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Broz M, Oostenbrink C, Bren U. The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach. J Chem Inf Model 2024; 64:2077-2083. [PMID: 38477115 PMCID: PMC10966651 DOI: 10.1021/acs.jcim.3c01937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Abstract
The impact of microwave (MW) irradiation on protein folding, potentially inciting misfolding, was investigated by employing molecular dynamics (MD) simulations. Twenty-nine proteins were subjected to MD simulations under equilibrium (300 K) and MW conditions, where the rotational temperature was elevated to 700 K. The utilized replacement model captures the microwave effects of δ- and γ-relaxation processes (frequency range of ∼300 MHz to ∼20 GHz). The results disclosed that MW heating incited a shift toward more compact protein conformations, as indicated by decreased root-mean-square deviations, root-mean-square fluctuations, head-to-tail distances, and radii of gyration. This compaction was attributed to the intensification of intramolecular electrostatic interactions and hydrogen bonds within the protein caused by MW-destabilized hydrogen bonds between the protein and solvent. The solvent-accessible surface area (SASA), particularly that of polar amino-acid residues, shrank under MW conditions, corresponding to a reduced polarity of the water solvent. However, MW irradiation produced no significant alterations in protein secondary structures; hence, MW heating was observed to primarily affect the protein tertiary structures.
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Affiliation(s)
- Matic Broz
- Faculty
of Chemistry and Chemical Engineering, University
of Maribor, Smetanova ulica 17, Maribor SI-2000, Slovenia
| | - Chris Oostenbrink
- Institute
of Molecular Modeling and Simulation, University
of Natural Resources and Life Sciences, Muthgasse 18, Vienna 1190, Austria
| | - Urban Bren
- Faculty
of Chemistry and Chemical Engineering, University
of Maribor, Smetanova ulica 17, Maribor SI-2000, Slovenia
- Faculty
of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, Koper SI-6000, Slovenia
- Institute
of Environmental Protection and Sensors, Beloruska ulica 7, Maribor SI-2000, Slovenia
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2
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Kishimoto F, Yoshioka T, Ishibashi R, Yamada H, Muraoka K, Taniguchi H, Wakihara T, Takanabe K. Direct microwave energy input on a single cation for outstanding selective catalysis. SCIENCE ADVANCES 2023; 9:eadi1744. [PMID: 37595044 PMCID: PMC10438448 DOI: 10.1126/sciadv.adi1744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023]
Abstract
Microwave (MW)-driven catalytic systems are attracting attention not only as an aggressive electrification strategy of the chemical industry but also as creating a unique catalytic reaction field that conventional equilibrium heating cannot achieve. This study unlocked direct and selective heating of single alkali metal cations in the pores of aluminosilicate zeolites under MW. Selectively heated Cs+ cations in FAU zeolite exhibited selective CH4 combustion performance, that is, COx generation at the heated Cs+ cations selectively occurred while side reactions in the low-temperature gas phase were suppressed. The Cs-O pair distribution function revealed by synchrotron-based in situ x-ray total scattering gave us direct evidence of peculiar displacement induced by MW, which was consistent with the results of molecular dynamics simulation mimicking MW heating. The concept of selective monoatomic heating by MW is expected to open a next stage in "microwave catalysis" science by providing physicochemical insights into "microwave effects."
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Affiliation(s)
- Fuminao Kishimoto
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tatsushi Yoshioka
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryo Ishibashi
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroki Yamada
- Japan Synchrotron Radiation Research Institute, SPring–8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Koki Muraoka
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroki Taniguchi
- Department of Physics, Nagoya University, Nagoya 464-8602, Japan
| | - Toru Wakihara
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Institute of Engineering Innovation, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazuhiro Takanabe
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Ogrin P, Urbic T. Isothermal-isobaric algorithm to study the effects of rotational degrees of freedom-Benz water model. J Mol Liq 2022; 349:118152. [PMID: 37727581 PMCID: PMC10508877 DOI: 10.1016/j.molliq.2021.118152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed isothermal-isobaric algorithm for non-equilibrium Monte Carlo simulations. As first we have shown that the new method correctly predict density by comparing it to the density determined in canonical Monte Carlo simulations through the virial pressure. The new method was then used to study the effect of translational and rotational degrees of freedom on the structural and thermodynamic properties of the simple Mercedes-Benz water model. By holding one of the temperatures constant and varying the other one, we investigated how the position of the density maxima changes. We have observed that upon increase of rotational temperature the fluid become more Lennard-Jones like and the density maxima disappears.
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Affiliation(s)
- Peter Ogrin
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna Pot 113, SI-1000 Ljubljana, Slovenia
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5
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Thermodynamic perturbation theory for rotational degrees of freedom. Application to the Mercedes–Benz water model. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ogrin P, Urbic T. Integral equation study of the effects of rotational degrees of freedom on properties of the Mercedes–Benz water model. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114880] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Petricci E, Cini E, Taddei M. Metal Catalysis with Microwaves in Organic Synthesis: a Personal Account. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Elena Petricci
- Dipartimento di Biotecnologie; Chimica e Farmacia; Università degli Studi di Siena; Via A. Moro, 2 53100 Siena Italy
| | - Elena Cini
- Dipartimento di Biotecnologie; Chimica e Farmacia; Università degli Studi di Siena; Via A. Moro, 2 53100 Siena Italy
| | - Maurizio Taddei
- Dipartimento di Biotecnologie; Chimica e Farmacia; Università degli Studi di Siena; Via A. Moro, 2 53100 Siena Italy
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Gladovic M, Oostenbrink C, Bren U. Could Microwave Irradiation Cause Misfolding of Peptides? J Chem Theory Comput 2020; 16:2795-2802. [PMID: 32163704 PMCID: PMC7309322 DOI: 10.1021/acs.jctc.9b01104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Indexed: 11/29/2022]
Abstract
Microwaves have been experimentally shown to affect the folding dynamics of peptides and proteins. Using molecular dynamics, we performed all-atom simulations of a model β-peptide in aqueous solution where individual degrees of freedom of solvent molecules were decoupled to allow for investigation at non-equilibrium microwave-irradiated conditions. An elevated rotational temperature of the water medium was found to significantly affect the conformation of the peptide due to the weakened hydrogen-bonding interactions with the surrounding solvent molecules. Cluster analysis revealed that microwave irradiation can indeed act as a promoter in the formation of new misfolded peptide structures of the hairpin type, which are generally associated with the onset of several neurodegenerative disorders such as Alzheimer's, Parkinson's, Huntington's, and Creutzfeldt-Jakob diseases as well as certain cancer types such as amyloidosis.
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Affiliation(s)
- Martin Gladovic
- Faculty
of Chemistry and Chemical Technology, University
of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia
| | - Chris Oostenbrink
- Institute
of Molecular Modeling and Simulation, University
of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Urban Bren
- Faculty
of Chemistry and Chemical Technology, University
of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia
- National
Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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11
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Mohorič T, Bren U. Microwave irradiation affects ion pairing in aqueous solutions of alkali halide salts. J Chem Phys 2018; 146:044504. [PMID: 28147548 DOI: 10.1063/1.4974759] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Using the molecular dynamics simulations with separate thermostats for translational and rotational degrees of freedom, we investigate the effects of water's rotational motion on the ion pairing of ionic solutes in aqueous solutions. The situation with rotational temperature higher than the translational one, Trot>Ttrs, is mimicking the non-equilibrium effects of microwaves on model solutions of alkali halide salts. The simulations reveal that an increase in the rotational temperature at constant translational temperature exerts significant changes in the structure of the solution. The latter are reflected in increased pairing of the oppositely charged ions, which can be explained by the weaker ability of rotationally excited water to screen and separate the opposite charges. It seems that Collins' law of matching water affinities retains its validity also in the non-equilibrium situation where the rotational temperature exceeds the translational one. On the other hand, the equilibrium effect (i.e., an increase in the solution's overall temperature T≡Trot = Ttrs) favors the formation of small-small (NaCl), while it has a little effect on large-large (CsI) ion pairs. This is in accordance with water becoming less polar solvent upon a temperature increase. Furthermore, we investigated the effects of excited translational motion of water (and ions) on the ion pairing by increasing the translational temperature, while keeping the rotational one unchanged (i.e., Ttrs>Trot). Interestingly, in certain cases the faster translational motion causes an increase in correlations. The temperature variations in the like-ion association constants, Kas++ and Kas--, are also examined. Here the situation is more complex but, in most cases, a decrease in the ion pairing is observed.
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Affiliation(s)
- Tomaž Mohorič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana,Večna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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Jeřábek P, Florián J, Martínek V. Membrane-Anchored Cytochrome P450 1A2–Cytochrome b5 Complex Features an X-Shaped Contact between Antiparallel Transmembrane Helices. Chem Res Toxicol 2016; 29:626-36. [DOI: 10.1021/acs.chemrestox.5b00349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Petr Jeřábek
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, Albertov 2030, 128 43 Prague 2, Czech Republic
| | - Jan Florián
- Department
of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan
Road, Chicago, Illinois 60660, United States
| | - Václav Martínek
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, Albertov 2030, 128 43 Prague 2, Czech Republic
- Department of Teaching and Didactics of Chemistry, Faculty of Science, Charles University in Prague, Albertov 3, 128 43 Prague 2, Czech Republic
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13
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Mohorič T, Bren U, Vlachy V. Fast rotational motion of water molecules increases ordering of hydrophobes in solutions and may cause hydrophobic chains to collapse. J Chem Phys 2015; 143:244510. [DOI: 10.1063/1.4939085] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tomaž Mohorič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
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14
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Mohorič T, Hribar-Lee B, Vlachy V. Effects of the translational and rotational degrees of freedom on the hydration of simple solutes. J Chem Phys 2015; 140:184510. [PMID: 24832291 DOI: 10.1063/1.4875280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics simulations with separate thermostats for rotational and translational motion were used to study the effect of these degrees of freedom on the structure of water around model solutes. To describe water molecules we used the SPC/E model. The simplest solute studied here, the hydrophobe, was represented as a Lennard-Jones particle. Since direct interaction between the hydrophobe and water molecules has no angular dependence the influence of the increase of the rotational temperature on the solvation of a hydrophobe is only indirect. In the next step the central solute was assumed to be charged with either a positive or a negative charge to mimic an ion in water. Hence, depending on the charge of the ion, the neighboring water molecules assumed different angular distributions. The principal conclusions of this work are: (i) an increase of the translational temperature always decreases the height of the first peak in the solute-water radial distribution function; (ii) an increase of the rotational temperature yields an increase in the first peak in the solute-water radial distribution function for hydrophobes and cations; (iii) in contrast to this, the solvation peak decreases around ions with sufficiently large negative charge; and (iv) an increase of the rotational temperature affects cations in an opposite way to anions. For this reason complex molecules with a small net charge may not be very sensitive to variation of the rotational temperature.
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Affiliation(s)
- Tomaž Mohorič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
| | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
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15
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Jeřábek P, Florián J, Stiborová M, Martínek V. Flexible docking-based molecular dynamics/steered molecular dynamics calculations of protein-protein contacts in a complex of cytochrome P450 1A2 with cytochrome b5. Biochemistry 2014; 53:6695-705. [PMID: 25313797 DOI: 10.1021/bi500814t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Formation of transient complexes of cytochrome P450 (P450) with another protein of the endoplasmic reticulum membrane, cytochrome b5 (cyt b5), dictates the catalytic activities of several P450s. Therefore, we examined formation and binding modes of the complex of human P450 1A2 with cyt b5. Docking of soluble domains of these proteins was performed using an information-driven flexible docking approach implemented in HADDOCK. Stabilities of the five unique binding modes of the P450 1A2-cyt b5 complex yielded by HADDOCK were evaluated using explicit 10 ns molecular dynamics (MD) simulations in aqueous solution. Further, steered MD was used to compare the stability of the individual P450 1A2-cyt b5 binding modes. The best binding mode was characterized by a T-shaped mutual orientation of the porphyrin rings and a 10.7 Å distance between the two redox centers, thus satisfying the condition for a fast electron transfer. Mutagenesis studies and chemical cross-linking, which, in the absence of crystal structures, were previously used to deduce specific P450-cyt b5 interactions, indicated that the negatively charged convex surface of cyt b5 binds to the positively charged concave surface of P450. Our simulations further elaborate structural details of this interface, including nine ion pairs between R95, R100, R138, R362, K442, K455, and K465 side chains of P450 1A2 and E42, E43, E49, D65, D71, and heme propionates of cyt b5. The universal heme-centric system of internal coordinates was proposed to facilitate consistent classification of the orientation of the two porphyrins in any protein complex.
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Affiliation(s)
- Petr Jeřábek
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Albertov 2030, 128 43 Prague 2, Czech Republic
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16
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Bren U, Janežič D. Individual degrees of freedom and the solvation properties of water. J Chem Phys 2012; 137:024108. [PMID: 22803529 DOI: 10.1063/1.4732514] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using molecular dynamics simulations in conjunction with home-developed Split Integration Symplectic Method we effectively decouple individual degrees of freedom of water molecules and connect them to corresponding thermostats. In this way, we facilitate elucidation of structural, dynamical, spectral, and hydration properties of bulk water at any given combination of rotational, translational, and vibrational temperatures. Elevated rotational temperature of the water medium is found to severely hinder hydration of polar molecules, to affect hydration of ionic species in a nonmonotonous way and to somewhat improve hydration of nonpolar species. As proteins consist of charged, polar, and nonpolar amino-acid residues, the developed methodology is also applied to critically evaluate the hypothesis that the overall decrease in protein hydration and the change in the subtle balance between hydration of various types of amino-acid residues provide a plausible physical mechanism through which microwaves enhance aberrant protein folding and aggregation.
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Affiliation(s)
- Urban Bren
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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Kanno M, Nakamura K, Kanai E, Hoki K, Kono H, Tanaka M. Theoretical Verification of Nonthermal Microwave Effects on Intramolecular Reactions. J Phys Chem A 2012; 116:2177-83. [DOI: 10.1021/jp212460v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manabu Kanno
- Department
of Chemistry, Graduate
School of Science, Tohoku University, Sendai
980-8578, Japan
| | - Kosuke Nakamura
- Department
of Chemistry, Graduate
School of Science, Tohoku University, Sendai
980-8578, Japan
| | - Eri Kanai
- Department
of Chemistry, Graduate
School of Science, Tohoku University, Sendai
980-8578, Japan
| | - Kunihito Hoki
- Department
of Chemistry, Graduate
School of Science, Tohoku University, Sendai
980-8578, Japan
| | - Hirohiko Kono
- Department
of Chemistry, Graduate
School of Science, Tohoku University, Sendai
980-8578, Japan
| | - Motohiko Tanaka
- College
of Engineering, Chubu University, 1200
Matsumoto-cho, Kasugai 487-8501,
Japan
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Mizrahi S. Mechanisms of Objectionable Textural Changes by Microwave Reheating of Foods: A Review. J Food Sci 2012; 77:R57-62. [DOI: 10.1111/j.1750-3841.2011.02515.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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de Moura AP, de Oliveira LH, Paris EC, Li MS, Andrés J, Varela JA, Longo E, Rosa ILV. Photolumiscent Properties of Nanorods and Nanoplates Y2O3:Eu3+. J Fluoresc 2011; 21:1431-8. [DOI: 10.1007/s10895-010-0827-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 12/29/2010] [Indexed: 11/28/2022]
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