1
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Demosthene B, Kravchuk P, Harmon CL, Kalae A, Kang EH. Small organic osmolytes accelerate actin filament assembly and stiffen filaments. Cytoskeleton (Hoboken) 2024. [PMID: 39276026 DOI: 10.1002/cm.21927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 08/27/2024] [Accepted: 09/03/2024] [Indexed: 09/16/2024]
Abstract
Actin filament assembly and mechanics are crucial for maintenance of cell structure, motility, and division. Actin filament assembly occurs in a crowded intracellular environment consisting of various types of molecules, including small organic molecules known as osmolytes. Ample evidence highlights the protective functions of osmolytes such as trimethylamine-N-oxide (TMAO), including their effects on protein stability and their ability to counteract cellular osmotic stress. Yet, how TMAO affects individual actin filament assembly dynamics and mechanics is not well understood. We hypothesize that, owing to its protective nature, TMAO will enhance filament dynamics and stiffen actin filaments due to increased stability. In this study, we investigate osmolyte-dependent actin filament assembly and bending mechanics by measuring filament elongation rates, steady-state filament lengths, and bending persistence lengths in the presence of TMAO using total internal reflection fluorescence microscopy and pyrene assays. Our results demonstrate that TMAO increases filament elongation rates as well as steady-state average filament lengths, and enhances filament bending stiffness. Together, these results will help us understand how small organic osmolytes modulate cytoskeletal protein assembly and mechanics in living cells.
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Affiliation(s)
- Bryan Demosthene
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Pavlo Kravchuk
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
| | - Connor L Harmon
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
| | - Abdulrazak Kalae
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
| | - Ellen H Kang
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
- Department of Physics, University of Central Florida, Orlando, Florida, USA
- Department of Materials Science and Engineering, University of Central Florida, Orlando, Florida, USA
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2
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Raghunathan S. Solvent accessible surface area-assessed molecular basis of osmolyte-induced protein stability. RSC Adv 2024; 14:25031-25041. [PMID: 39131493 PMCID: PMC11310836 DOI: 10.1039/d4ra02576h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
In solvent-modulated protein folding, under certain physiological conditions, an equilibrium exists between the unfolded and folded states of the protein without any need to break or make a covalent bond. In this process, interactions between various protein groups (peptides) and solvent molecules are known to play a major role in determining the directionality of the chemical reaction. However, an understanding of the mechanism of action of the co(solvent) by a generic theoretical underpinning is lacking. In this study, a generic solvation model is developed based on statistical mechanics and the thermodynamic transfer free energy model by considering the microenvironment polarity of the interacting co(solvent)-protein system. According to this model, polarity and the fractional solvent-accessible surface areas contribute to the interaction energies. The present model includes various orientations of participating interactant solvent surfaces of suitable areas. As model systems, besides the backbone we consider naturally occurring amino acid residues solvated in ten different osmolytes, small organic compounds known to modulate protein stability. The present model is able to predict the correct trend of the osmolyte-peptide interactions ranging from stabilizing to destabilizing not only for the backbone but also for side chains. Our model predicts Asn, Gln, Asp, Glu, Arg and Pro to be highly stable in most of the protecting osmolytes while Ala, Val, Ile, Leu, Thr, Met, Lys, Phe, Trp and Tyr are predicted to be moderately stable, and Ser, Cys and Histidine are predicted to be least stable. However, in denaturing solvents, both backbone and side chain models show similar stabilities in urea and guanidine. One of the important aspects of this model is that it is essentially parameter-free and consistent with the electrostatics of the interaction partners that make this model suitable for estimating any solute-solvent interaction energies.
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Affiliation(s)
- Shampa Raghunathan
- École Centrale School of Engineering, Mahindra University Hyderabad 500043 India
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3
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Kitamura K, Oshima A, Sasaki F, Shiramasa Y, Yamamoto R, Kameda T, Kitazawa S, Kitahara R. Modulation of Biomolecular Liquid-Liquid Phase Separation by Preferential Hydration and Interaction of Small Osmolytes with Proteins. J Phys Chem Lett 2024; 15:7620-7627. [PMID: 39029245 DOI: 10.1021/acs.jpclett.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
We examined the effects of trimethylamine N-oxide (TMAO) and urea (known osmolytes) on the liquid-liquid phase separation (LLPS) of fused in sarcoma (FUS) and three FUS-LLPS states: LLPS states at atmospheric pressure with low- and high-salt concentrations and a re-entrant LLPS state above 2 kbar. Temperature- and pressure-scan turbidity measurements revealed that TMAO and urea contributed to stabilizing and destabilizing LLPS, respectively. These results can be attributed to the excluded volume effect of TMAO (preferential hydration) and preferential interaction of urea with proteins. Additionally, TMAO counteracted the effects of equimolar urea on LLPS, a phenomenon not previously reported. The concept of the m-value for osmolyte-induced protein folding and unfolding can be applied to the osmolyte's effects on LLPS. In conclusion, biomolecular LLPS can be modulated by preferential hydration and the interaction of small osmolytes with proteins, thereby facilitating LLPS formation, even in extreme environments characterized by high-salt, high-urea, and high-pressure conditions.
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Affiliation(s)
- Keiji Kitamura
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ayano Oshima
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Fuka Sasaki
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Yutaro Shiramasa
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ryu Yamamoto
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ryo Kitahara
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
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4
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Shimizu S, Matubayasi N. Synergistic Solvation as the Enhancement of Local Mixing. J Phys Chem B 2024; 128:5713-5726. [PMID: 38829987 PMCID: PMC11182234 DOI: 10.1021/acs.jpcb.4c01582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/02/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024]
Abstract
Mixing two solvents can sometimes make a much better solvent than expected from their weighted mean. This phenomenon, called synergistic solvation, has commonly been explained via the Hildebrand and Hansen solubility parameters, yet their inability in other solubilization phenomena, most notably hydrotropy, necessitates an alternative route to elucidating solubilization. While, recently, the universal theory of solubilization was founded on the statistical thermodynamic fluctuation theory (as a generalization of the Kirkwood-Buff theory), its demand for experimental data processing has been a hindrance for its wider application. This can be overcome by the solubility isotherm theory, which is founded on the fluctuation theory yet reduces experimental data processing significantly to the level of isotherm analysis in sorption. The isotherm analysis identifies the driving force of synergistic solvation as the enhancement of solvent mixing around the solute, opposite in behavior to hydrotropy (characterized by the enhancement of demixing or self-association around the solute). Thus, the fluctuation theory, including its solubility isotherms, provides a universal language for solubilization across the historic subcategorization of solubilizers, for which different (and often contradictory) mechanistic models have been proposed.
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Affiliation(s)
- Seishi Shimizu
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Nobuyuki Matubayasi
- Division
of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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5
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Malik R, Chandra A. Counteracting Effects of Trimethylamine N-Oxide against Urea in Aqueous Solutions: Insights from Theoretical Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2023; 127:7372-7383. [PMID: 37566900 DOI: 10.1021/acs.jpcb.3c03864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
The study of small osmolytes in their aqueous solutions has gained significant attention because of their relevance to structure and thermodynamics of proteins in aqueous media. Special attention has been given to the binary and ternary aqueous solutions of urea and trimethylamine N-oxide (TMAO). Urea is a well-known protein denaturant, while TMAO protects proteins in their native states. Interestingly, TMAO counteracts urea's ability to denature proteins when present in solutions with approximately half of the concentration of urea. Vibrational spectroscopy can improve our understanding of the molecular origin of this counteracting effect because of its sensitivity to local structure and dynamics. We present results of theoretical linear vibrational and two-dimensional infrared (2DIR) spectroscopy of water in the binary and ternary aqueous solutions of TMAO and urea. The 2DIR spectra are calculated using the electronic structure/molecular dynamics approach. The non-Condon effects in spectral transitions are incorporated in the theoretical calculations of 2DIR spectra. It is found that TMAO disrupts the local structure of water, while urea leaves it essentially unaffected. The 2DIR results show that both TMAO and urea slow down the dynamics of spectral diffusion of water. The extent of slowing down is found to be particularly significant for both hydration and bulk water in the presence of TMAO which can be attributed to strong hydrogen bonds between the water and TMAO molecules. The water molecules present in the hydration layer of the solutes in the ternary solutions are found to relax at even slower rates compared to that in their binary solutions in water. The hydrogen bonds between TMAO and urea are found to be not stable. Thus, the counteracting effect of TMAO against urea is seen to take place mainly through water-mediated interactions. Such TMAO-induced effects giving rise to more structured and slower hydrogen-bonded network are successfully captured through 2DIR spectroscopic calculations.
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Affiliation(s)
- Ravi Malik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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6
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Boob MM, Sukenik S, Gruebele M, Pogorelov TV. TMAO: Protecting proteins from feeling the heat. Biophys J 2023; 122:1414-1422. [PMID: 36916005 PMCID: PMC10111349 DOI: 10.1016/j.bpj.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 03/14/2023] Open
Abstract
Osmolytes are ubiquitous in the cell and play an important role in controlling protein stability under stress. The natural osmolyte trimethylamine N-oxide (TMAO) is used by marine animals to counteract the effect of pressure denaturation at large depths. The molecular mechanism of TMAO stabilization against pressure and urea denaturation has been extensively studied, but unlike the case of other osmolytes, the ability of TMAO to protect proteins from high temperature has not been quantified. To reveal the effect of TMAO on folded and unfolded protein ensembles and the hydration shell at different temperatures, we study a mutant of the well-characterized, fast-folding model protein B (PRB). We carried out, in total, >190 μs all-atom simulations of thermal folding/unfolding of PRB at multiple temperatures and concentrations of TMAO. The simulations show increased thermal stability of PRB in the presence of TMAO. Partly structured, compact ensembles are favored over the unfolded state. TMAO forms two shells near the protein: an outer shell away from the protein surface has altered H-bond lifetimes of water molecules and increases hydration of the protein to help stabilize it; a less-populated inner shell with an opposite TMAO orientation closer to the protein surface binds exclusively to basic side chains. The cooperative cosolute effect of the inner and outer shell TMAO has a small number of TMAO molecules "herding" water molecules into two hydration shells at or near the protein surface. The stabilizing effect of TMAO on our protein saturates at 1 M despite higher TMAO solubility, so there may be little evolutionary pressure for extremophiles to produce higher intracellular TMAO concentrations, if true in general.
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Affiliation(s)
- Mayank M Boob
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Shahar Sukenik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| | - Taras V Pogorelov
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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7
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Oprzeska-Zingrebe EA, Smiatek J. Basket-type G-quadruplex with two tetrads in the presence of TMAO and urea: A molecular dynamics study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Urea counteracts trimethylamine N-oxide (TMAO) compaction of lipid membranes by modifying van der Waals interactions. J Colloid Interface Sci 2023; 629:165-172. [DOI: 10.1016/j.jcis.2022.08.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022]
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9
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Eronina TB, Mikhaylova VV, Chebotareva NA, Kleymenov SY, Pivovarova AV, Kurganov BI. Combined action of chemical chaperones on stability, aggregation and oligomeric state of muscle glycogen phosphorylase b. Int J Biol Macromol 2022; 203:406-416. [PMID: 35066023 DOI: 10.1016/j.ijbiomac.2022.01.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 01/19/2023]
Abstract
Chemical chaperones are a class of small molecules, which enhance protein stability, folding, inhibit protein aggregation, and are used for long-term storage of therapeutic proteins. The combined action of chemical chaperones trehalose, betaine and lysine on stability, aggregation and oligomeric state of muscle glycogen phosphorylase b (Phb) has been studied. Dynamic light scattering data indicate that the affinity of trehalose to Phb increased in the presence of betaine or lysine at both stages (stage of nucleation and aggregate growth) of enzyme aggregation at 48 °C, in contrast, the affinity of betaine to the enzyme in the presence of lysine remained practically unchanged. According to differential scanning calorimetry and analytical ultracentrifugation data, the mixture of trehalose and betaine stabilized Phb stronger than either of them in total. Moreover, the destabilizing effect of lysine on the enzyme was almost completely compensated by trehalose and only partially by betaine. The main protective effect of the mixtures of osmolytes and lysine is associated with their influence on the dissociation/denaturation stage, which is the rate-limiting one of Phb aggregation. Thus, a pair of chaperones affects the stability, oligomeric state, and aggregation of Phb differently than individual chaperones.
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Affiliation(s)
- Tatiana B Eronina
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia.
| | - Valeriya V Mikhaylova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Natalia A Chebotareva
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Sergey Y Kleymenov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia; Koltsov's Institute of Developmental Biology, Russian Academy of Sciences, Vavilova 26, Moscow 119991, Russia
| | - Anastasia V Pivovarova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Boris I Kurganov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
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10
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Contessoto VG, Ferreira PHB, Chahine J, Leite VBP, Oliveira RJ. Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics. J Phys Chem B 2021; 125:11673-11686. [PMID: 34644091 DOI: 10.1021/acs.jpcb.1c07663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular crowding is a ubiquitous phenomenon in biological systems, with significant consequences on protein folding and stability. Small compounds, such as the osmolyte trimethylamine N-oxide (TMAO), can also present similar effects. To analyze the effects arising from these solute-like molecules, we performed a series of crowded coarse-grained folding simulations. Two well-known proteins were chosen, CI2 and SH3, modeled by the alpha-carbon-structure-based model. In the simulations, the crowding molecules were represented by low-sized neutral atom beads in different concentrations. The results show that a low level of the volume fraction occupied by neutral agents can change protein stability and folding kinetics for the two systems. However, the kinetics were shown to be unaffected in their respective folding temperatures. The faster kinetics correlates with changes in the folding route for systems at the same temperature, where non-native contacts were shown to be relevant. The transition states of the two systems with and without crowders are similar. In the case of SH3, there are differences in the structuring of two strands, which may be associated with the increase in its folding rate, in addition to the destabilization of the denatured ensemble. The present study also detected a crossover in the thermodynamic stability behavior, previously observed experimentally and theoretically. As the temperature increases, crowders change from destabilizing to stabilizing agents.
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Affiliation(s)
- Vinícius G Contessoto
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Paulo H B Ferreira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba 38064-200, Brazil
| | - Jorge Chahine
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Vitor B P Leite
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Ronaldo J Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba 38064-200, Brazil
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11
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Folberth A, Polák J, Heyda J, van der Vegt NFA. Pressure, Peptides, and a Piezolyte: Structural Analysis of the Effects of Pressure and Trimethylamine- N-oxide on the Peptide Solvation Shell. J Phys Chem B 2020; 124:6508-6519. [PMID: 32615760 DOI: 10.1021/acs.jpcb.0c03319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The osmolyte trimethylamine-N-oxide (TMAO) is able to increase the thermodynamic stability of folded proteins, counteracting pressure denaturation. Herein, we report experimental solubility data on penta-alanine (pAla) in aqueous TMAO solutions (at pH = 7 and pH = 13) together with molecular simulation data for pAla, penta-serine (pSer), and an elastin-like peptide (ELP) sequence (VPGVG) under varying pH and pressure conditions. The effect of the peptide end groups on TMAO-peptide interactions is investigated by comparing the solvation of zwitterionic and negatively charged pentamers with the solvation of pentamers with charge-neutral C- and N-termini and linear, virtually infinite, peptide chains stretched across the periodic boundaries of the simulation cell. The experiments and simulations consistently show that TMAO is net-depleted from the pAla-water interface, but local accumulation of TMAO is observed just outside the first hydration shell of the peptide. While the same observations are also made in the simulations of the zwitterionic pentamers (Ala, Ser, and ELP) and virtually infinite peptide chains (Ala and ELP), weak preferential binding of TMAO is instead observed for pAla with neutral end groups at a 1 M TMAO concentration and for an ELP pentamer with capped neutral end groups at a 0.55 M TMAO concentration studied in previous work (Y.-T. Liao et al. Proc. Natl. Acad. Sci. USA, 2017, 114, 2479-2484). The above observations made at 1 bar ambient pressure remain qualitatively unchanged at 500 bar and 2 kbar. Local accumulation of TMAO correlates with a reduction in the total number of peptide-solvent hydrogen bonds, independent of the peptide's primary sequence and the applied pressure. By weakening water hydrogen bonds with the protein backbone, TMAO indirectly contributes to stabilizing internal hydrogen bonds in proteins, thus providing a protein stabilization mechanism beyond net depletion.
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Affiliation(s)
- Angelina Folberth
- Eduard-Zintl-Institut fuer Anorganische und Physikalische Chemie, Technical University of Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
| | - Jakub Polák
- Physical Chemistry Department, University of Chemistry and Technology, Prague Technicka 5, 16628 Prague 6, Czech Republic
| | - Jan Heyda
- Physical Chemistry Department, University of Chemistry and Technology, Prague Technicka 5, 16628 Prague 6, Czech Republic
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut fuer Anorganische und Physikalische Chemie, Technical University of Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
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12
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Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis. Sci Rep 2020; 10:9685. [PMID: 32546801 PMCID: PMC7297731 DOI: 10.1038/s41598-020-66710-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/20/2020] [Indexed: 12/24/2022] Open
Abstract
It has long been observed that trimethylamine N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work on these two osmolytes, various aspects of their underlying mechanisms still remain largely elusive. In this paper, we propose to use the weighted persistent homology to systematically study the osmolytes molecular aggregation and their hydrogen-bonding network from a local topological perspective. We consider two weighted models, i.e., localized persistent homology (LPH) and interactive persistent homology (IPH). Boltzmann persistent entropy (BPE) is proposed to quantitatively characterize the topological features from LPH and IPH, together with persistent Betti number (PBN). More specifically, from the localized persistent homology models, we have found that TMAO and urea have very different local topology. TMAO is found to exhibit a local network structure. With the concentration increase, the circle elements in these networks show a clear increase in their total numbers and a decrease in their relative sizes. In contrast, urea shows two types of local topological patterns, i.e., local clusters around 6 Å and a few global circle elements at around 12 Å. From the interactive persistent homology models, it has been found that our persistent radial distribution function (PRDF) from the global-scale IPH has same physical properties as the traditional radial distribution function. Moreover, PRDFs from the local-scale IPH can also be generated and used to characterize the local interaction information. Other than the clear difference of the first peak value of PRDFs at filtration size 4 Å, TMAO and urea also shows very different behaviors at the second peak region from filtration size 5 Å to 10 Å. These differences are also reflected in the PBNs and BPEs of the local-scale IPH. These localized topological information has never been revealed before. Since graphs can be transferred into simplicial complexes by the clique complex, our weighted persistent homology models can be used in the analysis of various networks and graphs from any molecular structures and aggregation systems.
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13
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Ganguly P, Polák J, van der Vegt NFA, Heyda J, Shea JE. Protein Stability in TMAO and Mixed Urea–TMAO Solutions. J Phys Chem B 2020; 124:6181-6197. [DOI: 10.1021/acs.jpcb.0c04357] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - 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
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14
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Teng X, Ichiye T. Dynamical Model for the Counteracting Effects of Trimethylamine N-Oxide on Urea in Aqueous Solutions under Pressure. J Phys Chem B 2020; 124:1978-1986. [PMID: 32059113 DOI: 10.1021/acs.jpcb.9b10844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Of cosolutes found in living cells, urea denatures and trimethylamine N-oxide (TMAO) stabilizes proteins; furthermore, these effects cancel at a 2:1 ratio of urea to TMAO. Interestingly, cartilaginous fish use urea and TMAO as osmolytes at similar ratios at the ocean surface but with increasing fractions of TMAO at increasing depths. Here, molecular dynamics simulations of aqueous solutions with different urea:TMAO ratios show that the diffusion coefficients of water in the solutions vary with pressure if the urea:TMAO ratio is constant, but strikingly, they are almost pressure independent at the ratio found in these fish as a function of depth. This suggests that this ratio may be maintaining a homeostasis of water dynamics. In addition, diffusion is determined by hydrogen-bond lifetimes of the different species in the solution. Based on these observations, a dynamical model in terms of hydrogen-bond lifetimes is developed for the hydrogen bonding propensities of cosolutes and water in an aqueous solution to proteins. This model provides an explanation for both the counteracting effects of TMAO on urea denaturation and the depth-dependent urea:TMAO ratio found in cartilaginous fish.
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Affiliation(s)
- Xiaojing Teng
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
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15
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Sahle CJ, Schroer MA, Niskanen J, Elbers M, Jeffries CM, Sternemann C. Hydration in aqueous osmolyte solutions: the case of TMAO and urea. Phys Chem Chem Phys 2020; 22:11614-11624. [DOI: 10.1039/c9cp06785j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-ray Raman scattering spectroscopy and first principles simulations reveal details of the hydration and hydrogen-bond topology of trimethylamine N-oxide (TMAO) and urea in aqueous solutions.
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Affiliation(s)
| | - Martin A. Schroer
- European Molecular Biology Laboratory (EMBL)
- Hamburg Outstation c/o DESY
- Hamburg 22607
- Germany
| | - Johannes Niskanen
- Department of Physics and Astronomy
- University of Turku
- FI-20014 Turun Yliopisto
- Finland
| | - Mirko Elbers
- Fakultät Physik/DELTA
- Technische Universität Dortmund
- 44221 Dortmund
- Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL)
- Hamburg Outstation c/o DESY
- Hamburg 22607
- Germany
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16
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Oprzeska-Zingrebe EA, Smiatek J. Aqueous Mixtures of Urea and Trimethylamine-N-oxide: Evidence for Kosmotropic or Chaotropic Behavior? J Phys Chem B 2019; 123:4415-4424. [PMID: 31046272 DOI: 10.1021/acs.jpcb.9b02598] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Trimethylamine-N-oxide (TMAO) and urea are commonly produced in many extremophilic microorganisms that live in harsh environments. In view of high temperature, high pressure, or high salt content, TMAO is known as a protein structure stabilizer, whereas urea destabilizes protein structures even under ambient conditions. Despite clear evidence, destabilizers are often regarded as chaotropes, meaning water-structure breakers, whereas kosmotropes as water-structure makers are classified as stabilizers. Using atomistic molecular dynamics simulations, we study aqueous mixtures of TMAO and urea in various biologically relevant concentrations to gain insight into the molecular details of their mutual cross-interactions and their influence on water dynamics and structure. Our results for binary and ternary solutions in combination with different mixing ratios show that both co-solutes strengthen the water network in terms of dynamic and structural aspects. Slight differences in the water binding behavior between both species result in only negligible compensation effects. The outcomes of our simulations thus question the validity and the ill-considered use of attributes like kosmotropic or chaotropic substances for stabilizers and destabilizers.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics , University of Stuttgart , D-70569 Stuttgart , Germany.,Helmholtz-Institute Münster: Ionics in Energy Storage (HIMS-IEK 12) , Forschungszentrum Jülich GmbH , D-48149 Münster , Germany
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17
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Harton K, Shimizu S. Statistical thermodynamics of casein aggregation: Effects of salts and water. Biophys Chem 2019; 247:34-42. [DOI: 10.1016/j.bpc.2019.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 11/30/2022]
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18
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Huang TQ, Shahid MQ, Baloch FS, Lin SQ, Yang XH. Effects of trimethylamine oxide (TMAO) and loading duration on the shoot tip cryopreservation of loquat ( Eriobotrya japonica). Turk J Biol 2019; 42:224-230. [PMID: 30814884 DOI: 10.3906/biy-1712-51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Two cryoprotectant solutions, including trimethylamine oxide (TMAO) and dimethyl sulfoxide (DMSO), and several loading durations were used to evaluate the cryopreservation of the shoot tip of Eriobotrya plants. The best results for regrowth (59.91%) were obtained from 10% TMAO compared to 10% DMSO as cryoprotectant, although nonsignificant differences were found for survival between the two cryoprotectants. We detected pronounced effects of loading duration on survival and regrowth rates of shoot tips. The maximum regrowth (56.36%) was observed at 9 h of loading duration. The cryoprotectants and loading durations greatly affected the regrowth of Eriobotrya shoot tips, and TMAO could be introduced as a nontoxic and efficient cryoprotectant. These results could lay a foundation for the cryopreservation of Eriobotrya.
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Affiliation(s)
- Tian-Qi Huang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture , Guangzhou , P.R. China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University , Guangzhou , P.R. China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University , Guangzhou , P.R. China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agriculture and Natural Sciences, Abant İzzet Baysal University , Bolu , Turkey
| | - Shun-Quan Lin
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture , Guangzhou , P.R. China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University , Guangzhou , P.R. China
| | - Xiang-Hui Yang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture , Guangzhou , P.R. China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University , Guangzhou , P.R. China
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19
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Teng X, Ichiye T. Dynamical Effects of Trimethylamine N-Oxide on Aqueous Solutions of Urea. J Phys Chem B 2019; 123:1108-1115. [PMID: 30638025 DOI: 10.1021/acs.jpcb.8b09874] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trimethylamine N-oxide (TMAO) stabilizes protein structures, whereas urea destabilizes proteins, and their opposing effects can be counteracted at a 1:2 ratio of TMAO to urea. To investigate how they affect solution dynamics, molecular dynamics simulations have been carried out for aqueous solutions of TMAO and urea at different concentrations. In the binary solutions, urea mainly slows the diffusion of waters that are hydrogen bonded to it (i.e., hydration water), whereas TMAO dramatically slows the diffusion of both hydration water and bulk water because of long-lived TMAO-water hydrogen bonds. In the ternary solutions, because TMAO decreases the diffusion rate of bulk water, the lifetimes of not only water-water but also urea-water hydrogen bonds increase. In addition, the constant forming and breaking of short lifetime hydrogen bonds between urea and water appears to impart energy into the bulk, whereas the long lifetime hydrogen bonds between TMAO and water slows down the bulk, resulting in the compensating effects on bulk water in the ternary solution. This suggests that the counteracting effects of TMAO on urea denaturation may be both to make longer lived hydrogen bonds to water and to counter the energizing effects of urea on bulk water.
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Affiliation(s)
- Xiaojing Teng
- Department of Chemistry , Georgetown University , Washington, D.C. 20057 , United States
| | - Toshiko Ichiye
- Department of Chemistry , Georgetown University , Washington, D.C. 20057 , United States
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20
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Xia K, Anand DV, Shikhar S, Mu Y. Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networks. Phys Chem Chem Phys 2019; 21:21038-21048. [DOI: 10.1039/c9cp03009c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dramatically different patterns can be observed in the topological fingerprints for hydrogen-bonding networks from two types of osmolyte systems.
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Affiliation(s)
- Kelin Xia
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - D. Vijay Anand
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Saxena Shikhar
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
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21
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Xie WJ, Cha S, Ohto T, Mizukami W, Mao Y, Wagner M, Bonn M, Hunger J, Nagata Y. Large Hydrogen-Bond Mismatch between TMAO and Urea Promotes Their Hydrophobic Association. Chem 2018. [DOI: 10.1016/j.chempr.2018.08.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Baz J, Gebhardt J, Kraus H, Markthaler D, Hansen N. Insights into Noncovalent Binding Obtained from Molecular Dynamics Simulations. CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201800050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jörg Baz
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Julia Gebhardt
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Hamzeh Kraus
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Daniel Markthaler
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Niels Hansen
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
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23
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Zetterholm SG, Verville GA, Boutwell L, Boland C, Prather JC, Bethea J, Cauley J, Warren KE, Smith SA, Magers DH, Hammer NI. Noncovalent Interactions between Trimethylamine N-Oxide (TMAO), Urea, and Water. J Phys Chem B 2018; 122:8805-8811. [PMID: 30165021 DOI: 10.1021/acs.jpcb.8b04388] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Trimethylamine N-oxide (TMAO) and urea are two important osmolytes with their main significance to the biophysical field being in how they uniquely interact with proteins. Urea is a strong protein destabilizing agent, whereas TMAO is known to counteract urea's deleterious effects. The exact mechanisms by which TMAO stabilizes and urea destabilizes folded proteins continue to be debated in the literature. Although recent evidence has suggested that urea binds directly to amino acid side chains to make protein folding less thermodynamically favored, it has also been suggested that urea acts indirectly to denature proteins by destabilizing the surrounding hydrogen bonding water networks. Here, we elucidate the molecular level mechanism of TMAO's unique ability to counteract urea's destabilizing nature by comparing Raman spectroscopic frequency shifts to the results of electronic structure calculations of microsolvated molecular clusters. Experimental and computational data suggest that the addition of TMAO into an aqueous solution of urea induces blue shifts in urea's H-N-H symmetric bending modes, which is evidence for direct interactions between the two cosolvents.
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Affiliation(s)
- Sarah G Zetterholm
- Department of Chemistry and Biochemistry , Mississippi College , P.O. Box 4036, Clinton , Mississippi 39058 , United States
| | - Genevieve A Verville
- Department of Chemistry and Biochemistry , University of Mississippi , P.O. Box 1848, University , Mississippi 38655 , United States
| | - Leeann Boutwell
- Department of Chemistry and Biochemistry , Mississippi College , P.O. Box 4036, Clinton , Mississippi 39058 , United States
| | - Christopher Boland
- Department of Chemistry and Biochemistry , University of Mississippi , P.O. Box 1848, University , Mississippi 38655 , United States
| | - John C Prather
- Department of Chemistry and Biochemistry , University of Mississippi , P.O. Box 1848, University , Mississippi 38655 , United States
| | - Jonathan Bethea
- Department of Chemistry and Biochemistry , Mississippi College , P.O. Box 4036, Clinton , Mississippi 39058 , United States
| | - Jordan Cauley
- Department of Chemistry and Biochemistry , University of Mississippi , P.O. Box 1848, University , Mississippi 38655 , United States.,Department of Chemistry and Biochemistry , Mississippi College , P.O. Box 4036, Clinton , Mississippi 39058 , United States
| | - Kayla E Warren
- Department of Chemistry and Biochemistry , University of Mississippi , P.O. Box 1848, University , Mississippi 38655 , United States
| | - Shelley A Smith
- Department of Chemistry and Biochemistry , Mississippi College , P.O. Box 4036, Clinton , Mississippi 39058 , United States
| | - David H Magers
- Department of Chemistry and Biochemistry , Mississippi College , P.O. Box 4036, Clinton , Mississippi 39058 , United States
| | - Nathan I Hammer
- Department of Chemistry and Biochemistry , University of Mississippi , P.O. Box 1848, University , Mississippi 38655 , United States
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24
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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.
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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
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25
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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.
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Affiliation(s)
- Anjeeta Rani
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
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26
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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
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27
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Zhang C, Yang M, Zhao K. Insight into the effect mechanism of urea-induced protein denaturation by dielectric spectroscopy. Phys Chem Chem Phys 2017; 19:32007-32015. [PMID: 29177311 DOI: 10.1039/c7cp05994a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dielectric relaxation spectroscopy was applied to study how urea affects the phase transition of a thermosensitive polymer, poly(N-isopropylacrylamide) (PNIPAM), which has been widely used as a protein model. It was found that there is a pronounced relaxation near 10 GHz for the ternary system of PNIPAM in urea aqueous solution. The temperature dependence of dielectric parameters indicates that urea can reduce the lower critical solution temperature (LCST) of PNIPAM, i.e., stabilize the globule state of PNIPAM and collapse the PNIPAM chains. Based on our results, the interaction mechanism of urea on the conformational transition of PNIPAM was presented: urea replaces water molecules directly bonding with PNIPAM and acts as the bridging agent for the adjacent side chains of PNIPAM. Accordingly, the mechanism with which urea denatures protein was deduced. In addition, it is worth mentioning that, from the temperature dependence of the dielectric parameters obtained in the presence of urea, an interesting phenomenon was found in which the effect of urea on PNIPAM seems to take 2 M as a unit. This result may be the reason why urea and TMAO exit marine fishes at a specific ratio of 2 : 1.
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Affiliation(s)
- Cancan Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
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28
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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
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29
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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]
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30
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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
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31
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Chand A, Chowdhuri S. A comparative study of hydrogen bonding structure and dynamics in aqueous urea solution of amides with varying hydrophobicity: Effect of addition of trimethylamine N -oxide (TMAO). J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.06.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Rani A, Taha M, Venkatesu P, Lee MJ. Coherent Experimental and Simulation Approach To Explore the Underlying Mechanism of Denaturation of Stem Bromelain in Osmolytes. J Phys Chem B 2017; 121:6456-6470. [DOI: 10.1021/acs.jpcb.7b01776] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anjeeta Rani
- Department
of Chemistry, University of Delhi, Delhi 110 007, India
| | - Mohamed Taha
- Department
of Chemistry, College of Science, Sultan Qaboos University, PO Box 36, PC 123 Muscat, Oman
| | | | - Ming- Jer Lee
- Department of Chemical Engineering, National Taiwan University of Science & Technology, Taipei 10607, Taiwan
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33
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Ghosh S, Dey S, Patel M, Chakrabarti R. Can an ammonium-based room temperature ionic liquid counteract the urea-induced denaturation of a small peptide? Phys Chem Chem Phys 2017; 19:7772-7787. [DOI: 10.1039/c6cp08842b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The folding/unfolding equilibrium of proteins in aqueous medium can be altered by adding small organic molecules generally termed as co-solvents.
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Affiliation(s)
- Soumadwip Ghosh
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Souvik Dey
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Mahendra Patel
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
| | - Rajarshi Chakrabarti
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai – 400076
- India
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34
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Ohto T, Hunger J, Backus EHG, Mizukami W, Bonn M, Nagata Y. Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations. Phys Chem Chem Phys 2017; 19:6909-6920. [DOI: 10.1039/c6cp07284d] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Vibrational spectroscopy and molecular simulations revealed the hydrophilicity and hydrophobicity of TMAO in aqueous solution.
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Affiliation(s)
- Tatsuhiko Ohto
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | | | | | - Wataru Mizukami
- Department of Energy and Material Sciences
- Faculty of Engineering Sciences
- Kyushu University
- Fukuoka
- Japan
| | - Mischa Bonn
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
- Department of Theoretical and Computational Molecular Science
- Institute for Molecular Science
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35
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Fedotova MV, Kruchinin SE, Chuev GN. Hydration structure of osmolyte TMAO: concentration/pressure-induced response. NEW J CHEM 2017. [DOI: 10.1039/c6nj03296f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of solute concentration/pressure on the TMAO hydration structure was studied to understand its protective action under abiotic stressors.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Sergey E. Kruchinin
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics
- The Russian Academy of Sciences
- Pushchino
- Russia
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36
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Ganguly P, van der Vegt NFA, Shea JE. Hydrophobic Association in Mixed Urea-TMAO Solutions. J Phys Chem Lett 2016; 7:3052-9. [PMID: 27440555 DOI: 10.1021/acs.jpclett.6b01344] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The formation of a hydrophobic core is key to the folding and resulting function of most proteins in the cell. In several organisms, as well as in many in vitro experiments, protein folding is modulated by the presence of osmolytes, but the mechanism by which hydrophobic association occurs is not well understood. We present a study of the solvation thermodynamics of hydrophobic self-association in mixed-osmolyte urea-TMAO solutions, with neopentane as a model hydrophobic molecule. Using molecular dynamics simulations and the Kirkwood-Buff theory of solutions, we show that a sensitive balance between the TMAO-water and the TMAO-urea interactions governs the osmolyte-induced changes in hydrophobic association in mixed urea-TMAO solutions. This balance must be correctly incorporated in force-field parametrization because hydrophobic association can be either enhanced or prevented all together by slightly increasing or decreasing the osmolyte-water affinity and osmolyte-osmolyte self-affinity of TMAO molecules.
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Affiliation(s)
- Pritam Ganguly
- 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
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and 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
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37
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Yancey PH, Siebenaller JF. Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms. ACTA ACUST UNITED AC 2016; 218:1880-96. [PMID: 26085665 DOI: 10.1242/jeb.114355] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Organisms experience a wide range of environmental factors such as temperature, salinity and hydrostatic pressure, which pose challenges to biochemical processes. Studies on adaptations to such factors have largely focused on macromolecules, especially intrinsic adaptations in protein structure and function. However, micromolecular cosolutes can act as cytoprotectants in the cellular milieu to affect biochemical function and they are now recognized as important extrinsic adaptations. These solutes, both inorganic and organic, have been best characterized as osmolytes, which accumulate to reduce osmotic water loss. Singly, and in combination, many cosolutes have properties beyond simple osmotic effects, e.g. altering the stability and function of proteins in the face of numerous stressors. A key example is the marine osmolyte trimethylamine oxide (TMAO), which appears to enhance water structure and is excluded from peptide backbones, favoring protein folding and stability and counteracting destabilizers like urea and temperature. Co-evolution of intrinsic and extrinsic adaptations is illustrated with high hydrostatic pressure in deep-living organisms. Cytosolic and membrane proteins and G-protein-coupled signal transduction in fishes under pressure show inhibited function and stability, while revealing a number of intrinsic adaptations in deep species. Yet, intrinsic adaptations are often incomplete, and those fishes accumulate TMAO linearly with depth, suggesting a role for TMAO as an extrinsic 'piezolyte' or pressure cosolute. Indeed, TMAO is able to counteract the inhibitory effects of pressure on the stability and function of many proteins. Other cosolutes are cytoprotective in other ways, such as via antioxidation. Such observations highlight the importance of considering the cellular milieu in biochemical and cellular adaptation.
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Affiliation(s)
- Paul H Yancey
- Department of Biology, Whitman College, Walla Walla, WA 99362, USA
| | - Joseph F Siebenaller
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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38
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Rani A, Jayaraj A, Jayaram B, Pannuru V. Trimethylamine-N-oxide switches from stabilizing nature: A mechanistic outlook through experimental techniques and molecular dynamics simulation. Sci Rep 2016; 6:23656. [PMID: 27025561 PMCID: PMC4812290 DOI: 10.1038/srep23656] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/08/2016] [Indexed: 12/13/2022] Open
Abstract
In adaptation biology of the discovery of the intracellular osmolytes, the osmolytes are found to play a central role in cellular homeostasis and stress response. A number of models using these molecules are now poised to address a wide range of problems in biology. Here, a combination of biophysical measurements and molecular dynamics (MD) simulation method is used to examine the effect of trimethylamine-N-oxide (TMAO) on stem bromelain (BM) structure, stability and function. From the analysis of our results, we found that TMAO destabilizes BM hydrophobic pockets and active site as a result of concerted polar and non-polar interactions which is strongly evidenced by MD simulation carried out for 250 ns. This destabilization is enthalpically favourable at higher concentrations of TMAO while entropically unfavourable. However, to the best of our knowledge, the results constitute first detailed unambiguous proof of destabilizing effect of most commonly addressed TMAO on the interactions governing stability of BM and present plausible mechanism of protein unfolding by TMAO.
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Affiliation(s)
- Anjeeta Rani
- Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Abhilash Jayaraj
- Department of Chemistry, Indian Institute of Technology, New Delhi-110 016, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology, New Delhi-110 016, India.,Supercomputing Facility for Bioinformatics &Computational Biology, Indian Institute of Technology, New Delhi-110 016, India.,Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi-110 016, India
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39
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Effect of glycine betaine on the hydrophobic interactions in the presence of denaturant: A molecular dynamics study. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.12.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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40
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Borgohain G, Paul S. Model Dependency of TMAO’s Counteracting Effect Against Action of Urea: Kast Model versus Osmotic Model of TMAO. J Phys Chem B 2016; 120:2352-61. [DOI: 10.1021/acs.jpcb.5b10968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gargi Borgohain
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
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41
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Yang Y, Mu Y, Li W. Microscopic significance of hydrophobic residues in the protein-stabilizing effect of trimethylamine N-oxide (TMAO). Phys Chem Chem Phys 2016; 18:22081-8. [DOI: 10.1039/c6cp01205a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteins with a higher hydrophobic content are better protected by TMAO against the deleterious effect of urea.
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Affiliation(s)
- Yanmei Yang
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Weifeng Li
- School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions
- Soochow University
- Suzhou
- China
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42
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Sahle CJ, Schroer MA, Juurinen I, Niskanen J. Influence of TMAO and urea on the structure of water studied by inelastic X-ray scattering. Phys Chem Chem Phys 2016; 18:16518-26. [DOI: 10.1039/c6cp01922f] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a study on the influence of the naturally occurring organic osmolytes tri-methylamine N-oxide (TMAO) and urea on the bulk structure of water using X-ray Raman scattering spectroscopy.
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Affiliation(s)
| | - Martin A. Schroer
- Deutsches Elektronen-Synchrotron DESY
- 22607 Hamburg
- Germany
- The Hamburg Centre for Ultrafast Imaging (CUI)
- 22761 Hamburg
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43
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Hamdane D, Velours C, Cornu D, Nicaise M, Lombard M, Fontecave M. A chemical chaperone induces inhomogeneous conformational changes in flexible proteins. Phys Chem Chem Phys 2016; 18:20410-21. [DOI: 10.1039/c6cp03635j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Organic osmolytes are major cellular compounds that favor protein's compaction and stabilization of the native state. Here, we have examined the chaperone effect of the naturally occurring trimethylamine N-oxide (TMAO) osmolyte on a flexible protein.
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Affiliation(s)
- Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques
- CNRS-UMR 8229
- Collège De France
- 75231 Paris Cedex 05
- France
| | - Christophe Velours
- Macromolecular Interaction Platform of I2BC
- UMR 9198
- Centre de Recherche de Gif
- Centre National de la Recherche Scientifique
- 91191 Gif Sur Yvette
| | - David Cornu
- CNRS
- Centre de Recherche de Gif
- SICaPS
- F-91198 Gif-sur-Yvette Cedex
- France
| | - Magali Nicaise
- Macromolecular Interaction Platform of I2BC
- UMR 9198
- Centre de Recherche de Gif
- Centre National de la Recherche Scientifique
- 91191 Gif Sur Yvette
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques
- CNRS-UMR 8229
- Collège De France
- 75231 Paris Cedex 05
- France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques
- CNRS-UMR 8229
- Collège De France
- 75231 Paris Cedex 05
- France
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44
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Yoo J, Aksimentiev A. Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields. J Chem Theory Comput 2015; 12:430-43. [DOI: 10.1021/acs.jctc.5b00967] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jejoong Yoo
- Center for the Physics of
Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Center for the Physics of
Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
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45
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Usui K, Hunger J, Sulpizi M, Ohto T, Bonn M, Nagata Y. Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution. J Phys Chem B 2015; 119:10597-606. [DOI: 10.1021/acs.jpcb.5b02579] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kota Usui
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Marialore Sulpizi
- Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz, Germany
| | - Tatsuhiko Ohto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
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46
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Rahman S, Warepam M, Singh LR, Dar TA. A current perspective on the compensatory effects of urea and methylamine on protein stability and function. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:129-36. [PMID: 26095775 DOI: 10.1016/j.pbiomolbio.2015.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 11/16/2022]
Abstract
Urea is a strong denaturant and inhibits many enzymes but is accumulated intracellularly at very high concentrations (up to 3-4 M) in mammalian kidney and in many marine fishes. It is known that the harmful effects of urea on the macromolecular structure and function is offset by the accumulation of an osmolytic agent called methylamine. Intracellular concentration of urea to methylamines falls in the ratio of 2:1 to 3:2 (molar ratio). At this ratio, the thermodynamic effects of urea and methylamines on protein stability and function are believed to be algebraically additive. The mechanism of urea-methylamine counteraction has been widely investigated on various approaches including, thermodynamic, structural and functional aspects. Recent advances have also revealed atomic level insights of counteraction and various molecular dynamic simulation studies have yielded significant molecular level informations on the interaction between urea and methylamines with proteins. It is worthwhile that urea-methylamine system not only plays pivotal role for the survival and functioning of the renal medullary cells but also is a key osmoregulatory component of the marine elasmobranchs, holocephalans and coelacanths. Therefore, it is important to combine all discoveries and discuss the developments in context to physiology of the mammalian kidney and adaptation of the marine organisms. In this article we have for the first time reviewed all major developments on urea-counteraction systems to date. We have also discussed about other additional urea-counteraction systems discovered so far including urea-NaCl, urea-myoinsoitol and urea-molecular chaperone systems. Insights for the possible future research have also been highlighted.
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Affiliation(s)
- Safikur Rahman
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Marina Warepam
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Laishram R Singh
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India
| | - Tanveer Ali Dar
- Clinical Biochemistry, University of Kashmir, Srinagar, Jammu & Kashmir 190006, India.
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47
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Ganguly P, Hajari T, Shea JE, van der Vegt NFA. Mutual Exclusion of Urea and Trimethylamine N-Oxide from Amino Acids in Mixed Solvent Environment. J Phys Chem Lett 2015; 6:581-5. [PMID: 26262470 DOI: 10.1021/jz502634k] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We study the solvation of amino acids in pure-osmolyte and mixed-osmolyte urea and trimethylamine N-oxide (TMAO) solutions using molecular dynamics simulations. Analysis of Kirkwood-Buff integrals between the solution components provides evidence that in the mixed osmolytic solution, both urea and TMAO are mutually excluded from the amino acid surface, accompanied by an increase in osmolyte-osmolyte aggregation. Similar observations are made in simulations of a model protein backbone, represented by triglycine, and suggest that TMAO stabilizes proteins under urea denaturation conditions by effectively removing urea from the protein surface. The effects of the mixed osmolytes on the solvation of the amino acids and the backbone are found to be highly nonlinear in terms of the effects of the individual osmolytes and independent of differences in the strength of the TMAO-water interactions, as observed with different TMAO force fields.
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Affiliation(s)
- Pritam Ganguly
- §Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Timir Hajari
- §Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | | | - Nico F A van der Vegt
- §Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
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48
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Ball P, Hallsworth JE. Water structure and chaotropicity: their uses, abuses and biological implications. Phys Chem Chem Phys 2015; 17:8297-305. [PMID: 25628033 DOI: 10.1039/c4cp04564e] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The concept of "water structure" has been invoked to explain all manner of aqueous phenomena. Here we look at the origins of this tendency to understand solute hydration in terms of structural changes in bulk water, and consider the validity of one particular example: the classification of small solutes as chaotropic or kosmotropic, and the putative relation of this terminology to notions of structure-making and structure-breaking in the solvent. We doubt whether complex phenomena such as Hofmeister and osmolyte effects on macromolecules can be understood simply on the basis of a change in solvent structure. Rather, we argue that chaotropicity, if understood in the original sense, arises from the activities that solutes exert on macromolecular systems, as well as from deviations of solvation water from bulk-like behaviour. If applied judiciously, chaotropicity remains a potent, biologically pertinent parameter useful for classifying and understanding solution phenomena in all types of living system.
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Affiliation(s)
- Philip Ball
- 18 Hillcourt Road, East Dulwich, London SE22 0PE, UK.
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49
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Abstract
Virtually all taxa use osmolytes to protect cells against biochemical stress. Osmolytes often occur in mixtures, such as the classical combination of urea with TMAO (trimethylamine N-oxide) in cartilaginous fish or the cocktail of at least six different osmolytes in the kidney. The concentration patterns of osmolyte mixtures found in vivo make it likely that synergy between them plays an important role. Using statistical mechanical n-component Kirkwood-Buff theory, we show from first principles that synergy in protein-osmolyte systems can arise from two separable sources: (1) mutual alteration of protein surface solvation and (2) effects mediated through bulk osmolyte chemical activities. We illustrate both effects in a four-component system with the experimental example of the unfolding of a notch ankyrin domain in urea-TMAO mixtures, which make urea a less effective denaturant and TMAO a more effective stabilizer. Protein surface effects are primarily responsible for this synergy. The specific patterns of surface solvation point to denatured state expansion as the main factor, as opposed to direct competition.
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Affiliation(s)
- Jörg Rösgen
- Department of Biochemistry
and Molecular Biology, Penn State University
College of Medicine, Hershey, Pennsylvania 17033, United States
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50
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Reddy PM, Taha M, Sharma YVRK, Venkatesu P, Lee MJ. Quantifying the co-solvent effects on trypsin from the digestive system of carp Catla catla by biophysical techniques and molecular dynamics simulations. RSC Adv 2015. [DOI: 10.1039/c5ra01302j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Urea molecules locate within 0.5 nm of the surface of trypsin.
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Affiliation(s)
- P. Madhusudhana Reddy
- Department of Chemistry
- University of Delhi
- Delhi – 110 007
- India
- Department of Chemical Engineering
| | - M. Taha
- CICECO
- Departamento de Química
- Universidade de Aveiro
- 3810-193 Aveiro
- Portugal
| | | | | | - Ming-Jer Lee
- Department of Chemical Engineering
- National Taiwan University of Science & Technology
- Taipei 10607
- Taiwan
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