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Molecules
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Protein Interactions—on the Frontier of Biochemistry and Biophysics
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Protein Interactions—on the Frontier of Biochemistry and Biophysics

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

Deadline for manuscript submissions: closed (15 September 2021) | Viewed by 23924

Special Issue Editor

Dr. Danuta Witkowska

E-Mail Website
Guest Editor
Institute of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland
Interests: protein–protein interactions; metal–protein interactions; biophysical methods; medicinal chemistry

Special Issue Information

Dear Colleagues,

Working on protein interactions can be extremely difficult, especially when working on metal–protein or metal-mediated protein–protein interactions. So many steps need to be taken into account: proper purification, choosing the right buffers, the right techniques to get as much data as possible, etc. Sometimes, it is helpful to design the analogs of protein fragments to “dig” deeper into metal–protein interaction. The aim of this Special Issue is to show the advantage of the collaboration of molecular biologists and researchers working in the field of the biochemistry and biophysics, to reflect the most reliable data and natural conditions of protein interactions. Recent advances with multidisciplinary approaches in understanding protein–protein and metal–protein interactions will be particularly welcomed.

Dr. Danuta Witkowska
Guest Editor

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

  • Protein–protein interactions
  • Metal–protein interactions
  • Protein–ligand complexes
  • Biochemical and biophysical techniques
  • Computational chemistry for biological interaction studies
  • Active site analogs
  • Importance of buffer system

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Published Papers (2 papers)

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Research

Jump to: Review

17 pages, 3677 KiB  
Article
Effect of Tetraphenylborate on Physicochemical Properties of Bovine Serum Albumin
by Ola Grabowska, Małgorzata M. Kogut, Krzysztof Żamojć, Sergey A. Samsonov, Joanna Makowska, Aleksandra Tesmar, Katarzyna Chmur, Dariusz Wyrzykowski and Lech Chmurzyński
Molecules 2021, 26(21), 6565; https://doi.org/10.3390/molecules26216565 - 29 Oct 2021
Cited by 7 | Viewed by 2700
Abstract
The binding interactions of bovine serum albumin (BSA) with tetraphenylborate ions ([B(Ph)4]−) have been investigated by a set of experimental methods (isothermal titration calorimetry, steady-state fluorescence spectroscopy, differential scanning calorimetry and circular dichroism spectroscopy) and molecular dynamics-based computational approaches. [...] Read more.
The binding interactions of bovine serum albumin (BSA) with tetraphenylborate ions ([B(Ph)4]−) have been investigated by a set of experimental methods (isothermal titration calorimetry, steady-state fluorescence spectroscopy, differential scanning calorimetry and circular dichroism spectroscopy) and molecular dynamics-based computational approaches. Two sets of structurally distinctive binding sites in BSA were found under the experimental conditions (10 mM cacodylate buffer, pH 7, 298.15 K). The obtained results, supported by the competitive interactions experiments of SDS with [B(Ph)4]− for BSA, enabled us to find the potential binding sites in BSA. The first site is located in the subdomain I A of the protein and binds two [B(Ph)4]− ions (logK(ITC)1 = 7.09 ± 0.10; ΔG(ITC)1 = −9.67 ± 0.14 kcal mol−1; ΔH(ITC)1 = −3.14 ± 0.12 kcal mol−1; TΔS(ITC)1 = −6.53 kcal mol−1), whereas the second site is localized in the subdomain III A and binds five ions (logK(ITC)2 = 5.39 ± 0.06; ΔG(ITC)2 = −7.35 ± 0.09 kcal mol−1; ΔH(ITC)2 = 4.00 ± 0.14 kcal mol−1; TΔS(ITC)2 = 11.3 kcal mol−1). The formation of the {[B(Ph)4]−}–BSA complex results in an increase in the thermal stability of the alfa-helical content, correlating with the saturation of the particular BSA binding sites, thus hindering its thermal unfolding. Full article
(This article belongs to the Special Issue Protein Interactions—on the Frontier of Biochemistry and Biophysics)
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Figure 1

Figure 1
<p>The secondary structure of BSA (grey cartoon) with marked Trp residues (magenta VDW representation). The first and second potential binding sites of SDS are shown with red and green rings, respectively.</p> Full article ">Figure 2
<p>Chemical structure of sodium tetraphenylborate (Na[B(Ph)<sub>4</sub>]) and sodium dodecyl sulfate (SDS).</p> Full article ">Figure 3
<p>Calorimetric titration isotherms of the binding interactions between SDS and BSA (LEFT) and Na[B(Ph)<sub>4</sub>] and BSA (RIGHT) in the10 mM Caco buffer of pH 7, at 298.15 K.</p> Full article ">Figure 4
<p>Calorimetric titration isotherms of the binding interactions between SDS and BSA in the presence of Na[B(Ph)<sub>4</sub>] in the Na[B(Ph)<sub>4</sub>]:BSA molar ratio 3:1 (<b>left</b>) and 7:1 (<b>right</b>) in the 10 mM Caco buffer of pH 7, at 298.15 K.</p> Full article ">Figure 5
<p>The fluorescence emission spectra of free BSA (<b>a</b>) and the solutions of BSA with Na[B(Ph)<sub>4</sub>] mixed in molar ratios 1:3 (<b>b</b>); 1:7 (<b>c</b>); and 1:15 (<b>d</b>) in the presence of increasing concentrations of SDS (0–25 μM) in the 10 mM Caco buffer of pH 7.0 at 298.15 K.</p> Full article ">Figure 6
<p>Stern–Volmer plots for the steady-state fluorescence quenching of BSA and its mixtures with Na[B(Ph)<sub>4</sub>] (1:3; 1:7; and 1:15) by SDS in the 10 mM Caco buffer of pH 7.0 at 298 K.</p> Full article ">Figure 7
<p>The raw heat capacity data for: (A) free BSA (0.015 mM) and the mixtures (B) with the Na[B(Ph)<sub>4</sub>]:BSA molar ratios 2.5:1 (0.0375 mM Na[B(Ph)<sub>4</sub>], 0.015 mM BSA) and (C) 7:1 (0.105 mM Na[B(Ph)<sub>4</sub>], 0.015 mM BSA) in the 10 mM Caco buffer of pH 7.</p> Full article ">Figure 8
<p>CD spectra of BSA in 10 mM Caco buffer at pH 7, in the temperature range 298.15–368.15 K. The concentration of BSA was maintained at 0.0015 mM.</p> Full article ">Figure 9
<p>CD spectra of the Na[B(Ph)<sub>4</sub>]/BSA mixture (Na[B(Ph)<sub>4</sub>]:BSA = 2.5:1 molar ratio) in 10 mM Caco buffer at pH 7, in the temperature range 298.15–368.15 K. The concentration of BSA was maintained at 0.0015 mM.</p> Full article ">Figure 10
<p>CD spectra of the Na[B(Ph)<sub>4</sub>]/BSA mixture (Na[B(Ph)<sub>4</sub>]:BSA = 7:1 molar ratio) in 10 mM Caco buffer at pH 7, in the temperature range 298.15–368.15 K. The concentration of BSA was maintained at 0.0015 mM.</p> Full article ">Figure 11
<p>On the left, BSA protein (grey cartoon), Trp residues (magenta VDW representation) and three clusters (licorice) representing [B(Ph)<sub>4</sub>]<sup>−</sup> ions that bound to the protein with the highest affinity. Colors of the clusters correspond to the color coding used in <a href="#molecules-26-06565-t004" class="html-table">Table 4</a>. On the right panel, a representative frame for one [B(Ph)<sub>4</sub>]<sup>−</sup> ion and its protein surrounding.</p> Full article ">

Review

Jump to: Research

16 pages, 1266 KiB  
Review
Heavy Metals and Human Health: Possible Exposure Pathways and the Competition for Protein Binding Sites
by Danuta Witkowska, Joanna Słowik and Karolina Chilicka
Molecules 2021, 26(19), 6060; https://doi.org/10.3390/molecules26196060 - 7 Oct 2021
Cited by 256 | Viewed by 20492
Abstract
Heavy metals enter the human body through the gastrointestinal tract, skin, or via inhalation. Toxic metals have proven to be a major threat to human health, mostly because of their ability to cause membrane and DNA damage, and to perturb protein function and [...] Read more.
Heavy metals enter the human body through the gastrointestinal tract, skin, or via inhalation. Toxic metals have proven to be a major threat to human health, mostly because of their ability to cause membrane and DNA damage, and to perturb protein function and enzyme activity. These metals disturb native proteins’ functions by binding to free thiols or other functional groups, catalyzing the oxidation of amino acid side chains, perturbing protein folding, and/or displacing essential metal ions in enzymes. The review shows the physiological and biochemical effects of selected toxic metals interactions with proteins and enzymes. As environmental contamination by heavy metals is one of the most significant global problems, some detoxification strategies are also mentioned. Full article
(This article belongs to the Special Issue Protein Interactions—on the Frontier of Biochemistry and Biophysics)
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Figure 1

Figure 1
<p>Routes of exposure, the impact of toxic metals on human health, and the ways of limiting the risk caused by contact with these elements (large arrow on the left). These adverse effects are caused by direct exposure to the toxic metals in the environment or indirectly due to anthropogenic activity.</p> Full article ">Figure 2
<p>General mechanisms utilized by bacteria, and plant cells for metal resistance and detoxification, which can be adapted in bioremediation techniques. Based on [<a href="#B130-molecules-26-06060" class="html-bibr">130</a>].</p> Full article ">
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