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Santander EA, Bravo G, Chang-Halabi Y, Olguín-Orellana GJ, Naulin PA, Barrera MJ, Montenegro FA, Barrera NP. The Adsorption of P2X2 Receptors Interacting with IgG Antibodies Revealed by Combined AFM Imaging and Mechanical Simulation. Int J Mol Sci 2023; 25:336. [PMID: 38203505 PMCID: PMC10778698 DOI: 10.3390/ijms25010336] [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: 10/30/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
The adsorption of proteins onto surfaces significantly impacts biomaterials, medical devices, and biological processes. This study aims to provide insights into the irreversible adsorption process of multiprotein complexes, particularly focusing on the interaction between anti-His6 IgG antibodies and the His6-tagged P2X2 receptor. Traditional approaches to understanding protein adsorption have centered around kinetic and thermodynamic models, often examining individual proteins and surface coverage, typically through Molecular Dynamics (MD) simulations. In this research, we introduce a computational approach employing Autodesk Maya 3D software for the investigation of multiprotein complexes' adsorption behavior. Utilizing Atomic Force Microscopy (AFM) imaging and Maya 3D-based mechanical simulations, our study yields real-time structural and kinetic observations. Our combined experimental and computational findings reveal that the P2X2 receptor-IgG antibody complex likely undergoes absorption in an 'extended' configuration. Whereas the P2X2 receptor is less adsorbed once is complexed to the IgG antibody compared to its individual state, the opposite is observed for the antibody. This insight enhances our understanding of the role of protein-protein interactions in the process of protein adsorption.
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Affiliation(s)
- Eduardo A. Santander
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Graciela Bravo
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Yuan Chang-Halabi
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Gabriel J. Olguín-Orellana
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Pamela A. Naulin
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Mario J. Barrera
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Felipe A. Montenegro
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
| | - Nelson P. Barrera
- Laboratory of Nanophysiology and Structural Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile; (E.A.S.); (G.B.); (G.J.O.-O.)
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Lousada CM. Interactions between glucosides of the tip of the S1 subunit of SARS-CoV-2 spike protein and dry and wet surfaces of CuO and Cu-A model for the surfaces of coinage metals. Colloids Surf B Biointerfaces 2022; 214:112465. [PMID: 35334309 PMCID: PMC8940556 DOI: 10.1016/j.colsurfb.2022.112465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022]
Abstract
Despite their importance there is little knowledge at the atomic scale on the interactions between fragments of SARS-CoV-2 and inorganic materials. Such knowledge is important to understand the survival of the virus at surfaces and for the development of antiviral materials. Here is reported a study of the interactions between glucoside monomers of the tip of the S1 subunit of SARS-CoV-2 spike protein with dry and wet surfaces of CuO and Cu, performed with dispersion corrected density functional theory—DFT. The three glucoside monomers that constitute the tip of S1: 6VSB, 6VXX and 6X6P, were adsorbed onto dry and wet CuO(111) and Cu(110) with different orientations and surface alignments. There are large differences—of up to 1.3 eV—in binding energies between these monomers and the surfaces. These differences depend on: the type of surface; if the surface is wet or dry; if the glucosidic O-atom points towards or away from the surfaces; and to a smaller extent on the surface alignment of the monomers. All monomers bind strongly to the surfaces via molecular adsorption that does not involve bond breaking in the monomers at this stage. 6VSB has the larger adsorption energies—that reach 2.2 eV—due to its larger dipole moment. Both materials bind the monomers more strongly when their surfaces are dry. At Cu(110) the bonds are on average 1 eV stronger when the surface is dry when compared to wet. The difference between dry and wet CuO(111) is smaller, in the order of 0.2 eV. Overall, it is here shown that the stability of the monomers of the tip of the spike protein of the virus is very different at different surfaces. For a given surface the larger binding energies in dry conditions could explain the differences in the surface stability of the spike protein depending on the presence of moisture.
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Affiliation(s)
- Cláudio M Lousada
- Department of Materials Science and Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
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4
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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: 1.7] [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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5
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Trusova VM, Gorbenko GP. Molecular dynamics simulations of lysozyme-lipid systems: probing the early steps of protein aggregation. J Biomol Struct Dyn 2017; 36:2249-2260. [PMID: 28665188 DOI: 10.1080/07391102.2017.1349691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Using the molecular dynamics simulation, the role of lipids in the lysozyme transition into the aggregation-competent conformation has been clarified. Analysis of the changes of lysozyme secondary structure upon its interactions with the model bilayer membranes composed of phosphatidylcholine and its mixtures with phosphatidylglycerol (10, 40, and 80 mol%) within the time interval of 100 ns showed that lipid-bound protein is characterized by the increased content of β-structures. Along with this, the formation of protein-lipid complexes was accompanied by the increase in the gyration radius and the decrease in RMSD of polypeptide chain. The results obtained were interpreted in terms of the partial unfolding of lysozyme molecule on the lipid matrix, with the magnitude of this effect being increased with increasing the fraction of anionic lipids. Based on the results of molecular dynamics simulation, a hypothetical model of the nucleation of lysozyme amyloid fibrils in a membrane environment was suggested.
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Affiliation(s)
- Valeriya M Trusova
- a Department of Nuclear and Medical Physics , V.N. Karazin Kharkov National University , 4 Svobody Sq., Kharkov 61022 , Ukraine
| | - Galyna P Gorbenko
- a Department of Nuclear and Medical Physics , V.N. Karazin Kharkov National University , 4 Svobody Sq., Kharkov 61022 , Ukraine
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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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7
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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: 8.6] [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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8
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Beckner W, He Y, Pfaendtner J. Chain Flexibility in Self-Assembled Monolayers Affects Protein Adsorption and Surface Hydration: A Molecular Dynamics Study. J Phys Chem B 2016; 120:10423-10432. [DOI: 10.1021/acs.jpcb.6b05882] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Wesley Beckner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Yi He
- College
of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, P.R. China
| | - Jim Pfaendtner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
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9
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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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10
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Romanowska J, Kokh DB, Wade RC. When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces. NANO LETTERS 2015; 15:7508-7513. [PMID: 26491986 DOI: 10.1021/acs.nanolett.5b03168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Fluorescent labels are often attached to proteins to monitor binding and adsorption processes. Docking simulations for native hen egg white lysozyme (HEWL) and HEWL labeled with fluorescein isothiocyanate show that these adsorb differently on charged surfaces. Attachment of even a small label can significantly change the interaction properties of a protein. Thus, the results of experiments with fluorescently labeled proteins should be interpreted by modeling the structures and computing the interaction properties of both labeled and unlabeled species.
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Affiliation(s)
- Julia Romanowska
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , 69117 Heidelberg, Germany
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , 69117 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , 69117 Heidelberg, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg University , 69117 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , 69117 Heidelberg, Germany
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11
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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: 5.8] [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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12
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Liang J, Fieg G, Jakobtorweihen S. Molecular Dynamics Simulations of a Binary Protein Mixture Adsorption onto Ion-Exchange Adsorbent. Ind Eng Chem Res 2015. [DOI: 10.1021/ie504374x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Liang
- Institute
of Process and Plant Engineering, Hamburg University of Technology, Schwarzenbergstrasse 95, 21073 Hamburg, Germany
| | - Georg Fieg
- Institute
of Process and Plant Engineering, Hamburg University of Technology, Schwarzenbergstrasse 95, 21073 Hamburg, Germany
| | - Sven Jakobtorweihen
- Institute
of Thermal Separation Processes, Hamburg University of Technology, Eissendorfer Strasse 38, 21073 Hamburg, Germany
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Wu E, Coppens MO, Garde S. Role of arginine in mediating protein-carbon nanotube interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:1683-1692. [PMID: 25575129 DOI: 10.1021/la5043553] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Arginine-rich proteins (e.g., lysozyme) or poly-L-arginine peptides have been suggested as solvating and dispersing agents for single-wall carbon nanotubes (CNTs) in water. In addition, protein structure-function in porous and hydrophobic materials is of broad interest. The amino acid residue, arginine (Arg(+)), has been implicated as an important mediator of protein/peptide-CNT interactions. To understand the structural and thermodynamic aspects of this interaction at the molecular level, we employ molecular dynamics (MD) simulations of the protein lysozyme in the interior of a CNT, as well as of free solutions of Arg(+) in the presence of a CNT. To dissect the Arg(+)-CNT interaction further, we also perform simulations of aqueous solutions of the guanidinium ion (Gdm(+)) and the norvaline (Nva) residue in the presence of a CNT. We show that the interactions of lysozyme with the CNT are mediated by the surface Arg(+) residues. The strong interaction of Arg(+) residue with the CNT is primarily driven by the favorable interactions of the Gdm(+) group with the CNT wall. The Gdm(+) group is not as well-hydrated on its flat sides, which binds to the CNT wall. This is consistent with a similar binding of Gdm(+) ions to a hydrophobic polymer. In contrast, the Nva residue, which lacks the Gdm(+) group, binds to the CNT weakly. We present details of the free energy of binding, molecular structure, and dynamics of these solutes on the CNT surface. Our results highlight the important role of Arg(+) residues in protein-CNT or protein-carbon-based material interactions. Such interactions could be manipulated precisely through protein engineering, thereby offering control over protein orientation and structure on CNTs, graphene, or other hydrophobic interfaces.
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Affiliation(s)
- Eugene Wu
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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14
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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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15
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Wei Q, Becherer T, Angioletti-Uberti S, Dzubiella J, Wischke C, Neffe AT, Lendlein A, Ballauff M, Haag R. Protein Interactions with Polymer Coatings and Biomaterials. Angew Chem Int Ed Engl 2014; 53:8004-31. [DOI: 10.1002/anie.201400546] [Citation(s) in RCA: 524] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Indexed: 01/07/2023]
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16
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Wei Q, Becherer T, Angioletti-Uberti S, Dzubiella J, Wischke C, Neffe AT, Lendlein A, Ballauff M, Haag R. Wechselwirkungen von Proteinen mit Polymerbeschichtungen und Biomaterialien. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400546] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Kastantin M, Langdon BB, Schwartz DK. A bottom-up approach to understanding protein layer formation at solid-liquid interfaces. Adv Colloid Interface Sci 2014; 207:240-52. [PMID: 24484895 PMCID: PMC4028386 DOI: 10.1016/j.cis.2013.12.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 12/05/2013] [Accepted: 12/17/2013] [Indexed: 11/25/2022]
Abstract
A common goal across different fields (e.g. separations, biosensors, biomaterials, pharmaceuticals) is to understand how protein behavior at solid-liquid interfaces is affected by environmental conditions. Temperature, pH, ionic strength, and the chemical and physical properties of the solid surface, among many factors, can control microscopic protein dynamics (e.g. adsorption, desorption, diffusion, aggregation) that contribute to macroscopic properties like time-dependent total protein surface coverage and protein structure. These relationships are typically studied through a top-down approach in which macroscopic observations are explained using analytical models that are based upon reasonable, but not universally true, simplifying assumptions about microscopic protein dynamics. Conclusions connecting microscopic dynamics to environmental factors can be heavily biased by potentially incorrect assumptions. In contrast, more complicated models avoid several of the common assumptions but require many parameters that have overlapping effects on predictions of macroscopic, average protein properties. Consequently, these models are poorly suited for the top-down approach. Because the sophistication incorporated into these models may ultimately prove essential to understanding interfacial protein behavior, this article proposes a bottom-up approach in which direct observations of microscopic protein dynamics specify parameters in complicated models, which then generate macroscopic predictions to compare with experiment. In this framework, single-molecule tracking has proven capable of making direct measurements of microscopic protein dynamics, but must be complemented by modeling to combine and extrapolate many independent microscopic observations to the macro-scale. The bottom-up approach is expected to better connect environmental factors to macroscopic protein behavior, thereby guiding rational choices that promote desirable protein behaviors.
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Affiliation(s)
- Mark Kastantin
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, United States
| | - Blake B Langdon
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309, United States.
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18
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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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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: 2.2] [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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Yang W, Zhang L, Li M, Pu X, Zhao N. Effects of Non‐specific and Specific Solvation on Adsorption of BPTI on Au Surface: Insight from Molecular Dynamics Simulation. CHINESE J CHEM PHYS 2013. [DOI: 10.1063/1674-0068/26/05/558-568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Hung A, Mager M, Hembury M, Stellacci F, Stevens MM, Yarovsky I. Amphiphilic amino acids: a key to adsorbing proteins to nanopatterned surfaces? Chem Sci 2013. [DOI: 10.1039/c2sc21639f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Kubiak-Ossowska K, Mulheran PA. Protein diffusion and long-term adsorption states at charged solid surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:15577-15585. [PMID: 23062108 DOI: 10.1021/la303323r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The diffusion pathways of lysozyme adsorbed to a model charged ionic surface are studied using fully atomistic steered molecular dynamics simulation. The simulations start from existing protein adsorption trajectories, where it has been found that one particular residue, Arg128 at the N,C-terminal face, plays a crucial role in anchoring the lysozyme to the surface [Langmuir 2010 , 26 , 15954 - 15965]. We first investigate the desorption pathway for the protein by pulling the Arg128 side chain away from the surface in the normal direction, and its subsequent readsorption, before studying diffusion pathways by pulling the Arg128 side chain parallel to the surface. We find that the orientation of this side chain plays a decisive role in the diffusion process. Initially, it is oriented normal to the surface, aligning in the electrostatic field of the surface during the adsorption process, but after resorption it lies parallel to the surface, being unable to return to its original orientation due to geometric constraints arising from structured water layers at the surface. Diffusion from this alternative adsorption state has a lower energy barrier of ∼0.9 eV, associated with breaking hydrogen bonds along the pathway, in reasonable agreement with the barrier inferred from previous experimental observation of lysozyme surface clustering. These results show the importance of studying protein diffusion alongside adsorption to gain full insight into the formation of protein clusters and films, essential steps in the future development of functionalized surfaces.
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Affiliation(s)
- Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde, Glasgow, United Kingdom
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Panos M, Sen TZ, Ahunbay MG. Molecular simulation of fibronectin adsorption onto polyurethane surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:12619-12628. [PMID: 22856639 DOI: 10.1021/la301546v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Poly(ethylene glycol)-based polyurethanes have been widely used in biomedical applications; however, they are prone to swelling. A natural polyol, castor oil, can be incorporated into these polyurethanes to control the degree of the swelling, which alters mechanical properties and protein adsorption characteristic of the polymers. In this work, we modeled poly(ethylene glycol) and castor oil copolymers of hexamethylene diisocyanate-based polyurethanes (PEG-HDI and CO-HDI, respectively) and compared their mechanisms for fibronectin adsorption using molecular mechanics and molecular dynamics simulations. Results showed that the interplay between the hydrophobic residues concentrated at the N-terminal end of the protein, the surface roughness, and the hydrophilicity of the polymer surface determine the overall protein adsorption affinity. Incorporating explicit water molecules in the simulations results in higher affinity for fibronectin adsorption to more hydrophobic surface of CO-HDI surfaces, emphasizing the role that water molecules play during adsorption. We also observed that the strain energies that are indicative of flexibility and consequently entropy are significantly affected by the changes in the patterns of β-sheet formation/breaking. Our study lends supports to the view that while castor oil controls the degree of swelling, it increases the adsorption of fibronectin to a limited extent due to the interplay between its hydrophobicity and its surface roughness, which needs to be taken into account during the design of polyurethane-based biomaterials.
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Affiliation(s)
- Melisa Panos
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
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Johnston CT, Premachandra GS, Szabo T, Lok J, Schoonheydt RA. Interaction of biological molecules with clay minerals: a combined spectroscopic and sorption study of lysozyme on saponite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:611-619. [PMID: 22047516 DOI: 10.1021/la203161n] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The interaction of hen egg white lysozyme (HEWL) with Na- and Cs-exchanged saponite was investigated using sorption, structural, and spectroscopic methods as a model system to study clay-protein interactions. HEWL sorption to Na- and Cs-saponite was determined using the bicinchoninic acid (BCA) assay, thermogravimetric analysis, and C and N analysis. For Na-saponite, the TGA and elemental analysis-derived sorption maximum was 600 mg/g corresponding to a surface coverage of 0.85 ng/mm(2) with HEWL occupying 526 m(2)/g based on a cross-sectional area of 13.5 nm(2)/molecule. HEWL sorption on Na-saponite was accompanied by the release of 9.5 Na(+) ions for every molecule of HEWL sorbed consistent with an ion exchange mechanism between the positively charged HEWL (IEP 11) and the negatively charged saponite surface. The d-spacing of the HEWL-Na-saponite complex increased to a value of 4.4 nm consistent with the crystallographic dimensions of HEWL of 3 × 3 × 4.5 nm. In the case of Cs-saponite, there was no evidence of interlayer sorption; however, sorption of HEWL to the "external" surface of Cs-saponite showed a high affinity isotherm. FTIR and Raman analysis of the amide I region of the HEWL-saponite films prepared from water and D(2)O showed little perturbation to the secondary structure of the protein. The overall hydrophilic nature of the HEWL-Na-saponite complex was determined by water vapor sorption measurements. The clay retained its hydrophilic character with a water content of 18% at high humidity corresponding to 240 H(2)O molecules per molecule of HEWL.
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Affiliation(s)
- Cliff T Johnston
- Birck Nanotechnology Center, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, United States.
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