1
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Gandhi ZA, Lu T, Guo W, Crisci R, Gao J, Wilson MC, So CR, Sarker P, Qin X, Wei T, Chen Z. Probing Molecular Interactions between Barnacle Peptides and Polymers In Situ to Understand Bioadhesion. J Phys Chem Lett 2025; 16:4031-4037. [PMID: 40231810 DOI: 10.1021/acs.jpclett.5c00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2025]
Abstract
Biofouling poses a significant issue in the maritime industry, where the attachment of biofoulants to ships greatly affects operational costs, surface durability, and marine pollution. Barnacles and barnacle proteins are widely used as models to study the biofouling mechanisms. With a combined in situ experimental and simulation approach, this study elucidated the molecular interaction mechanisms between barnacle cement-derived peptides (BCPs) and a polymer. The results showed that the peptide-charged segment plays a significant role in interfacial interactions, facilitating the formation of antiparallel β-sheets within the simple domain. This study reports the first in situ, real-time observation of β-sheet formation in adsorbed BCPs at the buried solution-polymer interface, which will prove to be essential for understanding overall BCP aggregation and barnacle fouling mechanisms.
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Affiliation(s)
- Zahra Asif Gandhi
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tieyi Lu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wen Guo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ralph Crisci
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jinpeng Gao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michael C Wilson
- NRC Postdoc Sited in Chemistry Division, Code 6176, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Christopher R So
- NRC Postdoc Sited in Chemistry Division, Code 6176, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Pranab Sarker
- Department of Biomedical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Xiaoxue Qin
- Department of Biomedical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Tao Wei
- Department of Biomedical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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2
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Rhodes ER, Day NB, Aldrich EC, Wyatt Shields C, Sprenger KG. Elucidating the role of carrier proteins in cytokine stabilization within double emulsion-based polymeric nanoparticles. Bioeng Transl Med 2025; 10:e10722. [PMID: 39801762 PMCID: PMC11711224 DOI: 10.1002/btm2.10722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/14/2024] [Accepted: 08/22/2024] [Indexed: 01/16/2025] Open
Abstract
Polymeric micro- and nanoparticles are useful vehicles for delivering cytokines to diseased tissues such as solid tumors. Double emulsion solvent evaporation is one of the most common techniques to formulate cytokines into vehicles made from hydrophobic polymers; however, the liquid-liquid interfaces formed during emulsification can greatly affect the stability and therapeutic performance of encapsulated cytokines. To develop more effective cytokine-delivery systems, a clear molecular understanding of the interactions between relevant proteins and solvents used in the preparation of such particles is needed. We utilized an integrated computational and experimental approach for studying the governing mechanisms by which interleukin-12 (IL-12), a clinically relevant cytokine, is protected from denaturation by albumin, a common stabilizing protein, at an organic-aqueous solvent interface formed during double emulsification. We investigated protein-protein interactions between human (h)IL-12 and albumin and simulated these components in pure water, dichloromethane (DCM), and along a water/DCM interface to replicate the solvent regimes formed during double emulsification. We observed that (i) hIL-12 experiences increased structural deviations near the water/DCM interface, and (ii) hIL-12 structural deviations are reduced in the presence of albumin. Experimentally, we found that hIL-12 bioactivity is retained when released from particles in which albumin is added to the aqueous phase in molar excess to hIL-12 and sufficient time is allowed for albumin-hIL-12 binding. Findings from this work have implications in establishing design principles to enhance the stability of cytokines and other unstable proteins in particles formed by double emulsification for improved stability and therapeutic efficacy.
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Affiliation(s)
- Emily R. Rhodes
- Department of Chemical and Biological EngineeringUniversity of Colorado BoulderBoulderColoradoUSA
| | - Nicole B. Day
- Department of Chemical and Biological EngineeringUniversity of Colorado BoulderBoulderColoradoUSA
| | - Emma C. Aldrich
- Department of Chemical and Biological EngineeringUniversity of Colorado BoulderBoulderColoradoUSA
| | - C. Wyatt Shields
- Department of Chemical and Biological EngineeringUniversity of Colorado BoulderBoulderColoradoUSA
- Biomedical Engineering ProgramUniversity of Colorado BoulderBoulderColoradoUSA
| | - Kayla G. Sprenger
- Department of Chemical and Biological EngineeringUniversity of Colorado BoulderBoulderColoradoUSA
- Biomedical Engineering ProgramUniversity of Colorado BoulderBoulderColoradoUSA
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3
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Salafsky J, Johansson PK, Abdelkader E, Otting G. Ligand-induced conformational changes in protein molecules detected by sum-frequency generation. Biophys J 2024; 123:3678-3687. [PMID: 39305014 PMCID: PMC11560303 DOI: 10.1016/j.bpj.2024.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/06/2024] [Accepted: 09/18/2024] [Indexed: 10/04/2024] Open
Abstract
We present the first demonstration of ligand-induced conformational changes in a biological molecule, a protein, by sum-frequency generation (SFG). Constructs of KRasG12D protein were prepared by selectively deuterating residues of a single amino acid type using isotope-labeled amino acids and cell-free protein synthesis. By attaching labeled protein to a supported bilayer membrane via a His-tag to Ni-NTA-bearing lipids, we ensured that single layers of ordered molecules were formed while preserving the protein's native structure. Exceptionally large SFG amide I signals were produced in both labeled and unlabeled proteins, demonstrating a high degree of orientational order upon attachment to the bilayer. Deuterated protein also produced SFG signals in the CDx spectral region, which were not present in the unlabeled protein. The CDx signals were measured before and after binding a peptide inhibitor, KRpep-2d, revealing shifts in SFG intensity due to conformational changes at the labeled sites. In particular, peaks associated with CDx stretching vibrations for alanine, valine, and glycine changed substantially in amplitude upon inhibitor binding. By inspection of the crystal structure, these three residues are uniquely colocated on the protein surface in and near the nucleotide binding site, which is in allosteric communication with the site of peptide inhibitor binding, suggesting an approach to identify a ligand's binding site. The technique offers a highly sensitive, nonperturbative method of mapping ligand-induced conformational changes and allosteric networks in biological molecules for studies of the relationship between structure and function and mechanisms of action in drug discovery.
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Affiliation(s)
- Joshua Salafsky
- Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, California; Skylight Discovery, Inc., Suite 300, Seattle, Washington.
| | | | - Elwy Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT, Australia
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4
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Ma YH, Wang C, Yang J, Li B, Han X, Lu X. Disulfide-Driven Charge and Hydrophobicity Rearrangement of Remodeled Membrane Proteins toward Amyloid-Type Aggregation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:16145-16150. [PMID: 39054779 DOI: 10.1021/acs.langmuir.4c01201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
As a common pathological hallmark, protein aggregation into amyloids is a highly complicated phenomenon, attracting extensive research interest for elucidating its structural details and formation mechanisms. Membrane deposition and disulfide-driven protein misfolding play critical roles in amyloid-type aggregation, yet the underlying molecular process remains unclear. Here, we employed sum frequency generation (SFG) vibrational spectroscopy to comprehensively investigate the remodeling process of lysozyme, as the model protein, into amyloid-type aggregates at the cell membrane interface. It was discovered that disulfide reduction concurrently induced the transition of membrane-bound lysozyme from predominantly α-helical to antiparallel β-sheet structures, under a mode switch of membrane interaction from electrostatic to hydrophobic, and subsequent oligomeric aggregation. These findings shed light on the systematic understanding of dynamic molecular mechanisms underlying membrane-interactive amyloid oligomer formation.
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Affiliation(s)
- Yong-Hao Ma
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Chu Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jingjing Yang
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Bolin Li
- Anhui Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory, HFIPS, Chinese Academy of Sciences, Hefei 230031, China
| | - Xiaofeng Han
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaolin Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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5
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Saurabh S, Lei L, Li Z, Seddon JM, Lu JR, Kalonia C, Bresme F. Adsorption of monoclonal antibody fragments at the water-oil interface: A coarse-grained molecular dynamics study. APL Bioeng 2024; 8:026128. [PMID: 38948350 PMCID: PMC11211994 DOI: 10.1063/5.0207959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/06/2024] [Indexed: 07/02/2024] Open
Abstract
Monoclonal antibodies (mAbs) can undergo structural changes due to interaction with oil-water interfaces during storage. Such changes can lead to aggregation, resulting in a loss of therapeutic efficacy. Therefore, understanding the microscopic mechanism controlling mAb adsorption is crucial to developing strategies that can minimize the impact of interfaces on the therapeutic properties of mAbs. In this study, we used MARTINI coarse-grained molecular dynamics simulations to investigate the adsorption of the Fab and Fc domains of the monoclonal antibody COE3 at the oil-water interface. Our aim was to determine the regions on the protein surface that drive mAb adsorption. We also investigate the role of protein concentration on protein orientation and protrusion to the oil phase. While our structural analyses compare favorably with recent neutron reflectivity measurements, we observe some differences. Unlike the monolayer at the interface predicted by neutron reflectivity experiments, our simulations indicate the presence of a secondary diffused layer near the interface. We also find that under certain conditions, protein-oil interaction can lead to a considerable distortion in the protein structure, resulting in enhanced adsorption behavior.
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Affiliation(s)
- Suman Saurabh
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College, W12 0BZ London, United Kingdom
| | - Li Lei
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College, W12 0BZ London, United Kingdom
| | - Zongyi Li
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, Oxford Road, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - John M. Seddon
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College, W12 0BZ London, United Kingdom
| | - Jian R. Lu
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, Oxford Road, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Cavan Kalonia
- Dosage Form Design and Development, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, USA
| | - Fernando Bresme
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College, W12 0BZ London, United Kingdom
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6
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Saurabh S, Zhang Q, Li Z, Seddon JM, Kalonia C, Lu JR, Bresme F. Mechanistic Insights into the Adsorption of Monoclonal Antibodies at the Water/Vapor Interface. Mol Pharm 2024; 21:704-717. [PMID: 38194618 PMCID: PMC10848294 DOI: 10.1021/acs.molpharmaceut.3c00821] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/11/2024]
Abstract
Monoclonal antibodies (mAbs) are active components of therapeutic formulations that interact with the water-vapor interface during manufacturing, storage, and administration. Surface adsorption has been demonstrated to mediate antibody aggregation, which leads to a loss of therapeutic efficacy. Controlling mAb adsorption at interfaces requires a deep understanding of the microscopic processes that lead to adsorption and identification of the protein regions that drive mAb surface activity. Here, we report all-atom molecular dynamics (MD) simulations of the adsorption behavior of a full IgG1-type antibody at the water/vapor interface. We demonstrate that small local changes in the protein structure play a crucial role in promoting adsorption. Also, interfacial adsorption triggers structural changes in the antibody, potentially contributing to the further enhancement of surface activity. Moreover, we identify key amino acid sequences that determine the adsorption of antibodies at the water-air interface and outline strategies to control the surface activity of these important therapeutic proteins.
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Affiliation(s)
- Suman Saurabh
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
| | - Qinkun Zhang
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
| | - Zongyi Li
- Biological
Physics Group, School of Physics and Astronomy, Faculty of Science
and Engineering, the University of Manchester, Manchester M13 9PL, U.K.
| | - John M. Seddon
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
| | - Cavan Kalonia
- Dosage
Form Design and Development, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Jian R. Lu
- Biological
Physics Group, School of Physics and Astronomy, Faculty of Science
and Engineering, the University of Manchester, Manchester M13 9PL, U.K.
| | - Fernando Bresme
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
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7
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Krevert C, Chavez D, Chatterjee S, Stelzl LS, Pütz S, Roeters SJ, Rudzinski JF, Fawzi NL, Girard M, Parekh SH, Hunger J. Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics. J Phys Chem Lett 2023; 14:11224-11234. [PMID: 38056002 PMCID: PMC10726384 DOI: 10.1021/acs.jpclett.3c02790] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Formation of liquid condensates plays a critical role in biology via localization of different components or via altered hydrodynamic transport, yet the hydrogen-bonding environment within condensates, pivotal for solvation, has remained elusive. We explore the hydrogen-bond dynamics within condensates formed by the low-complexity domain of the fused in sarcoma protein. Probing the hydrogen-bond dynamics sensed by condensate proteins using two-dimensional infrared spectroscopy of the protein amide I vibrations, we find that frequency-frequency correlations of the amide I vibration decay on a picosecond time scale. Interestingly, these dynamics are markedly slower for proteins in the condensate than in a homogeneous protein solution, indicative of different hydration dynamics. All-atom molecular dynamics simulations confirm that lifetimes of hydrogen-bonds between water and the protein are longer in the condensates than in the protein in solution. Altered hydrogen-bonding dynamics may contribute to unique solvation and reaction dynamics in such condensates.
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Affiliation(s)
- Carola
S. Krevert
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Chavez
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sayantan Chatterjee
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Lukas S. Stelzl
- KOMET 1,
Institute of Physics, Johannes Gutenberg
University, Staudingerweg 7, 55099 Mainz, Germany
- Faculty of
Biology, Johannes Gutenberg University Mainz, Gresemundweg 2, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), Ackermannweg 2, 55128 Mainz, Germany
| | - Sabine Pütz
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Steven J. Roeters
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Department
of Anatomy and Neurosciences, Amsterdam
UMC, Vrije Universiteit, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Joseph F. Rudzinski
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- IRIS
Adlershof, Humboldt-Universität zu
Berlin, Zum Großen
Windkanal 2, 12489 Berlin, Germany
| | - Nicolas L. Fawzi
- Department
of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Providence, Rhode Island 02912, United States
| | - Martin Girard
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Johannes Hunger
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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8
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Kurapati R, Natarajan U. Complex role of chemical nature and tacticity in the adsorption free energy of carboxylic acid polymers at the oil-water interface: molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:27783-27797. [PMID: 37814803 DOI: 10.1039/d3cp02754f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Scientific understanding of the molecular structure and adsorption of polymers at oil-water liquid interfaces is very limited. In this study the adsorption free energy at the oil (CCl4)-water interface was estimated using umbrella sampling molecular dynamics simulations for six carboxylate type vinyl polymers differing in hydrophobic nature and tacticity: isotactic and syndiotactic poly(acrylic acid) (i-PAA, s-PAA), isotactic and syndiotactic poly(methacrylic acid) (i-PMA, s-PMA), and atactic and syndiotactic poly(ethylacrylic acid) (a-PEA, s-PEA). ΔGads values are in the order i-PMA < a-PEA < s-PEA < s-PAA < i-PAA < s-PMA. The results show the significant and complex influence of the chemical nature as well as tacticity of the polymer on its adsorption free energy as related to hydrogen bonding and orientation of bonds with respect to oil and water phases. The influence of tacticity is found to be the highest for PMA, which is interpreted to occur due to the balance between interactions among side groups and those occurring between side groups and solvent. Interactions between side-groups are crucial for determining the conformation of PAA (most hydrophilic) and the solvation of the side-group in water is crucial for determining the conformation of PEA (most hydrophobic). The adsorption of PMA represents the transition between these two dominating effects. The molecular contributions to the enthalpy of adsorption indicate that adsorption is favored mainly through two interactions: polymer-CCl4 and water-water.
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Affiliation(s)
- Raviteja Kurapati
- Macromolecular Modeling and Simulation Laboratory, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai, 600036, India.
| | - Upendra Natarajan
- Macromolecular Modeling and Simulation Laboratory, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai, 600036, India.
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9
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Roeters SJ, Strunge K, Pedersen KB, Golbek TW, Bregnhøj M, Zhang Y, Wang Y, Dong M, Nielsen J, Otzen DE, Schiøtt B, Weidner T. Elevated concentrations cause upright alpha-synuclein conformation at lipid interfaces. Nat Commun 2023; 14:5731. [PMID: 37723164 PMCID: PMC10507035 DOI: 10.1038/s41467-023-39843-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/23/2023] [Indexed: 09/20/2023] Open
Abstract
The amyloid aggregation of α-synuclein (αS), related to Parkinson's disease, can be catalyzed by lipid membranes. Despite the importance of lipid surfaces, the 3D-structure and orientation of lipid-bound αS is still not known in detail. Here, we report interface-specific vibrational sum-frequency generation (VSFG) experiments that reveal how monomeric αS binds to an anionic lipid interface over a large range of αS-lipid ratios. To interpret the experimental data, we present a frame-selection method ("ViscaSelect") in which out-of-equilibrium molecular dynamics simulations are used to generate structural hypotheses that are compared to experimental amide-I spectra via excitonic spectral calculations. At low and physiological αS concentrations, we derive flat-lying helical structures as previously reported. However, at elevated and potentially disease-related concentrations, a transition to interface-protruding αS structures occurs. Such an upright conformation promotes lateral interactions between αS monomers and may explain how lipid membranes catalyze the formation of αS amyloids at elevated protein concentrations.
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Affiliation(s)
- Steven J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
- Department of Anatomy and Neurosciences, Amsterdam UMC, Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Kris Strunge
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Kasper B Pedersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Thaddeus W Golbek
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Mikkel Bregnhøj
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Yuge Zhang
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Yin Wang
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
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10
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Saurabh S, Li Z, Hollowell P, Waigh T, Li P, Webster J, Seddon JM, Kalonia C, Lu JR, Bresme F. Structure and interaction of therapeutic proteins in solution: a combined simulation and experimental study. Mol Phys 2023; 121:e2236248. [PMID: 38107421 PMCID: PMC10721229 DOI: 10.1080/00268976.2023.2236248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/30/2023] [Indexed: 12/19/2023]
Abstract
The aggregation of therapeutic proteins in solution has attracted significant interest, driving efforts to understand the relationship between microscopic structural changes and protein-protein interactions determining aggregation processes in solution. Additionally, there is substantial interest in being able to predict aggregation based on protein structure as part of molecular developability assessments. Molecular Dynamics provides theoretical tools to complement experimental studies and to interrogate and identify the microscopic mechanisms determining aggregation. Here we perform all-atom MD simulations to study the structure and inter-protein interaction of the Fab and Fc fragments of the monoclonal antibody (mAb) COE3. We unravel the role of ion-protein interactions in building the ionic double layer and determining effective inter-protein interaction. Further, we demonstrate, using various state-of-the-art force fields (charmm, gromos, amber, opls/aa), that the protein solvation, ionic structure and protein-protein interaction depend significantly on the force field parameters. We perform SANS and Static Light Scattering experiments to assess the accuracy of the different forcefields. Comparison of the simulated and experimental results reveal significant differences in the forcefields' performance, particularly in their ability to predict the protein size in solution and inter-protein interactions quantified through the second virial coefficients. In addition, the performance of the forcefields is correlated with the protein hydration structure.
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Affiliation(s)
- Suman Saurabh
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London, United Kingdom
| | - Zongyi Li
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Peter Hollowell
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Thomas Waigh
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
- Photon Science Institute, The University of Manchester, Manchester, UK
| | - Peixun Li
- STFC ISIS Facility, Rutherford Appleton Laboratory, Didcot, UK
| | - John Webster
- STFC ISIS Facility, Rutherford Appleton Laboratory, Didcot, UK
| | - John M. Seddon
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London, United Kingdom
| | - Cavan Kalonia
- Dosage Form Design and Development, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Jian R. Lu
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Fernando Bresme
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London, United Kingdom
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11
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Enders AA, Clark JB, Elliott SM, Allen HC. New Insights into Cation- and Temperature-Driven Protein Adsorption to the Air-Water Interface through Infrared Reflection Studies of Bovine Serum Albumin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5505-5513. [PMID: 37027519 DOI: 10.1021/acs.langmuir.3c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The chemistry and structure of the air-ocean interface modulate biogeochemical processes between the ocean and atmosphere and therefore impact sea spray aerosol properties, cloud and ice nucleation, and climate. Protein macromolecules are enriched in the sea surface microlayer and have complex adsorption properties due to the unique molecular balance of hydrophobicity and hydrophilicity. Additionally, interfacial adsorption properties of proteins are of interest as important inputs for ocean climate modeling. Bovine serum albumin is used here as a model protein to investigate the dynamic surface behavior of proteins under several variable conditions including solution ionic strength, temperature, and the presence of a stearic acid (C17COOH) monolayer at the air-water interface. Key vibrational modes of bovine serum albumin are examined via infrared reflectance-absorbance spectroscopy, a specular reflection method that ratios out the solution phase and highlights the aqueous surface to determine, at a molecular level, the surface structural changes and factors affecting adsorption to the solution surface. Amide band reflection absorption intensities reveal the extent of protein adsorption under each set of conditions. Studies reveal the nuanced behavior of protein adsorption impacted by ocean-relevant sodium concentrations. Moreover, protein adsorption is most strongly affected by the synergistic effects of divalent cations and increased temperature.
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Affiliation(s)
- Abigail A Enders
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jessica B Clark
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Scott M Elliott
- Computational Physics and Methods (CCS-2), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Heather C Allen
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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12
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Yang P, Guo W, Ramamoorthy A, Chen Z. Conformation and Orientation of Antimicrobial Peptides MSI-594 and MSI-594A in a Lipid Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5352-5363. [PMID: 37017985 DOI: 10.1021/acs.langmuir.2c03430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
There is significant interest in the development of antimicrobial compounds to overcome the increasing bacterial resistance to conventional antibiotics. Studies have shown that naturally occurring and de novo-designed antimicrobial peptides could be promising candidates. MSI-594 is a synthetic linear, cationic peptide that has been reported to exhibit a broad spectrum of antimicrobial activities. Investigation into how MSI-594 disrupts the cell membrane is important for better understanding the details of this antimicrobial peptide (AMP)'s action against bacterial cells. In this study, we used two different synthetic lipid bilayers: zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and anionic 7:3 POPC/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho(1'-rac-glycerol) (POPG). Sum frequency generation (SFG) vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) were used to determine the orientations of MSI-594 and its analogue MSI-594A associated with zwitterionic POPC and anionic 7:3 POPC/POPG lipid bilayers. The simulated ATR-FTIR and SFG spectra using nuclear magnetic resonance (NMR)-determined structures were compared with experimental spectra to optimize the bent angle between the N- (1-11) and C- (12-24) termini helices and the membrane orientations of the helices; since the NMR structure of the peptide was determined from lipopolysaccharide (LPS) micelles, the optimization was needed to find the most suitable conformation and orientation in lipid bilayers. The reported experimental results indicate that the optimized MSI-594 helical hairpin structure adopts a complete lipid bilayer surface-bound orientation (denoted "face-on") in both POPC and 7:3 POPC/POPG lipid bilayers. The analogue peptide, MSI-584A, on the other hand, exhibited a larger bent angle between the N- (1-11) and C- (12-24) termini helices with the hydrophobic C-terminal helix inserted into the hydrophobic region of the bilayer (denoted "membrane-inserted") when interacting with both POPC and 7:3 POPC/POPG lipid bilayers. These experimental findings on the membrane orientations suggest that both peptides are likely to disrupt the cell membrane through the carpet mechanism.
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Affiliation(s)
- Pei Yang
- Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Wen Guo
- Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Zhan Chen
- Department of Chemistry, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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13
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Guo W, Lu T, Crisci R, Nagao S, Wei T, Chen Z. Determination of protein conformation and orientation at buried solid/liquid interfaces. Chem Sci 2023; 14:2999-3009. [PMID: 36937592 PMCID: PMC10016606 DOI: 10.1039/d2sc06958j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Protein structures at solid/liquid interfaces mediate interfacial protein functions, which are important for many applications. It is difficult to probe interfacial protein structures at buried solid/liquid interfaces in situ at the molecular level. Here, a systematic methodology to determine protein molecular structures (orientation and conformation) at buried solid/liquid interfaces in situ was successfully developed with a combined approach using a nonlinear optical spectroscopic technique - sum frequency generation (SFG) vibrational spectroscopy, isotope labeling, spectra calculation, and computer simulation. With this approach, molecular structures of protein GB1 and its mutant (with two amino acids mutated) were investigated at the polymer/solution interface. Markedly different orientations and similar (but not identical) conformations of the wild-type protein GB1 and its mutant at the interface were detected, due to the varied molecular interfacial interactions. This systematic strategy is general and can be widely used to elucidate protein structures at buried interfaces in situ.
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Affiliation(s)
- Wen Guo
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Tieyi Lu
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Ralph Crisci
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Satoshi Nagao
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Ako-gun Kamigouri-cho Hyogo 678-1297 Japan
| | - Tao Wei
- Department of Chemical Engineering, Howard University 2366 Sixth Street NW Washington 20059 DC USA
| | - Zhan Chen
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
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14
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Zhang L, Yang L, Li Y, Ma J, Du X, Cao C, Jia Y, Li R. Ultrasonic treatment of foam for the prevention of foam-induced pepsin inactivation. Colloids Surf B Biointerfaces 2022; 221:113021. [DOI: 10.1016/j.colsurfb.2022.113021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
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15
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Jin H, Jin Y, Pan J, Sun Y, Sheng L. Multidimensional evaluation of structural properties of ovalbumin at the air-water interface: Spectroscopy and molecular dynamics simulations. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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16
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Yu CC, Seki T, Chiang KY, Tang F, Sun S, Bonn M, Nagata Y. Polarization-Dependent Heterodyne-Detected Sum-Frequency Generation Spectroscopy as a Tool to Explore Surface Molecular Orientation and Ångström-Scale Depth Profiling. J Phys Chem B 2022; 126:6113-6124. [PMID: 35849538 PMCID: PMC9421650 DOI: 10.1021/acs.jpcb.2c02178] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/01/2022] [Indexed: 11/28/2022]
Abstract
Sum-frequency generation (SFG) spectroscopy provides a unique optical probe for interfacial molecules with interface-specificity and molecular specificity. SFG measurements can be further carried out at different polarization combinations, but the target of the polarization-dependent SFG is conventionally limited to investigating the molecular orientation. Here, we explore the possibility of polarization-dependent SFG (PD-SFG) measurements with heterodyne detection (HD-PD-SFG). We stress that HD-PD-SFG enables accurate determination of the peak amplitude, a key factor of the PD-SFG data. Subsequently, we outline that HD-PD-SFG can be used not only for estimating the molecular orientation but also for investigating the interfacial dielectric profile and studying the depth profile of molecules. We further illustrate the variety of combined simulation and PD-SFG studies.
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Affiliation(s)
- Chun-Chieh Yu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Takakazu Seki
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kuo-Yang Chiang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Fujie Tang
- Department
of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Shumei Sun
- Department
of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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17
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Zhang M, Fan L, Liu Y, Huang S, Li J. Effects of proteins on emulsion stability: The role of proteins at the oil-water interface. Food Chem 2022; 397:133726. [PMID: 35908463 DOI: 10.1016/j.foodchem.2022.133726] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/26/2022] [Accepted: 07/14/2022] [Indexed: 11/15/2022]
Abstract
To obtain a stable protein-added emulsion system, researchers have focused on the design of the oil-water interface. This review discussed the updated details of protein adsorption behavior at the oil-water interface. We evaluated methods of monitoring interfacial proteins as well as their strengths and limitations. Based on the effects of structure on protein adsorption, we summarized the contribution of pre-changing methods to adsorption. In addition, the interaction of proteins and other surface-active molecules at the interface had been emphasized. Results showed that protein adsorption is affected by conformation, oil polarity and aqueous environments. The monitoring of interfacial proteins through spectroscopic properties in actual emulsion systems is an emerging trend. Pre-changing could improve the protein adsorption and the purpose of pre-changing of proteins is similar. In the interaction with other surface-active molecules, co-adsorption is desirable. By co-adsorption, the respective advantages can be exploited to obtain a more stable emulsion system.
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Affiliation(s)
- Mi Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liuping Fan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shengquan Huang
- Nuspower Greatsun (Guangdong) Biotechnology Co., Ltd., Guangzhou 510931, China
| | - Jinwei Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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18
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Strunge K, Hoinkis N, Lutz H, Alamdari S, Roeters SJ, Lu H, Pfaendtner J, Weidner T. Peptide Mimic of the Marine Sponge Protein Silicatein Fabricates Ultrathin Nanosheets of Silicon Dioxide and Titanium Dioxide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8087-8093. [PMID: 35727216 DOI: 10.1021/acs.langmuir.2c00918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Two-dimensional (2D) materials have attracted attention for potential applications in light harvesting, catalysis, and molecular electronics. Mineral proteins involved in hard tissue biogenesis can produce 2D structures with high fidelity by using sustainable production routes. This study shows that a peptide mimic based on the catalytic triad of the marine sponge protein silicatein catalyzes the formation of nanometer thin and stable sheets of silicon dioxide and titanium dioxide.
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Affiliation(s)
- Kris Strunge
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Nina Hoinkis
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Helmut Lutz
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sarah Alamdari
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
| | - Steven J Roeters
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Hao Lu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Department of Chemical Engineering, University of Washington, 105 Benson Hall, Seattle, Washington 98195-1750, United States
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19
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Andre JS, Grant J, Greyson E, Chen X, Tucker C, Drumright R, Mohler C, Chen Z. Molecular Interactions between Amino Silane Adhesion Promoter and Acrylic Polymer Adhesive at Buried Silica Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6180-6190. [PMID: 35512318 DOI: 10.1021/acs.langmuir.2c00602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this study, the influence of an amino silane (3-(2-aminoethylamino)-propyldimethoxymethylsilane, AEAPS) on the interfacial structure and adhesion of butyl acrylate/methyl methacrylate copolymers (BAMMAs) to silica was investigated by sum frequency generation vibrational spectroscopy (SFG). Small amounts of methacrylic acid, MAA, were included in the BAMMA polymerizations to assess the impact of carboxylic acid functionality on the glass interface. SFG was used to probe the O-H and C═O groups of incorporated MAA, ester C═O groups of BAMMA, and CH groups from all species at the silica interfaces. The addition of AEAPS resulted in a significant change in the molecular structure of the polymer at the buried interface with silica due to specific interactions between the BAMMA polymers and silane. SFG results were consistent with the formation of ionic bonds between the primary and secondary amines of the AEAPS tail group and the MAA component of the polymer, as evidenced by the loss of the MAA O-H and C═O signals at the interface. It is extensively reported in the literature that methoxy head groups of an amino silane chemically bind to the silanols of glass, leaving the amine groups available to react with various chemical functionalities. Our results are consistent with this scenario and support an adhesion promotion mechanism of amino silane with various aspects: (1) the ionic bond formation between the tail amine group and acid functionality on BAMMA, (2) the chemical coupling between the silane head group and glass, (3) migration of more ester C═O groups to the interface with order, and (4) disordering or reduced levels of CH groups at the interface. These results are important for better understanding of the mechanisms and effect of amino silanes on the adhesion between acrylate polymers and glass substrates in a variety of applications.
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Affiliation(s)
- John S Andre
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph Grant
- Dow Coating Materials, Collegeville, Pennsylvania 19426, United States
| | - Eric Greyson
- Dow Coating Materials, Collegeville, Pennsylvania 19426, United States
| | - Xiaoyun Chen
- The Dow Chemical Company, Core R&D, Midland, Michigan 48674, United States
| | - Christopher Tucker
- The Dow Chemical Company, Core R&D, Midland, Michigan 48674, United States
| | - Ray Drumright
- Dow Coating Materials, Midland, Michigan 48674, United States
| | - Carol Mohler
- The Dow Chemical Company, Core R&D, Midland, Michigan 48674, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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20
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Bregnhøj M, Roeters SJ, Chatterley AS, Madzharova F, Mertig R, Pedersen JS, Weidner T. Structure and Orientation of the SARS-Coronavirus-2 Spike Protein at Air-Water Interfaces. J Phys Chem B 2022; 126:3425-3430. [PMID: 35477296 PMCID: PMC9063992 DOI: 10.1021/acs.jpcb.2c01272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/06/2022] [Indexed: 11/28/2022]
Abstract
The SARS coronavirus 2 (SARS-CoV-2) spike protein is located at the outermost perimeter of the viral envelope and is the first component of the virus to make contact with surrounding interfaces. The stability of the spike protein when in contact with surfaces plays a deciding role for infection pathways and for the viability of the virus after surface contact. While cryo-EM structures of the spike protein have been solved with high resolution and structural studies in solution have provided information about the secondary and tertiary structures, only little is known about the folding when adsorbed to surfaces. We here report on the secondary structure and orientation of the S1 segment of the spike protein, which is often used as a model protein for in vitro studies of SARS-CoV-2, at the air-water interface using surface-sensitive vibrational sum-frequency generation (SFG) spectroscopy. The air-water interface plays an important role for SARS-CoV-2 when suspended in aerosol droplets, and it serves as a model system for hydrophobic surfaces in general. The SFG experiments show that the S1 segment of the spike protein remains folded at the air-water interface and predominantly binds in its monomeric state, while the combination of small-angle X-ray scattering and two-dimensional infrared spectroscopy measurements indicate that it forms hexamers with the same secondary structure in aqueous solution.
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Affiliation(s)
- Mikkel Bregnhøj
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C,
Denmark
| | - Steven J. Roeters
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C,
Denmark
| | - Adam S. Chatterley
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C,
Denmark
| | - Fani Madzharova
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C,
Denmark
| | - Rolf Mertig
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C,
Denmark
| | - Jan Skov Pedersen
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C,
Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C,
Denmark
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21
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Choose your own adventure: Picosecond or broadband vibrational sum-frequency generation spectroscopy. Biointerphases 2022; 17:031201. [PMID: 35513338 DOI: 10.1116/6.0001844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Vibrational sum-frequency generation (VSFG) spectroscopy is a method capable of measuring chemical structure and dynamics within the interfacial region between two bulk phases. At the core of every experimental system is a laser source that influences the experimental capabilities of the VSFG spectrometer. In this article, we discuss the differences between VSFG spectrometers built with picosecond and broadband laser sources as it will impact everything from material costs, experimental build time, experimental capabilities, and more. A focus is placed on the accessibility of the two different SFG systems to newcomers in the SFG field and provides a resource for laboratories considering incorporating VSFG spectroscopy into their research programs. This Tutorial provides a model decision tree to aid newcomers when determining whether the picosecond or femtosecond laser system is sufficient for their research program and navigates through it for a few specific scenarios.
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22
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Wang J, Woodley JM. In Situ Cofactor Regeneration Using NAD(P)H Oxidase: Enzyme Stability in a Bubble Column. ChemCatChem 2022. [DOI: 10.1002/cctc.202200255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jingyu Wang
- Technical University of Denmark Department of Chemical and Biochemical Engineerning Søltofts Plads Bygning 228A, 2800 Kgs. Lyngby 2800 2800 Kgs. Lyngby DENMARK
| | - John M. Woodley
- Technical University of Denmark Department of Chemical Engineering S�ltofts Plads DK-2800 Lyngby DENMARK
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23
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Rafe A, Glikman D, Rey NG, Haller N, Kulozik U, Braunschweig B. Structure-property relations of β-lactoglobulin/κ-carrageenan mixtures in aqueous foam. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Wang H, Xiong W. Revealing the Molecular Physics of Lattice Self-Assembly by Vibrational Hyperspectral Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3017-3031. [PMID: 35238562 DOI: 10.1021/acs.langmuir.1c03313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lattice self-assemblies (LSAs), which mimic protein assemblies, were studied using a new nonlinear vibrational imaging technique called vibrational sum-frequency generation (VSFG) microscopy. This technique successfully mapped out the mesoscopic morphology, microscopic geometry, symmetry, and ultrafast dynamics of an LSA formed by β-cyclodextrin (β-CD) and sodium dodecyl sulfate (SDS). The spatial imaging also revealed correlations between these different physical properties. Such knowledge shed light on the functions and mechanical properties of LSAs. In this Feature Article, we briefly introduce the fundamental principles of the VSFG microscope and then discuss the in-depth molecular physics of the LSAs revealed by this imaging technique. The application of the VSFG microscope to the artificial LSAs also paved the way for an alternative approach to studying the structure-dynamic-function relationships of protein assemblies, which were essential for life and difficult to study because of their various and complicated interactions. We expect that the hyperspectral VSFG microscope could be broadly applied to many noncentrosymmetric soft materials.
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25
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Yu CC, Imoto S, Seki T, Chiang KY, Sun S, Bonn M, Nagata Y. Accurate molecular orientation at interfaces determined by multimode polarization-dependent heterodyne-detected sum-frequency generation spectroscopy via multidimensional orientational distribution function. J Chem Phys 2022; 156:094703. [DOI: 10.1063/5.0081209] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many essential processes occur at soft interfaces, from chemical reactions on aqueous aerosols in the atmosphere to biochemical recognition and binding at the surface of cell membranes. The spatial arrangement of molecules specifically at these interfaces is crucial for many of such processes. The accurate determination of the interfacial molecular orientation has been challenging due to the low number of molecules at interfaces and the ambiguity of their orientational distribution. Here, we combine phase- and polarization-resolved sum-frequency generation (SFG) spectroscopy to obtain the molecular orientation at the interface. We extend an exponentially decaying orientational distribution to multiple dimensions, which, in conjunction with multiple SFG datasets obtained from the different vibrational modes, allows us to determine the molecular orientation. We apply this new approach to formic acid molecules at the air–water interface. The inferred orientation of formic acid agrees very well with ab initio molecular dynamics data. The phase-resolved SFG multimode analysis scheme using the multidimensional orientational distribution thus provides a universal approach for obtaining the interfacial molecular orientation.
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Affiliation(s)
- Chun-Chieh Yu
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Sho Imoto
- Analysis Technology Center, Fujifilm R&D, 210 Nakanuma, Minamiashigara, Kanagawa 250-0123, Japan
| | - Takakazu Seki
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Kuo-Yang Chiang
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Shumei Sun
- Applied Optics Beijing Area Major Laboratory, Department of Physics, Beijing Normal University, 100875 Beijing, China
| | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Yuki Nagata
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
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26
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Thi-Yen Le T, Hussain S, Tsay RY, Noskov BA, Akentiev A, Lin SY. On the equilibrium surface tension of aqueous protein solutions – Bovine serum albumin. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Sprenger K, Roeters SJ, Mauri S, Mertig R, Nishiyama Y, Pfaendtner J, Weidner T. Direct Evidence for Aligned Binding of Cellulase Enzymes to Cellulose Surfaces. J Phys Chem Lett 2021; 12:10684-10688. [PMID: 34709817 DOI: 10.1021/acs.jpclett.1c02757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The conversion of biomass into green fuels and chemicals is of great societal interest. Engineers have been designing new cellulase enzymes for the breakdown of otherwise insoluble cellulose materials. A barrier to the rational design of new enzymes has been our lack of a molecular picture of how cellulase binding occurs. A critical factor is the attachment via the enzyme's carbohydrate binding module (CBM). To elucidate the structural and mechanistic details of cellulase adsorption, we have combined experimental data from sum frequency generation spectroscopy with molecular dynamics simulations to probe the equilibrium structure and surface alignment of a 14-residue peptide mimicking the CBM. The data show that binding is driven by hydrogen bonding and that tyrosine side chains within the CBM align the cellulase with the registry of the cellulose surface. Such an alignment is favorable for the translocation and effective cellulose breakdown and is therefore likely an important parameter for the design of novel enzymes.
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Affiliation(s)
- Kayla Sprenger
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Steven J Roeters
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Sergio Mauri
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Rolf Mertig
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98192, United States
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98192, United States
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28
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Zhang S, Hsu L, Toolis A, Li B, Zhou J, Lin T, Chen Z. Investigation of the Atmospheric Moisture Effect on the Molecular Behavior of an Isocyanate-Based Primer Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12705-12713. [PMID: 34668715 DOI: 10.1021/acs.langmuir.1c02135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A primer coating is engineered to facilitate compatibility between products like adhesives, sealants, and potting compounds and targeted substrates. Prolonged exposure of isocyanate-based primer surfaces to the environment is known to negatively affect the interfacial adhesion between itself and the products subsequently applied on top of it. However, the molecular behavior behind this observed phenomenon remained to be further investigated. In this study, sum frequency generation (SFG) vibrational spectroscopy, a nonlinear optical spectroscopic technique, was applied to study the surface of an isocyanate-based primer exposed to different environments at the molecular level. Atmospheric moisture was considered to be a potential factor in impairing the adhesion performance of the primer, and thus, time- and humidity-dependent experiments were executed to monitor the molecular behavior at the primer surface using SFG. In addition, 180° peel testing experiments were conducted to measure the adhesion properties of primers after being exposed to the corresponding conditions to correlate to SFG results and establish a chemical structure-macroscopic performance relationship. This study on the changes at the primer surface in different environments with varied humidity levels as a function of time aims to provide an in-depth understanding of the moisture effect on isocyanate-based primers. These learnings may also be helpful toward exploring a broader range of coatings and surface layers and improving customer product use guidelines.
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Affiliation(s)
| | - Lorraine Hsu
- Coatings and Innovation Center, PPG, 4325 Rosanna Drive, Allison Park, Pennsylvania 15101, United States
| | - Amy Toolis
- Coatings and Innovation Center, PPG, 4325 Rosanna Drive, Allison Park, Pennsylvania 15101, United States
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29
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Weidner T, Castner DG. Developments and Ongoing Challenges for Analysis of Surface-Bound Proteins. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:389-412. [PMID: 33979545 PMCID: PMC8522203 DOI: 10.1146/annurev-anchem-091520-010206] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Proteins at surfaces and interfaces play important roles in the function and performance of materials in applications ranging from diagnostic assays to biomedical devices. To improve the performance of these materials, detailed molecular structure (conformation and orientation) along with the identity and concentrations of the surface-bound proteins on those materials must be determined. This article describes radiolabeling, surface plasmon resonance, quartz crystal microbalance with dissipation, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, sum frequency generation spectroscopy, and computational techniques along with the information each technique provides for characterizing protein films. A multitechnique approach using both experimental and computation methods is required for these investigations. Although it is now possible to gain much insight into the structure of surface-bound proteins, it is still not possible to obtain the same level of structural detail about proteins on surfaces as can be obtained about proteins in crystals and solutions, especially for large, complex proteins. However, recent results have shown it is possible to obtain detailed structural information (e.g., backbone and side chain orientation) about small peptides (5-20 amino sequences) on surfaces. Current studies are extending these investigations to small proteins such as protein G B1 (∼6 kDa). Approaches for furthering the capabilities for characterizing the molecular structure of surface-bound proteins are proposed.
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Affiliation(s)
- Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark;
| | - David G Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, Departments of Bioengineering and Chemical Engineering, University of Washington, Seattle, Washington 98195, USA;
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30
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Carpenter AP, Christoffersen EL, Mapile AN, Richmond GL. Assessing the Impact of Solvent Selection on Vibrational Sum-Frequency Scattering Spectroscopy Experiments. J Phys Chem B 2021; 125:3216-3229. [PMID: 33739105 DOI: 10.1021/acs.jpcb.1c00188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The development of vibrational sum-frequency scattering (S-VSF) spectroscopy has opened the door to directly probing nanoparticle surfaces with an interfacial and chemical specificity that was previously reserved for planar interfacial systems. Despite its potential, challenges remain in the application of S-VSF spectroscopy beyond simplified chemical systems. One such challenge includes infrared absorption by an absorptive continuous phase, which will alter the spectral lineshapes within S-VSF spectra. In this study, we investigate how solvent vibrational modes manifest in S-VSF spectra of surfactant stabilized nanoemulsions and demonstrate how corrections for infrared absorption can recover the spectral features of interfacial solvent molecules. We also investigate infrared absorption for systems with the absorptive phase dispersed in a nonabsorptive continuous phase to show that infrared absorption, while reduced, will still impact the S-VSF spectra. These studies are then used to provide practical recommendations for anyone wishing to use S-VSF to study nanoparticle surfaces where absorptive solvents are present.
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Affiliation(s)
- Andrew P Carpenter
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
| | - Evan L Christoffersen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
| | - Ashley N Mapile
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
| | - Geraldine L Richmond
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
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