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New Approaches in Structural and Biophysical Chemistry to Illuminate Molecular...
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New Approaches in Structural and Biophysical Chemistry to Illuminate Molecular Interactions

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 10161

Special Issue Editors

Dr. Antoine Loquet

E-Mail Website
Guest Editor
CNRS, CBMN, UMR5248, University of Bordeaux, F-33600 Pessac, France
Interests: NMR spectroscopy; structural biology; aggregates; filaments; supramolecular assembly; membrane proteins; lipid dynamics; amyloids; prions
Dr. Isabel D. Alves

E-Mail Website1 Website2
Guest Editor
CNRS, CBMN, UMR5248, University of Bordeaux, F-33600 Pessac, France
Interests: protein–lipid interaction characterisation; plasmon resonance; membrane proteins; membrane active peptides; mechanisms of action of G-protein-coupled receptors

Special Issue Information

Dear Colleagues,

A fundamental understanding of molecular mechanisms in chemistry and biology requires the study of the interactions between essential entities, such as small organic molecules, proteins, DNA/RNA and lipids. Biomolecular interactions can form a myriad of complexes that can adopt unique architectures, composed of single-to-multi-component molecules, that vary in stability and size, ranging from small chemical moieties of tens of Daltons to supramolecular structures larger than a mega-Dalton.

Regardless of the intricacies that these interactions adopt, they all rely on molecular forces that can be non-covalent in nature, highlighting the importance of understanding the role hydrogen bonds, hydrophobic effects or van der Waals and electrostatic interactions play in biomolecular structure/function. The timescales in which biomolecular interactions occur span picoseconds to real-time, hours to days, and occur through many different kinetic mechanisms. Importantly, the lifetime of these interactions can tune functional behaviour, which has consequences for how a biological response is generated. Deciphering molecular interactions is key in understanding how macroscopic cellular responses form. These are mediated between proteins, proteins and lipids, protein and ligands, and protein and DNA/RNA, as well as chemical reactions and complex supramolecular systems. The detection, identification and analysis of molecular interactions are crucial in a wide range of disciplines, including supramolecular chemistry, structural biology, pharmacology and analytical chemistry. In this context, the development of novel approaches to improve our knowledge of molecular interactions is imperative.

In this Special Issue of Molecules, we will focus on recent developments and applications of novel approaches in structural and biophysical chemistry that aim to study molecular interactions. The development and application of new (bio)chemical probes will be covered, as will new biophysical techniques for uncovering binding-site information and the kinetics of interactions at resolutions that cover the atomic to optical range. Methodological improvements with a focus on improving the sensitivity, specificity or selectivity with which interactions can be monitored are of interest. Additionally, advances in single-molecule detection and the application of computational techniques to improve the study of molecular interactions are welcomed.

Contributions to this Special Issue will be in the form of original research or review articles on novel approaches and their application in chemistry and biology to elucidate molecular interactions.

Dr. Antoine Loquet
Dr. Isabel D. Alves
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. Molecules is an international peer-reviewed open access semimonthly 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

  • biomolecular structure
  • molecular interactions
  • novel techniques in biophysics
  • techniques to detect molecular interactions
  • structural chemistry
  • weak interactions
  • molecular recognition
  • molecular modeling
  • computational biophysics
  • DNA–protein interaction

Published Papers (3 papers)

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Research

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8 pages, 980 KiB  
Article
Quantification of Structural Integrity and Stability Using Nanograms of Protein by Flow-Induced Dispersion Analysis
by Morten E. Pedersen, Jesper Østergaard and Henrik Jensen
Molecules 2022, 27(8), 2506; https://doi.org/10.3390/molecules27082506 - 13 Apr 2022
Viewed by 2529
Abstract
In the development of therapeutic proteins, analytical assessment of structural stability and integrity constitutes an important activity, as protein stability and integrity influence drug efficacy, and ultimately patient safety. Existing analytical methodologies solely rely on relative changes in optical properties such as fluorescence [...] Read more.
In the development of therapeutic proteins, analytical assessment of structural stability and integrity constitutes an important activity, as protein stability and integrity influence drug efficacy, and ultimately patient safety. Existing analytical methodologies solely rely on relative changes in optical properties such as fluorescence or scattering upon thermal or chemical perturbation. Here, we present an absolute analytical method for assessing protein stability, structure, and unfolding utilizing Taylor dispersion analysis (TDA) and LED-UV fluorescence detection. The developed TDA method measures the change in size (hydrodynamic radius) and intrinsic fluorescence of a protein during in-line denaturation with guanidinium hydrochloride (GuHCl). The conformational stability of the therapeutic antibody adalimumab and human serum albumin were characterized as a function of pH. The simple workflow and low sample consumption (40 ng protein per data point) of the methodology make it ideal for assessing protein characteristics related to stability in early drug development or when having a scarce amount of sample available. Full article
(This article belongs to the Special Issue New Approaches in Structural and Biophysical Chemistry to Illuminate Molecular Interactions)
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15 pages, 3165 KiB  
Article
The Impact of an Anchoring Layer on the Formation of Tethered Bilayer Lipid Membranes on Silver Substrates
by Indrė Aleknavičienė, Martynas Talaikis, Rima Budvytyte and Gintaras Valincius
Molecules 2021, 26(22), 6878; https://doi.org/10.3390/molecules26226878 - 15 Nov 2021
Cited by 2 | Viewed by 2033
Abstract
Tethered bilayer lipid membranes (tBLMs) have been known as stable and versatile experimental platforms for protein–membrane interaction studies. In this work, the assembly of functional tBLMs on silver substrates and the effect of the molecular chain-length of backfiller molecules on their properties were [...] Read more.
Tethered bilayer lipid membranes (tBLMs) have been known as stable and versatile experimental platforms for protein–membrane interaction studies. In this work, the assembly of functional tBLMs on silver substrates and the effect of the molecular chain-length of backfiller molecules on their properties were investigated. The following backfillers 3-mercapto-1-propanol (3M1P), 4-mercapto-1-butanol (4M1B), 6-mercapto-1-hexanol (6M1H), and 9-mercapto-1-nonanol (9M1N) mixed with the molecular anchor WC14 (20-tetradecyloxy-3,6,9,12,15,18,22 heptaoxahexatricontane-1-thiol) were used to form self-assembled monolayers (SAMs) on silver, which influenced a fusion of multilamellar vesicles and the formation of tBLMs. Spectroscopic analysis by SERS and RAIRS has shown that by using different-length backfiller molecules, it is possible to control WC14 anchor molecules orientation on the surface. An introduction of increasingly longer surface backfillers in the mixed SAM may be related to the increasing SAMs molecular order and more vertical orientation of WC14 at both the hydrophilic ethylenoxide segment and the hydrophobic lipid bilayer anchoring alkane chains. Since no clustering of WC14 alkane chains, which is deleterious for tBLM integrity, was observed on dry samples, the suitability of mixed-component SAMs for subsequent tBLM formation was further interrogated by electrochemical impedance spectroscopy (EIS). EIS showed the arrangement of well-insulating tBLMs if 3M1P was used as a backfiller. An increase in the length of the backfiller led to increased defectiveness of tBLMs. Despite variable defectiveness, all tBLMs responded to the pore-forming cholesterol-dependent cytolysin, vaginolysin in a manner consistent with the functional reconstitution of the toxin into phospholipid bilayer. This experiment demonstrates the biological relevance of tBLMs assembled on silver surfaces and indicates their utility as biosensing elements for the detection of pore-forming toxins in liquid samples. Full article
(This article belongs to the Special Issue New Approaches in Structural and Biophysical Chemistry to Illuminate Molecular Interactions)
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Review

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19 pages, 1543 KiB  
Review
Modeling the Dynamics of Protein–Protein Interfaces, How and Why?
by Ezgi Karaca, Chantal Prévost and Sophie Sacquin-Mora
Molecules 2022, 27(6), 1841; https://doi.org/10.3390/molecules27061841 - 11 Mar 2022
Cited by 3 | Viewed by 4731
Abstract
Protein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfaces. Although [...] Read more.
Protein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein–protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein–protein interface. Full article
(This article belongs to the Special Issue New Approaches in Structural and Biophysical Chemistry to Illuminate Molecular Interactions)
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