201
|
Ferrie JJ, Ieda N, Haney CM, Walters CR, Sungwienwong I, Yoon J, Petersson EJ. Multicolor protein FRET with tryptophan, selective coumarin-cysteine labeling, and genetic acridonylalanine encoding. Chem Commun (Camb) 2018; 53:11072-11075. [PMID: 28948265 DOI: 10.1039/c7cc05492k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Site-specific fluorescence probes can be used to measure distances within proteins when used as part of a Förster resonance energy transfer (FRET) pair. Here we report the synthesis of a coumarin maleimide (Mcm-Mal) that is fluorogenic upon reaction with cysteine. We demonstrate that cysteine, acridonylalanine (Acd) double mutant proteins can be produced by unnatural amino acid mutagenesis and reacted with Mcm-Mal to generate Mcm/Acd labeled proteins for FRET studies. The Mcm/Acd FRET pair is minimally-perturbing, easy to install, and well-suited to studying protein distances in the 15-40 Å range. Furthermore, Mcm/Acd labeling can be combined with tryptophan fluorescence in three color FRET to monitor multiple interactions in one experiment.
Collapse
Affiliation(s)
- John J Ferrie
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | | | | | | | | | | | | |
Collapse
|
202
|
Su Z, Ravindhran G, Dias CL. Effects of Trimethylamine-N-oxide (TMAO) on Hydrophobic and Charged Interactions. J Phys Chem B 2018; 122:5557-5566. [DOI: 10.1021/acs.jpcb.7b11847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Zhaoqian Su
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| | - Gopal Ravindhran
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| | - Cristiano L. Dias
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| |
Collapse
|
203
|
Nayar D, van der Vegt NFA. Cosolvent Effects on Polymer Hydration Drive Hydrophobic Collapse. J Phys Chem B 2018; 122:3587-3595. [PMID: 29443520 DOI: 10.1021/acs.jpcb.7b10780] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Water-mediated hydrophobic interactions play an important role in self-assembly processes, aqueous polymer solubility, and protein folding, to name a few. Cosolvents affect these interactions; however, the implications for hydrophobic polymer collapse and protein folding equilibria are not well-understood. This study examines cosolvent effects on the hydrophobic collapse equilibrium of a generic 32-mer hydrophobic polymer in urea, trimethylamine- N-oxide (TMAO), and acetone aqueous solutions using molecular dynamics simulations. Our results unveil a remarkable cosolvent-concentration-dependent behavior. Urea, TMAO, and acetone all shift the equilibrium toward collapsed structures below 2 M cosolvent concentration and, in turn, to unfolded structures at higher cosolvent concentrations, irrespective of the differences in cosolvent chemistry and the nature of cosolvent-water interactions. We find that weakly attractive polymer-water van der Waals interactions oppose polymer collapse in pure water, corroborating related observations reviewed by Ben-Amotz ( Annu. Rev. Phys. Chem. 2016, 67, 617-638). The cosolvents studied in the present work adsorb at the polymer/water interface and expel water molecules into the bulk, thereby effectively removing the dehydration energy penalty that opposes polymer collapse in pure water. At low cosolvent concentrations, this leads to cosolvent-induced stabilization of collapsed polymer structures. Only at sufficiently high cosolvent concentrations, polymer-cosolvent interactions favor polymer unfolding.
Collapse
Affiliation(s)
- Divya Nayar
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces , Technische Universität Darmstadt , Alarich-Weiss-Strasse 10 , 64287 , Darmstadt , Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Center of Smart Interfaces , Technische Universität Darmstadt , Alarich-Weiss-Strasse 10 , 64287 , Darmstadt , Germany
| |
Collapse
|
204
|
Diddens D, Lesch V, Heuer A, Smiatek J. Aqueous ionic liquids and their influence on peptide conformations: denaturation and dehydration mechanisms. Phys Chem Chem Phys 2018; 19:20430-20440. [PMID: 28737791 DOI: 10.1039/c7cp02897k] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Low concentrated aqueous ionic liquids (ILs) and their influence on protein structures have attracted a lot of interest over the last few years. This can be mostly attributed to the fact that aqueous ILs, depending on the ion species involved, can be used as protein protectants or protein denaturants. Atomistic molecular dynamics (MD) simulations are performed in order to study the influence of different aprotic ILs on the properties of a short hairpin peptide. Our results reveal distinct binding and denaturation effects for 1-ethyl-3-methylimidazolium (EMIM) in combination with different anions, namely, chloride (CL), tetrafluoroborate (BF4) and acetate (ACE). The simulation outcomes demonstrate that the studied ILs with larger anions reveal a more pronounced accumulation behavior of the individual ion species around the peptide, which is accomplished by a stronger dehydration effect. We can relate these findings to the implications of the Kirkwood-Buff theory, which provides a thermodynamic explanation for the denaturation strength in terms of the IL accumulation behavior. The results for the spatial distribution functions, the binding energies and the local/bulk partition coefficients are in good agreement with metadynamics simulations in order to determine the energetically most stable peptide conformations. The free energy landscapes indicate a decrease of the denaturation strength in the order EMIM/ACE, EMIM/BF4 and EMIM/CL, which coincides with a decreasing size of the anion species. An analysis of the potential binding energies reveals that this effect is mainly of enthalpic nature.
Collapse
Affiliation(s)
- Diddo Diddens
- Institute of Physical Chemistry, University of Münster, Corrensstrasse 28/30, 48149 Münster, Germany
| | | | | | | |
Collapse
|
205
|
Al-Ayoubi SR, Schummel PH, Golub M, Peters J, Winter R. Influence of cosolvents, self-crowding, temperature and pressure on the sub-nanosecond dynamics and folding stability of lysozyme. Phys Chem Chem Phys 2018; 19:14230-14237. [PMID: 28447688 DOI: 10.1039/c7cp00705a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We studied the effects of temperature and hydrostatic pressure on the dynamical properties and folding stability of highly concentrated lysozyme solutions in the absence and presence of the osmolytes trimethylamine-N-oxide (TMAO) and urea. Elastic incoherent neutron scattering (EINS) was applied to determine the mean-squared displacement (MSD) of the protein's hydrogen atoms to yield insights into the effects of these cosolvents on the averaged sub-nanosecond dynamics in the pressure range from ambient up to 4000 bar. To evaluate the additional effect of self-crowding, two protein concentrations (80 and 160 mg mL-1) were used. We observed a distinct effect of TMAO on the internal hydrogen dynamics, namely a reduced mobility. Urea, on the other hand, revealed no marked effect and consequently, no counteracting effect in an urea-TMAO mixture was observed. Different from the less concentrated protein solution, no significant effect of pressure on the MSD was observed for 160 mg mL-1 lysozyme. The EINS experiments were complemented by Fourier-transform infrared (FTIR) spectroscopy measurements, which led to additional insights into the folding stability of lysozyme under the various environmental conditions. We observed a stabilization of the protein in the presence of the compatible osmolyte TMAO and a destabilization in the presence of urea against temperature and pressure for both protein concentrations. Additionally, we noticed a slight destabilizing effect upon self-crowding at very high protein concentration (160 mg mL-1), which is attributable to transient destabilizing intermolecular interactions. Furthermore, a pressure-temperature diagram could be obtained for lysozyme at these high protein concentrations that mimics densely packed intracellular conditions.
Collapse
Affiliation(s)
- S R Al-Ayoubi
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
| | | | | | | | | |
Collapse
|
206
|
Meti MD, Dixit MK, Tembe BL. Salting-in of neopentane in the aqueous solutions of urea and glycine-betaine. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1431834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manjunath D. Meti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Mayank K. Dixit
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Bhalachandra L. Tembe
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| |
Collapse
|
207
|
Remsing RC, Xi E, Patel AJ. Protein Hydration Thermodynamics: The Influence of Flexibility and Salt on Hydrophobin II Hydration. J Phys Chem B 2018; 122:3635-3646. [DOI: 10.1021/acs.jpcb.7b12060] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard C. Remsing
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Erte Xi
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Amish J. Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
208
|
The opposing effect of urea and high pressure on the conformation of the protein β-hairpin: A molecular dynamics simulation study. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.12.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
209
|
Hall D, Kinjo AR, Goto Y. A new look at an old view of denaturant induced protein unfolding. Anal Biochem 2018; 542:40-57. [DOI: 10.1016/j.ab.2017.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/11/2017] [Accepted: 11/16/2017] [Indexed: 12/15/2022]
|
210
|
Budkov YA, Kiselev MG. Flory-type theories of polymer chains under different external stimuli. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:043001. [PMID: 29271365 DOI: 10.1088/1361-648x/aa9f56] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this Review, we present a critical analysis of various applications of the Flory-type theories to a theoretical description of the conformational behavior of single polymer chains in dilute polymer solutions under a few external stimuli. Different theoretical models of flexible polymer chains in the supercritical fluid are discussed and analysed. Different points of view on the conformational behavior of the polymer chain near the liquid-gas transition critical point of the solvent are presented. A theoretical description of the co-solvent-induced coil-globule transitions within the implicit-solvent-explicit-co-solvent models is discussed. Several explicit-solvent-explicit-co-solvent theoretical models of the coil-to-globule-to-coil transition of the polymer chain in a mixture of good solvents (co-nonsolvency) are analysed and compared with each other. Finally, a new theoretical model of the conformational behavior of the dielectric polymer chain under the external constant electric field in the dilute polymer solution with an explicit account for the many-body dipole correlations is discussed. The polymer chain collapse induced by many-body dipole correlations of monomers in the context of statistical thermodynamics of dielectric polymers is analysed.
Collapse
Affiliation(s)
- Yu A Budkov
- Tikhonov Moscow Institute of Electronics and Mathematics, School of Applied Mathematics, National Research University Higher School of Economics, Moscow, Russia. Laboratory of NMR Spectroscopy and Numerical Investigations of Liquids, G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo, Russia
| | | |
Collapse
|
211
|
Remsing RC, Duignan TT, Baer MD, Schenter GK, Mundy CJ, Weeks JD. Water Lone Pair Delocalization in Classical and Quantum Descriptions of the Hydration of Model Ions. J Phys Chem B 2018; 122:3519-3527. [DOI: 10.1021/acs.jpcb.7b10722] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard C. Remsing
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Timothy T. Duignan
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Marcel D. Baer
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Gregory K. Schenter
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Christopher J. Mundy
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States
- Affiliate Professor, Department of Chemical Engineering, University of Washington, Seattle, Washington, United States
| | - John D. Weeks
- Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
212
|
Senske M, Constantinescu-Aruxandei D, Havenith M, Herrmann C, Weingärtner H, Ebbinghaus S. The temperature dependence of the Hofmeister series: thermodynamic fingerprints of cosolute-protein interactions. Phys Chem Chem Phys 2018; 18:29698-29708. [PMID: 27806138 DOI: 10.1039/c6cp05080h] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Hofmeister series is a universal homologous series to rank ion-specific effects on biomolecular properties such as protein stability or aggregation propensity. Although this ranking is widely used, outliers and exceptions are discussed controversially and a molecular level understanding is still lacking. Studying the thermal unfolding equilibrium of RNase A, we here show that this ambiguity arises from the oversimplified approach to determine the ion rankings. Instead of measuring salt effects on a single point of the protein folding stability curve (e.g. the melting point Tm), we here consider the salt induced shifts of the entire protein 'stability curve' (the temperature dependence of the unfolding free energy change, ΔGu(T)). We found multiple intersections of these curves, pinpointing a widely ignored fact: the Hofmeister cation and anion rankings are temperature dependent. We further developed a novel classification scheme of cosolute effects based on their thermodynamic fingerprints, reaching beyond salt effects to non-electrolytes.
Collapse
Affiliation(s)
- Michael Senske
- Department of Physical Chemistry II, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | | | - Martina Havenith
- Department of Physical Chemistry II, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Christian Herrmann
- Department of Physical Chemistry I, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Hermann Weingärtner
- Department of Physical Chemistry II, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Simon Ebbinghaus
- Department of Physical Chemistry II, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| |
Collapse
|
213
|
Hahn MB, Uhlig F, Solomun T, Smiatek J, Sturm H. Combined influence of ectoine and salt: spectroscopic and numerical evidence for compensating effects on aqueous solutions. Phys Chem Chem Phys 2018; 18:28398-28402. [PMID: 27722327 DOI: 10.1039/c6cp05417j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ectoine is an important osmolyte, which allows microorganisms to survive in extreme environmental salinity. The hygroscopic effects of ectoine in pure water can be explained by a strong water binding behavior whereas a study on the effects of ectoine in salty solution is yet missing. We provide Raman spectroscopic evidence that the influence of ectoine and NaCl are opposing and completely independent of each other. The effect can be explained by the formation of strongly hydrogen-bonded water molecules around ectoine which compensate the influence of the salt on the water dynamics. The mechanism is corroborated by first principles calculations and broadens our understanding of zwitterionic osmolytes in aqueous solution. Our findings allow us to provide a possible explanation for the relatively high osmolyte concentrations in halotolerant bacteria.
Collapse
Affiliation(s)
- Marc Benjamin Hahn
- Federal Institute for Materials Research and Testing, D-12205 Berlin, Germany. and Free University Berlin, Department of Physics, D-14195 Berlin, Germany
| | - Frank Uhlig
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.
| | - Tihomir Solomun
- Federal Institute for Materials Research and Testing, D-12205 Berlin, Germany.
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany.
| | - Heinz Sturm
- Federal Institute for Materials Research and Testing, D-12205 Berlin, Germany. and Technical University Berlin, D-10587 Berlin, Germany
| |
Collapse
|
214
|
Zhang X, Zhang L, Jin T, Zhang Q, Zhuang W. Cosolvent effect on the dynamics of water in aqueous binary mixtures. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1424958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Xia Zhang
- Department of Chemistry, Bohai University, Jinzhou, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Tan Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Qiang Zhang
- Department of Chemistry, Bohai University, Jinzhou, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| |
Collapse
|
215
|
Rezaie M, Aminzadeh S, Heidari F, Mashhadi Akbar Boojar M, Karkhane AA. Biochemical Characterization of Recombinant Thermostable Cohnella sp. A01 β-Glucanase. IRANIAN BIOMEDICAL JOURNAL 2018; 22:345-54. [PMID: 29331014 PMCID: PMC6058188 DOI: 10.29252/ibj.22.5.345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Background Typically, non-cellulytic glucanase, including fungi and yeast cell wall hydrolyzing enzymes, are released by some symbiotic fungi and plants during the mycoparasitic fungi attack on plants. These enzymes are known as the defense mechanisms of plants. This study intends to investigate the biochemical properties of β-1,6-glucanase (bg16M) from native thermophilic bacteria, Cohnella A01. Methods bg16M gene was cloned and expressed in E. coli BL21 (DE3). The enzyme was purified utilizing Ni-NTA nikcle sepharose column. Pustulan and laminarin were selected as substrates in enzyme assay. The purified bg16M enzyme was treated with different pH, temperature, metal ions, and detergents. Results The expressed protein, including 639 amino acids, showed a high similarity with the hydrolytic glycosylated family 30. The molecular weight of enzyme was 64 kDa, and purification yield was 46%. The bg16M demonstrated activity as 4.83 U/ml on laminarin and 2.88 U/ml on pustulan. The optimum pH and temperature of the enzyme were 8 and 50 °C, respectively. The enzyme had an appropriate stability at high temperatures and in the pH range of 7 to 9, showing acceptable stability, while it did not lose enzymatic activity completely at acidic or basic pH. None of the studied metal ions and chemical compounds was the activator of bg16M, and urea, SDS, and copper acted as enzyme inhibitors. Conclusion Biochemical characterization of this enzyme revealed that bg16M can be applied in beverage industries and medical sectors because of its high activity, as well as thermal and alkaline stability.
Collapse
Affiliation(s)
- Meysam Rezaie
- National Institute for Genetic Engineering and Biotechnology (NIGEB), Institute of Industrial and Environmental Biotechnology, Bioprocess Engineering Research Group, Shahrak-E-Pajoohesh km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran.,Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Saeed Aminzadeh
- National Institute for Genetic Engineering and Biotechnology (NIGEB), Institute of Industrial and Environmental Biotechnology, Bioprocess Engineering Research Group, Shahrak-E-Pajoohesh km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
| | - Farid Heidari
- National Institute for Genetic Engineering and Biotechnology (NIGEB), Institute of Agricultural Biotechnology, Animal Biotechnology Department, Shahrak-E-Pajoohesh km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
| | | | - Ali Asghar Karkhane
- National Institute for Genetic Engineering and Biotechnology (NIGEB), Institute of Industrial and Environmental Biotechnology, Bioprocess Engineering Research Group, Shahrak-E-Pajoohesh km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
| |
Collapse
|
216
|
Effects of Cosolvents and Macromolecular Crowding on the Phase Transitions and Temperature-Pressure Stability of Chiral and Racemic Poly-Lysine. Z PHYS CHEM 2018. [DOI: 10.1515/zpch-2017-1012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abstract
FTIR spectroscopy has been used to reveal the effects of different types of cosolvents (TMAO, urea) as well as macromolecular crowding (using the crowding agent Ficoll) on the temperature and pressure dependent structure of poly-L-lysine, poly-D-lysine and their racemic mixture. Compared to the effects of cosolvents on the unfolding transition of proteins, their effects on the α-helix to aggregated β-sheet transition of polylysine are quite small. High hydrostatic pressure has been found to favor the α-helical state over the aggregated β-sheet structure which is reflected in a volume decrease of ΔV=−32 mL mol−1, indicating that the packing mode is more efficient in the α-helical structure. Both, addition of urea and TMAO lead to a decrease in pressure stability of the aggregated β-sheet structure, which is accompanied by a three-fold decrease in ΔV, whereas the macromolecular crowder has little effect on the β-to-α transition. The more than 3 kbar higher β-to-α transition pressure of the racemic mixture compared with PLL confirms the drastic stabilization of β-sheet aggregates if the stereoisomers PLL and PDL are combined. Changes in hydration and packing of the polypeptide occurs upon interaction and fine packing of the polypeptide’s chains of opposed chirality, which are slightly modulated by the properties of cosolute and crowding, only. The underlying solvational and packing mechanisms observed here may be decisive factors responsible for the spontaneous protein aggregation in general and, as such, may shed additional light on the molecular basis of amyloid-associated diseases.
Collapse
|
217
|
Aqueous ionic liquids influence the disulfide bond isoform equilibrium in conotoxin AuIB: a consequence of the Hofmeister effect? Biophys Rev 2018; 10:769-780. [PMID: 29294259 DOI: 10.1007/s12551-017-0391-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/13/2017] [Indexed: 12/13/2022] Open
Abstract
The appearance of several disulfide bond isoforms in multiple cysteine containing venom peptides poses a significant challenge in their synthesis and purification under laboratory conditions. Recent experiments suggest that careful tuning of solvent and temperature conditions can propel the disulfide bond isoform equilibrium in favor of the most potent, native form. Certain aqueous ionic liquids (ILs) have proven significantly useful as solvents for this purpose, while exceptions have also been noted. To elucidate the molecular level origin behind such a preference, we report a detailed explicit solvent replica exchange molecular dynamics study of a conotoxin, AuIB, in pure water and four different aqueous IL solutions (~45-60% v/v). The ILs studied here are comprised of cations like 1-ethyl-3-methyl-imidazolium (Im21+) or 1-butyl-3-methyl-imidazolium (Im41+) coupled with either acetate (OAc-) or chloride (Cl-) as the counter anion. Our simulations unfold interesting features of the conformational spaces sampled by the peptide and its solvation in pure water and aqueous IL solutions. Detailed investigation into populations of the globular disulfide bond isoform of AuIB in aqueous IL solutions reveal distinct trends which might be related to the Hofmeister effect of the cation and anion of the IL and of specific interactions of the aqueous IL solutions with the peptide. In accordance with experimental observations, the aqueous [Im21][OAc] solution is found to promote the highest globular isoform population in AuIB.
Collapse
|
218
|
Rani A, Venkatesu P. Changing relations between proteins and osmolytes: a choice of nature. Phys Chem Chem Phys 2018; 20:20315-20333. [DOI: 10.1039/c8cp02949k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stabilization and destabilization of the protein in the presence of any additive is mainly attributed to its preferential exclusion from protein surface and its preferential binding to the protein surface, respectively.
Collapse
Affiliation(s)
- Anjeeta Rani
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
| | | |
Collapse
|
219
|
Oprzeska-Zingrebe EA, Meyer S, Roloff A, Kunte HJ, Smiatek J. Influence of compatible solute ectoine on distinct DNA structures: thermodynamic insights into molecular binding mechanisms and destabilization effects. Phys Chem Chem Phys 2018; 20:25861-25874. [DOI: 10.1039/c8cp03543a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study ectoine-induced destabilization effects on DNA hairpins by a combination of atomistic molecular dynamics simulations, experiments, and theoretical approaches.
Collapse
Affiliation(s)
| | - Susann Meyer
- Federal Institute for Materials Research and Testing (BAM)
- D-12205 Berlin
- Germany
- Institute of Biochemistry and Biology
- University of Potsdam
| | - Alexander Roloff
- Federal Institute for Materials Research and Testing (BAM)
- D-12489 Berlin
- Germany
| | - Hans-Jörg Kunte
- Federal Institute for Materials Research and Testing (BAM)
- D-12205 Berlin
- Germany
| | - Jens Smiatek
- Institute for Computational Physics
- University of Stuttgart
- D-70569 Stuttgart
- Germany
- Helmholtz Institute Münster: Ionics in Energy Storage (HI MS IEK-12)
| |
Collapse
|
220
|
Jaworek MW, Schuabb V, Winter R. The effects of glycine, TMAO and osmolyte mixtures on the pressure dependent enzymatic activity of α-chymotrypsin. Phys Chem Chem Phys 2018; 20:1347-1354. [DOI: 10.1039/c7cp06042d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different natural osmolytes modulate the pressure dependent enzyme kinetics in different ways.
Collapse
Affiliation(s)
- Michel W. Jaworek
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Vitor Schuabb
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| |
Collapse
|
221
|
Imoto S, Forbert H, Marx D. Aqueous TMAO solutions as seen by theoretical THz spectroscopy: hydrophilic versus hydrophobic water. Phys Chem Chem Phys 2018; 20:6146-6158. [DOI: 10.1039/c7cp07003a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
All THz resonances of aqueous TMAO solutions are computed and assigned based on ab initio molecular dynamics simulations.
Collapse
Affiliation(s)
- Sho Imoto
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Harald Forbert
- Center for Solvation Science ZEMOS
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| |
Collapse
|
222
|
Schummel PH, Jaworek MW, Rosin C, Högg J, Winter R. Exploring the influence of natural cosolvents on the free energy and conformational landscape of filamentous actin and microtubules. Phys Chem Chem Phys 2018; 20:28400-28411. [DOI: 10.1039/c8cp03041c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural osmolytes have a significant influence on the temperature- and pressure-dependent stability of filamentous actin and microtubules.
Collapse
Affiliation(s)
- Paul Hendrik Schummel
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Michel W. Jaworek
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Christopher Rosin
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Jessica Högg
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| |
Collapse
|
223
|
Sahle CJ, Schroer MA, Jeffries CM, Niskanen J. Hydration in aqueous solutions of ectoine and hydroxyectoine. Phys Chem Chem Phys 2018; 20:27917-27923. [DOI: 10.1039/c8cp05308a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We explore the influence of the two osmolytes ectoine and hydroxyectoine on the structure of pure water and aqueous NaCl solutions using non-resonant X-ray Raman scattering spectroscopy at the oxygen K-edge.
Collapse
Affiliation(s)
- Christoph J. Sahle
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs
- 38000 Grenoble
- France
| | - Martin A. Schroer
- European Molecular Biology Laboratory (EMBL)
- Hamburg Outstation c/o DESY
- 22607 Hamburg
- Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL)
- Hamburg Outstation c/o DESY
- 22607 Hamburg
- Germany
| | - Johannes Niskanen
- University of Turku
- Department of Physics and Astronomy
- FI-20014 Turun yliopisto
- Finland
| |
Collapse
|
224
|
Ganguly P, Boserman P, van der Vegt NFA, Shea JE. Trimethylamine N-oxide Counteracts Urea Denaturation by Inhibiting Protein–Urea Preferential Interaction. J Am Chem Soc 2017; 140:483-492. [DOI: 10.1021/jacs.7b11695] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pritam Ganguly
- Department
of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Pablo Boserman
- Department
of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut
für Anorganische und Physikalische Chemie, Center of Smart
Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße
10, Darmstadt 64287, Germany
| | - Joan-Emma Shea
- Department
of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
- Department
of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| |
Collapse
|
225
|
The Effect of Natural Osmolyte Mixtures on the Temperature-Pressure Stability of the Protein RNase A. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/zpch-2017-1039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In biological cells, osmolytes appear as complex mixtures with variable compositions, depending on the particular environmental conditions of the organism. Based on various spectroscopic, thermodynamic and small-angle scattering data, we explored the effect of two different natural osmolyte mixtures, which are found in shallow-water and deep-sea shrimps, on the temperature and pressure stability of a typical monomeric protein, RNase A. Both natural osmolyte mixtures stabilize the protein against thermal and pressure denaturation. This effect seems to be mainly caused by the major osmolyte components of the osmolyte mixtures, i.e. by glycine and trimethylamine-N-oxide (TMAO), respectively. A minor compaction of the structure, in particular in the unfolded state, seems to be largely due to TMAO. Differences in thermodynamic properties observed for glycine and TMAO, and hence also for the two osmolyte mixtures, are most likely due to different solvation properties and interactions with the protein. Different from TMAO, glycine seems to interact with the amino acid side chains and/or the backbone of the protein, thus competing with hydration water and leading to a less hydrated protein surface.
Collapse
|
226
|
Stirnemann G, Duboué-Dijon E, Laage D. Ab Initio Simulations of Water Dynamics in Aqueous TMAO Solutions: Temperature and Concentration Effects. J Phys Chem B 2017; 121:11189-11197. [PMID: 29200289 DOI: 10.1021/acs.jpcb.7b09989] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use ab initio molecular dynamics simulation to study the effect of hydrophobic groups on the dynamics of water molecules in aqueous solutions of trimethylamine N-oxide (TMAO). We show that hydrophobic groups induce a moderate (<2-fold) slowdown of water reorientation and hydrogen-bond dynamics in dilute solutions, but that this slowdown rapidly increases with solute concentration. In addition, the slowdown factor is found to vary very little with temperature, thus suggesting an entropic origin. All of these results are in quantitative agreement with prior classical molecular dynamics simulations and with the previously suggested excluded-volume model. The hydrophilic TMAO headgroup is found to affect water dynamics more strongly than the hydrophobic moiety, and the magnitude of this slowdown is very sensitive to the strength of the water-solute hydrogen-bond.
Collapse
Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Univ. Paris Diderot, Sorbonne Paris Cité, PSL Research University , 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Elise Duboué-Dijon
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS , 75005 Paris, France
| | - Damien Laage
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS , 75005 Paris, France
| |
Collapse
|
227
|
Jamal S, Kumari A, Singh A, Goyal S, Grover A. Conformational Ensembles of α-Synuclein Derived Peptide with Different Osmolytes from Temperature Replica Exchange Sampling. Front Neurosci 2017; 11:684. [PMID: 29270108 PMCID: PMC5725442 DOI: 10.3389/fnins.2017.00684] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/22/2017] [Indexed: 11/13/2022] Open
Abstract
Intrinsically disordered proteins (IDP) are a class of proteins that do not have a stable three-dimensional structure and can adopt a range of conformations playing various vital functional role. Alpha-synuclein is one such IDP which can aggregate into toxic protofibrils and has been associated largely with Parkinson's disease (PD) along with other neurodegenerative diseases. Osmolytes are small organic compounds that can alter the environment around the proteins by acting as denaturants or protectants for the proteins. In the present study, we have conducted a series of replica exchange molecular dynamics simulations to explore the role of osmolytes, urea which is a denaturant and TMAO (trimethylamine N-oxide), a protecting osmolyte, in aggregation and conformations of the synuclein peptide. We observed that both the osmolytes have significantly distinct impacts on the peptide and led to transitions of the conformations of the peptide from one state to other. Our findings highlighted that urea attenuated peptide aggregation and resulted in the formation of extended peptide structures whereas TMAO led to compact and folded forms of the peptide.
Collapse
Affiliation(s)
- Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, India
| | - Anchala Kumari
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi, India
| | - Aditi Singh
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi, India
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
228
|
Stepanian L, Son I, Chalikian TV. Effect of urea on protein-ligand association. Biophys Chem 2017; 231:15-19. [DOI: 10.1016/j.bpc.2016.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 11/26/2022]
|
229
|
Martínez L, Shimizu S. Molecular Interpretation of Preferential Interactions in Protein Solvation: A Solvent-Shell Perspective by Means of Minimum-Distance Distribution Functions. J Chem Theory Comput 2017; 13:6358-6372. [DOI: 10.1021/acs.jctc.7b00599] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leandro Martínez
- Institute of Chemistry and Center for Computational Engineering & Science, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Seishi Shimizu
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10
5DD, U.K
| |
Collapse
|
230
|
Markthaler D, Zeman J, Baz J, Smiatek J, Hansen N. Validation of Trimethylamine-N-oxide (TMAO) Force Fields Based on Thermophysical Properties of Aqueous TMAO Solutions. J Phys Chem B 2017; 121:10674-10688. [DOI: 10.1021/acs.jpcb.7b07774] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Daniel Markthaler
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Johannes Zeman
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Jörg Baz
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Jens Smiatek
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering and ‡Institute for Computational
Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| |
Collapse
|
231
|
Anikeenko A, Kadtsyn E, Medvedev N. Statistical geometry characterization of global structure of TMAO and TBA aqueous solutions. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
232
|
Goyal S, Chattopadhyay A, Kasavajhala K, Priyakumar UD. Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State. J Am Chem Soc 2017; 139:14931-14946. [DOI: 10.1021/jacs.7b05463] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Siddharth Goyal
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Aditya Chattopadhyay
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Koushik Kasavajhala
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| |
Collapse
|
233
|
van der Vegt NFA, Nayar D. The Hydrophobic Effect and the Role of Cosolvents. J Phys Chem B 2017; 121:9986-9998. [DOI: 10.1021/acs.jpcb.7b06453] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nico F. A. van der Vegt
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Divya Nayar
- Eduard-Zintl-Institut für
Anorganische und Physikalische Chemie, Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| |
Collapse
|
234
|
Gao M, Held C, Patra S, Arns L, Sadowski G, Winter R. Crowders and Cosolvents-Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses. Chemphyschem 2017; 18:2951-2972. [DOI: 10.1002/cphc.201700762] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/15/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mimi Gao
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Christoph Held
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Satyajit Patra
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Loana Arns
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Gabriele Sadowski
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Roland Winter
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| |
Collapse
|
235
|
Su Z, Mahmoudinobar F, Dias CL. Effects of Trimethylamine-N-oxide on the Conformation of Peptides and its Implications for Proteins. PHYSICAL REVIEW LETTERS 2017; 119:108102. [PMID: 28949191 DOI: 10.1103/physrevlett.119.108102] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 05/16/2023]
Abstract
To provide insights into the stabilizing mechanisms of trimethylamine-N-oxide (TMAO) on protein structures, we perform all-atom molecular dynamics simulations of peptides and the Trp-cage miniprotein. The effects of TMAO on the backbone and charged residues of peptides are found to stabilize compact conformations, whereas effects of TMAO on nonpolar residues lead to peptide swelling. This suggests competing mechanisms of TMAO on proteins, which accounts for hydrophobic swelling, backbone collapse, and stabilization of charge-charge interactions. These mechanisms are observed in Trp cage.
Collapse
Affiliation(s)
- Zhaoqian Su
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Farbod Mahmoudinobar
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Cristiano L Dias
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| |
Collapse
|
236
|
Hausrath AC, Kingston RL. Conditionally disordered proteins: bringing the environment back into the fold. Cell Mol Life Sci 2017; 74:3149-3162. [PMID: 28597298 PMCID: PMC11107710 DOI: 10.1007/s00018-017-2558-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/01/2017] [Indexed: 12/19/2022]
Abstract
For many proteins, biological function requires the folding of the polypeptide chain into a unique and persistent tertiary structure. This review concerns proteins that adopt a specific tertiary structure to function, but are otherwise partially or completely disordered. The biological cue for protein folding is environmental perturbation or minor post-translational modification. Hence, we term these proteins conditionally disordered. Many of these proteins recognize and bind other molecules, and conditional disorder has been hypothesized to allow for more nuanced control and regulation of binding processes. However, this remains largely unproven. The sequences of conditionally disordered proteins suggest their propensity to fold; yet, under the standard laboratory conditions, they do not do so, which may appear surprising. We argue that the surprise results from the failure to consider the role of the environment in protein structure formation and that conditional disorder arises as a natural consequence of the marginal stability of the folded state.
Collapse
Affiliation(s)
- Andrew C Hausrath
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand.
| |
Collapse
|
237
|
Jethva PN, Udgaonkar JB. Modulation of the Extent of Cooperative Structural Change During Protein Folding by Chemical Denaturant. J Phys Chem B 2017; 121:8263-8275. [DOI: 10.1021/acs.jpcb.7b04473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Prashant N. Jethva
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| |
Collapse
|
238
|
Papini CM, Pandharipande PP, Royer CA, Makhatadze GI. Putting the Piezolyte Hypothesis under Pressure. Biophys J 2017; 113:974-977. [PMID: 28803626 DOI: 10.1016/j.bpj.2017.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/15/2017] [Accepted: 07/25/2017] [Indexed: 12/01/2022] Open
Abstract
A group of small molecules that stabilize proteins against high hydrostatic pressure has been classified as piezolytes, a subset of stabilizing cosolutes. This distinction would imply that piezolytes counteract the effects of high hydrostatic pressure through effects on the volumetric properties of the protein. The purpose of this study was to determine if cosolutes proposed to be piezolytes have an effect on the volumetric properties of proteins through direct experimental measurements of volume changes upon unfolding of model proteins lysozyme and ribonuclease A, in solutions containing varying cosolute concentrations. Solutions containing the proposed piezolytes glutamate, sarcosine, and betaine were used, as well as solutions containing the denaturants guanidinium hydrochloride and urea. Changes in thermostability were monitored using differential scanning calorimetry whereas changes in volume were monitored using pressure perturbation calorimetry. Our findings indicate that increasing stabilizing cosolute concentration increases the stability and transition temperature of the protein, but does not change the temperature dependence of volume changes upon unfolding. The results suggest that the pressure stability of a protein in solution is not directly affected by the presence of these proposed piezolytes, and so they cannot be granted this distinction.
Collapse
Affiliation(s)
- Christina M Papini
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - Pranav P Pandharipande
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Catherine A Royer
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York.
| |
Collapse
|
239
|
Amin MA, Halder R, Ghosh C, Jana B, Bhattacharyya K. Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations. J Chem Phys 2017; 145:235102. [PMID: 28010091 DOI: 10.1063/1.4972065] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Effect of ethanol on the size and structure of a protein cytochrome C (Cyt C) is investigated using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. For FCS studies, Cyt C is covalently labeled with a fluorescent probe, alexa 488. FCS studies indicate that on addition of ethanol, the size of the protein varies non-monotonically. The size of Cyt C increases (i.e., the protein unfolds) on addition of alcohol (ethanol) up to a mole fraction of 0.2 (44.75% v/v) and decreases at higher alcohol concentration. In order to provide a molecular origin of this structural transition, we explore the conformational free energy landscape of Cyt C as a function of radius of gyration (Rg) at different compositions of water-ethanol binary mixture using MD simulations. Cyt C exhibits a minimum at Rg ∼ 13 Å in bulk water (0% alcohol). Upon increasing ethanol concentration, a second minimum appears in the free energy surface with gradually larger Rg up to χEtOH ∼ 0.2 (44.75% v/v). This suggests gradual unfolding of the protein. At a higher concentration of alcohol (χEtOH > 0.2), the minimum at large Rg vanishes, indicating compaction. Analysis of the contact map and the solvent organization around protein indicates a preferential solvation of the hydrophobic residues by ethanol up to χEtOH = 0.2 (44.75% v/v) and this causes the gradual unfolding of the protein. At high concentration (χEtOH = 0.3 (58% v/v)), due to structural organization in bulk water-ethanol binary mixture, the extent of preferential solvation by ethanol decreases. This causes a structural transition of Cyt C towards a more compact state.
Collapse
Affiliation(s)
- Md Asif Amin
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Catherine Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| |
Collapse
|
240
|
Cheng X, Shkel IA, O'Connor K, Henrich J, Molzahn C, Lambert D, Record MT. Experimental Atom-by-Atom Dissection of Amide-Amide and Amide-Hydrocarbon Interactions in H 2O. J Am Chem Soc 2017; 139:9885-9894. [PMID: 28678492 PMCID: PMC5580340 DOI: 10.1021/jacs.7b03261] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Quantitative information about amide interactions in water is needed to understand their contributions to protein folding and amide effects on aqueous processes and to compare with computer simulations. Here we quantify interactions of urea, alkylated ureas, and other amides by osmometry and amide-aromatic hydrocarbon interactions by solubility. Analysis of these data yields strengths of interaction of ureas and naphthalene with amide sp2O, amide sp2N, aliphatic sp3C, and amide and aromatic sp2C unified atoms in water. Interactions of amide sp2O with urea and naphthalene are favorable, while amide sp2O-alkylurea interactions are unfavorable, becoming more unfavorable with increasing alkylation. Hence, amide sp2O-amide sp2N interactions (proposed n-σ* hydrogen bond) and amide sp2O-aromatic sp2C (proposed n-π*) interactions are favorable in water, while amide sp2O-sp3C interactions are unfavorable. Interactions of all ureas with sp3C and amide sp2N are favorable and increase in strength with increasing alkylation, indicating favorable sp3C-amide sp2N and sp3C-sp3C interactions. Naphthalene results show that aromatic sp2C-amide sp2N interactions in water are unfavorable while sp2C-sp3C interactions are favorable. These results allow interactions of amide and hydrocarbon moieties and effects of urea and alkylureas on aqueous processes to be predicted or interpreted in terms of structural information. We predict strengths of favorable urea-benzene and N-methylacetamide interactions from experimental information to compare with simulations and indicate how amounts of hydrocarbon and amide surfaces buried in protein folding and other biopolymer processes and transition states can be determined from analysis of urea and diethylurea effects on equilibrium and rate constants.
Collapse
Affiliation(s)
- Xian Cheng
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Irina A Shkel
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Kevin O'Connor
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - John Henrich
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Cristen Molzahn
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - David Lambert
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - M Thomas Record
- Program in Biophysics and ‡Departments of Biochemistry and §Chemistry University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| |
Collapse
|
241
|
Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B 2017; 121:8009-8025. [PMID: 28666087 PMCID: PMC5582368 DOI: 10.1021/acs.jpcb.7b03570] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The
effects of crowding in biological environments on biomolecular
structure, dynamics, and function remain not well understood. Computer
simulations of atomistic models of concentrated peptide and protein
systems at different levels of complexity are beginning to provide
new insights. Crowding, weak interactions with other macromolecules
and metabolites, and altered solvent properties within cellular environments
appear to remodel the energy landscape of peptides and proteins in
significant ways including the possibility of native state destabilization.
Crowding is also seen to affect dynamic properties, both conformational
dynamics and diffusional properties of macromolecules. Recent simulations
that address these questions are reviewed here and discussed in the
context of relevant experiments.
Collapse
Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States.,Quantitative Biology Center, RIKEN , Kobe, Japan
| | - Isseki Yu
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan
| | - Po-Hung Wang
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States
| | - Yuji Sugita
- Quantitative Biology Center, RIKEN , Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan.,Advanced Institute for Computational Science, RIKEN , Kobe, Japan
| |
Collapse
|
242
|
Aslanyan L, Ko J, Kim BG, Vardanyan I, Dalyan YB, Chalikian TV. Effect of Urea on G-Quadruplex Stability. J Phys Chem B 2017; 121:6511-6519. [DOI: 10.1021/acs.jpcb.7b03479] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lusine Aslanyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Jordan Ko
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Byul G. Kim
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Ishkhan Vardanyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Yeva B. Dalyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Tigran V. Chalikian
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| |
Collapse
|
243
|
Hong J, Xiong S. TMAO-Protein Preferential Interaction Profile Determines TMAO's Conditional In Vivo Compatibility. Biophys J 2017; 111:1866-1875. [PMID: 27806268 DOI: 10.1016/j.bpj.2016.09.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/16/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022] Open
Abstract
Trimethylamine N-oxide (TMAO) exemplifies how Nature uses the solute effect as a simple chemical strategy to cope with hydrodynamic pressure or urea stress to maintain proteostasis. It is a gut-microbe-generated metabolite that strongly promotes the development of atherosclerosis. It remains unclear how TMAO exerts its effects. In this study, we experimentally characterized the profile of the preferential interaction potential of TMAO with proteins, a thermodynamic key to understanding the effects of TMAO on protein processes and the distinction of TMAO among osmolytes. TMAO is thus found to be highly preferentially excluded from most types of protein surface, which explains why TMAO is a strong globular protein stabilizer and identifies the dominant stabilizing factor as the unfavorable interaction of TMAO with the hydrophobic surface exposed upon unfolding. We dissected the mechanism of the counteracting effects of TMAO and urea: the contrary feature of the interaction profiles of the two solutes maximizes the possibility for them to offset each other's perturbing effect on protein processes. The interaction profile also predicts that TMAO promotes aggregation of amyloidogenic intrinsically disordered peptide, as demonstrated here in Aβ42, and that TMAO has a strong potential to impact protein processes in the absence of stressors. Our data suggest that although TMAO is an evolutionally selected chemical chaperone for some organisms or organs, its compatibility in vivo is conditional and determined by its interaction profile with biopolymers and the nature of the essential biopolymer processes. Our thermodynamic framework plus the TMAO-protein interaction profile provides a basis for exploring the broad biological significance of TMAO, including its pathological impact in the absence of stressors. We argue for the general importance of controlling in vivo background solutes and the pathological significance of a control failure.
Collapse
Affiliation(s)
- Jiang Hong
- School of Life Sciences, Shanghai University, Shanghai, China; Experimental Center for Life Sciences, School of Life Sciences, Shanghai University, Shanghai, China.
| | - Shangqin Xiong
- School of Life Sciences, Shanghai University, Shanghai, China
| |
Collapse
|
244
|
Yamamori Y, Matubayasi N. Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme. J Chem Phys 2017; 146:225103. [DOI: 10.1063/1.4985222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| |
Collapse
|
245
|
Smiatek J. Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:233001. [PMID: 28398214 DOI: 10.1088/1361-648x/aa6c9d] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization or denaturation mechanisms for various ILs. In this review, we summarize the main findings and discuss the implications with regard to molecular theories of solutions and specific ion effects. A preferential binding model is introduced in order to discuss protein-IL effects from a statistical mechanics perspective. The value of the preferential binding coefficient determines the strength of the ion influence and indicates a shift of the chemical equilibrium either to the native or the denatured state of the protein. We highlight the role of water in order to explain the self-association behavior of the IL species and discuss recent experimental and simulation results in the light of the observed binding effects.
Collapse
Affiliation(s)
- Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| |
Collapse
|
246
|
Oh KI, Rajesh K, Stanton JF, Baiz CR. Quantifying Hydrogen-Bond Populations in Dimethyl Sulfoxide/Water Mixtures. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry; University of Texas at Austin; 105 E 24th St. Stop A5300 Austin TX 78712-1224 USA
| | - Kavya Rajesh
- Department of Chemistry; University of Texas at Austin; 105 E 24th St. Stop A5300 Austin TX 78712-1224 USA
| | - John F. Stanton
- Department of Chemistry; University of Texas at Austin; 105 E 24th St. Stop A5300 Austin TX 78712-1224 USA
| | - Carlos R. Baiz
- Department of Chemistry; University of Texas at Austin; 105 E 24th St. Stop A5300 Austin TX 78712-1224 USA
| |
Collapse
|
247
|
Oh KI, Rajesh K, Stanton JF, Baiz CR. Quantifying Hydrogen-Bond Populations in Dimethyl Sulfoxide/Water Mixtures. Angew Chem Int Ed Engl 2017; 56:11375-11379. [DOI: 10.1002/anie.201704162] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry; University of Texas at Austin; 105 E 24th St. Stop A5300 Austin TX 78712-1224 USA
| | - Kavya Rajesh
- Department of Chemistry; University of Texas at Austin; 105 E 24th St. Stop A5300 Austin TX 78712-1224 USA
| | - John F. Stanton
- Department of Chemistry; University of Texas at Austin; 105 E 24th St. Stop A5300 Austin TX 78712-1224 USA
| | - Carlos R. Baiz
- Department of Chemistry; University of Texas at Austin; 105 E 24th St. Stop A5300 Austin TX 78712-1224 USA
| |
Collapse
|
248
|
Pandey RB, Jacobs DJ, Farmer BL. Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation. J Chem Phys 2017; 146:195101. [PMID: 28527439 PMCID: PMC5438306 DOI: 10.1063/1.4983222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/26/2017] [Indexed: 11/14/2022] Open
Abstract
The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ∼ 1.3), random-coil (D ∼ 1.75), and globular (D ∼ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.
Collapse
Affiliation(s)
- R B Pandey
- Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - D J Jacobs
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina 28223, USA
| | - B L Farmer
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio 45433, USA and Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA
| |
Collapse
|
249
|
Pathak AK, Bandyopadhyay T. Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study. J Chem Phys 2017; 146:165104. [DOI: 10.1063/1.4982049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Arup K. Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| |
Collapse
|
250
|
Ploetz EA, Smith PE. Simulated pressure denaturation thermodynamics of ubiquitin. Biophys Chem 2017; 231:135-145. [PMID: 28576277 DOI: 10.1016/j.bpc.2017.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/14/2017] [Accepted: 04/17/2017] [Indexed: 01/09/2023]
Abstract
Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues.
Collapse
Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, 213 CBC Building, 1212 Mid Campus Dr. North, Kansas State University, Manhattan, KS 66506-0401, United States
| | - Paul E Smith
- Department of Chemistry, 213 CBC Building, 1212 Mid Campus Dr. North, Kansas State University, Manhattan, KS 66506-0401, United States.
| |
Collapse
|