Mechanisms and Kinetics of Interactions of Biomolecules at Interfaces II

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biological and Bio- Materials".

Deadline for manuscript submissions: 15 October 2024 | Viewed by 5988

Special Issue Editors


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Guest Editor
Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, Niezapominajek 8, 30-239 Cracow, Poland
Interests: protein adsorption; mechanisms of protein adsorption; stability of biocolloidal suspensions; adsorption of biocolloidal particles; streaming potential; biosensors
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Guest Editor
Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
Interests: biocompatible polyelectrolyte films; polysaccharides; biomaterials; application of electrokinetic techniques for determination of the properties of nanocomposites; binding proteins to polyelectrolyte multilayers; determination of the stability of polyelectrolyte mono- and multilayers; determination of the physicochemical properties of polyelectrolytes in bulk
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
Interests: preparation and characterization of mono-, bi-, and multilayers of macroions and nanoparticles; mechanisms of macroion and nanoparticle adsorption; kinetics adsorption and desorption of macromolecules and nanoparticles; macroion adsorption at homogeneous and heterogeneous surfaces; stability of monolayers and bilayers composed of macromolecules and nanoparticles; biocompatibility of composed layered materials; electrokinetic potential at solid/liquid interfaces; streaming potential at solid/liquid interfaces; layer by layer deposition of colloidal particles; polypeptides and their monolayers; nanoparticles/macroions composite material; biological applications of macromolecules and nanoparticles
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following a very successful first run, we are pleased to announce the launch of a second edition of a Special Issue on the mechanisms and kinetics of interactions of biomolecules at interfaces.

The adsorption of biocolloids, particularly proteins, at solid/liquid interfaces is important both in terms of their industrial preparation, purification, or storage and due to the wide spectrum of other practical applications. Especially important are the control of protein and cell separation, the production of biosensors and biochips, the transport of medicines, and the bio-integration of materials used for the production of medical implants.

Although deposited biomolecules play a crucial role in many processes, the mechanisms and kinetics of the immobilization processes are poorly understood. There is a lack of systematic investigations of the relationship between the deposition conditions and resulting biomolecules’ coverage, local distribution, the orientation of adsorbed particles, and their bioactivity. There is no doubt that all investigations related to biomolecule adsorption at solid substrates are desired.

This Special Issue is devoted to the most recent research focused on the determination of the mechanisms of biomolecules (proteins, peptides, and biocompatible macroions) at solid substrates. Potential topics also include the application of new techniques in biomolecule deposition research and the analysis of biomolecules’ interactions with cells, viruses, etc.

Dr. Monika Wasilewska
Dr. Aneta Michna
Dr. Maria Morga
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomolecule adsorption
  • kinetics of biomolecule adsorption
  • mechanisms of biomolecule deposition
  • interactions of biomolecules
  • techniques for the detection of biomolecules at solid substrates
  • interactions of proteins with biomolecules/biopolymers
  • protein and biomolecule systems
  • protein and biomolecule complexes

Related Special Issue

Published Papers (4 papers)

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Research

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20 pages, 12704 KiB  
Article
Mechanisms of Fibroblast Growth Factor 21 Adsorption on Macroion Layers: Molecular Dynamics Modeling and Kinetic Measurements
by Monika Wasilewska, Maria Dąbkowska, Agata Pomorska, Piotr Batys, Bogusław Kowalski, Aneta Michna and Zbigniew Adamczyk
Biomolecules 2023, 13(12), 1709; https://doi.org/10.3390/biom13121709 - 26 Nov 2023
Viewed by 1640
Abstract
Molecular dynamic modeling and various experimental techniques, including multi-angle dynamic light scattering (MADLS), streaming potential, optical waveguide light spectroscopy (OWLS), quartz crystal microbalance with dissipation (QCM), and atomic force microscopy (AFM), were applied to determine the basic physicochemical parameters of fibroblast growth factor [...] Read more.
Molecular dynamic modeling and various experimental techniques, including multi-angle dynamic light scattering (MADLS), streaming potential, optical waveguide light spectroscopy (OWLS), quartz crystal microbalance with dissipation (QCM), and atomic force microscopy (AFM), were applied to determine the basic physicochemical parameters of fibroblast growth factor 21 in electrolyte solutions. The protein size and shape, cross-section area, dependence of the nominal charge on pH, and isoelectric point of 5.3 were acquired. These data enabled the interpretation of the adsorption kinetics of FGF 21 on bare and macrocation-covered silica investigated by OWLS and QCM. It was confirmed that the protein molecules irreversibly adsorbed on the latter substrate, forming layers with controlled coverage up to 0.8 mg m−2, while their adsorption on bare silica was much smaller. The viability of two cell lines, CHO-K1 and L-929, on both bare and macrocation/FGF 21-covered substrates was also determined. It is postulated that the acquired results can serve as useful reference systems for designing complexes that can extend the half-life of FGF 21 in its active state. Full article
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13 pages, 2865 KiB  
Article
Mechanism of Anti-Salmonella Rabbit Immunoglobulin Adsorption on Polymer Particles
by Paulina Żeliszewska, Monika Wasilewska, Jolanta Szych and Zbigniew Adamczyk
Biomolecules 2023, 13(9), 1390; https://doi.org/10.3390/biom13091390 - 15 Sep 2023
Viewed by 712
Abstract
The adsorption of anti-Salmonella rabbit immunoglobulin (IgaR) on negatively charged polymer particles leading to the formation of immunolatex was studied using various techniques comprising atomic force microscopy (AFM) and laser Doppler velocimetry (LDV). Initially, the basic physicochemical properties of IgaR molecules and the [...] Read more.
The adsorption of anti-Salmonella rabbit immunoglobulin (IgaR) on negatively charged polymer particles leading to the formation of immunolatex was studied using various techniques comprising atomic force microscopy (AFM) and laser Doppler velocimetry (LDV). Initially, the basic physicochemical properties of IgaR molecules and the particles, inter alia their electrophoretic mobilities, the zeta potentials and hydrodynamic diameters, were determined under different ionic strengths and pHs. Applying AFM, single immunoglobulin molecules adsorbed on mica were also imaged, which allowed to determine their size. The adsorption of the IgaR molecules on the particles leading to changes in their electrophoretic mobility was monitored in situ using the LDV method. The obtained results were interpreted applying a general electrokinetic model which yielded quantitative information about the molecule coverage on the particles. The obtained immunolatex was thoroughly characterized with respect to its acid–base properties and its stability upon storage. Notably, the developed procedure demonstrated better efficiency compared to commercially applied methods, characterized by a higher immunoglobulin consumption. Full article
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15 pages, 5533 KiB  
Article
Comparative Analysis of pH and Target-Induced Conformational Changes of an Oxytetracycline Aptamer in Solution Phase and Surface-Immobilized Form
by Kristóf Jakab, Nikitas Melios, George Tsekenis, Abdul Shaban, Viola Horváth and Zsófia Keresztes
Biomolecules 2023, 13(9), 1363; https://doi.org/10.3390/biom13091363 - 7 Sep 2023
Cited by 1 | Viewed by 1191
Abstract
To date, numerous aptamer-based biosensing platforms have been developed for sensitive and selective monitoring of target analytes, relying on analyte-induced conformational changes in the aptamer for the quantification of the analyte and the conversion of the binding event into a measurable signal. Despite [...] Read more.
To date, numerous aptamer-based biosensing platforms have been developed for sensitive and selective monitoring of target analytes, relying on analyte-induced conformational changes in the aptamer for the quantification of the analyte and the conversion of the binding event into a measurable signal. Despite the impact of these conformational rearrangements on sensor performance, the influence of the environment on the structural conformations of aptamers has rarely been investigated, so the link between parameters directly influencing aptamer folding and the ability of the aptamer to bind to the target analyte remains elusive. Herein, the effect a number of variables have on an aptamer’s 3D structure was examined, including the pH of the buffering medium, as well as the anchoring of the aptamer on a solid support, with the use of two label-free techniques. Circular dichroism spectroscopy was utilized to study the conformation of an aptamer in solution along with any changes induced to it by the environment (analyte binding, pH, composition and ionic strength of the buffer solution), while quartz crystal microbalance with dissipation monitoring was employed to investigate the surface-bound aptamer’s behavior and performance. Analysis was performed on an aptamer against oxytetracycline, serving as a model system, representative of aptamers selected against small molecule analytes. The obtained results highlight the influence of the environment on the folding and thus analyte-binding capacity of an aptamer and emphasize the need to deploy appropriate surface functionalization protocols in sensor development as a means to minimize the steric obstructions and undesirable interactions of an aptamer with a surface onto which it is tethered. Full article
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Review

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12 pages, 1532 KiB  
Review
Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery
by Zoe Li, Ruili Huang, Menghang Xia, Tucker A. Patterson and Huixiao Hong
Biomolecules 2024, 14(1), 72; https://doi.org/10.3390/biom14010072 - 5 Jan 2024
Cited by 1 | Viewed by 1827
Abstract
Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular [...] Read more.
Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) structural interaction fingerprints offer enhanced structural features specific to target proteins. Machine learning models trained on interaction fingerprints enable precise binding prediction. Recent focus has shifted to structure-based predictive modeling, with machine-learning scoring functions excelling due to feature engineering guided by key interactions. Notably, 3D interaction fingerprints are gaining ground due to their robustness. Various structural interaction fingerprints have been developed and used in drug discovery, each with unique capabilities. This review recapitulates the developed structural interaction fingerprints and provides two case studies to illustrate the power of interaction fingerprint-driven machine learning. The first elucidates structure–activity relationships in β2 adrenoceptor ligands, demonstrating the ability to differentiate agonists and antagonists. The second employs a retrosynthesis-based pre-trained molecular representation to predict protein–ligand dissociation rates, offering insights into binding kinetics. Despite remarkable progress, challenges persist in interpreting complex machine learning models built on 3D fingerprints, emphasizing the need for strategies to make predictions interpretable. Binding site plasticity and induced fit effects pose additional complexities. Interaction fingerprints are promising but require continued research to harness their full potential. Full article
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