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Xue C, You J, Xiong S, Yin T, Du W, Huang Q. Myosin head as the main off-odors binding region: Key binding residues and conformational changes in the binding process. Food Chem 2023; 403:134437. [DOI: 10.1016/j.foodchem.2022.134437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/24/2022]
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2
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Zheng K, Ji MH, Chu FH, Jiang YH, Yang CK, Xue L, Jiang C. The Effect of External Electric Field on the Conformational Integrity of Trypsin Inhibitor: A Molecular Model Study. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422110103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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3
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Noble BB, Todorova N, Yarovsky I. Electromagnetic bioeffects: a multiscale molecular simulation perspective. Phys Chem Chem Phys 2022; 24:6327-6348. [PMID: 35245928 DOI: 10.1039/d1cp05510k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.
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Affiliation(s)
- Benjamin B Noble
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Nevena Todorova
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
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4
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Gorai B, Vashisth H. Progress in Simulation Studies of Insulin Structure and Function. Front Endocrinol (Lausanne) 2022; 13:908724. [PMID: 35795141 PMCID: PMC9252437 DOI: 10.3389/fendo.2022.908724] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 01/02/2023] Open
Abstract
Insulin is a peptide hormone known for chiefly regulating glucose level in blood among several other metabolic processes. Insulin remains the most effective drug for treating diabetes mellitus. Insulin is synthesized in the pancreatic β-cells where it exists in a compact hexameric architecture although its biologically active form is monomeric. Insulin exhibits a sequence of conformational variations during the transition from the hexamer state to its biologically-active monomer state. The structural transitions and the mechanism of action of insulin have been investigated using several experimental and computational methods. This review primarily highlights the contributions of molecular dynamics (MD) simulations in elucidating the atomic-level details of conformational dynamics in insulin, where the structure of the hormone has been probed as a monomer, dimer, and hexamer. The effect of solvent, pH, temperature, and pressure have been probed at the microscopic scale. Given the focus of this review on the structure of the hormone, simulation studies involving interactions between the hormone and its receptor are only briefly highlighted, and studies on other related peptides (e.g., insulin-like growth factors) are not discussed. However, the review highlights conformational dynamics underlying the activities of reported insulin analogs and mimetics. The future prospects for computational methods in developing promising synthetic insulin analogs are also briefly highlighted.
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5
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Zhu Y, Wang J, Vanga SK, Raghavan V. Visualizing structural changes of egg avidin to thermal and electric field stresses by molecular dynamics simulation. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112139] [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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6
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Todorova N, Bentvelzen A, Yarovsky I. Electromagnetic field modulates aggregation propensity of amyloid peptides. J Chem Phys 2020; 152:035104. [DOI: 10.1063/1.5126367] [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] Open
Affiliation(s)
- N. Todorova
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia
- Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - A. Bentvelzen
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia
- Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - I. Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia
- Australian Centre for Electromagnetic Bioeffects Research, Australia
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7
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Saxena R, Vanga SK, Raghavan V. Effect of thermal and microwave processing on secondary structure of bovine β-lactoglobulin: A molecular modeling study. J Food Biochem 2019; 43:e12898. [PMID: 31353721 DOI: 10.1111/jfbc.12898] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 01/26/2019] [Accepted: 04/08/2019] [Indexed: 11/30/2022]
Abstract
Milk allergy is known to cause severe allergic reactions in hypersensitive patients, especially in infants and children. β-Lactoglobulin is one of the major allergens in bovine milk. The influence of thermal and microwave processing on the structural deviations of β-lactoglobulin protein have been studied using molecular modeling techniques. The structural deviations are studied using root mean square deviations, radius of gyration, dipole moment, and solvent accessible surface area. STRIDE analysis showed significant changes in the β-lactoglobulin, especially when oscillating electric fields were applied along with heat. Root mean square fluctuations (RMSF) has been assessed for known epitopes in the β-lactoglobulin molecule. This showed that when the protein is exposed to certain thermal stress, it compacts by burying hydrophobic residues in the core. However, few allergic epitope residues also exhibit increased RMSF leading to higher reactive sites on the surface of the protein molecule. PRACTICAL APPLICATIONS: This study showed that molecular modeling can be used to gain valuable insights regarding the structural changes during processing. In the future, with more computational capacity, it can be used to make comparison between results obtained from simulations and real-time experiments. The current techniques used in food industries such as Nuclear Magnetic Resonance Imaging, Fourier Transformation Infrared Spectroscopy, X-ray diffraction can analyze pre- and post-processing effects. Hence, it become necessary to understand the changes that takes place during the processing techniques. Molecular dynamic simulation could be a useful technique in analyzing the changes occurring during the processing.
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Affiliation(s)
- Rachit Saxena
- Faculty of Agricultural and Environmental Sciences, Department of Bioresource Engineering, McGill University, Montreal, Quebec, Canada
| | - Sai Kranthi Vanga
- Faculty of Agricultural and Environmental Sciences, Department of Bioresource Engineering, McGill University, Montreal, Quebec, Canada
| | - Vijaya Raghavan
- Faculty of Agricultural and Environmental Sciences, Department of Bioresource Engineering, McGill University, Montreal, Quebec, Canada
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8
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Todorova N, Yarovsky I. The Enigma of Amyloid Forming Proteins: Insights From Molecular Simulations. Aust J Chem 2019. [DOI: 10.1071/ch19059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular level insight into the interplay between protein sequence, structure, and conformational dynamics is crucial for the comprehensive understanding of protein folding, misfolding, and aggregation phenomena that are pertinent to the formation of amyloid fibrils implicated in several degenerative diseases. Computational modelling provides insight into protein behaviour at spatial and temporal resolution still largely outside the reach of experiments. Herein we present an account of our theoretical modelling research conducted in collaboration with several experimental groups where we explored the effects of local environment on the structure and aggregation propensity of several types of amyloidogenic peptides and proteins, including apolipoprotein C-II, insulin, amylin, and amyloid-β using a variety of computational approaches.
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9
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Changes in soybean trypsin inhibitor by varying pressure and temperature of processing: A molecular modeling study. INNOV FOOD SCI EMERG 2018. [DOI: 10.1016/j.ifset.2018.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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10
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Singh A, Vanga SK, Orsat V, Raghavan V. Application of molecular dynamic simulation to study food proteins: A review. Crit Rev Food Sci Nutr 2017; 58:2779-2789. [DOI: 10.1080/10408398.2017.1341864] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ashutosh Singh
- School of Engineering, University of Guelph, Guelph, Ontario, Canada
| | - Sai Kranthi Vanga
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Valerie Orsat
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Vijaya Raghavan
- Faculty of Agriculture and Environmental Studies, Department of Bioresource Engineering, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
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11
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Alizadeh H, Davoodi J, Rafii-Tabar H. Deconstruction of the human connexin 26 hemichannel due to an applied electric field; A molecular dynamics simulation study. J Mol Graph Model 2017; 73:108-114. [PMID: 28259639 DOI: 10.1016/j.jmgm.2017.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
Abstract
Connexins are a 21-member membrane protein family constituting channels evolved in direct communication between adjacent cells by passaging cytoplasmic molecules and ions. Hexametrical assembly of connexin proteins in plasma membrane forms a wide aqueous pore known as connexin hemichannel. These hemichannels mediate cytoplasm and extracellular milieu communication both in many external tissues and in the central nervous system. In this study, a series of molecular dynamics simulations has been performed to investigate the effect of applied static and alternating electric fields on the stability and conformation of human connexin26 hemichannel. The root mean square deviations of C-alpha atoms, the dipole moment distribution, the number of inter-protein hydrogen bonds and the number of water-protein hydrogen bonds were used to assess connexin26 hemichannel stability. In the static field case, our results show that although the lowest field used in this study (0.1V/nm) does not lead to the hemichannel deconstruction, stronger fields (>0.1V/nm), however, disrupt the protein structure during the simulations time period. Furthermore, in the alternating case, compared to static field case, field effects on the connexin26 hemichannel conformation are reduced and consequently the protein maintains its native structure for longer times. Specifically, for the highest frequency used in this study (50GHz), the hemichannel keeps its structure even under the effect of the strongest field (0.4V/nm). According to our results, the protein secondary structure is preserved in the characteristic times determined for the protein deconstruction. Consequently, we suggest that the protein deconstruction is due to the tertiary and quaternary structure loss.
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Affiliation(s)
- Hadi Alizadeh
- Department of Physics, Faculty of Sciences, University of Zanjan, Zanajn, Iran
| | - Jamal Davoodi
- Department of Physics, Faculty of Sciences, University of Zanjan, Zanajn, Iran
| | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering, School of Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran.
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12
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Atabay M, Jahanbin Sardroodi J, Rastkar Ebrahimzadeh A. Adsorption and immobilisation of human insulin on graphene monoxide, silicon carbide and boron nitride nanosheets investigated by molecular dynamics simulation. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1270452] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Maryam Atabay
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Lab, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Rastkar Ebrahimzadeh
- Department of Chemistry, Azarbaijan Shahid Madani University, Tabriz, Iran
- Department of Physics, Azarbaijan Shahid Madani University, Tabriz, Iran
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13
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Todorova N, Bentvelzen A, English NJ, Yarovsky I. Electromagnetic-field effects on structure and dynamics of amyloidogenic peptides. J Chem Phys 2016; 144:085101. [PMID: 26931725 DOI: 10.1063/1.4941108] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (>0.04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (<0.004 V/nm) promote the formation of the amyloid-prone hairpin structures relative to the ambient conditions. These findings suggest that intermediate-strength electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.
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Affiliation(s)
- Nevena Todorova
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne, Australia
| | - Alan Bentvelzen
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne, Australia
| | - Niall J English
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Irene Yarovsky
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne, Australia
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14
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Harish Vagadia B, Vanga SK, Singh A, Raghavan V. Effects of thermal and electric fields on soybean trypsin inhibitor protein: A molecular modelling study. INNOV FOOD SCI EMERG 2016. [DOI: 10.1016/j.ifset.2016.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Effect of thermal and electric field treatment on the conformation of Ara h 6 peanut protein allergen. INNOV FOOD SCI EMERG 2015. [DOI: 10.1016/j.ifset.2015.03.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Vashisth H. Theoretical and computational studies of peptides and receptors of the insulin family. MEMBRANES 2015; 5:48-83. [PMID: 25680077 PMCID: PMC4384091 DOI: 10.3390/membranes5010048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/28/2015] [Indexed: 01/05/2023]
Abstract
Synergistic interactions among peptides and receptors of the insulin family are required for glucose homeostasis, normal cellular growth and development, proliferation, differentiation and other metabolic processes. The peptides of the insulin family are disulfide-linked single or dual-chain proteins, while receptors are ligand-activated transmembrane glycoproteins of the receptor tyrosine kinase (RTK) superfamily. Binding of ligands to the extracellular domains of receptors is known to initiate signaling via activation of intracellular kinase domains. While the structure of insulin has been known since 1969, recent decades have seen remarkable progress on the structural biology of apo and liganded receptor fragments. Here, we review how this useful structural information (on ligands and receptors) has enabled large-scale atomically-resolved simulations to elucidate the conformational dynamics of these biomolecules. Particularly, applications of molecular dynamics (MD) and Monte Carlo (MC) simulation methods are discussed in various contexts, including studies of isolated ligands, apo-receptors, ligand/receptor complexes and intracellular kinase domains. The review concludes with a brief overview and future outlook for modeling and computational studies in this family of proteins.
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Affiliation(s)
- Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, 33 Academic Way, Durham, NH 03824, USA.
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17
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Astrakas LG, Gousias C, Tzaphlidou M. Electric field effects on alanine tripeptide in sodium halide solutions. Electromagn Biol Med 2014; 34:361-9. [PMID: 25006865 DOI: 10.3109/15368378.2014.936065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The electric field effects on conformational properties of trialanine in different halide solutions were explored with long-scale molecular dynamics simulations. NaF, NaCl, NaBr and NaI solutions of low (0.2 M) and high (2 M) concentrations were exposed to a constant electric field of 1000 V/m. Generally, the electric field does not disturb trialanine's structure. Large structural changes appear only in the case of the supersaturated 2.0 M NaF solution containing NaF crystals. Although the electric field affects in a complex way, all the ions-water-peptide interactions, it predominantly affects the electroselectivity effect, which describes specific interactions such as the ion-pair formation.
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Affiliation(s)
- Loukas G Astrakas
- a Laboratories of Medical Physics , Medical School, University of Ioannina , Ioannina , Greece
| | - Christos Gousias
- a Laboratories of Medical Physics , Medical School, University of Ioannina , Ioannina , Greece
| | - Margaret Tzaphlidou
- a Laboratories of Medical Physics , Medical School, University of Ioannina , Ioannina , Greece
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18
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Ilizaliturri-Flores I, Correa-Basurto J, Benítez-Cardoza CG, Zamorano-Carrillo A. A study of the structural properties and thermal stability of human Bcl-2 by molecular dynamics simulations. J Biomol Struct Dyn 2013; 32:1707-19. [PMID: 24028527 DOI: 10.1080/07391102.2013.833858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The anti-apoptotic B-cell lymphoma 2 (Bcl-2) protein interacts with several proteins that regulate the apoptotic properties of cells. In this research, we conduct several all-atom molecular dynamics (MD) simulations under high-temperature unfolding conditions, from 400 to 800 K, for 25 ns. These simulations were performed using a model of an engineered Bcl-2 human protein (Bcl-2-Δ22Σ3), which lacks 22 C-terminal residues of the transmembrane domain. The aim of this study is to gain insight into the structural behavior of Bcl-2-Δ22Σ3 by mapping the conformational movements involved in Bcl-2 stability and its biological function. To build a Bcl-2-Δ22Σ3 three-dimensional model, the protein core was built by homology modeling and the flexible loop domain (FLD, residues 33-91) by ab initio methods. Further, the entire protein model was refined by MD simulations. Afterwards, the production MD simulations showed that the FLD at 400 and 500 K has several conformations reaching into the protein core, whereas at 600 K some of the alpha-helices were lost. At 800 K, the Bcl-2 core is destabilized suggesting a possible mechanism for protein unfolding, where the alpha helices 1 and 6 were the most stable, and a reduction in the number of hydrogen bonds initially occurs. In conclusion, the structural changes and the internal protein interactions suggest that the core and the FLD are crucial components of Bcl-2 in its function of regulate ng access to the recognition sites of kinases and caspases.
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Affiliation(s)
- Ian Ilizaliturri-Flores
- a Laboratorio de Investigación Bioquímica, Doctorado en Ciencias en Biotecnología , ENMH, Instituto Politécnico Nacional , Guillermo Massieu Helguera #239 Fracc. "La Escalera" Ticoman, C.P. 07320, D.F. México , Mexico
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19
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Effect of External Electric Field Stress on Gliadin Protein Conformation. Proteomes 2013; 1:25-39. [PMID: 28250397 PMCID: PMC5302742 DOI: 10.3390/proteomes1020025] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/05/2013] [Accepted: 06/20/2013] [Indexed: 11/17/2022] Open
Abstract
A molecular dynamic (MD) modeling approach was applied to evaluate the effect of external electric field on gliadin protein structure and surface properties. Static electric field strengths of 0.001 V/nm and 0.002 V/nm induced conformational changes in the protein but had no significant effect on its surface properties. The study of hydrogen bond evolution during the course of simulation revealed that the root mean square deviation, radius of gyration and secondary structure formation, all depend significantly on the number hydrogen bonds formed. This study demonstrated that it is necessary to gain insight into protein dynamics under external electric field stress, in order to develop the novel food processing techniques that can be potentially used to reduce or eradicate food allergens.
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20
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Marracino P, Apollonio F, Liberti M, d’Inzeo G, Amadei A. Effect of High Exogenous Electric Pulses on Protein Conformation: Myoglobin as a Case Study. J Phys Chem B 2013; 117:2273-9. [DOI: 10.1021/jp309857b] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Paolo Marracino
- Dipartimento di Ingegneria dell’Informazione,
Elettronica e Telecomunicazioni Sapienza, Università di Roma, Roma, Italy
| | - Francesca Apollonio
- Dipartimento di Ingegneria dell’Informazione,
Elettronica e Telecomunicazioni Sapienza, Università di Roma, Roma, Italy
| | - Micaela Liberti
- Dipartimento di Ingegneria dell’Informazione,
Elettronica e Telecomunicazioni Sapienza, Università di Roma, Roma, Italy
| | - Guglielmo d’Inzeo
- Dipartimento di Ingegneria dell’Informazione,
Elettronica e Telecomunicazioni Sapienza, Università di Roma, Roma, Italy
| | - Andrea Amadei
- Dipartimento di Scienze e Tecnologie
Chimiche, Università di Roma ‘Tor Vergata’, Roma, Italy
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21
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Singh A, Orsat V, Raghavan V. Soybean hydrophobic protein response to external electric field: a molecular modeling approach. Biomolecules 2013; 3:168-79. [PMID: 24970163 PMCID: PMC4030879 DOI: 10.3390/biom3010168] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 01/30/2013] [Accepted: 02/04/2013] [Indexed: 11/28/2022] Open
Abstract
The molecular dynamic (MD) modeling approach was applied to evaluate the effect of an external electric field on soybean hydrophobic protein and surface properties. Nominal electric field strengths of 0.002 V/nm and 0.004 V/nm had no major effect on the structure and surface properties of the protein isolate but the higher electric field strength of 3 V/nm significantly affected the protein conformation and solvent accessible surface area. The response of protein isolate to various external field stresses demonstrated that it is necessary to gain insight into protein dynamics under electromagnetic fields in order to be able to develop the techniques utilizing them for food processing and other biological applications.
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Affiliation(s)
- Ashutosh Singh
- Department of Bioresource Engineering, McGill University, 21,111 Rue Lakeshore, Ste-anne-de-bellevue, QC, H9X 3V9, Canada.
| | - Valérie Orsat
- Department of Bioresource Engineering, McGill University, 21,111 Rue Lakeshore, Ste-anne-de-bellevue, QC, H9X 3V9, Canada.
| | - Vijaya Raghavan
- Department of Bioresource Engineering, McGill University, 21,111 Rue Lakeshore, Ste-anne-de-bellevue, QC, H9X 3V9, Canada.
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22
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Ganim Z, Jones KC, Tokmakoff A. Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2010; 12:3579-88. [DOI: 10.1039/b923515a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A structurally sensitive probe of the monomer/dimer equilibrium of insulin was developed using 2DIR spectroscopy and interpreted using calculated spectra.
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Affiliation(s)
- Ziad Ganim
- Department of Chemistry
- Massachusetts Institute of Technology
- Cambridge
- USA
| | - Kevin C. Jones
- Department of Chemistry
- Massachusetts Institute of Technology
- Cambridge
- USA
| | - Andrei Tokmakoff
- Department of Chemistry
- Massachusetts Institute of Technology
- Cambridge
- USA
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23
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Todorova N, Marinelli F, Piana S, Yarovsky I. Exploring the folding free energy landscape of insulin using bias exchange metadynamics. J Phys Chem B 2009; 113:3556-64. [PMID: 19243106 DOI: 10.1021/jp809776v] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bias exchange metadynamics (BE-META) technique was applied to investigate the folding mechanism of insulin, one of the most studied and biologically important proteins. The BE-META simulations were performed starting from an extended conformation of chain B of insulin, using only eight replicas and seven reaction coordinates. The folded state, together with the intermediate states along the folding pathway were identified and their free energy was determined. Three main basins were found separated from one another by a large free energy barrier. The characteristic native fold of chain B was observed in one basin, while the other two most populated basins contained "molten-globule" conformations stabilized by electrostatic and hydrophobic interactions, respectively. Transitions between the three basins occur on the microsecond time scale. The implications and relevance of this finding to the folding mechanisms of insulin were investigated.
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Affiliation(s)
- Nevena Todorova
- Applied Physics, School of Applied Sciences, RMIT University, Melbourne, Victoria, Australia
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Todorova N, Legge FS, Treutlein H, Yarovsky I. Systematic Comparison of Empirical Forcefields for Molecular Dynamic Simulation of Insulin. J Phys Chem B 2008; 112:11137-46. [DOI: 10.1021/jp076825d] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nevena Todorova
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria, 3001, Australia, and Cytopia Research Pty. Ltd., PO Box 6492, St. Kilda Road Central, Melbourne, Victoria, 8008, Australia
| | - F. Sue Legge
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria, 3001, Australia, and Cytopia Research Pty. Ltd., PO Box 6492, St. Kilda Road Central, Melbourne, Victoria, 8008, Australia
| | - Herbert Treutlein
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria, 3001, Australia, and Cytopia Research Pty. Ltd., PO Box 6492, St. Kilda Road Central, Melbourne, Victoria, 8008, Australia
| | - Irene Yarovsky
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria, 3001, Australia, and Cytopia Research Pty. Ltd., PO Box 6492, St. Kilda Road Central, Melbourne, Victoria, 8008, Australia
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Budi A, Legge FS, Treutlein H, Yarovsky I. Comparative Study of Insulin Chain-B in Isolated and Monomeric Environments under External Stress. J Phys Chem B 2008; 112:7916-24. [DOI: 10.1021/jp800350v] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akin Budi
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria, 3001, Australia, and Cytopia Research Pty. Ltd., PO Box 6492, St. Kilda Road Central, Melbourne, Victoria, 8008, Australia
| | - F. Sue Legge
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria, 3001, Australia, and Cytopia Research Pty. Ltd., PO Box 6492, St. Kilda Road Central, Melbourne, Victoria, 8008, Australia
| | - Herbert Treutlein
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria, 3001, Australia, and Cytopia Research Pty. Ltd., PO Box 6492, St. Kilda Road Central, Melbourne, Victoria, 8008, Australia
| | - Irene Yarovsky
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria, 3001, Australia, and Cytopia Research Pty. Ltd., PO Box 6492, St. Kilda Road Central, Melbourne, Victoria, 8008, Australia
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Budi A, Legge FS, Treutlein H, Yarovsky I. Electric field effects on insulin chain-B conformation. J Phys Chem B 2007; 109:22641-8. [PMID: 16853947 DOI: 10.1021/jp052742q] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The response of proteins to different forms of stress continues to be a topic of major interest, especially with the proliferation of electromagnetic devices conjectured to have detrimental effects on human health. In this paper, we have performed molecular dynamics simulations on insulin chain-B under the influence of both static and oscillating electric fields, ranging from 10(7) to 10(9) V/m. We have found that both variants have an effect on the normal behavior of the protein, with oscillating fields being more disruptive to the structure as compared to static fields of similar effective strength. The application of a static field had a stabilizing effect on the secondary structure, restricting the inherent flexibility that is crucial for insulin's biological activity.
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Affiliation(s)
- Akin Budi
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria, 3001, Australia
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Budi A, Legge FS, Treutlein H, Yarovsky I. Effect of frequency on insulin response to electric field stress. J Phys Chem B 2007; 111:5748-56. [PMID: 17472363 DOI: 10.1021/jp067248g] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There are many unanswered questions regarding the precise way in which proteins respond to external stress. Since the function of proteins is critically linked to their three-dimensional structures, exposure to any form of stress which may induce changes in conformation can potentially initiate severe cellular dysfunction. This is particularly relevant with regard to the increasing presence of electromagnetic devices in today's environment and the possible effects on human health. Previously, we investigated the effect of electric field of various strengths on insulin chain-B under static and oscillating conditions. This paper expands on our previous work by subjecting the peptide to an oscillating electric field of different frequencies. We observed a frequency-dependent effect where the application of lower-frequency oscillating fields resulted in static-field-like behavior of the peptide, whereby the intrinsic flexibility of the protein is constrained, thus potentially restricting access to the protein's active state.
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Affiliation(s)
- Akin Budi
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria 3001, Australia
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Legge FS, Budi A, Treutlein H, Yarovsky I. Protein flexibility: multiple molecular dynamics simulations of insulin chain B. Biophys Chem 2005; 119:146-57. [PMID: 16129550 DOI: 10.1016/j.bpc.2005.08.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 08/03/2005] [Accepted: 08/03/2005] [Indexed: 11/15/2022]
Abstract
Multiple molecular dynamics simulations totaling more than 100 ns were performed on chain B of insulin in explicit solvent at 300 K and 400 K. Despite some individual variations, a comparison of the protein dynamics of each simulation showed similar trends and most structures were consistent with NMR experimental values, even at the elevated temperature. The importance of packing interactions in determining the conformational transitions of the protein was observed, sometimes resulting in conformations induced by localized hydrophobic interactions. The high temperature simulation generated a more diverse range of structures with similar elements of secondary structure and populated conformations to the simulations at room temperature. A broad sampling of the conformational space of insulin chain B illustrated a wide range of conformational states with many transitions at room temperature in addition to the conformational states observed experimentally. The T-state conformation associated with insulin activity was consistently present and a possible mechanism of behavior was suggested.
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Affiliation(s)
- F S Legge
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria 3001, Australia
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