1
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Doveiko D, Kubiak-Ossowska K, Chen Y. Estimating Binding Energies of π-Stacked Aromatic Dimers Using Force Field-Driven Molecular Dynamics. Int J Mol Sci 2024; 25:5783. [PMID: 38891971 PMCID: PMC11171666 DOI: 10.3390/ijms25115783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
π-π stacking are omnipresent interactions, crucial in many areas of chemistry, and often studied using quantum chemical methods. Here, we report a simple and computationally efficient method of estimating the binding energies of stacked polycyclic aromatic hydrocarbons based on steered molecular dynamics. This method leverages the force field parameters for accurate calculation. The presented results show good agreement with those obtained through DFT at the ωB97X-D3/cc-pVQZ level of theory. It is demonstrated that this force field-driven SMD method can be applied to other aromatic molecules, allowing insight into the complexity of the stacking interactions and, more importantly, reporting π-π stacking energy values with reasonable precision.
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Affiliation(s)
- Daniel Doveiko
- Photophysics Group, Department of Physics, University of Strathclyde, Scottish Universities Physics Alliance, Glasgow G4 0NG, UK;
| | | | - Yu Chen
- Photophysics Group, Department of Physics, University of Strathclyde, Scottish Universities Physics Alliance, Glasgow G4 0NG, UK;
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2
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Doveiko D, Kubiak-Ossowska K, Chen Y. Impact of the Crystal Structure of Silica Nanoparticles on Rhodamine 6G Adsorption: A Molecular Dynamics Study. ACS OMEGA 2024; 9:4123-4136. [PMID: 38284092 PMCID: PMC10809255 DOI: 10.1021/acsomega.3c06657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/21/2023] [Accepted: 12/25/2023] [Indexed: 01/30/2024]
Abstract
Understanding the mechanism of adsorption of Rhodamine 6G (R6G) to various crystal structures of silica nanoparticles (SNPs) is important to elucidate the impact of dye size when measuring the size of the dye-SNP complex via the time-resolved fluorescence anisotropy method. In this work, molecular dynamics (MD) simulations were used to get an insight into the R6G adsorption process, which cannot be observed using experimental methods. It was found that at low pH, α-Cristobalite structured SNPs have a strong affinity to R6G; however, at high pH, more surface silanol groups undergo ionization when compared with α-Quartz, preventing the adsorption. Therefore, α-Quartz structured SNPs are more suitable for R6G adsorption at high pH than the α-Cristobalite ones. Furthermore, it was found that stable adsorption can occur only when the R6G xanthene core is oriented flat with respect to the SNP surface, indicating that the dye size does not contribute significantly to the measured size of the dye-SNP complex. The requirement of correct dipole moment orientation indicates that only one R6G molecule can adsorb on any sized SNP, and the R6G layer formation on SNP is not possible. Moreover, the dimerization process of R6G and its competition with the adsorption has been explored. It has been shown that the highest stable R6G aggregate is a dimer, and in this form, R6G does not adsorb to SNPs. Finally, using steered molecular dynamics (SMD) with constant-velocity pulling, the binding energies of R6G dimers and R6G complexes with both α-Quartz and α-Cristobalite SNPs of 40 Å diameter were estimated. These confirm that R6G adsorption is most stable on 40 Å α-Quartz at pH 7, although dimerization is equally possible.
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Affiliation(s)
- Daniel Doveiko
- Photophysics
Group, Department of Physics, University of Strathclyde, Scottish Universities Physics Alliance, 107 Rottenrow, Glasgow G4 0NG, U.K.
| | - Karina Kubiak-Ossowska
- Chemical
Engineering, James Weir Building, University
of Strathclyde, Glasgow G1 1XJ, U.K.
| | - Yu Chen
- Photophysics
Group, Department of Physics, University of Strathclyde, Scottish Universities Physics Alliance, 107 Rottenrow, Glasgow G4 0NG, U.K.
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3
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Hudek M, Kubiak-Ossowska K, Johnston K, Ferro VA, Mulheran PA. Chitin and Chitosan Binding to the α-Chitin Crystal: A Molecular Dynamics Study. ACS OMEGA 2023; 8:3470-3477. [PMID: 36713729 PMCID: PMC9878639 DOI: 10.1021/acsomega.2c07495] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
Understanding the binding of chitosan oligomers to the surface of a chitin nanocrystal is important for improving the enzymatic deacetylation of chitin and for the design of chitin/chitosan composite films. Here, we study the binding of several chito-oligomers to the (100) surface of an α-chitin crystal using molecular dynamics (MD), steered MD, and umbrella sampling. The convergence of the free energy was carefully considered and yielded a binding energies of -12.5 and -2 kcal mol-1 for 6-monomer-long chitin and uncharged chitosan oligomers, respectively. We also found that the results for the umbrella sampling were consistent with the force profile from the steered MD and with classical MD simulations of the adsorption process. Our results give insight into the molecular-scale interactions, which can be helpful for the design of new chitin composite films. Furthermore, the free energy curves we present can be used to validate coarse-grained models for chitin and chitosan, which are necessary to study the self-assembly of chitin crystals due to the long time scale of the process.
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Affiliation(s)
- Magdalena Hudek
- Department
of Chemical and Process Engineering, University
of Strathclyde, 75 Montrose Street, GlasgowG1 1XJ, Scotland
| | - Karina Kubiak-Ossowska
- ARCHIE-WeSt,
Department of Physics, University of Strathclyde, 107 Rottenrow East, GlasgowG4 0NG, Scotland
| | - Karen Johnston
- Department
of Chemical and Process Engineering, University
of Strathclyde, 75 Montrose Street, GlasgowG1 1XJ, Scotland
| | - Valerie A. Ferro
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, GlasgowG4 0RE, Scotland
| | - Paul A. Mulheran
- Department
of Chemical and Process Engineering, University
of Strathclyde, 75 Montrose Street, GlasgowG1 1XJ, Scotland
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4
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Zhang H, Zheng J, Lin C, Yuan S. Molecular dynamics study on adsorption and desorption of lysozyme above polymer antifouling membranes. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Farouq MAH, Kubiak-Ossowska K, Al Qaraghuli MM, Ferro VA, Mulheran PA. Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study. Int J Mol Sci 2022; 23:ijms23094832. [PMID: 35563221 PMCID: PMC9103475 DOI: 10.3390/ijms23094832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/07/2022] Open
Abstract
Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles.
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Affiliation(s)
- Mohammed A. H. Farouq
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (M.M.A.Q.); (P.A.M.)
- Correspondence: ; Tel.: +44-01-4155-24400
| | - Karina Kubiak-Ossowska
- Department of Physics/Archie-West HPC, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, UK;
| | - Mohammed M. Al Qaraghuli
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (M.M.A.Q.); (P.A.M.)
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
- EPSRC Future Manufacturing Research Hub for Continuous Manufacturing and Advanced Crystallisation (CMAC), University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK
| | - Valerie A. Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
| | - Paul A. Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (M.M.A.Q.); (P.A.M.)
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6
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Caetano DLZ, Metzler R, Cherstvy AG, de Carvalho SJ. Adsorption of lysozyme into a charged confining pore. Phys Chem Chem Phys 2021; 23:27195-27206. [PMID: 34821240 DOI: 10.1039/d1cp03185f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Several applications arise from the confinement of proteins on surfaces because their stability and biological activity are enhanced. It is also known that the way in which a protein adsorbs on the surface is important for its biological function since its active sites should not be obstructed. In this study, the adsorption properties of hen egg-white lysozyme, HEWL, into a negatively charged silica pore is examined by employing a coarse-grained model and constant-pH Monte Carlo simulations. The role of electrostatic interactions is taken into account via including the Debye-Hückel potentials into the Cα structure-based model. We evaluate the effects of pH, salt concentration, and pore radius on the protein preferential orientation and spatial distribution of its residues regarding the pore surface. By mapping the residues that stay closer to the pore surface, we find that the increase of pH leads to orientational changes of the adsorbed protein when the solution pH gets closer to the HEWL isoelectric point. Under these conditions, the pKa shift of these important residues caused by the adsorption into the charged confining surface results in a HEWL charge distribution that stabilizes the adsorption in the observed protein orientation. We compare our observations to the results of the pKa shift for HEWL available in the literature and to some experimental data.
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Affiliation(s)
- Daniel L Z Caetano
- Institute of Chemistry, State University of Campinas (UNICAMP), Campinas, Brazil.,Center for Computational Engineering and Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Andrey G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.,Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Sidney J de Carvalho
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, Brazil.
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7
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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: 0.5] [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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8
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Mieda S. Analysis of the Interaction between a Protein and Polymer Membranes Using Steered Molecular Dynamics Simulation to Interpret the Fouling Behavior. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shunsuke Mieda
- Platform Laboratory for Science & Technology, Asahi Kasei Corporation, 2-1 Samejima, Fuji, Shizuoka 416-8501, Japan
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9
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Kawagoe Y, Surblys D, Matsubara H, Kikugawa G, Ohara T. Cross-Plane and In-Plane Heat Conductions in Layer-by-Layer Membrane: Molecular Dynamics Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6482-6493. [PMID: 32447958 DOI: 10.1021/acs.langmuir.0c00845] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A material with anisotropic heat conduction characteristics, which is determined by molecular scale structure, provides a way of controlling heat flow in nanoscale spaces. As such, here, we consider layer-by-layer (LbL) membranes, which are an electrostatic assembly of polyelectrolyte multilayers and are expected to have different heat conduction characteristics between cross-plane and in-plane directions. We constructed models of a poly(acrylic acid)/polyethylenimine (PAA/PEI) LbL membrane sandwiched by charged solid walls and investigated their anisotropic heat conduction using molecular dynamics simulations. In the cross-plane direction, the thermal boundary resistance between the solid wall and the LbL membrane and that between the constituent PAA and PEI layers decrease with increasing degree of ionization (solid surface charge density and the number of electric charges per PAA/PEI molecule). When the degree of ionization is low, the cross-plane thermal conductivity of a constituent layer is higher than that of the bulk state. As the degree of ionization increases, however, the cross-plane thermal conductivity of PAA, a linear polymer, decreases because of the increase in the number of in-plane oriented polymer chains. In the in-plane direction, we investigated the heat conduction of each layer and found the enhancement of effective in-plane thermal conductivity again due to the in-plane oriented chain alignment. The heat conduction in the LbL membrane is three-dimensionally enhanced compared to those in the bulk states of the constituent polymers because of the electrostatic interactions in the cross-plane direction and the molecular alignment in the in-plane direction.
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Affiliation(s)
- Yoshiaki Kawagoe
- Department of Aerospace Engineering, Tohoku University, 6-6-01, Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Donatas Surblys
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Hiroki Matsubara
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Gota Kikugawa
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Taku Ohara
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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10
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11
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Adsorption of Fibronectin Fragment on Surfaces Using Fully Atomistic Molecular Dynamics Simulations. Int J Mol Sci 2018; 19:ijms19113321. [PMID: 30366398 PMCID: PMC6275015 DOI: 10.3390/ijms19113321] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/15/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023] Open
Abstract
The effect of surface chemistry on the adsorption characteristics of a fibronectin fragment (FNIII8⁻10) was investigated using fully atomistic molecular dynamics simulations. Model surfaces were constructed to replicate self-assembled monolayers terminated with methyl, hydroxyl, amine, and carboxyl moieties. It was found that adsorption of FNIII8⁻10 on charged surfaces is rapid, specific, and driven by electrostatic interactions, and that the anchoring residues are either polar uncharged or of opposing charge to that of the targeted surfaces. On charged surfaces the presence of a strongly bound layer of water molecules and ions hinders FNIII8⁻10 adsorption. In contrast, adsorption kinetics on uncharged surfaces are slow and non-specific, as they are driven by van der Waals interactions, and the anchoring residues are polar uncharged. Due to existence of a positively charged area around its cell-binding region, FNIII8⁻10 is available for subsequent cell binding when adsorbed on a positively charged surface, but not when adsorbed on a negatively charged surface. On uncharged surfaces, the availability of the fibronectin fragment's cell-binding region is not clearly distinguished because adsorption is much less specific.
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12
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Hildebrand N, Wei G, Köppen S, Colombi Ciacchi L. Simulated and experimental force spectroscopy of lysozyme on silica. Phys Chem Chem Phys 2018; 20:19595-19605. [PMID: 30009290 DOI: 10.1039/c8cp03747g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The force spectra of proteins detaching from oxide surfaces measured by atomic force microscopy (AFM) often present complex patterns of peaks, which are difficult to correlate with individual bond-breaking events at the atomic scale. In this work we rationalize experimental AFM force spectra of hen-egg-white lysozyme detaching from silica by means of all-atom steered molecular dynamics (SMD) simulations. In particular, we demonstrate that the native tertiary structure of lysozyme is preserved if, and only if, its four intramolecular disulfide bridges are intact. Otherwise, the protein pulled off the surface undergoes severe unfolding, which is well captured by SMD simulations in explicit solvent. Implicit solvent simulations, on the contrary, wrongly predict protein unfolding even in the presence of S-S bridges, due to the lack of additional structural stabilization provided by the water's hydrogen-bond network within and surrounding the protein. On the basis of our combined experimental and theoretical findings, we infer that the rugged force spectra characteristic of lysozyme/silica interfaces are not due to the successive breaking of internal disulfide bonds leading to partial unfolding events. Rather, they reflect the detachment of several molecules bound to the same AFM tip, each anchored to the surface via multiple hydrogen and ionic bonds.
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Affiliation(s)
- Nils Hildebrand
- Hybrid Materials Interfaces Group, Faculty Production Engineering, Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany.
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13
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Tokarczyk K, Kubiak-Ossowska K, Jachimska B, Mulheran PA. Energy Landscape of Negatively Charged BSA Adsorbed on a Negatively Charged Silica Surface. J Phys Chem B 2018. [PMID: 29536734 DOI: 10.1021/acs.jpcb.7b12484] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We study the energy landscape of the negatively charged protein bovine serum albumin adsorbed on a negatively charged silica surface at pH 7. We use fully atomistic molecular dynamics (MD) and steered MD (SMD) to probe the energy of adsorption and the pathway for the surface diffusion of the protein and its associated activation energy. We find an adsorption energy ∼1.2 eV, which implies that adsorption is irreversible even on experimental time scales of hours. In contrast, the activation energy for surface diffusion is ∼0.4 eV so that it is observable on the MD simulation time scale of 100 ns. This analysis paves the way for a more detailed understanding of how a protein layer forms on biomaterial surfaces, even when the protein and surface share the same electrical polarity.
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Affiliation(s)
- Karolina Tokarczyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry (PAS) , Niezapominajek 8 , 30-239 Cracow , Poland
| | - Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering , University of Strathclyde , James Weir Building, 75 Montrose Street , G1 1XJ Glasgow , U.K
| | - Barbara Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry (PAS) , Niezapominajek 8 , 30-239 Cracow , Poland
| | - Paul A Mulheran
- Department of Chemical and Process Engineering , University of Strathclyde , James Weir Building, 75 Montrose Street , G1 1XJ Glasgow , U.K
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14
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Kubiak-Ossowska K, Tokarczyk K, Jachimska B, Mulheran PA. Bovine Serum Albumin Adsorption at a Silica Surface Explored by Simulation and Experiment. J Phys Chem B 2017; 121:3975-3986. [PMID: 28350173 DOI: 10.1021/acs.jpcb.7b01637] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Molecular details of BSA adsorption on a silica surface are revealed by fully atomistic molecular dynamics (MD) simulations (with a 0.5 μs trajectory), supported by dynamic light scattering (DLS), zeta potential, multiparametric surface plasmon resonance (MP-SPR), and contact angle experiments. The experimental and theoretical methods complement one another and lead to a wider understanding of the mechanism of BSA adsorption across a range of pH 3-9. The MD results show how the negatively charged BSA at pH7 adsorbs to the negatively charged silica surface, and reveal a unique orientation with preserved secondary and tertiary structure. The experiments then show that the protein forms complete monolayers at ∼ pH6, just above the protein's isoelectric point (pH5.1). The surface contact angle is maximum when it is completely coated with protein, and the hydrophobicity of the surface is understood in terms of the simulated protein conformation. The adsorption behavior at higher pH > 6 is also consistently interpreted using the MD picture; both the contact angle and the adsorbed protein mass density decrease with increasing pH, in line with the increasing magnitude of negative charge on both the protein and the surface. At lower pH < 5 the protein starts to unfold, and the adsorbed mass dramatically decreases. The comprehensive picture that emerges for the formation of oriented protein films with preserved native conformation will help guide efforts to create functional films for new technologies.
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Affiliation(s)
- Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde , James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, U.K
| | - Karolina Tokarczyk
- J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science (PAS) , Niezapominajek 8, 30-239 Cracow, Poland
| | - Barbara Jachimska
- J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science (PAS) , Niezapominajek 8, 30-239 Cracow, Poland
| | - Paul A Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde , James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, U.K
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15
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Abstract
Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
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16
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Kubiak-Ossowska K, Jachimska B, Mulheran PA. How Negatively Charged Proteins Adsorb to Negatively Charged Surfaces: A Molecular Dynamics Study of BSA Adsorption on Silica. J Phys Chem B 2016; 120:10463-10468. [PMID: 27657173 DOI: 10.1021/acs.jpcb.6b07646] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How proteins adsorb to inorganic material surfaces is critically important for the development of new biotechnologies, since the orientation and structure of the adsorbed proteins impacts their functionality. While it is known that many negatively charged proteins readily adsorb to negatively charged oxide surfaces, a detailed understanding of how this process occurs is lacking. In this work we study the adsorption of BSA, an important transport protein that is negatively charged at physiological conditions, to a model silica surface that is also negatively charged. We use fully atomistic molecular dynamics to provide detailed understanding of the noncovalent interactions that bind the BSA to the silica surface. Our results provide new insight into the competing roles of long-range electrostatics and short-range forces, and the consequences this has for the orientation and structure of the adsorbed proteins.
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Affiliation(s)
- Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde , James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Barbara Jachimska
- J. Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science (PAS) , Niezapominajek 8, 30-239 Cracow, Poland
| | - Paul A Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde , James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
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17
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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: 2.2] [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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18
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Joyeux M. Equilibration of complexes of DNA and H-NS proteins on charged surfaces: a coarse-grained model point of view. J Chem Phys 2015; 141:115102. [PMID: 25240378 DOI: 10.1063/1.4895819] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes, the precise structure of complexes of DNA and H-NS proteins is still not well understood. In particular, it is not clear whether the structure of DNA/H-NS complexes in the living cell is similar to that of complexes deposited on mica surfaces, which may be observed by AFM microscopy. A coarse-grained model, which helps getting more insight into this question, is described and analyzed in the present paper. This model is able of describing both the bridging of bacterial DNA by H-NS in the bulk and the deposition and equilibration of the complex on a charged surface. Simulations performed with the model reveal that a slight attraction between DNA and the charged surface is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar plasmids bridged by H-NS proteins similar to those observed by AFM microscopy. They furthermore highlight the antagonistic effects of the interactions between DNA and the surface. Indeed, increasing these interactions slows down the equilibration of naked plasmids on the surface but, on the other hand, enables a faster equilibration of DNA/H-NS complexes. Based on the distribution of the lifetimes of H-NS bridges and the time evolution of the number of trans-binding protein dimers during equilibration of the complexes on the surface, it is argued that the decrease of the equilibration time of the complex upon increase of the interaction strength between DNA and the surface is ascribable to the associated decrease of the probability to form new bridges between DNA and the proteins.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique (CNRS UMR5588), Université Joseph Fourier Grenoble 1, BP 87, 38402 St Martin d'Hères, France
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19
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Kubiak-Ossowska K, Cwieka M, Kaczynska A, Jachimska B, Mulheran PA. Lysozyme adsorption at a silica surface using simulation and experiment: effects of pH on protein layer structure. Phys Chem Chem Phys 2015; 17:24070-7. [PMID: 26315945 DOI: 10.1039/c5cp03910j] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hen Egg White Lysozyme (HEWL) is a widely used exemplar to study protein adsorption on surfaces and interfaces. Here we use fully atomistic Molecular Dynamics (MD) simulations, Multi-Parametric Surface Plasmon Resonance (MP-SPR), contact angle and zeta potential measurements to study HEWL adsorption at a silica surface. The simulations provide a detailed description of the adsorption mechanism and indicate that at pH7 the main adsorption driving force is electrostatics, supplemented by weaker hydrophobic forces. Moreover, they reveal the preferred orientation of the adsorbed protein and show that its structure is only slightly altered at the interface with the surface. This provides the basis for interpreting the experimental results, which indicate the surface adsorbs a close-packed monolayer at about pH10 where the surface has a large negative zeta potential and the HEWL is positively charged. At higher pH, the adsorption amount of the protein layer is greatly reduced due to the loss of charge on the protein. At lower pH, the smaller zeta potential of the surface leads to lower HEWL adsorption. These interpretations are complemented by the contact angle measurements that show how the hydrophobicity of the surface is greatest when the surface coverage is highest. The simulations provide details of the hydrophobic residues exposed to solution by the adsorbed HEWL, completing the picture of the protein layer structure.
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Affiliation(s)
- Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, UK.
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20
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Wang X, Liu L, Wang P, Li W, Zhang J, Yan Y. How the Inhibition Performance Is Affected by Inhibitor Concentration: A Perspective from Microscopic Adsorption Behavior. Ind Eng Chem Res 2014. [DOI: 10.1021/ie502790c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xiao Wang
- College
of Science, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
| | - Liang Liu
- College
of Science, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
| | - Pan Wang
- College
of Science, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
| | - Wen Li
- College
of Science, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
| | - Jun Zhang
- College
of Science, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
| | - Youguo Yan
- College
of Science, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong, China University of Petroleum, 266580 Qingdao, Shandong People’s Republic of China
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21
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Adsorption and catalytic activity of glucose oxidase accumulated on OTCE upon the application of external potential. J Colloid Interface Sci 2014; 435:164-70. [PMID: 25261840 DOI: 10.1016/j.jcis.2014.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 11/21/2022]
Abstract
This article describes the adsorption of glucose oxidase (GOx) onto optically transparent carbon electrodes (OTCE) under the effect of applied potential and the analysis of the enzymatic activity of the resulting GOx/OTCE substrates. In order to avoid electrochemical interferences with the enzyme redox center, control electrochemical experiments were performed using flavin adenine dinucleotide (FAD) and GOx/OTCE substrates. Then, the enzyme adsorption experiments were carried out as a function of the potential applied (ranged from the open circuit potential to +950mV), the pH solution, the concentration of enzyme, and the ionic strength on the environment. The experimental results demonstrated that an increase in the adsorbed amount of GOx on the OTCE can be achieved when the potential was applied. Although the increase in the adsorbed amount was examined as a function of the potential, a maximum enzymatic activity was observed in the GOx/OTCE substrate achieved at +800mV. These experiments suggest that although an increase in the amount of enzyme adsorbed can be obtained by the application of an external potential to the electrode, the magnitude of such potential can produce detrimental effects in the conformation of the adsorbed protein and should be carefully considered. As such, the article describes a simple and rational approach to increase the amount of enzyme adsorbed on a surface and can be applied to improve the sensitivity of a variety of biosensors.
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22
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Kubiak-Ossowska K, Mulheran PA, Nowak W. Fibronectin Module FNIII9 Adsorption at Contrasting Solid Model Surfaces Studied by Atomistic Molecular Dynamics. J Phys Chem B 2014; 118:9900-8. [DOI: 10.1021/jp5020077] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Karina Kubiak-Ossowska
- Department
of Chemical and Process Engineering, University of Strathclyde, James
Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudziadzka 5/7, 87-100 Torun, Poland
| | - Paul A. Mulheran
- Department
of Chemical and Process Engineering, University of Strathclyde, James
Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Wieslaw Nowak
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudziadzka 5/7, 87-100 Torun, Poland
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23
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Kubiak-Ossowska K, Burley G, Patwardhan SV, Mulheran PA. Spontaneous membrane-translocating peptide adsorption at silica surfaces: a molecular dynamics study. J Phys Chem B 2013; 117:14666-75. [PMID: 24176015 PMCID: PMC3871889 DOI: 10.1021/jp409130s] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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Spontaneous membrane-translocating
peptides (SMTPs) have recently
been shown to directly penetrate cell membranes. Adsorption of a SMTP,
and some engineered extensions, at model silica surfaces is studied
herein using fully atomistic molecular dynamics simulations in order
to assess their potential to construct novel drug delivery systems.
The simulations are designed to reproduce the electric fields above
single, siloxide-rich charged surfaces, and the trajectories indicate
that the main driving force for adsorption is electrostatic. An increase
in the salt concentration slows down but does not prevent adsorption
of the SMTP to the surface; it also does not result in peptide desorption,
suggesting additional binding via hydrophobic forces. The results
are used to design extensions to the peptide sequence which we find
enhance adsorption but do not affect the adsorbed conformation. We
also investigate the effect of surface hydroxylation on the peptide
adsorption. In all cases, the final adsorbed conformations are with
the peptide flattened to the surface with arginine residues, which
are key to the peptide’s function, anchoring it to the surface
so that they are not exposed to solution. This conformation could
impact their role in membrane translocation and thus has important
implications for the design of future drug delivery vehicles.
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Affiliation(s)
- Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde , James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
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