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Zhang L, Ma M, Li J, Qiao K, Xie Y, Zheng Y. Stimuli-responsive microcarriers and their application in tissue repair: A review of magnetic and electroactive microcarrier. Bioact Mater 2024; 39:147-162. [PMID: 38808158 PMCID: PMC11130597 DOI: 10.1016/j.bioactmat.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/07/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Microcarrier applications have made great advances in tissue engineering in recent years, which can load cells, drugs, and bioactive factors. These microcarriers can be minimally injected into the defect to help reconstruct a good microenvironment for tissue repair. In order to achieve more ideal performance and face more complex tissue damage, an increasing amount of effort has been focused on microcarriers that can actively respond to external stimuli. These microcarriers have the functions of directional movement, targeted enrichment, material release control, and providing signals conducive to tissue repair. Given the high controllability and designability of magnetic and electroactive microcarriers, the research progress of these microcarriers is highlighted in this review. Their structure, function and applications, potential tissue repair mechanisms, and challenges are discussed. In summary, through the design with clinical translation ability, meaningful and comprehensive experimental characterization, and in-depth study and application of tissue repair mechanisms, stimuli-responsive microcarriers have great potential in tissue repair.
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Affiliation(s)
- LiYang Zhang
- School of Material Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Mengjiao Ma
- Beijing Wanjie Medical Device Co., Ltd, Beijing, China
| | - Junfei Li
- School of Material Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Kun Qiao
- Beijing Gerecov Technology Company Ltd., Beijing, China
| | - Yajie Xie
- Beijing Gerecov Technology Company Ltd., Beijing, China
| | - Yudong Zheng
- School of Material Science and Engineering, University of Science and Technology Beijing, Beijing, China
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2
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Khursandov J, Mashalov R, Makhkamov M, Turgunboev F, Sharipov A, Razzokov J. Exploring α-synuclein stability under the external electrostatic fields: Effect of repeat unit. J Struct Biol 2024; 216:108109. [PMID: 38964522 DOI: 10.1016/j.jsb.2024.108109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Parkinson's disease (PD) is a category of neurodegenerative disorders (ND) that currently lack comprehensive and definitive treatment strategies. The etiology of PD can be attributed to the presence and aggregation of a protein known as α-synuclein. Researchers have observed that the application of an external electrostatic field holds the potential to induce the separation of the fibrous structures into peptides. To comprehend this phenomenon, our investigation involved simulations conducted on the α-synuclein peptides through the application of Molecular Dynamics (MD) simulation techniques under the influence of a 0.1 V/nm electric field. The results obtained from the MD simulations revealed that in the presence of external electric field, the monomer and oligomeric forms of α-synuclein are experienced significant conformational changes which could prevent them from further aggregation. However, as the number of peptide units in the model system increases, forming trimers and tetramers, the stability against the electric field also increases. This enhanced stability in larger aggregates indicates a critical threshold in α-synuclein assembly where the electric field's effectiveness in disrupting the aggregation diminishes. Therefore, our findings suggest that early diagnosis and intervention could be crucial in preventing PD progression. When α-synuclein predominantly exists in its monomeric or dimeric form, applying even a lower electric field could effectively disrupt the initial aggregation process. Inhibition of α-synuclein fibril formation at early stages might serve as a viable solution to combat PD by halting the formation of more stable and pathogenic α-synuclein fibrils.
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Affiliation(s)
- Javokhir Khursandov
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan; Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Universitet 7, Tashkent 100174, Uzbekistan
| | - Rasulbek Mashalov
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan; Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Universitet 7, Tashkent 100174, Uzbekistan
| | - Mukhriddin Makhkamov
- Department of Chemistry, National University of Uzbekistan, Universitet 4, 100174 Tashkent, Uzbekistan; Department of Information Technologies, Tashkent International University of Education, Imom Bukhoriy 6, Tashkent 100207, Uzbekistan
| | - Farkhad Turgunboev
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
| | - Avez Sharipov
- Depatment of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan; Department of Natural Sciences, Shakhrisabz State Pedagogical Institute, Shakhrisabz Street 10, Kashkadarya 181301, Uzbekistan; Department of Biotechnology, Tashkent State Technical University, Universitet 2, Tashkent 100095, Uzbekistan
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Dorčák V, Kroutil O, Kabeláč M, Janata J, Vacek J. Cysteamine Chemisorption at Mercury-Solution Interfaces in the Context of Redox and Microdissociation Equilibria. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:6253-6260. [PMID: 38489512 DOI: 10.1021/acs.langmuir.3c03744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
The redox behavior and chemisorption of cysteamine (CA) at a charged mercury surface are described, with an emphasis on its acid-base properties supported by molecular dynamics and quantum mechanical calculations. It was found that CA forms chemisorbed layers on the surface of the mercury electrode. The formation of Hg-CA complexes is connected to mercury disproportionation, as reflected in peaks SII and SI at potentials higher than the electrode potential of zero charge (p.z.c.). Both the process of chemisorption of CA and its consequent redox transformation are proton-dependent. Also, depending on the protonation of CA, the formation of typical populations of chemisorbed conformers can be observed. In addition, cystamine (CA disulfide dimer) can be reduced on the mercury surface. Between the potentials of this reduction and peak SI, the p.z.c. of the electrode used can be found. Furthermore, CA can serve as an LMW catalyst for hydrogen evolution. The mechanistic insights presented here can be used for follow-up research on CA chemisorption and targeted modification of other metallic surfaces.
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Affiliation(s)
- Vlastimil Dorčák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, Olomouc 775 15, Czech Republic
| | - Ondřej Kroutil
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Martin Kabeláč
- Department of Chemistry, Faculty of Science, University of South Bohemia, Branisovska 31, Ceske Budejovice 370 05, Czech Republic
| | - Jiří Janata
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, Olomouc 775 15, Czech Republic
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4
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Vacek J, Zatloukalová M, Dorčák V, Cifra M, Futera Z, Ostatná V. Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field. Mikrochim Acta 2023; 190:442. [PMID: 37847341 PMCID: PMC10582152 DOI: 10.1007/s00604-023-05999-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.
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Affiliation(s)
- Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic.
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Vlastimil Dorčák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, 18200, Prague, Czech Republic
| | - Zdeněk Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Sciences, v.v.i., Kralovopolska 135, 61200, Brno, Czech Republic
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5
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Huang Z, Wang C, Chen X, Ding S, Xiang Q, Xie M, Huang Y, Li H. Regulation of recombinant humanized collagen on HAP growth and its molecule simulation. RSC Adv 2023; 13:26031-26040. [PMID: 37664193 PMCID: PMC10472339 DOI: 10.1039/d3ra03810f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/13/2023] [Indexed: 09/05/2023] Open
Abstract
Hydroxyapatite (HAP) in natural bone is formed under the regulation of natural collagen I. Here, we report how recombinant humanized collagen I (rhCol I) regulates the growth of HAP nanocrystals in a long belt shape 100-150 nm in width and 200-300 nm in length. MD simulation results showed that the interactions between rhCol I and the (001), (100), and (211) planes of HAP mainly contributed to the electrostatic force and van der Waals forces via COO⋯Ca, -NH⋯Ca, CH⋯OPO3, and NH⋯OPO3 bonds, respectively. On the (001) plane, the interaction between -COO- and Ca was stronger than on the (100) and (211) planes, resulting in a large electrostatic force, which inhibited the growth of the (001) plane. The lowest energy of adsorption to the (211) plane resulted in the preferential growth of the (211) plane due to the weakest interaction with rhCol I. The detailed correlation between HAP and rhCol I could explain HAP growth under regulation by rhCol I. This study provides a reference for the bio-application of recombinant collagen.
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Affiliation(s)
- Zhilin Huang
- College of Chemistry and Materials Science, Jinan University Guangzhou 510632 China
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education Guangzhou 510632 China
| | - Chucheng Wang
- College of Chemistry and Materials Science, Jinan University Guangzhou 510632 China
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education Guangzhou 510632 China
| | - Xiaohui Chen
- College of Chemistry and Materials Science, Jinan University Guangzhou 510632 China
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education Guangzhou 510632 China
| | - Shan Ding
- College of Chemistry and Materials Science, Jinan University Guangzhou 510632 China
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education Guangzhou 510632 China
| | - Qi Xiang
- Institute of Biomedicine and Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University Guangzhou 510632 China
| | - Mo Xie
- College of Chemistry and Materials Science, Jinan University Guangzhou 510632 China
- Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications Guangzhou 510632 China
| | - Yadong Huang
- Institute of Biomedicine and Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University Guangzhou 510632 China
| | - Hong Li
- College of Chemistry and Materials Science, Jinan University Guangzhou 510632 China
- Engineering Research Center of Artificial Organs and Materials, Ministry of Education Guangzhou 510632 China
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Bhattacharjee N, Alonso-Cotchico L, Lucas MF. Enzyme immobilization studied through molecular dynamic simulations. Front Bioeng Biotechnol 2023; 11:1200293. [PMID: 37362217 PMCID: PMC10285225 DOI: 10.3389/fbioe.2023.1200293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.
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Cartus JJ, Jeindl A, Werkovits A, Hörmann L, Hofmann OT. Polymorphism mediated by electric fields: a first principles study on organic/inorganic interfaces. NANOSCALE ADVANCES 2023; 5:2288-2298. [PMID: 37056613 PMCID: PMC10089127 DOI: 10.1039/d2na00851c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/19/2023] [Indexed: 06/19/2023]
Abstract
Organic/inorganic interfaces are known to exhibit rich polymorphism, where different polymorphs often possess significantly different properties. Which polymorph forms during an experiment depends strongly on environmental parameters such as deposition temperature and partial pressure of the molecule to be adsorbed. To prepare desired polymorphs these parameters are varied. However, many polymorphs are difficult to access within the experimentally available temperature-pressure ranges. In this contribution, we investigate how electric fields can be used as an additional lever to make certain structures more readily accessible. On the example of tetracyanoethylene (TCNE) on Cu(111), we analyze how electric fields change the energy landscape of interface systems. TCNE on Cu(111) can form either lying or standing polymorphs, which exhibit significantly different work functions. We combine first-principles calculations with a machine-learning based structure search algorithm and ab initio thermodynamics to demonstrate that electric fields can be exploited to shift the temperature of the phase transition between standing and lying polymorphs by up to 100 K.
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Affiliation(s)
- Johannes J Cartus
- Institute of Solid State Physics, Graz University of Technology, NAWI Graz Petersgasse 16 8010 Graz Austria
| | - Andreas Jeindl
- Institute of Solid State Physics, Graz University of Technology, NAWI Graz Petersgasse 16 8010 Graz Austria
| | - Anna Werkovits
- Institute of Solid State Physics, Graz University of Technology, NAWI Graz Petersgasse 16 8010 Graz Austria
| | - Lukas Hörmann
- Institute of Solid State Physics, Graz University of Technology, NAWI Graz Petersgasse 16 8010 Graz Austria
| | - Oliver T Hofmann
- Institute of Solid State Physics, Graz University of Technology, NAWI Graz Petersgasse 16 8010 Graz Austria
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8
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Razzokov J, Fazliev S, Makhkamov M, Marimuthu P, Baev A, Kurganov E. Effect of Electric Field on α-Synuclein Fibrils: Revealed by Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24076312. [PMID: 37047286 PMCID: PMC10094641 DOI: 10.3390/ijms24076312] [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: 12/23/2022] [Revised: 02/24/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The self-association of amylogenic proteins to the fibril form is considered a pivotal factor in the pathogenesis of neurodegenerative diseases, including Parkinson’s disease (PD). PD causes unintended or uncontrollable movements in its common symptoms. α-synuclein is the major cause of PD development and thus has been the main target of numerous studies to suppress and sequester its expression or effectively degrade it. Nonetheless, to date, there are no efficient and proven ways to prevent pathological protein aggregation. Recent investigations proposed applying an external electric field to interrupt the fibrils. This method is a non-invasive approach that has a certain benefit over others. We performed molecular dynamics (MD) simulations by applying an electric field on highly toxic fibrils of α-synuclein to gain a molecular-level insight into fibril disruption mechanisms. The results revealed that the applied external electric field induces substantial changes in the conformation of the α-synuclein fibrils. Furthermore, we show the threshold value for electric field strength required to completely disrupt the α-synuclein fibrils by opening the hydrophobic core of the fibril. Thus, our findings might serve as a valuable foundation to better understand molecular-level mechanisms of the α-synuclein fibrils disaggregation process under an applied external electric field.
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Affiliation(s)
- Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- R&D Center, New Uzbekistan University, Mustaqillik Avenue 54, Tashkent 100007, Uzbekistan
- Institute of Material Sciences, Academy of Sciences, Chingiz Aytmatov 2b, Tashkent 100084, Uzbekistan
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
- Correspondence: ; Tel.: +998-90-116-23-20
| | - Sunnatullo Fazliev
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
- Faculty of Engineering Sciences, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Mukhriddin Makhkamov
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
| | - Parthiban Marimuthu
- Pharmaceutical Science Laboratory (PSL–Pharmacy) and Structural Bioinformatics Laboratory (SBL–Biochemistry), Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
| | - Artyom Baev
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
- Department of Biophysics, Biological Faculty, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
| | - Erkin Kurganov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Kritikos EM, Lele A, van Duin ACT, Giusti A. Atomistic insight into the effects of electrostatic fields on hydrocarbon reaction kinetics. J Chem Phys 2023; 158:054109. [PMID: 36754820 DOI: 10.1063/5.0134785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Reactive Molecular Dynamics (MD) and Density Functional Theory (DFT) computations are performed to provide insight into the effects of external electrostatic fields on hydrocarbon reaction kinetics. By comparing the results from MD and DFT, the suitability of the MD method in modeling electrodynamics is first assessed. Results show that the electric field-induced polarization predicted by the MD charge equilibration method is in good agreement with various DFT charge partitioning schemes. Then, the effects of oriented external electric fields on the transition pathways of non-redox reactions are investigated. Results on the minimum energy path suggest that electric fields can cause catalysis or inhibition of oxidation reactions, whereas pyrolysis reactions are not affected due to the weaker electronegativity of the hydrogen and carbon atoms. MD simulations of isolated reactions show that the reaction kinetics is also affected by applied external Lorentz forces and interatomic Coulomb forces since they can increase or decrease the energy of collision depending on the molecular conformation. In addition, electric fields can affect the kinetics of polar species and force them to align in the direction of field lines. These effects are attributed to energy transfer via intermolecular collisions and stabilization under the external Lorentz force. The kinetics of apolar species is not significantly affected mainly due to the weak induced dipole moment even under strong electric fields. The dynamics and reaction rates of species are studied by means of large-scale combustion simulations of n-dodecane and oxygen mixtures. Results show that under strong electric fields, the fuel, oxidizer, and most product molecules experience translational and rotational acceleration mainly due to close charge transfer along with a reduction in their vibrational energy due to stabilization. This study will serve as a basis to improve the current methods used in MD and to develop novel methodologies for the modeling of macroscale reacting flows under external electrostatic fields.
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Affiliation(s)
- Efstratios M Kritikos
- Department of Mechanical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Aditya Lele
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Adri C T van Duin
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrea Giusti
- Department of Mechanical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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10
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Urzúa SA, Sauceda-Oloño PY, García CD, Cooper CD. Predicting the Orientation of Adsorbed Proteins Steered with Electric Fields Using a Simple Electrostatic Model. J Phys Chem B 2022; 126:5231-5240. [PMID: 35819287 DOI: 10.1021/acs.jpcb.2c03118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is a spontaneous process that leads to a rather compact layer of randomly oriented molecules. However, controlling such orientation is critically important for the development of catalytic surfaces. In this regard, the use of electric fields is one of the most promising alternatives. Our work is motivated by experimental observations that show important differences in catalytic activity of a trypsin-covered surface, which depended on the applied potential during the adsorption. Even though adsorption results from the combination of several processes, we were able to determine that (under the selected conditions) mean-field electrostatics play a dominant role, determining the orientation and yielding a difference in catalytic activity. We simulated the electrostatic potential numerically, using an implicit-solvent model based on the linearized Poisson-Boltzmann equation. This was implemented in an extension of the code PyGBe that included an external electric field, and rendered the electrostatic component of the solvation free energy. Our model (extensions available at the Github repository) allowed estimating the overall affinity of the protein with the surface, and their most likely orientation as a function of the potential applied. Our results show that the active sites of trypsin are, on average, more exposed when the electric field is negative, which agrees with the experimental results of catalytic activity, and confirm the premise that electrostatic interactions can be used to control the orientation of adsorbed proteins.
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Affiliation(s)
- Sergio A Urzúa
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, Valparaíso, 2390123, Chile
| | - Perla Y Sauceda-Oloño
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Carlos D García
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Christopher D Cooper
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, Valparaíso, 2390123, Chile.,Centro Científico Tecnológico de Valparaíso, Valparaíso, 2390123, Chile
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11
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Benavides T, Guerra J, Garcia C. Dielectric Spectroscopy can Predict the Effect of External AC Fields on the Dynamic Adsorption of Lysozyme. Chemphyschem 2022; 23:e202100914. [PMID: 35226788 PMCID: PMC9311058 DOI: 10.1002/cphc.202100914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/25/2022] [Indexed: 11/08/2022]
Abstract
This report describes the application of dielectric spectroscopy as a simple and fast way to guide protein adsorption experiments. Specifically, the polarization behavior of a layer of adsorbed lysozyme was investigated using a triangular‐wave signal with frequencies varying from 0.5 to 2 Hz. The basic experiment, which can be performed in less than 5 min and with a single sample, not only allowed confirming the susceptibility of the selected protein towards the electric signal but also identified that this protein would respond more efficiently to signals with lower frequencies. To verify the validity of these observations, the adsorption behavior of lysozyme onto optically transparent carbon electrodes was also investigated under the influence of an applied alternating potential. In these experiments, the applied signal was defined by a sinusoidal wave with an amplitude of 100 mV and superimposed to +800 mV (applied as a working potential) and varying the frequency in the 0.1–10000 Hz range. The experimental data showed that the greatest adsorbed amounts of lysozyme were obtained at the lowest tested frequencies (0.1–1.0 Hz), results that are in line with the corresponding dielectric features of the protein.
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Affiliation(s)
- Tomas Benavides
- Universidad Nacional de Córdoba: Universidad Nacional de Cordoba, Physical-Chemistry, ARGENTINA
| | - Jose Guerra
- Federal University of Uberlandia: Universidade Federal de Uberlandia, physics, BRAZIL
| | - Carlos Garcia
- Clemson University, Chemistry, 211 S. Palmetto Blvd, 29634, Clemson, UNITED STATES
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12
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Zhang Q, Shao D, Xu P, Jiang Z. Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies. Polymers (Basel) 2021; 14:polym14010123. [PMID: 35012145 PMCID: PMC8747415 DOI: 10.3390/polym14010123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 12/21/2022] Open
Abstract
The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary structure analysis were used to assess the protein samples’ structural characteristics. In the simulation, we found that the higher frequency of the electric field influences the rapid response to the secondary structural transitions. However, the conformational changes measured by RMSD are diminished by applying the electrical field with a higher frequency. During the dipole moment analysis, we found that the magnitude and frequency of the dipole moment was directly related to the strength and frequency of the external electric field. In terms of the type of electric fields, we found that the average values of RMSD and RMSF of whole molecular protein are larger when the protein is exposed in the pulsed electric field. Concerning the typical sample 1BBL, the secondary structure analysis showed that two alpha-helix segments both transit to turns or random coils almost simultaneously when it is exposed in a pulsed electric field. Meanwhile, two segments present the different characteristic times when the transition occurs in the condition of an oscillating electric field. This study also demonstrated that the protein with fewer charged residues or more residues in forming α-helical structures display the higher conformational stability. These conclusions, achieved using MD simulations, provide a theoretical understanding of the effect of the frequency and expression form of external electric fields on the conformational changes of the all-α proteins with charged residues and the guidance for anticipative applications.
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13
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Chao Y, Zhang L. Biomimetic design of inhibitors of immune checkpoint LILRB4. Biophys Chem 2021; 282:106746. [PMID: 34963077 DOI: 10.1016/j.bpc.2021.106746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 12/20/2022]
Abstract
Immune checkpoint inhibitors have become a hot spot in the treatment of acute myeloid leukemia (AML), the most common acute leukemia (blood cancer) in adults. In the present study, molecular insights into the molecular interactions between an immune checkpoint leukocyte immunoglobulin-like receptor b4 (LILRB4) and its mAb h128-3 was explored using molecular dynamics (MD) simulation for the biomimetic design of peptide inhibitor of LILRB4. Both hydrophobic interaction and electrostatic interaction were found favorable for the binding of the mAb h128-3 on LILRB4, and hydrophobic interaction was identified as the main driving force. The key amino acid residues for the binding of mAb h128-3 on LILRB4 were identified as Y93, D94, D106, Y34, S103, W107, Y61, N30, E27, Y33, Y59, W95, S92 through MM-PBSA (molecular mechanics-Poisson-Boltzmann surface area) method. Based on this, an inhibitor library with the sequence of SXDXYXSY (Where X is an arbitrary amino acid residue) were designed. Two peptide inhibitors, SADHYHSY and SVDWYHSY were obtained through screening using molecular docking and MD simulations, and then validated by successful blocking of LILRB4 through the covering of LILRB4 surface by these inhibitors. These results would be helpful for the research and development of therapies for AML.
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Affiliation(s)
- Yuanyuan Chao
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Lin Zhang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China.
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14
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Hierro-Oliva M, Gallardo-Moreno AM, González-Martín ML. Surface Characterisation of Human Serum Albumin Layers on Activated Ti6Al4V. MATERIALS (BASEL, SWITZERLAND) 2021; 14:7416. [PMID: 34885570 PMCID: PMC8658959 DOI: 10.3390/ma14237416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 12/14/2022]
Abstract
Adpsortion of protein layers on biomaterials plays an important role in the interactions between implants and the bio-environment. In this context, human serum albumin (HSA) layers have been deposited on modified Ti6Al4V surfaces at different ultraviolet (UV-C) irradiation times to observe possible changes in the adsorbed protein layer. Protein adsorption was done from solutions at concentraions lower than the serum protein concentration, to follow the surface modifications at the beginning of the albumin adhesion process. For this purpose, the surface of the protein-coated samples has been characterized by time of flight secondary ion mass spectrometry (ToF-SIMS), contact angle and zeta potential measurements. The results obtained show a reduction in the total surface tension and zeta potential of samples treated with UV-C light when coated with a protein layer. Furthermore, the UV-C light treatment applied to titanium alloy surfaces is able to modify the conformation, orientation and packing of the proteins arranged in the adsorbed layer. Low irradiation time generates an unstable surface with the lowest protein adsorption and the highest hydrophobic/hydrophilic protein ratio, indicating a possible denaturalization of the protein on these surfaces. However, surface changes are stabilized after 15 h or UV-C irradiation, favoring the protein adsorption through electrical interactions.
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Affiliation(s)
- Margarita Hierro-Oliva
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 06006 Badajoz, Spain; (M.H.-O.); (M.L.G.-M.)
- Department of Applied Physics, Faculty of Science, University of Extremadura, 06006 Badajoz, Spain
- University Institute of Extremadura Sanity Research (INUBE), 06006 Badajoz, Spain
| | - Amparo M. Gallardo-Moreno
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 06006 Badajoz, Spain; (M.H.-O.); (M.L.G.-M.)
- Department of Applied Physics, Faculty of Science, University of Extremadura, 06006 Badajoz, Spain
- University Institute of Extremadura Sanity Research (INUBE), 06006 Badajoz, Spain
| | - María Luisa González-Martín
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 06006 Badajoz, Spain; (M.H.-O.); (M.L.G.-M.)
- Department of Applied Physics, Faculty of Science, University of Extremadura, 06006 Badajoz, Spain
- University Institute of Extremadura Sanity Research (INUBE), 06006 Badajoz, Spain
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15
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Fritz PA, Boom RM, Schroën C. Electrochemically driven adsorptive separation techniques: From ions to proteins and cells in liquid streams. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.118754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Ferreira-Santos P, Miranda SM, Belo I, Spigno G, Teixeira JA, Rocha CM. Sequential multi-stage extraction of biocompounds from Spirulina platensis: Combined effect of ohmic heating and enzymatic treatment. INNOV FOOD SCI EMERG 2021. [DOI: 10.1016/j.ifset.2021.102707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Zhao D, Huang C, Quan X, Li L, Wang Y, Zhou J. Lysozyme Adsorption on Different Functionalized MXenes: A Multiscale Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5932-5942. [PMID: 33961443 DOI: 10.1021/acs.langmuir.1c00480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recently, MXenes, due to their abundant advantages, have been widely applied in energy storage, separation, catalysis, biosensing, et al. In this study, parallel tempering Monte Carlo and molecular dynamics methods were performed to investigate lysozyme adsorption on different functionalized Ti3C2Tx (-O, -OH, and -F). The simulation results show that lysozyme can adsorb effectively on Ti3C2Tx surfaces, and the order of interaction strength is Ti3C2O2 > Ti3C2F2 > Ti3C2(OH)2. Electrostatics together with van der Waals interactions control protein adsorption. The orientation distributions of lysozyme adsorbed on the Ti3C2O2 and Ti3C2F2 surfaces are more concentrated than that on the Ti3C2(OH)2 surface. During adsorption, the conformation of lysozyme remains stable, suggesting the good biocompatibility of Ti3C2Tx. Besides, the distribution of the interfacial water layer on the Ti3C2Tx surface has a certain impact on protein adsorption. This study provides theoretical insights for understanding the biocompatibility of 2D Ti3C2Tx materials and may help us evaluate the engineering of their surfaces for future biorelated applications.
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Affiliation(s)
- Daohui Zhao
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P.R. China
| | - Chu Huang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P.R. China
| | - Xuebo Quan
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Libo Li
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Yuqing Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, School of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P.R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
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18
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Arruebo-Rivera PL, Castillo-Alfonso F, Troya A, Cárdenas-Moreno Y, Pérez-Ramos P, González-Bacerio J, Seijas JMG, Del Monte-Martínez A. Modeling and Experimental Validation of Algorithms for Maximum Quantity of Protein to be Immobilized on Solid Supports by Electrostatic Adsorption in the Strategy of Rational Design of Immobilized Derivatives. Protein J 2021; 40:576-588. [PMID: 33973097 DOI: 10.1007/s10930-021-09992-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 11/29/2022]
Abstract
Protein immobilization by electrostatic adsorption to a support could represent a good option. On the other hand, lysozyme (EC 3.2.1.17) is a little and basic protein. The objective of this work was to test the functionality of the strategy of Rational Design of Immobilized Derivatives for the immobilization by electrostatic adsorption of egg white lysozyme on SP-Sepharose FastFlow support. The RDID1.0 software was used to predict the superficial lysozyme clusters, the electrostatic configuration probability for each cluster, and the theoretical and estimated maximum quantity of protein to be immobilized. In addition, immobilization was performed and the experimental parameter practical maximum quantity of protein to be immobilized and the enzymatic activity of the immobilized derivative were assessed. The estimated maximum quantity of protein to be immobilized (9.49 protein mg/support g) was close to the experimental practical maximum quantity of protein to be immobilized (14.73 ± 0.09 protein mg/support g). The enzymatic activity assay with the chitosan substrate showed the catalytic functionality of the lysozyme-SP-Sepharose immobilized derivative (35.85 ± 3.07 U/support g), which preserved 78% functional activity. The used algorithm to calculate the estimated maximum quantity of protein to be immobilized works for other proteins, porous solid supports and immobilization methods, and this parameter has a high predictive value, useful for obtaining optimum immobilized derivatives. The applied methodology is valid to predict the most probable protein-support configurations and their catalytic competences, which concur with the experimental results. The produced biocatalyst had a high retention of functional activity. This indicates its functionality in enzymatic bioconversion processes.
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Affiliation(s)
- Pedro L Arruebo-Rivera
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba
| | - Freddy Castillo-Alfonso
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.,Posgrado en Ciencias Naturales E Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, 05348, Mexico City, Mexico
| | - Amanda Troya
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.,Instituto de Farmacia y Alimentos, Universidad de La Habana, San Lázaro y L, Vedado, 10400, Havana, Cuba
| | - Yosberto Cárdenas-Moreno
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.,Departamento de Microbiología y Virología, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba
| | - Patricia Pérez-Ramos
- Instituto de Farmacia y Alimentos, Universidad de La Habana, San Lázaro y L, Vedado, 10400, Havana, Cuba
| | - Jorge González-Bacerio
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.
| | - José M Guisán Seijas
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica, Consejo Superior de Investigaciones Científicas (CSIC), Campus Cantoblanco, 28049, Madrid, Spain
| | - Alberto Del Monte-Martínez
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25, #455, e/ J e I, Vedado, 10400, Havana, Cuba.
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19
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Xu Z, He Z, Quan X, Sun D, Miao Z, Yu H, Yang S, Chen Z, Zeng J, Zhou J. Molecular simulations of charged complex fluids: A review. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Song X, Bu Y. Electric field controlled uphill electron migration along α-helical oligopeptides. Phys Chem Chem Phys 2021; 23:1464-1474. [PMID: 33399139 DOI: 10.1039/d0cp05085g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic study on applied electric field effects (Eapp) on electron transfer along the peptides is very important for the regulation of electron transfer behaviors so as to realize the functions of proteins. In this work, we computationally investigated the uphill migration behaviors of excess electrons along the peptide chains under Eapp using the density functional theory method. We examined the electronic property changes of the model α-helical oligopeptides, the dynamics behavior of an excess electron along the peptide chains under Eapp opposite to the internal dipole field of peptides. We found that Eapp of different intensities can effectively modulate the electron-binding abilities, Frontier molecular orbital (FMO) energies and distributions, dipole moments and other corresponding properties with different degrees. The electron-binding abilities of α-helical oligopeptides revealed by vertical electron affinity and FMO energies decrease in weak Eapp and then increase greatly in high Eapp, while the dipole moments change mildly in weak Eapp and increase significantly until a threshold and then become gentle in high Eapp. Analysis of FMO and electron distributions indicates that an excess electron can migrate uphill from the N-terminus to the C-terminus of the α-helical peptides in an irregular jump mode as Eapp linearly increases. Another interesting finding is that α-helical peptides with diverse chain lengths have different sensitivities to Eapp. The longer the peptide is, the more obvious the effects of Eapp are. Additionally, compared to the Eapp effect on linear oligopeptides, we summarized the systematic rule about the Eapp effect on excess electron migration uphill along the peptide chains. Clearly, this work not only enriches the information of the Eapp effect on electronic properties and electron transfers in the helical peptides, but also provides a new perspective for modulating electron migration behaviors in protein electronics engineering.
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Affiliation(s)
- Xiufang Song
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.
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21
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Basu S, Gorai B, Basu B, Maiti PK. Electric Field-Mediated Fibronectin-Hydroxyapatite Interaction: A Molecular Insight. J Phys Chem B 2021; 125:3-16. [PMID: 33395296 DOI: 10.1021/acs.jpcb.0c08255] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In experimental research-driven biomaterials science, the influence of different material properties (elastic stiffness, surface energy, etc.) and, to a relatively lesser extent, biophysical stimulation (electric/magnetic) on cell-material interactions has been extensively investigated. Despite the central importance of protein adsorption on cell-material interactions, the quantitative analysis to probe into the role of physicochemical factors in protein adsorption remains largely unexplored in biomaterials science. In recent studies, the critical role of electric field stimulation toward the modulation of cell functionality in implantable biomaterials has been experimentally demonstrated. Given this background, we investigated the influence of external electric field stimulation (upto 1.00 V/nm) on fibronectin (FN) adsorption on a hydroxyapatite (HA) (001) surface at 300 K using the all-atom molecular dynamics (MD) simulation method. FN adsorption was found to be governed by attractive electrostatic interactions, which changed with the electric field strength. Nonmonotonous changes in the structural integrity of FN were recorded with the change in the field strength and direction. This can be attributed to the spatial rearrangement of the positions of local charges and the global structural changes of proteins. The dipole moment vectors of FN, water, and HA quantitatively exhibited a similar pattern of orienting themselves parallel to the field direction, with field strength-dependent increase in their magnitudes. No significant change has been recorded for the radial distribution function of water surrounding FN. Field-dependent variation in the salt bridge nets and the number of hydrogen bonds between FN and HA were also examined. One of the important results in the context of cell-material interaction is that the RGD (Arg-Gly-Asp) sequence of FN was exposed to the solvent side when the field was applied along an outward direction perpendicular to the HA (001) surface. In summary, the present study provides molecular insights into the influence of electric field stimulation on phenomenological interactions involved in FN adsorption on the HA surface.
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Affiliation(s)
- Subhadip Basu
- Materials Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Biswajit Gorai
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Bikramjit Basu
- Materials Research Centre, Indian Institute of Science, Bangalore 560012, India.,Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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22
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Baruah I, Borgohain G. Structural and functional changes of the protein β-lactoglobulin under thermal and electrical processing conditions. Biophys Chem 2020; 267:106479. [PMID: 33027745 DOI: 10.1016/j.bpc.2020.106479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
In the present study we have tried to explore the effect of static external electric field of strength 3.0 V/nm on the conformational changes adopted by the protein β-lactoglobulin. We have chosen different temperatures viz. 300 K, 400 K and 450 K to evaluate the temperature dependent effect of electric field. We have observed that combined effect of high temperature and static external electric field show significant changes on the structural conformation of the protein which in turn may affect the functional properties of the protein. Calculations of root mean square deviations reveal that both helical and β-sheet regions of the protein are noticeably affected at high temperature. We have used solvent accessible surface area (SASA) and dipole moment values to explain that there is changes in hydrophobicity of the protein surface due to presence of external electric field. The study reveals that electric field in combination with high temperature can be used to alter the conformation of the protein and the effect of external electric field is more pronounced at high temperature than that of low temperature. The study provides a better understanding of the conformational changes adopted by the protein under the stress of external electric field and high temperature and provide guidance to choose optimum conditions for processing without loss of nutritional properties.
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Affiliation(s)
- Indrani Baruah
- Department of Chemistry, Cotton University, Guwahati, Assam 781001, India
| | - Gargi Borgohain
- Department of Chemistry, Cotton University, Guwahati, Assam 781001, India.
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23
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Elucidating the Effect of Static Electric Field on Amyloid Beta 1-42 Supramolecular Assembly. J Mol Graph Model 2020; 96:107535. [PMID: 31978828 DOI: 10.1016/j.jmgm.2020.107535] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/06/2019] [Accepted: 01/09/2020] [Indexed: 02/07/2023]
Abstract
Amyloid-β (Aβ) aggregation is recognized to be a key toxic factor in the pathogenesis of Alzheimer disease, which is the most common progressive neurodegenerative disorder. In vitro experiments have elucidated that Aβ aggregation depends on several factors, such as pH, temperature and peptide concentration. Despite the research effort in this field, the fundamental mechanism responsible for the disease progression is still unclear. Recent research has proposed the application of electric fields as a non-invasive therapeutic option leading to the disruption of amyloid fibrils. In this regard, a molecular level understanding of the interactions governing the destabilization mechanism represents an important research advancement. Understanding the electric field effects on proteins, provides a more in-depth comprehension of the relationship between protein conformation and electrostatic dipole moment. The present study focuses on investigating the effect of static Electric Field (EF) on the conformational dynamics of Aβ fibrils by all-atom Molecular Dynamics (MD) simulations. The outcome of this work provides novel insight into this research field, demonstrating how the Aβ assembly may be destabilized by the applied EF.
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24
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Kroutil O, Kabeláč M, Dorčák V, Vacek J. Structures of Peptidic H‐wires at Mercury Surface: Molecular Dynamics Study. ELECTROANAL 2019. [DOI: 10.1002/elan.201900314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ondřej Kroutil
- Institute of Physics and Biophysics, Faculty of ScienceUniversity of South Bohemia Branisovska 1760 370 05 Ceske Budejovice Czech Republic
| | - Martin Kabeláč
- Department of Chemistry, Faculty of ScienceUniversity of South Bohemia Branisovska 31 370 05 Ceske Budejovice Czech Republic
| | - Vlastimil Dorčák
- Institute of Biophysics of the CAS Kralovopolska 135 612 65 Brno Czech Republic
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and DentistryPalacky University Hnevotinska 3 775 15 Olomouc Czech Republic
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25
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Rotavirus VP6 protein as a bio-electrochemical scaffold: Molecular dynamics and experimental electrochemistry. Bioelectrochemistry 2019; 127:180-186. [DOI: 10.1016/j.bioelechem.2019.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/24/2019] [Accepted: 02/24/2019] [Indexed: 11/23/2022]
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26
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Quan X, Liu J, Zhou J. Multiscale modeling and simulations of protein adsorption: progresses and perspectives. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Jiang Z, You L, Dou W, Sun T, Xu P. Effects of an Electric Field on the Conformational Transition of the Protein: A Molecular Dynamics Simulation Study. Polymers (Basel) 2019; 11:polym11020282. [PMID: 30960266 PMCID: PMC6419079 DOI: 10.3390/polym11020282] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 12/30/2022] Open
Abstract
The effect of the electric field on the conformational properties of the protein 1BBL was investigated by molecular dynamics simulations. Our simulation results clearly capture the structural transitions of the protein sample from helix to turn or random coil conformation induced by the increasing strength of the electric field. During our analysis, we found that the conformational stability is weakened, and the protein sample is stretched as an unfolded structure when it was exposed in a sufficiently high electric field. The characteristic time when the jump occurs in the time evolution curves of root mean square deviation (RMSD) and radius of gyration Rg decreases with increasing electric strength, which demonstrates the rapidly conformational transition that occurs. The number of intra-protein hydrogen bonds, which is the key factor for stabilizing the protein structure, is related to the overall size of the protein. The value of the dipole moment and characteristic time are both influenced by the strength, but are independent of the direction of the external field. The protein sample becomes rotated with the electric field direction. These conclusions provide a theoretical realization of understanding the protein conformational transition in an electric field and the guidance for anticipative applications.
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Affiliation(s)
- Zhouting Jiang
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| | - Le You
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| | - Wenhui Dou
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| | - Tingting Sun
- Department of Physics, Zhejiang University of Science and Technology, No. 318 Liuhe Road, Hangzhou 310023, China.
| | - Peng Xu
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
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28
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Ning C, Zhou Z, Tan G, Zhu Y, Mao C. Electroactive polymers for tissue regeneration: Developments and perspectives. Prog Polym Sci 2018; 81:144-162. [PMID: 29983457 PMCID: PMC6029263 DOI: 10.1016/j.progpolymsci.2018.01.001] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human body motion can generate a biological electric field and a current, creating a voltage gradient of -10 to -90 mV across cell membranes. In turn, this gradient triggers cells to transmit signals that alter cell proliferation and differentiation. Several cell types, counting osteoblasts, neurons and cardiomyocytes, are relatively sensitive to electrical signal stimulation. Employment of electrical signals in modulating cell proliferation and differentiation inspires us to use the electroactive polymers to achieve electrical stimulation for repairing impaired tissues. Electroactive polymers have found numerous applications in biomedicine due to their capability in effectively delivering electrical signals to the seeded cells, such as biosensing, tissue regeneration, drug delivery, and biomedical implants. Here we will summarize the electrical characteristics of electroactive polymers, which enables them to electrically influence cellular function and behavior, including conducting polymers, piezoelectric polymers, and polyelectrolyte gels. We will also discuss the biological response to these electroactive polymers under electrical stimulation. In particular, we focus this review on their applications in regenerating different tissues, including bone, nerve, heart muscle, cartilage and skin. Additionally, we discuss the challenges in tissue regeneration applications of electroactive polymers. We conclude that electroactive polymers have a great potential as regenerative biomaterials, due to their ability to stimulate desirable outcomes in various electrically responsive cells.
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Affiliation(s)
- Chengyun Ning
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Key Laboratory of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou 510006, China
| | - Zhengnan Zhou
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510006, China
- Institute of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China
- Guangdong Key Laboratory of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou 510006, China
| | - Guoxin Tan
- Institute of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China
| | - Ye Zhu
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5300, United States
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5300, United States
- School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, China
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29
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He Z, Cui H, Hao S, Wang L, Zhou J. Electric-Field Effects on Ionic Hydration: A Molecular Dynamics Study. J Phys Chem B 2018; 122:5991-5998. [DOI: 10.1021/acs.jpcb.8b02773] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Zhongjin He
- School of Chemical Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Haishuai Cui
- School of Chemical Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Shihua Hao
- School of Chemical Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Liping Wang
- School of Chemical Engineering, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
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30
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Liu J, Xie Y, Peng C, Yu G, Zhou J. Molecular Understanding of Laccase Adsorption on Charged Self-Assembled Monolayers. J Phys Chem B 2017; 121:10610-10617. [DOI: 10.1021/acs.jpcb.7b08738] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie Liu
- School
of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab
for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
- Key
Laboratory for Green Chemical Process of Ministry of Education, School
of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, P. R. China
| | - Yun Xie
- Huizhou University, Huizhou 516007, P. R. China
| | - Chunwang Peng
- School
of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab
for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Gaobo Yu
- School
of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab
for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
- School
of Materials and Chemical Engineering, Hainan University, Haikou 570228, P. R. China
| | - Jian Zhou
- School
of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab
for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
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31
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Marracino P, Liberti M, Vernier PT, Apollonio F. A statistical analytical model for hydrophilic electropore characterization: a comparison study. RSC Adv 2017. [DOI: 10.1039/c7ra03812g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A new procedure for lipid pore characterization, which extracts the pore geometry from a statistical analysis of the tridimensional surface of the pore, is compared with other methods in the literature.
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Affiliation(s)
- P. Marracino
- Department of Information Engineering, Electronics, and Telecommunications
- Sapienza University of Rome
- Rome
- Italy
| | - M. Liberti
- Department of Information Engineering, Electronics, and Telecommunications
- Sapienza University of Rome
- Rome
- Italy
| | - P. T. Vernier
- Frank Reidy Research Center for Bioelectrics
- Old Dominion University
- Norfolk
- USA
| | - F. Apollonio
- Department of Information Engineering, Electronics, and Telecommunications
- Sapienza University of Rome
- Rome
- Italy
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32
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Zhang JL, Zheng QC, Yu LY, Li ZQ, Zhang HX. Effect of External Electric Field on Substrate Transport of a Secondary Active Transporter. J Chem Inf Model 2016; 56:1539-46. [PMID: 27472561 DOI: 10.1021/acs.jcim.6b00212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Substrate transport across a membrane accomplished by a secondary active transporter (SAT) is essential to the normal physiological function of living cells. In the present research, a series of all-atom molecular dynamics (MD) simulations under different electric field (EF) strengths was performed to investigate the effect of an external EF on the substrate transport of an SAT. The results show that EF both affects the interaction between substrate and related protein's residues by changing their conformations and tunes the timeline of the transport event, which collectively reduces the height of energy barrier for substrate transport and results in the appearance of two intermediate conformations under the existence of an external EF. Our work spotlights the crucial influence of external EFs on the substrate transport of SATs and could provide a more penetrating understanding of the substrate transport mechanism of SATs.
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Affiliation(s)
- Ji-Long Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University , Changchun 130021, Jilin, People's Republic of China.,Department of Chemistry and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Qing-Chuan Zheng
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
| | - Li-Ying Yu
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
| | - Zheng-Qiang Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University , Changchun 130021, Jilin, People's Republic of China
| | - Hong-Xing Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University , Changchun 130023, Jilin, People's Republic of China
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33
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Zhu Y, Ruan Y, Wu X, Lu X, Zhang Y, Lu L. Electric Field-Responsive Nanopores with Ion Selectivity: Controlling Based on Transport Resistance. Chem Eng Technol 2016. [DOI: 10.1002/ceat.201500637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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34
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Mulheran PA, Connell DJ, Kubiak-Ossowska K. Steering protein adsorption at charged surfaces: electric fields and ionic screening. RSC Adv 2016. [DOI: 10.1039/c6ra16391b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Protein adsorption at charged surfaces is a common process in the development of functional technological devices.
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Affiliation(s)
- Paul A. Mulheran
- Department of Chemical and Process Engineering
- University of Strathclyde
- Glasgow G1 1XJ
- UK
| | - David J. Connell
- Department of Chemical and Process Engineering
- University of Strathclyde
- Glasgow G1 1XJ
- UK
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35
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Beykal B, Herzberg M, Oren Y, Mauter MS. Influence of surface charge on the rate, extent, and structure of adsorbed Bovine Serum Albumin to gold electrodes. J Colloid Interface Sci 2015; 460:321-8. [DOI: 10.1016/j.jcis.2015.08.055] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 08/15/2015] [Accepted: 08/22/2015] [Indexed: 11/30/2022]
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36
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Ma X, Shrotriya P. Molecular Dynamics Simulation of Conformational Transition and Frictional Performance Modulation of Densely Packed Self-Assembled Monolayers Based on Electrostatic Stimulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6729-6741. [PMID: 26053128 DOI: 10.1021/acs.langmuir.5b00956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Self-assembled monolayers (SAMs) terminated with functional end groups such as polyethylene glycols (PEG) have attracted considerable attention because of their unique and flexible structure that exhibits conformational transition under electrostatic stimulation. Molecular dynamics simulations are used to investigate the conformational transition and associated modulation of frictional performance of densely packed PEG-terminated SAMs subjected to electrical field stimulation. Previously reported empirical potentials and atomic charges were used to model the intrachain bonds and electrostatic and interchain interactions. Simulation results indicate that significant conformational transition is generated because of the electrostatic forces. Under positive electrical fields, PEG groups are compressed and twisted into the helical form, "gauche" state, whereas under negative electrical fields, PEG groups are stretched into the straight form, "all-trans" state. Such conformational transition may lead to substantial alteration of frictional response upon SAMs. By shallow penetration and sliding using a repulsive indenter, the SAMs under positive electrical fields exhibit a level of frictional response that is comparatively lower than those under zero and negative potentials, which may be attributed to reduced interchain space for deformation, limited conformational transition, and less energy absorption. The simulation results demonstrate that with appropriate selection of functional end groups attached to SAM backbone chains it is possible to modulate frictional performance of densely packed SAMs via electrostatic stimuli.
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Affiliation(s)
- Xiao Ma
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Pranav Shrotriya
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
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37
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Yu G, Liu J, Zhou J. Mesoscopic coarse-grained simulations of hydrophobic charge induction chromatography (HCIC) for protein purification. AIChE J 2015. [DOI: 10.1002/aic.14805] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Gaobo Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology; Guangzhou 510640 P.R. China
| | - Jie Liu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology; Guangzhou 510640 P.R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology; Guangzhou 510640 P.R. China
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38
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Liu J, Yu G, Zhou J. Ribonuclease A adsorption onto charged self-assembled monolayers: A multiscale simulation study. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2014.07.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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39
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Chen B, Zhang H, Xi W, Zhao L, Liang L, Chen Y. Unfolding mechanism of lysozyme in various urea solutions: Insights from fluorescence spectroscopy. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Mashamba-Thompson T, Soliman MES. Insight into the binding theme of CA-074Me to cathepsin B: molecular dynamics simulations and scaffold hopping to identify potential analogues as anti-neurodegenerative diseases. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1145-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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41
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Liao C, Zhou J. Replica-Exchange Molecular Dynamics Simulation of Basic Fibroblast Growth Factor Adsorption on Hydroxyapatite. J Phys Chem B 2014; 118:5843-52. [DOI: 10.1021/jp501463r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chenyi Liao
- School
of Chemistry and Chemical
Engineering, Guangdong Provincial Key Lab for Green Chemical Product
Technology, South China University of Technology, Guangzhou, 510640, P. R. China
| | - Jian Zhou
- School
of Chemistry and Chemical
Engineering, Guangdong Provincial Key Lab for Green Chemical Product
Technology, South China University of Technology, Guangzhou, 510640, P. R. China
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42
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Wang X, Li Y, He X, Chen S, Zhang JZH. Effect of strong electric field on the conformational integrity of insulin. J Phys Chem A 2014; 118:8942-52. [PMID: 24796962 DOI: 10.1021/jp501051r] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A series of molecular dynamics (MD) simulations up to 1 μs for bovine insulin monomer in different external electric fields were carried out to study the effect of external electric field on conformational integrity of insulin. Our results show that the secondary structure of insulin is kept intact under the external electric field strength below 0.15 V/nm, but disruption of secondary structure is observed at 0.25 V/nm or higher electric field strength. Although the starting time of secondary structure disruption of insulin is not clearly correlated with the strength of the external electric field ranging between 0.15 and 0.60 V/nm, long time MD simulations demonstrate that the cumulative effect of exposure time under the electric field is a major cause for the damage of insulin's secondary structure. In addition, the strength of the external electric field has a significant impact on the lifetime of hydrogen bonds when it is higher than 0.60 V/nm. The fast evolution of some hydrogen bonds of bovine insulin in the presence of the 1.0 V/nm electric field shows that different microwaves could either speed up protein folding or destroy the secondary structure of globular proteins deponding on the intensity of the external electric field.
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Affiliation(s)
- Xianwei Wang
- State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China
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43
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Yu G, Liu J, Zhou J. Mesoscopic coarse-grained simulations of lysozyme adsorption. J Phys Chem B 2014; 118:4451-60. [PMID: 24785197 DOI: 10.1021/jp409326f] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Coarse-grained simulations are adopted to study the adsorption behavior of lysozyme on different (hydrophobic, neutral hydrophilic, zwitterionic, negatively charged, and positively charged) surfaces at the mesoscopic microsecond time scale (1.2 μs). Simulation results indicate the following: (i) the conformation change of lysozyme on the hydrophobic surface is bigger than any other studied surfaces; (ii) the active sites of lysozyme are faced to the hydrophobic surface with a "top end-on" orientation, while they are exposed to the liquid phase on the hydrophilic surface with a "back-on" orientation; (iii) the neutral hydrophilic surface can induce the adsorption of lysozyme, while the nonspecific protein adsorption can be resisted by the zwitterionic surface; (iv) when the solution ionic strength is low, lysozyme can anchor on the negatively charged surface easily but cannot adsorb on the positively charged surface; (v) when the solution ionic strength is high, the positively charged lysozyme can also adsorb on the like-charged surface; (vi) the major positive potential center of lysozyme, especially the residue ARG128, plays a vital role in leading the adsorption of lysozyme on charged surfaces; (vii) when the ionic strength is high, a counterion layer is formed above the positively charged surface, which is the key factor why lysozyme can adsorb on a like-charged surface. The coarse-grained method based on the MARTINI force field for proteins and the BMW water model could provide an efficient way to understand protein interfacial adsorption behavior at a greater length scale and time scale.
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Affiliation(s)
- Gaobo Yu
- School of Chemistry and Chemical Engineering, South China University of Technology , Guangzhou, Guangdong 510640, China
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44
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Liao C, Xie Y, Zhou J. Computer simulations of fibronectin adsorption on hydroxyapatite surfaces. RSC Adv 2014. [DOI: 10.1039/c3ra47381c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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45
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Benavidez TE, Garcia CD. Potential-assisted adsorption of bovine serum albumin onto optically transparent carbon electrodes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14154-14162. [PMID: 24156567 PMCID: PMC3867293 DOI: 10.1021/la4029657] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This article describes the effect of the applied potential on the adsorption of bovine serum albumin (BSA) to optically transparent carbon electrodes (OTCE). To decouple the effect of the applied potential from the high affinity of the protein for the bare surface, the surface of the OTCE was initially saturated with a layer of BSA. Experiments described in the article show that potential values higher than +500 mV induced a secondary adsorption process (not observed at open-circuit potential), yielding significant changes in the thickness (and adsorbed amount) of the BSA layer obtained. Although the process showed a significant dependence on the experimental conditions selected, the application of higher potentials, selection of pH values around the isoelectric point (IEP) of the protein, high concentrations of protein, and low ionic strengths yielded faster kinetics and the accumulation of larger amounts of protein on the substrate. These experiments, obtained around the IEP of the protein, contrast with the traditional hypothesis that enhanced electrostatic interactions between the polarized substrate and the (oppositely charged) protein are solely responsible for the enhanced adsorption. These results suggest that the potential applied to the electrode is able to polarize the adsorbed layer and induce dipole-dipole interactions between the adsorbed and the incoming protein. This mechanism could be responsible for the potential-dependent oversaturation of the surface and could bolster to the development of surfaces with enhanced catalytic activity and implants with improved biocompatibility.
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Affiliation(s)
| | - Carlos D. Garcia
- To whom correspondence should be addressed. One UTSA Circle, San Antonio, TX 78249, USA. Ph: (210) 458-5774, Fax: (210) 458-7428,
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46
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Liu J, Liao C, Zhou J. Multiscale simulations of protein G B1 adsorbed on charged self-assembled monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11366-11374. [PMID: 23947739 DOI: 10.1021/la401171v] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The orientation of an antibody plays an important role in the development of immunosensors. Protein G is an antibody binding protein, which specifically targets the Fc fragment of an antibody. In this work, the orientation of prototypical and mutated protein G B1 adsorbed on positively and negatively charged self-assembled monolayers was studied by parallel tempering Monte Carlo and all-atom molecular dynamics simulations. Both methods present generally similar orientation distributions of protein G B1 for each kind of surface. The root-mean-square deviation, DSSP, gyration radius, eccentricity, dipole moment, and superimposed structures of protein G B1 were analyzed. Moreover, the orientation of binding antibody was also predicted in this work. Simulation results show that with the same orientation trends, the mutant exhibits narrower orientation distributions than does the prototype, which was mainly caused by the stronger dipole of the mutant. Both kinds of proteins adsorbed on charged surfaces were induced by the competition of electrostatic interaction and vdW interaction; the electrostatic interaction energy dominated the adsorption behavior. The protein adsorption was also largely affected by the distribution of charged residues within the proteins. Thus, the prototype could adsorb on a negatively charged surface, although it keeps a net charge of -4 e. The mutant has imperfect opposite orientation when it adsorbed on oppositely charged surfaces. For the mutant on a carboxyl-functionalized self-assembled monolayer (COOH-SAM), the orientation was the same as that inferred by experiments. While for the mutant on amine-functionalized self-assembled monolayer (NH2-SAM), the orientation was induced by the competition between attractive interactions (led by ASP40 and GLU56) and repulsive interactions (led by LYS10); thus, the perfect opposite orientation could not be obtained. On both surfaces, the adsorbed protein could retain its native conformation. The desired orientation of protein G B1, which would increase the efficiency of binding antibodies, could be obtained on a negatively charged surface adsorbed with the prototype. Further, we deduced that with the packing density of 12,076 protein G B1 domain per μm(2), the efficiency of the binding IgG would be maximized. The simulation results could be applied to control the orientation of protein G B1 in experiments and to provide a better understanding to maximize the efficiency of antibody binding.
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Affiliation(s)
- Jie Liu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou, Guangdong, 510640, People's Republic of China
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