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Day EC, Chittari SS, Cunha KC, Zhao RJ, Dodds JN, Davis DC, Baker ES, Berlow RB, Shea JE, Kulkarni RU, Knight AS. A High-Throughput Workflow to Analyze Sequence-Conformation Relationships and Explore Hydrophobic Patterning in Disordered Peptoids. Chem 2024; 10:3444-3458. [PMID: 39582487 PMCID: PMC11580747 DOI: 10.1016/j.chempr.2024.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2024]
Abstract
Understanding how a macromolecule's primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. Herein, we introduce a high-throughput workflow that implements a practical colorimetric conformational assay, introduces a semi-automated sequencing protocol using MALDI-MS/MS, and develops a generalizable sequence-structure algorithm. Using a model system of 20mer peptidomimetics containing polar glycine and hydrophobic N-butylglycine residues, we identified nine classifications of conformational disorder and isolated 122 unique sequences across varied compositions and conformations. Conformational distributions of three compositionally identical library sequences were corroborated through atomistic simulations and ion mobility spectrometry coupled with liquid chromatography. A data-driven strategy was developed using existing sequence variables and data-derived 'motifs' to inform a machine learning algorithm towards conformation prediction. This multifaceted approach enhances our understanding of sequence-conformation relationships and offers a powerful tool for accelerating the discovery of materials with conformational control.
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Affiliation(s)
- Erin C. Day
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Supraja S. Chittari
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Keila C. Cunha
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - Roy J. Zhao
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - James N. Dodds
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Delaney C. Davis
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Erin S. Baker
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Rebecca B. Berlow
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 USA
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | | | - Abigail S. Knight
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lead contact
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Vahid H, Scacchi A, Sammalkorpi M, Ala-Nissila T. Adsorption of polyelectrolytes in the presence of varying dielectric discontinuity between solution and substrate. J Chem Phys 2024; 161:134907. [PMID: 39360687 DOI: 10.1063/5.0223124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
We examine the interactions between polyelectrolytes (PEs) and uncharged substrates under conditions corresponding to a dielectric discontinuity between the aqueous solution and the substrate. To this end, we vary the relevant system characteristics, in particular the substrate dielectric constant ɛs under different salt conditions. We employ coarse-grained molecular dynamics simulations with rodlike PEs in salt solutions with explicit ions and implicit water solvent with dielectric constant ɛw = 80. As expected, at low salt concentrations, PEs are repelled from the substrates with ɛs < ɛw but are attracted to substrates with a high dielectric constant due to image charges. This attraction considerably weakens for high salt and multivalent counterions due to enhanced screening. Furthermore, for monovalent salt, screening enhances adsorption for weakly charged PEs, but weakens it for strongly charged ones. Meanwhile, multivalent counterions have little effect on weakly charged PEs, but prevent adsorption of highly charged PEs, even at low salt concentrations. We also find that correlation-induced charge inversion of a PE is enhanced close to the low dielectric constant substrates, but suppressed when the dielectric constant is high. To explore the possibility of a PE monolayer formation, we examine the interaction of a pair of like-charged PEs aligned parallel to a high dielectric constant substrate with ɛs = 8000. Our main conclusion is that monolayer formation is possible only for weakly charged PEs at high salt concentrations of both monovalent and multivalent counterions. Finally, we also consider the energetics of a PE approaching the substrate perpendicular to it, in analogy to polymer translocation. Our results highlight the complex interplay between electrostatic and steric interactions and contribute to a deeper understanding of PE-substrate interactions and adsorption at substrate interfaces with varying dielectric discontinuities from solution, ubiquitous in biointerfaces, PE coating applications, and designing adsorption setups.
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Affiliation(s)
- Hossein Vahid
- Department of Applied Physics, Aalto University, P.O. Box 15600, FI-00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Alberto Scacchi
- Department of Applied Physics, Aalto University, P.O. Box 15600, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Mechanical and Materials Engineering, University of Turku, Vesilinnantie 5, FI-20014 Turku, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Tapio Ala-Nissila
- Department of Applied Physics, Aalto University, P.O. Box 15600, FI-00076 Aalto, Finland
- Quantum Technology Finland Center of Excellence, Department of Applied Physics, Aalto University, P.O. Box 15600, FI-00076 Aalto, Finland
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough Leicestershire LE11 3TU, United Kingdom
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Sáringer S, Terjéki G, Varga Á, Maléth J, Szilágyi I. Optimization of Interfacial Properties Improved the Stability and Activity of the Catalase Enzyme Immobilized on Plastic Nanobeads. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:16338-16348. [PMID: 39066719 PMCID: PMC11308775 DOI: 10.1021/acs.langmuir.4c01508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
The immobilization of catalase (CAT), a crucial oxidoreductase enzyme involved in quenching reactive oxygen species, on colloids and nanoparticles presents a promising strategy to improve dispersion and storage stability while maintaining its activity. Here, the immobilization of CAT onto polymeric nanoparticles (positively (AL) or negatively (SL) charged) was implemented directly (AL) or via surface functionalization (SL) with water-soluble chitosan derivatives (glycol chitosan (GC) and methyl glycol chitosan (MGC)). The interfacial properties were optimized to obtain highly stable AL-CAT, SL-GC-CAT, and SL-MGC-CAT dispersions, and confocal microscopy confirmed the presence of CAT in the composites. Assessment of hydrogen peroxide decomposition ability revealed that applying chitosan derivatives in the immobilization process not only enhanced colloidal stability but also augmented the activity and reusability of CAT. In particular, the use of MGC has led to significant advances, indicating its potential for industrial and biomedical applications. Overall, the findings highlight the advantages of using chitosan derivatives in CAT immobilization processes to maintain the stability and activity of the enzyme as well as provide important data for the development of processable enzyme-based nanoparticle systems to combat reactive oxygen species.
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Affiliation(s)
- Szilárd Sáringer
- MTA-SZTE
Lendület Biocolloids Research Group, Interdisciplinary Excellence
Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
| | - Gergő Terjéki
- MTA-SZTE
Lendület Biocolloids Research Group, Interdisciplinary Excellence
Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
| | - Árpád Varga
- MTA-SZTE
Lendület Epithelial Cell Signaling and Secretion Research Group,
Interdisciplinary Excellence Centre, University
of Szeged, H-6720 Szeged, Hungary
| | - József Maléth
- MTA-SZTE
Lendület Epithelial Cell Signaling and Secretion Research Group,
Interdisciplinary Excellence Centre, University
of Szeged, H-6720 Szeged, Hungary
| | - István Szilágyi
- MTA-SZTE
Lendület Biocolloids Research Group, Interdisciplinary Excellence
Center, Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
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Glagoleva AA, Yaroslavov AA, Vasilevskaya VV. Computer Simulation Insight into the Adsorption and Diffusion of Polyelectrolytes on Oppositely Charged Surface. Polymers (Basel) 2023; 15:2845. [PMID: 37447491 DOI: 10.3390/polym15132845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
In the present work, by means of computer simulation, we studied the adsorption and diffusion of polyelectrolyte macromolecules on oppositely charged surfaces. We considered the surface coverage and the charge of the adsorbed layer depending on the ionization degree of the macromolecules and the charge of the surface and carried out a computer experiment on the polymer diffusion within the adsorbed layers, taking into account its strong dependency on the surface coverage and the macromolecular ionization degree. The different regimes were distinguished that provided maximal mobility of the polymer chains along with a high number of charged groups in the layer, which could be beneficial for the development of the functional coatings. The results were compared with those of previous experiments on the adsorption of polyelectrolyte layers that may be applied as biocidal renewable coatings that can reversibly desorb from the surface.
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Affiliation(s)
- Anna A Glagoleva
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander A Yaroslavov
- Department of Chemistry, M.V. Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russia
| | - Valentina V Vasilevskaya
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russia
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5
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The Influence of Solvents and Colloidal Particles on the Efficiency of Molecular Antioxidants. Antioxidants (Basel) 2022; 12:antiox12010099. [PMID: 36670961 PMCID: PMC9855148 DOI: 10.3390/antiox12010099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/22/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
The radical scavenging activity of three molecular antioxidants (trolox, rutin and ellagic acid) was investigated in different solvents with and without added polymer-based colloidal particles (SL-IP-2). Rutin and ellagic acid showed poor solubility in water, preventing the accurate measurement of the effective antioxidant concentration values, which were determined in ethanol/water (EtOH/H2O) mixtures. The presence of trolox and rutin changed neither the surface charge properties nor the size of SL-IP-2 in these solvents, while significant adsorption on SL-IP-2 was observed for ellagic acid leading to overcharging and rapid particle aggregation at appropriately high antioxidant concentrations in EtOH/H2O. The differences in the radical scavenging capacity of trolox and ellagic acid that was observed in homogeneous solutions using water or EtOH/H2O as solvents vanished in the presence of the particles. Rutin lost its activity after addition of SL-IP-2 due to the larger molecular size and lower exposure of the functional groups to the substrate upon interaction with the particles. The obtained results shed light on the importance of the type of solvent and particle-antioxidant interfacial effects on the radical decomposition ability of molecular antioxidants, which is of crucial importance in industrial processes involving heterogeneous systems.
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Qing L, Jiang J. Double-Edged Sword of Ion-Size Asymmetry in Energy Storage of Supercapacitors. J Phys Chem Lett 2022; 13:1438-1445. [PMID: 35129327 DOI: 10.1021/acs.jpclett.1c03900] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The advanced supercapacitor is of great significance for renewable energy storage. Achieving its high energy and high power densities remains a huge challenge. Herein, the contribution of ion-size asymmetry to the charging behavior of a supercapacitor is systematically studied using time-dependent density functional theory (TDDFT). We track the time evolution of the ionic microstructure inside the porous electrode and its reservoir and reveal a kinetic charge inversion in the asymmetrical ion-size cases. Compared with the symmetrical ion-size case, we find that the ion-size asymmetry has a double-edged sword effect on the energy storage of a supercapacitor: it accelerates the charging process yet reduces the differential capacitance. Additionally, the energy density and power density can simultaneously increase in the asymmetrical cases, which provides important insights toward the experimental design of supercapacitors with high energy and high power densities.
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Affiliation(s)
- Leying Qing
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Jian Jiang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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Chang Q, Jiang J. Sequence Effects on the Salt-Enhancement Behavior of Polyelectrolytes Adsorption. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Qiuhui Chang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jian Jiang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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8
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Szerlauth A, Szalma L, Muráth S, Sáringer S, Varga G, Li L, Szilágyi I. Nanoclay-based sensor composites for the facile detection of molecular antioxidants. Analyst 2022; 147:1367-1374. [DOI: 10.1039/d1an02352g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A paper-based sensor containing nanoclay particles, a polyelectrolyte and a metal complex as sensing elements was developed for the facile detection of molecular antioxidants.
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Affiliation(s)
- Adél Szerlauth
- MTA-SZTE Lendület Biocolloids Research Group, University of Szeged, H-6720 Szeged, Hungary
- Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
| | - Lilla Szalma
- Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
| | - Szabolcs Muráth
- MTA-SZTE Lendület Biocolloids Research Group, University of Szeged, H-6720 Szeged, Hungary
- Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
| | - Szilárd Sáringer
- MTA-SZTE Lendület Biocolloids Research Group, University of Szeged, H-6720 Szeged, Hungary
- Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
| | - Gábor Varga
- Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
| | - Li Li
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD-4072, Australia
| | - István Szilágyi
- MTA-SZTE Lendület Biocolloids Research Group, University of Szeged, H-6720 Szeged, Hungary
- Department of Physical Chemistry and Materials Science, University of Szeged, H-6720 Szeged, Hungary
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9
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Software Package: An Advanced Theoretical Tool for Inhomogeneous Fluids (Atif). CHINESE JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1007/s10118-021-2646-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Huang C, Podgornik R, Man X. Selective Adsorption of Confined Polymers: Self-Consistent Field Theory Studies. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Changhang Huang
- Center of Soft Matter Physics and its Applications, Beihang University, Beijing 100191, China
- School of Physics, Beihang University, Beijing 100191, China
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences (CAS), Beijing 100190, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Xingkun Man
- Center of Soft Matter Physics and its Applications, Beihang University, Beijing 100191, China
- School of Physics, Beihang University, Beijing 100191, China
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