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Protein-Protein and Protein-Ligand Interactions: Current Challenges and Perspectives
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Protein-Protein and Protein-Ligand Interactions: Current Challenges and Perspectives

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Macromolecules".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 3748

Special Issue Editor

Dr. Mariapina D'Onofrio

E-Mail Website
Guest Editor
Department of Biotechnology, University of Verona, Verona, Italy
Interests: structure; functional interactions; post translational modifications of proteins; NMR spectroscopy; intrinsically disordered proteins
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein–protein and protein–ligand interactions play central roles in all processes of living organisms, participating in their activation and regulation. The identification of the actors of cellular networks based on molecular recognition, as well as the clear definition of the transient and persistent interactions are crucial to elucidate biomolecular communication pathways.

Protein interactions are often at the basis of many pathological states, therefore, their in-depth understanding could open new perspectives in the treatment of many diseases.

 A key aspect to advance our knowledge is the availability of reliable novel bioinformatic methods to efficiently predict protein interactions as well as the development and improvement of experimental approaches to fully characterize the structure and thermodynamics of functional biomolecular associations to unveil biologically relevant pathways. 

In this Special Issue of IJMS, we aim to collect contributions in the form of either original research articles or reviews, to add new insight into the role of protein–protein and protein–ligand interactions in biological processes and to highlight the state of the art, the challenges, and the open issues in this varied field of investigation.

Dr. Mariapina D'Onofrio
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 interaction networks
  • Biological processes
  • Protein complexes
  • Molecular recognition

Published Papers (2 papers)

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Research

17 pages, 3568 KiB  
Article
Mapping PP1c and Its Inhibitor 2 Interactomes Reveals Conserved and Specific Networks in Asexual and Sexual Stages of Plasmodium
by Caroline De Witte, El Moukhtar Aliouat, Cerina Chhuon, Ida Chiara Guerrera, Christine Pierrot and Jamal Khalife
Int. J. Mol. Sci. 2022, 23(3), 1069; https://doi.org/10.3390/ijms23031069 - 19 Jan 2022
Cited by 1 | Viewed by 1574
Abstract
Malaria parasites require multiple phosphorylation and dephosphorylation steps to drive signaling pathways for proper differentiation and transformation. Several protein phosphatases, including protein phosphatase 1 (PP1), one of the main dephosphorylation enzymes, have been shown to be indispensable for the Plasmodium life cycle. The [...] Read more.
Malaria parasites require multiple phosphorylation and dephosphorylation steps to drive signaling pathways for proper differentiation and transformation. Several protein phosphatases, including protein phosphatase 1 (PP1), one of the main dephosphorylation enzymes, have been shown to be indispensable for the Plasmodium life cycle. The catalytic subunit of PP1 (PP1c) participates in cellular processes via dynamic interactions with a vast number of binding partners that contribute to its diversity of action. In this study, we used Plasmodium berghei transgenic parasite strains stably expressing PP1c or its inhibitor 2 (I2) tagged with mCherry, combined with the mCherry affinity pulldown of proteins from asexual and sexual stages, followed by mass spectrometry analyses. Mapped proteins were used to identify interactomes and to cluster functionally related proteins. Our findings confirm previously known physical interactions of PP1c and reveal enrichment of common biological processes linked to cellular component assembly in both schizonts and gametocytes to biosynthetic processes/translation in schizonts and to protein transport exclusively in gametocytes. Further, our analysis of PP1c and I2 interactomes revealed that nuclear export mediator factor and peptidyl-prolyl cis-trans isomerase, suggested to be essential in P. falciparum, could be potential targets of the complex PP1c/I2 in both asexual and sexual stages. Our study emphasizes the adaptability of Plasmodium PP1 and provides a fundamental study of the protein interaction landscapes involved in a myriad of events in Plasmodium, suggesting why it is crucial to the parasite and a source for alternative therapeutic strategies. Full article
(This article belongs to the Special Issue Protein-Protein and Protein-Ligand Interactions: Current Challenges and Perspectives)
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12 pages, 1451 KiB  
Article
In Vitro Investigation of Binding Interactions between Albumin–Gliclazide Model and Typical Hypotensive Drugs
by Ewa Zurawska-Plaksej, Rafal Wiglusz, Agnieszka Piwowar and Katarzyna Wiglusz
Int. J. Mol. Sci. 2022, 23(1), 286; https://doi.org/10.3390/ijms23010286 - 28 Dec 2021
Cited by 5 | Viewed by 1522
Abstract
Type 2 diabetes management usually requires polytherapy, which increases the risk of drug-to-drug interactions. Among the multiple diabetes comorbidities, hypertension is the most prevalent. This study aimed to investigate the binding interactions between the model protein, bovine albumin, and the hypoglycemic agent gliclazide [...] Read more.
Type 2 diabetes management usually requires polytherapy, which increases the risk of drug-to-drug interactions. Among the multiple diabetes comorbidities, hypertension is the most prevalent. This study aimed to investigate the binding interactions between the model protein, bovine albumin, and the hypoglycemic agent gliclazide (GLICL) in the presence of typical hypotensive drugs: quinapril hydrochloride (QUI), valsartan (VAL), furosemide (FUR), amlodipine besylate (AML), and atenolol (ATN). Spectroscopic techniques (fluorescence quenching, circular dichroism) and thermodynamic experiments were employed. The binding of the gliclazide to the albumin molecule was affected by the presence of an additional drug ligand, which was reflected by the reduced binding constant of the BSA–DRUG–GLICL system. This may indicate a possible GLICL displacement and its enhanced pharmacological effect, as manifested in clinical practice. The analysis of the thermodynamic parameters indicated the spontaneity of the reaction and emphasized the role of hydrogen bonding and van der Waals forces in these interactions. The secondary structure of the BSA remained almost unaffected. Full article
(This article belongs to the Special Issue Protein-Protein and Protein-Ligand Interactions: Current Challenges and Perspectives)
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