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Protein-Ligand Interactions
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Protein-Ligand Interactions

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

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 2151

Special Issue Editor

Dr. Małgorzata Maciążek-Jurczyk

E-Mail Website
Guest Editor
Department of Physical Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Sosnowiec, Poland
Interests: protein-ligand interactions; protein modification
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Interactions between proteins and ligands support the whole of biological science. The subject of protein–ligand interactions, especially serum protein, is one of the most exciting subjects in modern science. Due to the physicochemical properties of studied substances, there are numerous methods and techniques used in order to analyse their structure–function relationships. Understanding such interactions is crucial for gaining a fundamental knowledge base relating to cellular behaviour. The field of protein–ligand interaction studies is at an auspicious stage of development, as well as being in a very active growth phase. The main goal of this Special Issue is to provide a platform for publishing research on protein–ligand interactions, by using useful multi-disciplinary techniques applied in laboratories worldwide for investigating the basic principles and practical applications, especially in the pharmaceutical and biomedical fields.

Dr. Małgorzata Maciążek-Jurczyk
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.

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Keywords

  • protein–ligand interactions
  • binding affinity
  • protein structure and function

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Published Papers (2 papers)

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Research

22 pages, 7364 KiB  
Article
NMR Studies on the Structure of Yeast Sis1 and the Dynamics of Its Interaction with Ssa1-EEVD
by Carolina O. Matos, Glaucia M. S. Pinheiro, Icaro P. Caruso, Gisele C. Amorim, Fabio C. L. Almeida and Carlos H. I. Ramos
Molecules 2025, 30(1), 11; https://doi.org/10.3390/molecules30010011 - 24 Dec 2024
Viewed by 262
Abstract
HSP70 chaperones play pivotal roles in facilitating protein folding, refolding, and disaggregation through their binding and releasing activities. This intricate process is further supported by J-domain proteins (JDPs), also known as DNAJs or HSP40s, which can be categorized into classes A and B. [...] Read more.
HSP70 chaperones play pivotal roles in facilitating protein folding, refolding, and disaggregation through their binding and releasing activities. This intricate process is further supported by J-domain proteins (JDPs), also known as DNAJs or HSP40s, which can be categorized into classes A and B. In yeast, these classes are represented by Ydj1 and Sis1, respectively. While both classes stimulate the ATPase activity of Ssa1 (yeast HSP70) through the J-domain, only class B JDPs possess the unique ability to efficiently stimulate Ssa1 in disaggregation processes. The C-terminal EEVD motif of HSP70 plays a crucial role in mediating these interactions by connecting with both client proteins and JDPs. However, the removal of the EEVD motif disrupts the capacity of HSP70 to associate with class B JDPs, and the intricacies of the interaction between these two proteins remain incompletely understood. We employed NMR spectroscopy to investigate the structure and dynamics of the class B J domain protein (JDP) of S. cerevisiae (Sis1) complexed with an EEVD peptide of Ssa1. Our study is based on the extraordinary 70.5% residue assignment of the full-length (352 residues long) Sis1. Our findings revealed that EEVD binds to two distinct sites within the C-terminal domain I (CTDI) of Sis1, to the J domain and to the GF-rich loop located between the J domain and α-helix 6 (a structure identified by this work). We propose that the interaction between EEVD and Sis1 facilitates the dissociation of α-helix 6, promoting a conformational state that is more favorable for interaction with Ssa1. We also employed α-synuclein as a substrate to investigate the competitive nature between EEVD and the client protein. Our experimental findings provide evidence supporting the interaction of EEVD with the client protein at multiple sites and essential insights into the mechanistic cycle of class B JDPs. Full article
(This article belongs to the Special Issue Protein-Ligand Interactions)
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13 pages, 5173 KiB  
Article
Impact of Transglutaminase-Mediated Crosslinking on the Conformational Changes in a Dual-Protein System and IgE Reactivity of Soy Protein
by Guangliang Xing, Tianran Hui, Jia Liu and Siran Yang
Molecules 2024, 29(14), 3371; https://doi.org/10.3390/molecules29143371 - 18 Jul 2024
Cited by 1 | Viewed by 1156
Abstract
Transglutaminase (TGase)-catalyzed crosslinking has gained substantial traction as a novel strategy for reducing allergenic risk in food proteins, particularly within the realm of hypoallergenic food production. This study explored the impact of TGase crosslinking on conformational changes in a binary protein system composed [...] Read more.
Transglutaminase (TGase)-catalyzed crosslinking has gained substantial traction as a novel strategy for reducing allergenic risk in food proteins, particularly within the realm of hypoallergenic food production. This study explored the impact of TGase crosslinking on conformational changes in a binary protein system composed of soy protein isolate (SPI) and sodium caseinate (SC) at varying mass ratios (10:0, 7:3, 5:5, 3:7 (w/w)). Specifically, the immunoglobulin E (IgE) binding capacity of soy proteins within this system was examined. Prolonged TGase crosslinking (ranging from 0 h to 15 h) resulted in a gradual reduction in IgE reactivity across all SPI-SC ratios, with the order of IgE-binding capability as follows: SPI > SPI5-SC5 > SPI7-SC3 > SPI3-SC7. These alterations in protein conformation following TGase crosslinking, as demonstrated by variable intrinsic fluorescence, altered surface hydrophobicity, increased ultraviolet absorption and reduced free sulfhydryl content, were identified as the underlying causes. Additionally, ionic bonds were found to play a significant role in maintaining the structure of the dual-protein system after crosslinking, with hydrophobic forces and hydrogen bonds serving as supplementary forces. Generally, the dual-protein system may exhibit enhanced efficacy in reducing the allergenicity of soy protein. Full article
(This article belongs to the Special Issue Protein-Ligand Interactions)
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