1
|
Wernersson S, Birgersson S, Akke M. Cosolvent Dimethyl Sulfoxide Influences Protein-Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein-Ligand Encounter. Biochemistry 2023; 62:44-52. [PMID: 36542811 DOI: 10.1021/acs.biochem.2c00507] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein-ligand-exchange kinetics determines the duration of biochemical signals and consequently plays an important role in drug design. Binding studies commonly require solubilization of designed ligands in solvents such as dimethyl sulfoxide (DMSO), resulting in residual amounts of DMSO following titration of solubilized ligands into aqueous protein samples. Therefore, it is critical to establish whether DMSO influences protein-ligand binding. Here, we address the general and indirect effect of DMSO on protein-ligand binding caused by solvent viscosity, which is strongly dependent on the relative concentrations of DMSO and water. As a model system, we studied the binding of a drug-like ligand to the carbohydrate recognition domain of galectin-3 in the presence of variable amounts of DMSO. We used isothermal titration calorimetry to characterize binding thermodynamics and 15N NMR relaxation to monitor kinetics. The binding enthalpy is not affected, but we observe a subtle trend of increasingly unfavorable entropy of binding, and consequently decreased affinity, with increasing DMSO concentration. The increasing concentration of DMSO results in a reduced association rate of binding, while the dissociation rate is less affected. The observed association rate is inversely proportional to the viscosity of the DMSO-water mixture, as expected from theory, but significantly reduced from the diffusion-controlled limit. By comparing the viscosity dependence of the observed association rate with that of the theoretical diffusion-controlled association rate, we estimate the success rate of productive complex formation following an initial encounter of proteins and ligands, showing that only one out of several hundred binding "attempts" are successful.
Collapse
Affiliation(s)
- Sven Wernersson
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden
| | - Simon Birgersson
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden
| |
Collapse
|
2
|
Heterogeneous Off-Target Effects of Ultra-Low Dose Dimethyl Sulfoxide (DMSO) on Targetable Signaling Events in Lung Cancer In Vitro Models. Int J Mol Sci 2021; 22:ijms22062819. [PMID: 33802212 PMCID: PMC8001778 DOI: 10.3390/ijms22062819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/28/2021] [Accepted: 03/05/2021] [Indexed: 12/17/2022] Open
Abstract
Targetable alterations in cancer offer novel opportunities to the drug discovery process. However, pre-clinical testing often requires solubilization of these drugs in cosolvents like dimethyl sulfoxide (DMSO). Using a panel of cell lines commonly used for in vitro drug screening and pre-clinical testing, we explored the DMSO off-target effects on functional signaling networks, drug targets, and downstream substrates. Eight Non-Small Cell Lung Cancer (NSCLC) cell lines were incubated with three concentrations of DMSO (0.0008%, 0.002%, and 0.004% v/v) over time. Expression and activation levels of 187 proteins, of which 137 were kinases and downstream substrates, were captured using the Reverse Phase Protein Array (RPPA). The DMSO effect was heterogeneous across cell lines and varied based on concentration, exposure time, and cell line. Of the 187 proteins measured, all were statistically different in at least one comparison at the highest DMSO concentration, followed by 99.5% and 98.9% at lower concentrations. Only 46% of the proteins were found to be statistically different in more than 5 cell lines, indicating heterogeneous response across models. These cell line specific alterations modulate response to in vitro drug screening. Ultra-low DMSO concentrations have broad and heterogeneous effects on targetable signaling proteins. Off-target effects need to be carefully evaluated in pre-clinical drug screening and testing.
Collapse
|
3
|
Bleisinger N, Dittrich R, Strahl O, Brauweiler R, Hoffmann I, Beckmann MW, Volk T. Me2SO perfusion time for whole-organ cryopreservation can be shortened: Results of micro-computed tomography monitoring during Me2SO perfusion of rat hearts. PLoS One 2020; 15:e0238519. [PMID: 32877442 PMCID: PMC7467318 DOI: 10.1371/journal.pone.0238519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
Cryopreservation of whole organs and specific tissues is an important and continually expanding field of medicine. The protocols currently used for organ preservation do not ensure survivability and functionality; the protocols for ovarian tissue lead to acceptable outcomes, but these are still capable of further improvement. In general, cryopreservation protocols need to be optimized. One important approach to improving cryopreservation protocols in general involves reducing exposure to cytotoxic cryoprotective agents prior to freezing. This study, therefore, evaluated the real-time tissue penetration of dimethyl sulfoxide, a cryoprotective agent that is widely used in cryopreservation. Dimethyl sulfoxide penetration in rat hearts perfused with a 15% (v/v) dimethyl sulfoxide solution was examined in real-time using dynamic contrast-enhanced micro-computed tomography imaging. Viability of cardiomyocytes was not significantly affected by the dimethyl sulfoxide perfusion procedure. Two different perfusion rates were evaluated and compared with perfusion using a common iodine-based contrast agent (iomeprol). The dynamic contrast-enhanced micro-computed tomography imaging data showed that dimethyl sulfoxide flushes both the extracellular and intracellular spaces in rat heart tissue to 95% equilibration after ≈ 35 s via perfusion. Subsequent wash-out via perfusion is completed to 95% within ≈ 49 s. The equilibration duration routinely used in dimethyl sulfoxide–based protocols for cryopreservation should therefore be questioned. Shorter incubation duration would perhaps be sufficient, as well as being beneficial in relation to cell survivability. It would be helpful to have techniques for non-invasive real-time monitoring of the penetration of cryoprotective agents and such techniques should be used to revise cryopreservation protocols. Switching to perfusion-based equilibration procedures might be beneficial, if feasible.
Collapse
Affiliation(s)
- Nathalie Bleisinger
- Department of Obstetrics and Gynaecology, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Ralf Dittrich
- Department of Obstetrics and Gynaecology, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- * E-mail:
| | - Olga Strahl
- Department of Obstetrics and Gynaecology, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Brauweiler
- Institute of Medical Physics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Inge Hoffmann
- Department of Obstetrics and Gynaecology, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias W. Beckmann
- Department of Obstetrics and Gynaecology, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Tilmann Volk
- Institute of Cellular and Molecular Physiology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
4
|
Wallerstein J, Akke M. Minute Additions of DMSO Affect Protein Dynamics Measurements by NMR Relaxation Experiments through Significant Changes in Solvent Viscosity. Chemphyschem 2019; 20:326-332. [PMID: 30102005 PMCID: PMC6391962 DOI: 10.1002/cphc.201800626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 11/07/2022]
Abstract
Studies of protein-ligand binding often rely on dissolving the ligand in dimethyl sulfoxide (DMSO) to achieve sufficient solubility, and then titrating the ligand solution into the protein solution. As a result, the final protein-ligand solution contains small amounts of DMSO in the buffer. Here we report how the addition of DMSO impacts studies of protein conformational dynamics. We used 15 N NMR relaxation to compare the rotational diffusion correlation time (τC ) of proteins in aqueous buffer with and without DMSO. We found that τC scales with the viscosity of the water-DMSO mixture, which depends sensitively on the amount of DMSO and varies by a factor of 2 across the relevant concentration range. NMR relaxation studies of side chains dynamics are commonly interpreted using τC as a fixed parameter, obtained from backbone 15 N relaxation data acquired on a separate sample. Model-free calculations show that errors in τC , arising from mismatched DMSO concentration between samples, lead to significant errors in order parameters. Our results highlight the importance of determining τC for each sample or carefully matching the DMSO concentrations between samples.
Collapse
Affiliation(s)
- Johan Wallerstein
- Biophysical Chemistry, Center for Molecular Protein Science Department of ChemistryLund UniversityBox 124SE-221 00LundSweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science Department of ChemistryLund UniversityBox 124SE-221 00LundSweden
| |
Collapse
|
5
|
van Haren MJ, Thomas MG, Sartini D, Barlow DJ, Ramsden DB, Emanuelli M, Klamt F, Martin NI, Parsons RB. The kinetic analysis of the N-methylation of 4-phenylpyridine by nicotinamide N-methyltransferase: Evidence for a novel mechanism of substrate inhibition. Int J Biochem Cell Biol 2018; 98:127-136. [PMID: 29549048 DOI: 10.1016/j.biocel.2018.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/23/2018] [Accepted: 03/12/2018] [Indexed: 12/17/2022]
Abstract
The N-methylation of 4-phenylpyridine produces the neurotoxin 1-methyl-4-phenylpyridinium ion (MPP+). We investigated the kinetics of 4-phenylpyridine N-methylation by nicotinamide N-methyltransferase (NNMT) and its effect upon 4-phenylpyridine toxicity in vitro. Human recombinant NNMT possessed 4-phenylpyridine N-methyltransferase activity, with a specific activity of 1.7 ± 0.03 nmol MPP+ produced/h/mg NNMT. Although the Km for 4-phenylpyridine was similar to that reported for nicotinamide, its kcat of 9.3 × 10-5 ± 2 × 10-5 s-1 and specificity constant, kcat/Km, of 0.8 ± 0.8 s-1 M-1 were less than 0.15% of the respective values for nicotinamide, demonstrating that 4-phenylpyridine is a poor substrate for NNMT. At low (<2.5 mM) substrate concentration, 4-phenylpyridine N-methylation was competitively inhibited by dimethylsulphoxide, with a Ki of 34 ± 8 mM. At high (>2.5 mM) substrate concentration, enzyme activity followed substrate inhibition kinetics, with a Ki of 4 ± 1 mM. In silico molecular docking suggested that 4-phenylpyridine binds to the active site of NNMT in two non-redundant poses, one a substrate binding mode and the other an inhibitory mode. Finally, the expression of NNMT in the SH-SY5Y cell-line had no effect cell death, viability, ATP content or mitochondrial membrane potential. These data demonstrate that 4-phenylpyridine N-methylation by NNMT is unlikely to serve as a source of MPP+. The possibility for competitive inhibition by dimethylsulphoxide should be considered in NNMT-based drug discovery studies. The potential for 4-phenylpyridine to bind to the active site in two binding orientations using the same active site residues is a novel mechanism of substrate inhibition.
Collapse
Affiliation(s)
- Matthijs J van Haren
- Utrecht University, Utrecht Institute for Pharmaceutical Science, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Martin G Thomas
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street, London SE1 9NH, UK
| | - Davide Sartini
- Universitá Politecnica delle Marche, Department of Clinical Sciences, School of Medicine, Ancona, Italy
| | - David J Barlow
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street, London SE1 9NH, UK
| | - David B Ramsden
- University of Birmingham, Institute of Metabolism and Systems Research, Edgbaston, Birmingham B15 2TH, UK
| | - Monica Emanuelli
- Universitá Politecnica delle Marche, Department of Clinical Sciences, School of Medicine, Ancona, Italy
| | - Fábio Klamt
- Universidade Federal do Rio Grande do Sul, Departmento de Bioquímica, Instituto de Ciêncas Básicas de Saúde, Rua Ramiro Barcelos, Porto Alegre, RS 90035 003, Brazil
| | - Nathaniel I Martin
- Utrecht University, Utrecht Institute for Pharmaceutical Science, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
| | - Richard B Parsons
- King's College London, Institute of Pharmaceutical Science, 150 Stamford Street, London SE1 9NH, UK.
| |
Collapse
|
6
|
Liu M, Kim Y, Hilty C. Characterization of Chemical Exchange Using Relaxation Dispersion of Hyperpolarized Nuclear Spins. Anal Chem 2017; 89:9154-9158. [PMID: 28714674 DOI: 10.1021/acs.analchem.7b01896] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chemical exchange phenomena are ubiquitous in macromolecules, which undergo conformational change or ligand complexation. NMR relaxation dispersion (RD) spectroscopy based on a Carr-Purcell-Meiboom-Gill pulse sequence is widely applied to identify the exchange and measure the lifetime of intermediate states on the millisecond time scale. Advances in hyperpolarization methods improve the applicability of NMR spectroscopy when rapid acquisitions or low concentrations are required, through an increase in signal strength by several orders of magnitude. Here, we demonstrate the measurement of chemical exchange from a single aliquot of a ligand hyperpolarized by dissolution dynamic nuclear polarization (D-DNP). Transverse relaxation rates are measured simultaneously at different pulsing delays by dual-channel 19F NMR spectroscopy. This two-point measurement is shown to allow the determination of the exchange term in the relaxation rate expression. For the ligand 4-(trifluoromethyl)benzene-1-carboximidamide binding to the protein trypsin, the exchange term is found to be equal within error limits in neutral and acidic environments from D-DNP NMR spectroscopy, corresponding to a pre-equilibrium of trypsin deprotonation. This finding illustrates the capability for determination of binding mechanisms using D-DNP RD. Taking advantage of hyperpolarization, the ligand concentration in the exchange measurements can reach on the order of tens of μM and protein concentration can be below 1 μM, i.e., conditions typically accessible in drug discovery.
Collapse
Affiliation(s)
- Mengxiao Liu
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Yaewon Kim
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Christian Hilty
- Department of Chemistry, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| |
Collapse
|
7
|
Preferential solvation of lysozyme in dimethyl sulfoxide/water binary mixture probed by terahertz spectroscopy. Biophys Chem 2016; 216:31-36. [DOI: 10.1016/j.bpc.2016.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 11/21/2022]
|
8
|
Dachuri V, Boyineni J, Choi S, Chung HS, Jang SH, Lee C. Organic solvent-tolerant, cold-adapted lipases PML and LipS exhibit increased conformational flexibility in polar organic solvents. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
9
|
Bae SW, Eom D, Mai NL, Koo YM. Refolding of horseradish peroxidase is enhanced in presence of metal cofactors and ionic liquids. Biotechnol J 2016; 11:464-72. [PMID: 26901453 DOI: 10.1002/biot.201500142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 01/04/2016] [Accepted: 02/19/2016] [Indexed: 11/11/2022]
Abstract
The effects of various refolding additives, including metal cofactors, organic co-solvents, and ionic liquids, on the refolding of horseradish peroxidase (HRP), a well-known hemoprotein containing four disulfide bonds and two different types of metal centers, a ferrous ion-containing heme group and two calcium atoms, which provide a stabilizing effect on protein structure and function, were investigated. Both metal cofactors (Ca(2+) and hemin) and ionic liquids have positive impact on the refolding of HRP. For instance, the HRP refolding yield remarkably increased by over 3-fold upon addition of hemin and calcium chloride to the refolding buffer as compared to that in the conventional urea-containing refolding buffer. Moreover, the addition of ionic liquids [EMIM][Cl] to the hemin and calcium cofactor-containing refolding buffer further enhanced the HRP refolding yield up to 80% as compared to 12% in conventional refolding buffer at relatively high initial protein concentration (5 mg/ml). These results indicated that refolding method utilizing metal cofactors and ionic liquids could enhance the yield and efficiency for metalloprotein.
Collapse
Affiliation(s)
- Sang-Woo Bae
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea
| | - Doyoung Eom
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea
| | - Ngoc Lan Mai
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Yoon-Mo Koo
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea.
| |
Collapse
|
10
|
Abstract
Solution-state NMR has been widely applied to determine the three-dimensional structure, dynamics, and molecular interactions of proteins. The designs of experiments used in protein NMR differ from those used for small-molecule NMR, primarily because the information available prior to an experiment, such as molecular mass and knowledge of the primary structure, is unique for proteins compared to small molecules. In this review article, protein NMR for structural biology is introduced with comparisons to small-molecule NMR, such as descriptions of labeling strategies and the effects of molecular dynamics on relaxation. Next, applications for protein NMR are reviewed, especially practical aspects for protein-observed ligand-protein interaction studies. Overall, the following topics are described: (1) characteristics of protein NMR, (2) methods to detect protein-ligand interactions by NMR, and (3) practical aspects of carrying out protein-observed inhibitor-protein interaction studies.
Collapse
Affiliation(s)
- Rieko Ishima
- Address correspondence to Rieko Ishima: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Tel: 412-648-9056; Fax: 412-648-9008;
| |
Collapse
|
11
|
Koley Seth B, Ray A, Biswas S, Basu S. NiII–Schiff base complex as an enzyme inhibitor of hen egg white lysozyme: a crystallographic and spectroscopic study. Metallomics 2014; 6:1737-47. [DOI: 10.1039/c4mt00098f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
Landreh M, Alvelius G, Johansson J, Jörnvall H. Protective effects of dimethyl sulfoxide on labile protein interactions during electrospray ionization. Anal Chem 2014; 86:4135-9. [PMID: 24754426 DOI: 10.1021/ac500879c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrospray ionization mass spectrometry is a valuable tool to probe noncovalent interactions. However, the integrity of the interactions in the gas-phase is heavily influenced by the ionization process. Investigating oligomerization and ligand binding of transthyretin (TTR) and the chaperone domain from prosurfactant protein C, we found that dimethyl sulfoxide (DMSO) can improve the stability of the noncovalent interactions during the electrospray process, both regarding ligand binding and the protein quaternary structure. Low amounts of DMSO can reduce in-source dissociation of native protein oligomers and their interactions with hydrophobic ligands, even under destabilizing conditions. We interpret the effects of DMSO as being derived from its enrichment in the electrospray droplets during evaporation. Protection of labile interactions can arise from the decrease in ion charges to reduce the contributions from Coulomb repulsions, as well as from the cooling effect of adduct dissociation. The protective effects of DMSO on labile protein interactions are an important property given its widespread use in protein analysis by electrospray ionization mass spectrometry (ESI-MS).
Collapse
Affiliation(s)
- Michael Landreh
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Stockholm, S-171 77, Sweden
| | | | | | | |
Collapse
|
13
|
Grulich M, Štěpánek V, Kyslík P. Perspectives and industrial potential of PGA selectivity and promiscuity. Biotechnol Adv 2013; 31:1458-72. [DOI: 10.1016/j.biotechadv.2013.07.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 07/02/2013] [Accepted: 07/06/2013] [Indexed: 11/26/2022]
|
14
|
Kamerzell TJ, Pace AL, Li M, Danilenko DM, Mcdowell M, Gokarn YR, John Wang Y. Polar Solvents Decrease the Viscosity of High Concentration IgG1 Solutions Through Hydrophobic Solvation and Interaction: Formulation and Biocompatibility Considerations. J Pharm Sci 2013; 102:1182-93. [DOI: 10.1002/jps.23453] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 12/23/2012] [Accepted: 01/03/2013] [Indexed: 02/06/2023]
|
15
|
Tretyakova T, Shushanyan M, Partskhaladze T, Makharadze M, van Eldik R, Khoshtariya DE. Simplicity within the complexity: bilateral impact of DMSO on the functional and unfolding patterns of α-chymotrypsin. Biophys Chem 2013; 175-176:17-27. [PMID: 23524288 DOI: 10.1016/j.bpc.2013.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 02/05/2013] [Accepted: 02/09/2013] [Indexed: 10/27/2022]
Abstract
New understanding of the fundamental links between protein stability, conformational flexibility and function, can be gained through synergic studies on their catalytic and folding/unfolding properties under the influence of stabilizing/destabilizing additives. We explored an impact of dimethyl sulfoxide (DMSO), the moderate effector of multilateral action, on the kinetic (functional) and thermodynamic (thermal unfolding) patterns of a hydrolytic enzyme, α-chymotrypsin (α-CT), over a wide range of additive concentrations, 0-70% (v/v). Both the calorimetric and kinetic data exhibited rich behavior pointing to the complex interplay of global/local stability (and flexibility) patterns. The complex action of DMSO is explained through the negative and positive preferential solvation motifs that prevail for the extreme opposite, native-like and unfolded states, respectively, implying essential stabilization of compact domains by enhancement of interfacial water networks and destabilization of a flexible active site by direct binding of DMSO to the unoccupied specific positions intended for elongated polypeptide substrates.
Collapse
Affiliation(s)
- Tatyana Tretyakova
- Institute for Biophysics and Bionanosciences at the Department of Physics, I. Javakhishvili Tbilisi State University, I. Chavchavadze Ave. 3, 0128 Tbilisi, Georgia
| | | | | | | | | | | |
Collapse
|
16
|
Cubrilovic D, Zenobi R. Influence of dimehylsulfoxide on protein-ligand binding affinities. Anal Chem 2013; 85:2724-30. [PMID: 23347283 DOI: 10.1021/ac303197p] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Because of its favorable physicochemical properties, DMSO is the standard solvent for sample storage and handling of compounds in drug discovery. To date, little attention was given to how DMSO influences protein-ligand binding strengths. In this study we investigated the effects of DMSO on different noncovalent protein-ligand complexes, in particular in terms of the binding affinities, which we determined using nanoESI-MS. For the investigation, three different protein-ligand complexes were chosen: trypsin-Pefabloc, lysozyme-tri-N-acetylchitotriose (NAG3), and carbonic anhydrase-chlorothiazide. The DMSO content in the nanoESI buffer was increased systematically from 0.5 to 8%. For all three model systems, it was shown that the binding affinity decreases upon addition of DMSO. Even 0.5-1% DMSO alters the KD values, in particular for the tight binding system carbonic anhydrase-chlorothiazide. The determined dissociation constant (KD) is up to 10 times higher than for a DMSO-free sample in the case of carbonic anhydrase-chlorothiazide binding. For the trypsin-Pefabloc and lysozyme-NAG3 complexes, the dissociation constants are 7 and 3 times larger, respectively, in the presence of DMSO. This work emphasizes the importance of effects of DMSO as a co-solvent for quantification of protein-ligand binding strengths in the early stages of drug discovery.
Collapse
Affiliation(s)
- Dragana Cubrilovic
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | | |
Collapse
|
17
|
Design and characterization of protein-quercetin bioactive nanoparticles. J Nanobiotechnology 2011; 9:19. [PMID: 21586116 PMCID: PMC3116464 DOI: 10.1186/1477-3155-9-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 05/17/2011] [Indexed: 11/10/2022] Open
Abstract
Background The synthesis of bioactive nanoparticles with precise molecular level control is a major challenge in bionanotechnology. Understanding the nature of the interactions between the active components and transport biomaterials is thus essential for the rational formulation of bio-nanocarriers. The current study presents a single molecule of bovine serum albumin (BSA), lysozyme (Lys), or myoglobin (Mb) used to load hydrophobic drugs such as quercetin (Q) and other flavonoids. Results Induced by dimethyl sulfoxide (DMSO), BSA, Lys, and Mb formed spherical nanocarriers with sizes less than 70 nm. After loading Q, the size was further reduced by 30%. The adsorption of Q on protein is mainly hydrophobic, and is related to the synergy of Trp residues with the molecular environment of the proteins. Seven Q molecules could be entrapped by one Lys molecule, 9 by one Mb, and 11 by one BSA. The controlled releasing measurements indicate that these bioactive nanoparticles have long-term antioxidant protection effects on the activity of Q in both acidic and neutral conditions. The antioxidant activity evaluation indicates that the activity of Q is not hindered by the formation of protein nanoparticles. Other flavonoids, such as kaempferol and rutin, were also investigated. Conclusions BSA exhibits the most remarkable abilities of loading, controlled release, and antioxidant protection of active drugs, indicating that such type of bionanoparticles is very promising in the field of bionanotechnology.
Collapse
|
18
|
Xia Y, Park YD, Mu H, Zhou HM, Wang XY, Meng FG. The protective effects of osmolytes on arginine kinase unfolding and aggregation. Int J Biol Macromol 2007; 40:437-43. [PMID: 17173966 DOI: 10.1016/j.ijbiomac.2006.10.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 10/30/2006] [Accepted: 10/30/2006] [Indexed: 11/28/2022]
Abstract
Osmolytes are a series of different kinds of small molecules that can maintain the correct conformation of protein by acting as molecular chaperons. In this study, the protective effects of four compatible osmolytes, i.e., proline, sucrose, DMSO and glycerol, were studied during arginine kinase (EC 2.7.3.3) unfolding and aggregation. The results showed that all the osmolytes applied in this study obviously prevented AK unfolding and inactivation that was due to a GdnHCl denaturant by reducing the inactivation rate constants (k(i)), increasing the transition free energy changes (DeltaDeltaG(i)) and increasing the value for the midpoint of denaturation (C(m)). Furthermore, the osmolytes remarkably prevented AK aggregation in a concentration-dependent manner during AK refolding. Our results strongly indicated that osmolytes were not only metabolism substrates, but they were also important compounds with significant physiological protective functions for proteins, especially in some extremely harsh environments.
Collapse
Affiliation(s)
- Yong Xia
- College of Life Science, Shandong Agricultural University, Shandong, Taian 271018, PR China
| | | | | | | | | | | |
Collapse
|
19
|
Kim SH, Yan YB, Zhou HM. Role of osmolytes as chemical chaperones during the refolding of aminoacylase. Biochem Cell Biol 2006; 84:30-8. [PMID: 16462887 DOI: 10.1139/o05-148] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The refolding and reactivation of aminoacylase is particularly difficult because of serious off-pathway aggregation. The effects of 4 osmolytes--dimethylsulphoxide, glycerol, proline, and sucrose--on the refolding and reactivation of guanidine-denatured aminoacylase were studied by measuring aggregation, enzyme activity, intrinsic fluorescence spectra, 1-anilino-8-naphthalenesulfonate (ANS) fluorescence spectra, and circular dichroism (CD) spectra. The results show that all the osmolytes not only inhibit aggregation but also recover the activity of aminoacylase during refolding in a concentration-dependent manner. In particularly, a 40% glycerol concentration and a 1.5 mol/L sucrose concentration almost completely suppressed the aminoacylase aggregation. The enzyme activity measurements revealed that the influence of glycerol is more significant than that of any other osmolyte. The intrinsic fluorescence results showed that glycerol, proline, and sucrose stabilized the aminoacylase conformation effectively, with glycerol being the most effective. All 4 kinds of osmolytes reduced the exposure of the hydrophobic surface, indicating that osmolytes facilitate the formation of protein hydrophobic collapse. The CD results indicate that glycerol and sucrose facilitate the return of aminoacylase to its native secondary structure. The results of this study suggest that the ability of the various osmolytes to facilitate the refolding and renaturation of aminoacylase is not the same. A survey of the results in the literature, as well as those presented here, suggests that although the protective effect of osmolytes on protein activity and structure is equal for different osmolytes, the ability of osmolytes to facilitate the refolding of various proteins differs from case to case. In all cases, glycerol was found to be the best stabilizer and a folding aid.
Collapse
Affiliation(s)
- Sung-Hye Kim
- Laboratory of Molecular Enzymology, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, PR China
| | | | | |
Collapse
|
20
|
Huang H, Melacini G. High-resolution protein hydration NMR experiments: Probing how protein surfaces interact with water and other non-covalent ligands. Anal Chim Acta 2006; 564:1-9. [PMID: 17723356 DOI: 10.1016/j.aca.2005.10.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 10/13/2005] [Accepted: 10/20/2005] [Indexed: 10/25/2022]
Abstract
High-resolution solution NMR experiments are extremely useful to characterize the location and the dynamics of hydrating water molecules at atomic resolution. However, these methods are severely limited by undesired incoherent transfer pathways such as those arising from exchange-relayed intra-molecular cross-relaxation. Here, we review several complementary exchange network editing methods that can be used in conjunction with other types of NMR hydration experiments such as magnetic relaxation dispersion and 1J(NC') measurements to circumvent these limitations. We also review several recent contributions illustrating how the original solution hydration NMR pulse sequence architecture has inspired new approaches to map other types of non-covalent interactions going well beyond the initial scope of hydration. Specifically, we will show how hydration NMR methods have evolved and have been adapted to binding site mapping, ligand screening, protein-peptide and peptide-lipid interaction profiling.
Collapse
Affiliation(s)
- Hao Huang
- Department of Chemistry, McMaster University, 1280 Main Street, W. Hamilton, Ont., Canada L8S 4M1
| | | |
Collapse
|
21
|
Tjernberg A, Markova N, Griffiths WJ, Hallén D. DMSO-Related Effects in Protein Characterization. ACTA ACUST UNITED AC 2005; 11:131-7. [PMID: 16490773 DOI: 10.1177/1087057105284218] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
DMSO is the standard solvent for preparing stock solutions of compounds for drug discovery. The assay concentration of DMSO is normally 0.1% to 5% (v/v) or 14 to 715 mM. Thus, DMSO is often one of the principal additives in assay buffers. This standardization of stock solutions does not eliminate possible pitfalls associated with the effects of the DMSO-containing solutions on individual proteins. In this article, the authors want to emphasize the importance of detailed studies of these effects in the early stages of drug discovery. Two protein systems, the extracellular soluble domain of the human growth hormone receptor (hGHbp) and the phosphatase domain of PFKFB1 (BPase), were used for the study on effects of DMSO on protein stability, protein aggregation, and binding of drug compounds. The study revealed significant differences in the proteins’ behavior in the presence and absence of low amounts of DMSO. The addition of DMSO resulted in destabilization of the proteins investigated and also changed the apparent binding property of 1 protein. The authors have also shown that low DMSO concentrations influence the ionization process in electrospray ionization mass spectrometry (ESI-MS).
Collapse
|
22
|
KORB JEANPIERRE, BRYANT ROBERTG. MAGNETIC RELAXATION DISPERSION IN POROUS AND DYNAMICALLY HETEROGENEOUS MATERIALS. ADVANCES IN INORGANIC CHEMISTRY 2005. [DOI: 10.1016/s0898-8838(05)57006-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
23
|
Modig K, Kurian E, Prendergast FG, Halle B. Water and urea interactions with the native and unfolded forms of a beta-barrel protein. Protein Sci 2004; 12:2768-81. [PMID: 14627737 PMCID: PMC2366985 DOI: 10.1110/ps.03262603] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A fundamental understanding of protein stability and the mechanism of denaturant action must ultimately rest on detailed knowledge about the structure, solvation, and energetics of the denatured state. Here, we use (17)O and (2)H magnetic relaxation dispersion (MRD) to study urea-induced denaturation of intestinal fatty acid-binding protein (I-FABP). MRD is among the few methods that can provide molecular-level information about protein solvation in native as well as denatured states, and it is used here to simultaneously monitor the interactions of urea and water with the unfolding protein. Whereas CD shows an apparently two-state transition, MRD reveals a more complex process involving at least two intermediates. At least one water molecule binds persistently (with residence time >10 nsec) to the protein even in 7.5 M urea, where the large internal binding cavity is disrupted and CD indicates a fully denatured protein. This may be the water molecule buried near the small hydrophobic folding core at the D-E turn in the native protein. The MRD data also provide insights about transient (residence time <1 nsec) interactions of urea and water with the native and denatured protein. In the denatured state, both water and urea rotation is much more retarded than for a fully solvated polypeptide. The MRD results support a picture of the denatured state where solvent penetrates relatively compact clusters of polypeptide segments.
Collapse
Affiliation(s)
- Kristofer Modig
- Department of Biophysical Chemistry, Lund University, SE-22100 Lund, Sweden
| | | | | | | |
Collapse
|
24
|
Abstract
Although the MRD method has a long record in biomolecular systems, it has undergone a renaissance in the past few years as methodological developments have provided access to new types of information. In particular, MRD studies of quadrupolar nuclei such as 17O and 23Na have yielded valuable insights about the interactions of proteins and oligonucleotides with their solvent environment. The biomolecular MRD literature is still dominated by hydration studies, but the method has also been used to study the interaction of organic cosolvents and inorganic counterions with biomolecules. The MRD method can potentially make important contributions to the understanding of the mechanisms whereby protein conformational stability is affected by nonaqueous solvent components, such as denaturants, stabilizers, and helix promoters. Residence times of water molecules and other low molecular weight species in association with biomolecules can be determined by MRD. Such residence times are of general interest for understanding the kinetics of biomolecule-ligand interactions and, when exchange is gated by the biomolecule, can be used to characterize large-scale conformational fluctuations on nanosecond-millisecond time scales. By monitoring the integrity and specific internal hydration sites as well as the global solvent exposure, the MRD method can also shed light on the structure and dynamics of biomolecules in fluctuating nonnative states. Because it does not rely on high resolution, the MRD method is also applicable to very large biomolecules and complexes and has even been used to investigate protein crystals, gels, and biological tissues. In fact, dynamic studies of solids and liquid crystals were among the earliest applications of the MRD method. In many of its diverse applications, the MRD method provides unique information, complementing that available from high-resolution NMR.
Collapse
Affiliation(s)
- B Halle
- Department of Physical Chemistry 2, Condensed Matter Magnetic Resonance Group, Lund University, S-221 00 Lund, Sweden
| | | |
Collapse
|
25
|
Korzun AM, Nurminsky VN, Rozinov SV, Salyaev RK. The effect of dimethylsulphoxide (DMSO) on the membrane conductivity of an isolated vacuole. DOKL BIOCHEM BIOPHYS 2001; 381:409-11. [PMID: 11813556 DOI: 10.1023/a:1013319714716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- A M Korzun
- Siberian Institute of Plant Physiology and Biochemistry, Russian Academy of Sciences, ul. Lermontova 132, Irkutsk, 664033 Russia
| | | | | | | |
Collapse
|
26
|
Schmitt L, Boniface JJ, Davis MM, McConnell HM. Conformational isomers of a class II MHC-peptide complex in solution. J Mol Biol 1999; 286:207-18. [PMID: 9931260 DOI: 10.1006/jmbi.1998.2463] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A number of kinetic measurements of peptide dissociation from class II MHC-peptide complexes provide compelling evidence for the existence of conformational isomers in solution. There is evidence that T-lymphocytes can distinguish such isomers. However, virtually nothing is known about the structure of these isomers. Accordingly, we have investigated a water-soluble version of the murine class II MHC molecule I-Ek complexed with an antigenic peptide derived from pigeon cytochrome c residues 89-104 (PCC) by 19F-NMR. Two fluorine labels were placed on the PCC peptide; one fluorine label was placed at a MHC contact site, the other at a position involved in T-cell receptor (TCR) recognition. Introduction of these labels did not alter the observed kinetics of the PCC/I-Ek complex. The NMR data show two conformational isomers of this immunogenic complex. The presence of conformational isomers at a TCR contact site suggests that these structures may be recognized differently by the TCR. The agreement between the dissociation kinetics and the 19F-NMR data demonstrate that kinetic heterogeneity is correlated with structural counterparts observed by NMR. Dissociations in the presence of dimethyl sulfoxide were used to show that the rate of interconversion of these conformational isomers at pH 7.0 is low, with a lifetime on the order of hours or more. Modification of a peptide residue of PCC occupying the minor MHC binding pocket P6 alters the 19F-NMR spectra of both labels. This demonstrates that distant changes of amino acid residues can influence the conformation of the whole antigenic peptide inside the MHC binding cleft.
Collapse
Affiliation(s)
- L Schmitt
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | | | | | | |
Collapse
|
27
|
Yu ZW, Quinn PJ. The modulation of membrane structure and stability by dimethyl sulphoxide (review). Mol Membr Biol 1998; 15:59-68. [PMID: 9724923 DOI: 10.3109/09687689809027519] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Dimethyl sulphoxide is a widely used agent in cell biology. It is well known as a cryoprotectant, cell fusogen and a permeability enhancing agent. These applications depend, to a greater or lesser extent, on the effect of dimethyl sulphoxide on the stability and dynamics of biomembranes. The aim of this review is to examine progress of the research which has been directed towards studies of the interactions between dimethyl sulphoxide and membranes, particularly that with the lipid components of cell membranes, as seen in its effects on model membrane systems. Models are proposed to explain the mechanism whereby dimethyl sulphoxide may mediate its effects on biological functions by its effects on the stability and properties of the membrane lipid matrix.
Collapse
Affiliation(s)
- Z W Yu
- Division of Life Sciences, King's College London, UK
| | | |
Collapse
|