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Ouyang J, Sheng Y, Wang W. Recent Advances of Studies on Cell-Penetrating Peptides Based on Molecular Dynamics Simulations. Cells 2022; 11:cells11244016. [PMID: 36552778 PMCID: PMC9776715 DOI: 10.3390/cells11244016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
With the ability to transport cargo molecules across cell membranes with low toxicity, cell-penetrating peptides (CPPs) have become promising candidates for next generation peptide-based drug delivery vectors. Over the past three decades since the first CPP was discovered, a great deal of work has been done on the cellular uptake mechanisms and the applications for the delivery of therapeutic molecules, and significant advances have been made. But so far, we still do not have a precise and unified understanding of the structure-activity relationship of the CPPs. Molecular dynamics (MD) simulations provide a method to reveal peptide-membrane interactions at the atomistic level and have become an effective complement to experiments. In this paper, we review the progress of the MD simulations on CPP-membrane interactions, including the computational methods and technical improvements in the MD simulations, the research achievements in the CPP internalization mechanism, CPP decoration and coupling, and the peptide-induced membrane reactions during the penetration process, as well as the comparison of simulated and experimental results.
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Affiliation(s)
- Jun Ouyang
- School of Public Courses, Bengbu Medical College, Bengbu 233030, China
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yuebiao Sheng
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- High Performance Computing Center, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
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3
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Is It Possible to Find an Antimicrobial Peptide That Passes the Membrane Bilayer with Minimal Force Resistance? An Attempt at a Predictive Approach by Molecular Dynamics Simulation. Int J Mol Sci 2022; 23:ijms23115997. [PMID: 35682676 PMCID: PMC9180591 DOI: 10.3390/ijms23115997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/04/2022] Open
Abstract
There is still no answer to the mechanism of penetration of AMP peptides through the membrane bilayer. Several mechanisms for such a process have been proposed. It is necessary to understand whether it is possible, using the molecular dynamics method, to determine the ability of peptides of different compositions and lengths to pass through a membrane bilayer. To explain the passage of a peptide through a membrane bilayer, a method for preparing a membrane phospholipid bilayer was proposed, and 656 steered molecular dynamics calculations were carried out for pulling 7 amyloidogenic peptides with antimicrobial potential, and monopeptides (homo-repeats consisting of 10 residues of the same amino acid: Poly (Ala), Poly (Leu), Poly (Met), Poly (Arg), and Poly (Glu)) with various sequences through the membrane. Among the 15 studied peptides, the peptides exhibiting the least force resistance when passing through the bilayer were found, and the maximum reaction occurred at the boundary of the membrane bilayer entry. We found that the best correlation between the maximum membrane reaction force and the calculated parameters corresponds to the instability index (the correlation coefficient is above 0.9). One of the interesting results of this study is that the 10 residue amyloidogenic peptides and their extended peptides, with nine added residue cell-penetrating peptides and four residue linkers, both with established antimicrobial activity, have the same bilayer resistance force. All calculated data are summarized and posted on the server.
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4
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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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Pujol-Navarro N, Kubiak-Ossowska K, Ferro V, Mulheran P. Simulating Peptide Monolayer Formation: GnRH-I on Silica. Int J Mol Sci 2021; 22:ijms22115523. [PMID: 34073815 PMCID: PMC8197186 DOI: 10.3390/ijms22115523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Molecular dynamics (MD) simulations can provide a detailed view of molecule behaviour at an atomic level, which can be useful when attempting to interpret experiments or design new systems. The decapeptide gonadotrophin-releasing hormone I (GnRH-I) is known to control fertility in mammals for both sexes. It was previously shown that inoculation with silica nanoparticles (SiNPs) coated with GnRH-I makes an effective anti-fertility vaccine due to how the peptide adsorbs to the nanoparticle and is presented to the immune system. In this paper, we develop and employ a protocol to simulate the development of a GnRH-I peptide adlayer by allowing peptides to diffuse and adsorb in a staged series of trajectories. The peptides start the simulation in an immobile state in solution above the model silica surface, and are then released sequentially. This facile approach allows the adlayer to develop in a natural manner and appears to be quite versatile. We find that the GnRH-I adlayer tends to be sparse, with electrostatics dominating the interactions. The peptides are collapsed to the surface and are seemingly free to interact with additional solutes, supporting the interpretations of the GNRH-I/SiNP vaccine system.
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Affiliation(s)
- Neret Pujol-Navarro
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK;
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
- Correspondence:
| | - Karina Kubiak-Ossowska
- ARCHIE-WeSt, Department of Physics, University of Strathclyde, 107 Rottenrow East, Glasgow G4 0NG, UK;
| | - Valerie Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
| | - Paul Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK;
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Affiliation(s)
- Yunqiao Ma
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Singapore
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute Nanyang Technological University Singapore Singapore
| | - Andrew L. Zydney
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania USA
| | - Jia Wei Chew
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Singapore
- Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute Nanyang Technological University Singapore Singapore
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Chiarpotti MV, Longo GS, Del Pópolo MG. Nanoparticles modified with cell penetrating peptides: Assessing adsorption on membranes containing acidic lipids. Colloids Surf B Biointerfaces 2021; 197:111373. [DOI: 10.1016/j.colsurfb.2020.111373] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/07/2020] [Accepted: 09/17/2020] [Indexed: 01/12/2023]
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Xiong H, Devegowda D, Huang L. Water Bridges in Clay Nanopores: Mechanisms of Formation and Impact on Hydrocarbon Transport. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:723-733. [PMID: 31910022 DOI: 10.1021/acs.langmuir.9b03244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Clays are prevalent in the earth's crust and usually deposited in the presence of water. An unusual finding in clays is that under certain conditions, water molecules can collectively form a bridge across a clay-hosted pore. However, there are relatively few studies focused on the formation mechanism of the water bridge in clay nanopores. In this work, we use molecular dynamics simulations to investigate the formation of the water bridge and its influence on fluid transport in slit-shaped illite nanopores. Two different basal illite surface chemistries are constructed: potassium-hydroxyl (P-H) and hydroxyl-hydroxyl (H-H) structures. Because pore size and water concentration are expected to control the formation of the water bridge, our simulations span a wide range of pore sizes and water concentrations. Generally, positive potassium layers and negative hydroxyl groups in P-H nanopore can induce partial charges which in return produce instant and local electric fields, favoring the formation of the water bridge. In P-H nanopores, the water bridge happens at a relatively low water concentration. However, in H-H nanopores, the water bridge only forms at high water concentrations. Additionally, smaller pore sizes favor the formation of water bridges. However, the presence of an electric field promotes the formation of a water bridge even in larger pore sizes in P-H pores. The results also indicate that in both P-H and H-H nanopores, water adsorption films initially create a smooth surface to promote the hydrocarbon flow. In P-H nanopores, further increases in the water concentration causes a sharp decline in the self-diffusion coefficients of the hydrocarbon and water due to the formation of the water bridge. The presence of electric fields in P-H pores can however weaken the confinement effect of illite and promote the hydrocarbon flow. In contrast, in H-H nanopores, the self-diffusion coefficients decline slowly with the increase of water concentration. This is because no water bridge is formed at low water concentrations in H-H nanopores.
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Affiliation(s)
- Hao Xiong
- Mewbourne School of Petroleum and Geological Engineering , The University of Oklahoma , Norman , Oklahoma 73019 , United States
| | - Deepak Devegowda
- Mewbourne School of Petroleum and Geological Engineering , The University of Oklahoma , Norman , Oklahoma 73019 , United States
| | - Liangliang Huang
- Chemical, Biological & Materials Engineering , The University of Oklahoma , Norman , Oklahoma 73019 , United States
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9
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Grasso G, Mercuri S, Danani A, Deriu MA. Biofunctionalization of Silica Nanoparticles with Cell-Penetrating Peptides: Adsorption Mechanism and Binding Energy Estimation. J Phys Chem B 2019; 123:10622-10630. [DOI: 10.1021/acs.jpcb.9b08106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928, Switzerland
| | - Stefano Mercuri
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128, Torino, Italy
| | - Andrea Danani
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928, Switzerland
| | - Marco A. Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128, Torino, Italy
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11
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Molecular simulation of protein adsorption and conformation at gas-liquid, liquid–liquid and solid–liquid interfaces. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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12
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Connell DJ, Gebril A, Khan MAH, Patwardhan SV, Kubiak-Ossowska K, Ferro VA, Mulheran PA. Rationalising drug delivery using nanoparticles: a combined simulation and immunology study of GnRH adsorbed to silica nanoparticles. Sci Rep 2018; 8:17115. [PMID: 30459397 PMCID: PMC6244087 DOI: 10.1038/s41598-018-35143-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/26/2018] [Indexed: 11/30/2022] Open
Abstract
Silica nanoparticles (SiNPs) have been shown to have significant potential for drug delivery and as adjuvants for vaccines. We have simulated the adsorption of GnRH-I (gonadotrophin releasing hormone I) and a cysteine-tagged modification (cys-GnRH-I) to model silica surfaces, as well as its conjugation to the widely-used carrier protein bovine serum albumin (BSA). Our subsequent immunological studies revealed no significant antibody production was caused by the peptide-SiNP systems, indicating that the treatment was not effective. However, the testosterone response with the native peptide-SiNPs indicated a drug effect not found with cys-GnRH-I-SiNPs; this behaviour is explained by the specific orientation of the peptides at the silica surface found in the simulations. With the BSA systems, we found significant testosterone reduction, particularly for the BSA-native conjugates, and an antibody response that was notably higher with the SiNPs acting as an adjuvant; this behaviour again correlates well with the epitope presentation predicted by the simulations. The range of immunological and hormone response can therefore be interpreted and understood by the simulation results and the presentation of the peptides to solution, paving the way for the future rational design of drug delivery and vaccine systems guided by biomolecular simulation.
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Affiliation(s)
- David J Connell
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK
| | - Ayman Gebril
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Mohammad A H Khan
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Siddharth V Patwardhan
- Department of Chemical and Biological Engineering, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, 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.
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13
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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: 2.2] [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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14
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Ruan M, Seydou M, Noel V, Piro B, Maurel F, Barbault F. Molecular Dynamics Simulation of a RNA Aptasensor. J Phys Chem B 2017; 121:4071-4080. [PMID: 28363022 DOI: 10.1021/acs.jpcb.6b12544] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.
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Affiliation(s)
- Min Ruan
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France.,School of Materials and Metallurgy, Hubei Polytechnic University , Huangshi, Hubei, China
| | - Mahamadou Seydou
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Vincent Noel
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Benoit Piro
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - François Maurel
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
| | - Florent Barbault
- Université Paris Diderot , Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J-A de Baïf, 75013 Paris, France
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15
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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: 11.9] [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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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: 68] [Impact Index Per Article: 8.5] [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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Davidson S, Lamprou DA, Urquhart AJ, Grant MH, Patwardhan SV. Bioinspired Silica Offers a Novel, Green, and Biocompatible Alternative to Traditional Drug Delivery Systems. ACS Biomater Sci Eng 2016; 2:1493-1503. [DOI: 10.1021/acsbiomaterials.6b00224] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Scott Davidson
- Department
of Chemical and Process Engineering, University of Strathclyde, 75 Montrose
Street, Glasgow G1 1XJ, United Kingdom
| | - Dimitrios A. Lamprou
- Strathclyde
Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
- EPSRC
Centre for Innovative Manufacturing in Continuous Manufacturing and
Crystallization (CMAC), University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Andrew J. Urquhart
- Department
of Micro- and Nanotechnology, Technical University of Denmark, Produktionstorvet, Building 423, 2800 Kongens Lyngby, Denmark
| | - M. Helen Grant
- Department
of Biomedical Engineering, University of Strathclyde, 106 Rottenrow
East, Glasgow G4 0NW, United Kingdom
| | - Siddharth V. Patwardhan
- Department
of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
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18
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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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Wei T, Sajib MSJ, Samieegohar M, Ma H, Shing K. Self-Assembled Monolayers of an Azobenzene Derivative on Silica and Their Interactions with Lysozyme. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13543-52. [PMID: 26597057 DOI: 10.1021/acs.langmuir.5b03603] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The capability of the photoresponsive isomerization of azobenzene derivatives in self-assembled monolayer (SAM) surfaces to control protein adsorption behavior has very promising applications in antifouling materials and biotechnology. In this study, we performed an atomistic molecular dynamics (MD) simulation in combination with free-energy calculations to study the morphology of azobenzene-terminated SAMs (Azo-SAMs) grafted on a silica substrate and their interactions with lysozyme. Results show that the Azo-SAM surface morphology and the terminal benzene rings' packing are highly correlated with the surface density and the isomer state. Higher surface coverage and the trans-isomer state lead to a more ordered polycrystalline backbone as well as more ordered local packing of benzene rings. On the Azo-SAM surface, water retains a high interfacial diffusivity, whereas the adsorbed lysozyme is found to have extremely low mobility but a relative stable secondary structure. The moderate desorption free energy (∼60 kT) from the trans-Azo-SAM surface was estimated by using both the nonequilibrium-theorem-based Jarzynski's equality and equilibrium umbrella sampling.
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Affiliation(s)
- Tao Wei
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Md Symon Jahan Sajib
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Mohammadreza Samieegohar
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Heng Ma
- Dan F. Smith Department of Chemical Engineering, Lamar University , Beaumont, Texas 77710, United States
| | - Katherine Shing
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California , Los Angeles, California 90089, United States
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20
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Köhler S, Schmid F, Settanni G. Molecular Dynamics Simulations of the Initial Adsorption Stages of Fibrinogen on Mica and Graphite Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13180-90. [PMID: 26569042 DOI: 10.1021/acs.langmuir.5b03371] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Fibrinogen, a blood glycoprotein of vertebrates, plays an essential role in blood clotting by polymerizing into fibrin when activated. Upon adsorption on material surfaces, it also contributes to determine their biocompatibility and has been implicated in the onset of thrombosis and inflammation at medical implants. Here we present the first fully atomistic simulations of the initial stages of the adsorption process of fibrinogen on mica and graphite surfaces. The simulations reveal a weak adsorption on mica that allows frequent desorption and reorientation events. This adsorption is driven by electrostatic interactions between the protein and the silicate surface as well as the counterion layer. Preferred adsorption orientations for the globular regions of the protein are identified. The adsorption on graphite is found to be stronger with fewer reorientation and desorption events and shows the onset of denaturation of the protein.
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Affiliation(s)
- Stephan Köhler
- Institut für Physik, ‡Graduate School Materials Science in Mainz, and §Max Planck Graduate Center, Johannes Gutenberg-Universität , Mainz 55099, Germany
| | - Friederike Schmid
- Institut für Physik, ‡Graduate School Materials Science in Mainz, and §Max Planck Graduate Center, Johannes Gutenberg-Universität , Mainz 55099, Germany
| | - Giovanni Settanni
- Institut für Physik, ‡Graduate School Materials Science in Mainz, and §Max Planck Graduate Center, Johannes Gutenberg-Universität , Mainz 55099, Germany
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21
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Grasso G, Deriu MA, Prat M, Rimondini L, Vernè E, Follenzi A, Danani A. Cell Penetrating Peptide Adsorption on Magnetite and Silica Surfaces: A Computational Investigation. J Phys Chem B 2015; 119:8239-46. [PMID: 26042722 DOI: 10.1021/jp512782e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Magnetic nanoparticles (MNPs) represent one of the most promising materials as they can act as a versatile platform in the field of bionanotechnology for enhanced imaging, diagnosis, and treatment of various diseases. Silica is the most common compound for preparing coated iron oxide NPs since it improves colloidal stability and the binding affinity for various organic molecules. Biomolecules such as cell penetrating peptides (CPPs) might be employed to decorate MNPs, combining their promising physicochemical properties with a cell penetrating ability. In this work, a computational investigation on adsorption of Antennapedia homeodomain-derived penetrating peptide (pAntp) on silica and magnetite (MAG) surfaces is presented. By employing umbrella sampling molecular dynamics, we provided a quantitative estimation of the pAntp-surface adsorption free energy to highlight the influence of surface hydroxylation state on the adsorption mechanism. The interaction between peptide and surface has shown to be mainly driven by electrostatics. In case of MAG surface, also an important contribution of van der Waals (VdW) attraction was observed. Our data suggest that a competitive mechanism between MNPs and cell membrane might partially inhibit the CPP to carry out its membrane penetrating function.
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Affiliation(s)
- Gianvito Grasso
- †Department of Innovative Technologies, University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno CH-6928, Switzerland.,‡Department of Health Sciences, Università degli Studi del Piemonte Orientale "A. Avogadro", via Paolo Solaroli 17, Novara IT-28100, Italy
| | - Marco A Deriu
- †Department of Innovative Technologies, University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno CH-6928, Switzerland
| | - Maria Prat
- ‡Department of Health Sciences, Università degli Studi del Piemonte Orientale "A. Avogadro", via Paolo Solaroli 17, Novara IT-28100, Italy
| | - Lia Rimondini
- ‡Department of Health Sciences, Università degli Studi del Piemonte Orientale "A. Avogadro", via Paolo Solaroli 17, Novara IT-28100, Italy
| | - Enrica Vernè
- §Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino IT-10129, Italy
| | - Antonia Follenzi
- ‡Department of Health Sciences, Università degli Studi del Piemonte Orientale "A. Avogadro", via Paolo Solaroli 17, Novara IT-28100, Italy
| | - Andrea Danani
- †Department of Innovative Technologies, University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno CH-6928, Switzerland
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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: 2.2] [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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Cohen-Avrahami M, Shames AI, Ottaviani MF, Aserin A, Garti N. HIV-TAT Enhances the Transdermal Delivery of NSAID Drugs from Liquid Crystalline Mesophases. J Phys Chem B 2014; 118:6277-87. [DOI: 10.1021/jp412739p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Marganit Cohen-Avrahami
- Casali
Institute of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Alexander I. Shames
- Department
of Physics, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
| | - M. Francesca Ottaviani
- Department
of Earth, Life and Environment Sciences, University of Urbino, Località
Crocicchia, Urbino 61029, Italy
| | - Abraham Aserin
- Casali
Institute of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Nissim Garti
- Casali
Institute of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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