREs of
the former residues increase linearly with the hGH concentration in
the entire concentration range because of a reduction of the diffusion
caused by the transient, nonspecific protein–protein interactions,
while the PREs of the latter residues increase only at the lower hGH
concentrations but decrease at the higher concentrations because of
specific protein–protein associations that impede the access
of gadodiamide to the residues of the interaction surface. Finally,
it is found that the ultraweak aggregation of hGH involves several
interaction sites that are located in patches covering a large part
of the protein surface.
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Affiliation(s)
- Helle Johansson
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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16
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Yuwen T, Skrynnikov NR. Proton-decoupled CPMG: a better experiment for measuring (15)N R2 relaxation in disordered proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:155-169. [PMID: 24120537 DOI: 10.1016/j.jmr.2013.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/15/2013] [Accepted: 08/16/2013] [Indexed: 06/02/2023]
Abstract
(15)N R2 relaxation is one of the most informative experiments for characterization of intrinsically disordered proteins (IDPs). Small changes in nitrogen R2 rates are often used to determine how IDPs respond to various biologically relevant perturbations such as point mutations, posttranslational modifications and weak ligand interactions. However collecting high-quality (15)N relaxation data can be difficult. Of necessity, the samples of IDPs are often prepared with low protein concentration and the measurement time can be limited because of rapid sample degradation. Furthermore, due to hardware limitations standard experiments such as (15)N spin-lock and CPMG can sample the relaxation decay only to ca. 150ms. This is much shorter than (15)N T2 times in disordered proteins at or near physiological temperature. As a result, the sampling of relaxation decay profiles in these experiments is suboptimal, which further lowers the precision of the measurements. Here we report a new implementation of the proton-decoupled (PD) CPMG experiment which allows one to sample (15)N R2 relaxation decay up to ca. 0.5-1s. The new experiment has been validated through comparison with the well-established spin-lock measurement. Using dilute samples of denatured ubiquitin, we have demonstrated that PD-CPMG produces up to 3-fold improvement in the precision of the data. It is expected that for intrinsically disordered proteins the gains may be even more substantial. We have also shown that this sequence has a number of favorable properties: (i) the spectra are recorded with narrow linewidth in nitrogen dimension; (ii) (15)N offset correction is small and easy to calculate; (iii) the experiment is immune to various spurious effects arising from solvent exchange; (iv) the results are stable with respect to pulse miscalibration and rf field inhomogeneity; (v) with minimal change, the pulse sequence can also be used to measure R2 relaxation of (15)N(ε) spins in arginine side chains. We anticipate that the new experiment will be a valuable addition to the NMR toolbox for studies of IDPs.
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Affiliation(s)
- Tairan Yuwen
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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17
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Kovács K, Bánóczi G, Varga A, Szabó I, Holczinger A, Hornyánszky G, Zagyva I, Paizs C, Vértessy BG, Poppe L. Expression and properties of the highly alkalophilic phenylalanine ammonia-lyase of thermophilic Rubrobacter xylanophilus. PLoS One 2014; 9:e85943. [PMID: 24475062 PMCID: PMC3903478 DOI: 10.1371/journal.pone.0085943] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 12/04/2013] [Indexed: 11/18/2022] Open
Abstract
The sequence of a phenylalanine ammonia-lyase (PAL; EC: 4.3.1.24) of the thermophilic and radiotolerant bacterium Rubrobacter xylanophilus (RxPAL) was identified by screening the genomes of bacteria for members of the phenylalanine ammonia-lyase family. A synthetic gene encoding the RxPAL protein was cloned and overexpressed in Escherichia coli TOP 10 in a soluble form with an N-terminal His6-tag and the recombinant RxPAL protein was purified by Ni-NTA affinity chromatography. The activity assay of RxPAL with l-phenylalanine at various pH values exhibited a local maximum at pH 8.5 and a global maximum at pH 11.5. Circular dichroism (CD) studies showed that RxPAL is associated with an extensive α-helical character (far UV CD) and two distinctive near-UV CD peaks. These structural characteristics were well preserved up to pH 11.0. The extremely high pH optimum of RxPAL can be rationalized by a three-dimensional homology model indicating possible disulfide bridges, extensive salt-bridge formation and an excess of negative electrostatic potential on the surface. Due to these properties, RxPAL may be a candidate as biocatalyst in synthetic biotransformations leading to unnatural l- or d-amino acids or as therapeutic enzyme in treatment of phenylketonuria or leukemia.
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Affiliation(s)
- Klaudia Kovács
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences of Hungarian Academy of Sciences, Budapest, Hungary
| | - Gergely Bánóczi
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Andrea Varga
- Biocatalysis Research Group, Babeş-Bolyai University of Cluj-Napoca, Cluj-Napoca, Romania
| | - Izabella Szabó
- Biocatalysis Research Group, Babeş-Bolyai University of Cluj-Napoca, Cluj-Napoca, Romania
| | - András Holczinger
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gábor Hornyánszky
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Imre Zagyva
- Institute of Enzymology, Research Centre for Natural Sciences of Hungarian Academy of Sciences, Budapest, Hungary
| | - Csaba Paizs
- Biocatalysis Research Group, Babeş-Bolyai University of Cluj-Napoca, Cluj-Napoca, Romania
| | - Beáta G. Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences of Hungarian Academy of Sciences, Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Budapest, Hungary
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18
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Berbasova T, Nosrati M, Vasileiou C, Wang W, Lee KSS, Yapici I, Geiger JH, Borhan B. Rational design of a colorimetric pH sensor from a soluble retinoic acid chaperone. J Am Chem Soc 2013; 135:16111-9. [PMID: 24059243 PMCID: PMC4104655 DOI: 10.1021/ja404900k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Reengineering of cellular retinoic acid binding protein II (CRABPII) to be capable of binding retinal as a protonated Schiff base is described. Through rational alterations of the binding pocket, electrostatic perturbations of the embedded retinylidene chromophore that favor delocalization of the iminium charge lead to exquisite control in the regulation of chromophoric absorption properties, spanning the visible spectrum (474-640 nm). The pKa of the retinylidene protonated Schiff base was modulated from 2.4 to 8.1, giving rise to a set of proteins of varying colors and pH sensitivities. These proteins were used to demonstrate a concentration-independent, ratiometric pH sensor.
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Affiliation(s)
- Tetyana Berbasova
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Meisam Nosrati
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Wenjing Wang
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kin Sing Stephen Lee
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Ipek Yapici
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - James H. Geiger
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Babak Borhan
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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19
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Kitevski-LeBlanc JL, Hoang J, Thach W, Larda ST, Prosser RS. 19F NMR Studies of a Desolvated Near-Native Protein Folding Intermediate. Biochemistry 2013; 52:5780-9. [DOI: 10.1021/bi4010057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Julianne L. Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - Joshua Hoang
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - William Thach
- Department of Biochemistry, University of Toronto, 1 King’s College Circle,
Toronto, Ontario M5S 1A8, Canada
| | - Sacha Thierry Larda
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
- Department of Biochemistry, University of Toronto, 1 King’s College Circle,
Toronto, Ontario M5S 1A8, Canada
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20
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Gromiha MM, Pathak MC, Saraboji K, Ortlund EA, Gaucher EA. Hydrophobic environment is a key factor for the stability of thermophilic proteins. Proteins 2013; 81:715-21. [PMID: 23319168 DOI: 10.1002/prot.24232] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/16/2012] [Accepted: 11/28/2012] [Indexed: 11/07/2022]
Affiliation(s)
- M Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India.
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21
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Hayashi Y, Nagao S, Osuka H, Komori H, Higuchi Y, Hirota S. Domain Swapping of the Heme and N-Terminal α-Helix in Hydrogenobacter thermophilus Cytochrome c552 Dimer. Biochemistry 2012; 51:8608-16. [DOI: 10.1021/bi3011303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yugo Hayashi
- Graduate School
of Materials
Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate School
of Materials
Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hisao Osuka
- Department of Life Science,
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hirofumi Komori
- Department of Life Science,
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department of Life Science,
Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Shun Hirota
- Graduate School
of Materials
Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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22
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Sabo TM, Bakhtiari D, Walter KFA, McFeeters RL, Giller K, Becker S, Griesinger C, Lee D. Thermal coefficients of the methyl groups within ubiquitin. Protein Sci 2012; 21:562-70. [PMID: 22334336 PMCID: PMC3375756 DOI: 10.1002/pro.2045] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 11/11/2022]
Abstract
Physiological processes such as protein folding and molecular recognition are intricately linked to their dynamic signature, which is reflected in their thermal coefficient. In addition, the local conformational entropy is directly related to the degrees of freedom, which each residue possesses within its conformational space. Therefore, the temperature dependence of the local conformational entropy may provide insight into understanding how local dynamics may affect the stability of proteins. Here, we analyze the temperature dependence of internal methyl group dynamics derived from the cross-correlated relaxation between dipolar couplings of two CH bonds within ubiquitin. Spanning a temperature range from 275 to 308 K, internal methyl group dynamics tend to increase with increasing temperature, which translates to a general increase in local conformational entropy. With this data measured over multiple temperatures, the thermal coefficient of the methyl group order parameter, the characteristic thermal coefficient, and the local heat capacity were obtained. By analyzing the distribution of methyl group thermal coefficients within ubiquitin, we found that the N-terminal region has relatively high thermostability. These results indicate that methyl groups contribute quite appreciably to the total heat capacity of ubiquitin through the regulation of local conformational entropy.
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Affiliation(s)
- T Michael Sabo
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical ChemistryGöttingen 37077, Germany
| | - Davood Bakhtiari
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical ChemistryGöttingen 37077, Germany
| | - Korvin F A Walter
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical ChemistryGöttingen 37077, Germany
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama in HuntsvilleHuntsville, Alabama 35899
| | - Karin Giller
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical ChemistryGöttingen 37077, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical ChemistryGöttingen 37077, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical ChemistryGöttingen 37077, Germany
| | - Donghan Lee
- Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical ChemistryGöttingen 37077, Germany
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23
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Nebot VJ, Armengol J, Smets J, Prieto SF, Escuder B, Miravet JF. Molecular hydrogels from bolaform amino acid derivatives: a structure-properties study based on the thermodynamics of gel solubilization. Chemistry 2012; 18:4063-72. [PMID: 22354848 DOI: 10.1002/chem.201103193] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Indexed: 11/07/2022]
Abstract
Insight is provided into the aggregation thermodynamics associated to hydrogel formation by molecular gelators derived from L-valine and L-isoleucine. Solubility data from NMR measurements are used to extract thermodynamic parameters for the aggregation in water. It is concluded that at room temperature and up to 55 °C, these systems form self-assembled fibrillar networks in water with quite low or zero enthalpic component, whereas the entropy of the aggregation is favorable. These results are explained by considering that the hydrophobic effect is dominant in the self-assembly. However, studies by NMR and IR spectroscopy reveal that intermolecular hydrogen bonding is also a key issue in the aggregation process of these molecules in water. The low enthalpy values measured for the self-assembly process are ascribed to the result of a compensation of the favorable intermolecular hydrogen-bond formation and the unfavorable enthalpy component of the hydrophobic effect. Additionally, it is shown that by using the hydrophobic character as a design parameter, enthalpy-controlled hydrogel formation, as opposed to entropy-controlled hydrogel formation, can be achieved in water if the gelator is polar enough. It is noteworthy that these two types of hydrogels, enthalpy-versus entropy-driven hydrogels, present quite different response to temperature changes in properties such as the minimum gelator concentration (mgc) or the rheological moduli. Finally, the presence of a polymorphic transition in a hydrogel upon heating above 70 °C is reported and ascribed to the weakening of the hydrophobic effect upon heating. The new soft polymorphic materials present dramatically different solubility and rheological properties. Altogether these results are aimed to contribute to the rational design of molecular hydrogelators, which could be used for the tailored preparation of this type of soft materials. The reported results could also provide ground for the rationale of different self-assembly processes in aqueous media.
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Affiliation(s)
- Vicent J Nebot
- Department de Química Inorgánica i Orgánica, Universitat Jaume I, 12071 Castelló, Spain
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24
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Marcos E, Jiménez A, Crehuet R. Dynamic Fingerprints of Protein Thermostability Revealed by Long Molecular Dynamics. J Chem Theory Comput 2012; 8:1129-42. [DOI: 10.1021/ct200877z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Enrique Marcos
- Department
of Biological Chemistry and Molecular Modelling,
Institute of Advanced Chemistry of Catalonia (IQAC - CSIC), E-08034
Barcelona, Spain
| | - Aurora Jiménez
- Department
of Biological Chemistry and Molecular Modelling,
Institute of Advanced Chemistry of Catalonia (IQAC - CSIC), E-08034
Barcelona, Spain
| | - Ramon Crehuet
- Department
of Biological Chemistry and Molecular Modelling,
Institute of Advanced Chemistry of Catalonia (IQAC - CSIC), E-08034
Barcelona, Spain
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25
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Pistolesi S, Tjandra N. Temperature dependence of molecular interactions involved in defining stability of glutamine binding protein and its complex with L-glutamine. Biochemistry 2012; 51:643-52. [PMID: 22206385 PMCID: PMC3513781 DOI: 10.1021/bi201494h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The temperature dependence of dynamic parameters derived from nuclear magnetic resonance (NMR) relaxation data is related to conformational entropy of the system under study. This provides information such as macromolecules stability and thermodynamics of ligand binding. We studied the temperature dependence of NMR order parameter of glutamine binding protein (GlnBP), a periplasmic binding protein (PBP) highly specific to L-glutamine associated with its ABC transporter, with the goal of elucidating the dynamical differences between the respective ligand bound and free forms. We found that the protein-ligand interaction, which is stabilized at higher temperature, has a striking effect on the stability of the hydrophobic core of the large domain of GlnBP. Moreover, in contrast to what was found for less specific PBPs, the decreasing backbone motion of the hinge region at increasing temperature supports the idea that the likelihood that GlnBP can adopt a ligand free closed conformation in solution diminishes at higher temperatures. Our results support the induced-fit model as mode of action for GlnBP. In addition, we found that the backbones of residues involved in a salt bridge do not necessarily become more rigid as the temperature rises as it was previously suggested [Vinther, J. M., et al. (2011) J. Am. Chem. Soc., 133, 271-278]. Our results show that for this to happen these residues have to also directly interact with a region of the protein that is becoming more rigid as the temperature increases.
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Affiliation(s)
- Sara Pistolesi
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892
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26
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Neira JL, Sevilla P, García-Blanco F. The C-terminal sterile alpha motif (SAM) domain of human p73 is a highly dynamic protein, which acquires high thermal stability through a decrease in backbone flexibility. Phys Chem Chem Phys 2012; 14:10308-23. [DOI: 10.1039/c2cp41179b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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27
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Marcos E, Mestres P, Crehuet R. Crowding induces differences in the diffusion of thermophilic and mesophilic proteins: a new look at neutron scattering results. Biophys J 2011; 101:2782-9. [PMID: 22261067 PMCID: PMC3297780 DOI: 10.1016/j.bpj.2011.09.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/20/2011] [Accepted: 09/23/2011] [Indexed: 10/14/2022] Open
Abstract
The dynamical basis underlying the increased thermal stability of thermophilic proteins remains uncertain. Here, we challenge the new paradigm established by neutron scattering experiments in solution, in which the adaptation of thermophilic proteins to high temperatures lies in the lower sensitivity of their flexibility to temperature changes. By means of a combination of molecular dynamics and Brownian dynamics simulations, we report a reinterpretation of those experiments and show evidence that under crowding conditions, such as in vivo, thermophilic and homolog mesophilic proteins have diffusional properties with different thermal behavior.
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Affiliation(s)
| | | | - Ramon Crehuet
- Department of Biological Chemistry and Molecular Modeling, Institute of Advanced Chemistry of Catalonia (IQAC – CSIC), Barcelona, Spain
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28
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Substitution of Asp189 residue alters the activity and thermostability of Geobacillus sp. NTU 03 lipase. Biotechnol Lett 2011; 33:1841-6. [DOI: 10.1007/s10529-011-0635-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 04/19/2011] [Indexed: 11/26/2022]
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29
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Tai H, Irie K, Mikami SI, Yamamoto Y. Enhancement of the thermostability of Hydrogenobacter thermophilus cytochrome c(552) through introduction of an extra methylene group into its hydrophobic protein interior. Biochemistry 2011; 50:3161-9. [PMID: 21417336 DOI: 10.1021/bi200256d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Careful scrutiny of the protein interior of Hydrogenobacter thermophilus cytochrome c(552) (HT) on the basis of its X-ray structure [Travaglini-Allocatelli, C., Gianni, S., Dubey, V. K., Borgia, A., Di Matteo, A., Bonivento, D., Cutruzzola, F., Bren, K. L., and Brunori, M. (2005) J. Biol. Chem. 280, 25729-25734] indicated that a void space, which is large enough to accommodate a methyl group, exists in the hydrophobic protein interior near the heme. We tried to reduce the void space through the replacement of a Val by Ile or Leu (Val/Ile or Val/Leu mutation), and then the structural and functional consequences of these two mutations were characterized in order to elucidate the relationship between the nature of the packing of hydrophobic residues and the functional properties of the protein. The study demonstrated striking differences in the structural and functional consequences between the two mutations. The Val/Ile mutation was found to cause further enhancement of the thermostability of the oxidized HT, as reflected in the increase of the denaturation temperature (T(m)) value by ∼ 3 deg, whereas the thermostability of the reduced form was essentially unaffected. As a result, the redox potential (E(m)) of the Val/Ile mutant exhibited a negative shift of ∼ 50 mV relative to that of the wild-type protein in an enthalpic manner, this being consistent with our previous finding that a protein with higher stability in its oxidized form exhibits a lower E(m) value [Terui, N., Tachiiri, N., Matsuo, H., Hasegawa, J., Uchiyama, S., Kobayashi, Y., Igarashi, Y., Sambongi, Y., and Yamamoto, Y. (2003) J. Am. Chem. Soc. 125, 13650-13651]. In contrast, the Val/Leu mutation led to a decrease in thermostability of both the redox forms of the protein, as reflected in the decreases of the T(m) values of the oxidized and reduced proteins by ∼ 3 and ∼ 5 deg, respectively, and the E(m) value of the Val/Leu mutant happened to be similar to that of the Val/Ile one. The E(m) value of the Val/Leu mutant could be reasonably interpreted in terms of the different effects of the mutation on the stabilities of the two different redox forms of the protein. Thus, the present study demonstrated that the stability of the protein is affected quite sensitively by the contextual stereochemical packing of hydrophobic residues in the protein interior and that the structural properties of the hydrophobic core in the protein interior are crucial for control of the redox function of the protein. These findings provide novel insights as to functional control of a protein, which could be utilized for tuning of the T(m) and E(m) values of the protein by means of protein engineering.
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Affiliation(s)
- Hulin Tai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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