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Special Issue Editors

Special Issue Information

Dear Colleagues,

The study of the structure–function relationship in proteins is considered one of the building blocks in biochemistry, with important consequences in diverse fields such as molecular biology, genetics, and protein engineering and represents a challenge that requires a lot of effort to succeed. So far, the understanding of the structure–function relationship of a newly identified pharmacological target combined both with cell-based assays and with the data collected when mutations or improper folding of such a target are associated with serious diseases are all information that is critical for drug discovery and medicine. A peculiar role in predicting the protein function of a target and for deep understanding of the molecular mechanisms in a living cell is assigned to protein–protein interactions. All researchers working in the field are cordially invited to contribute original research papers or reviews to this Special Issue, which reports on the structure–function relationship studies of proteins correlated with the insurgence of pathologies.

Dr. Emilia Pedone
Dr. Luciano Pirone
Guest Editors

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Keywords

structure–function relationship
protein–protein interactions
disease-associated mutations
folding and improper folding
protein structural and functional characterization

Published Papers (2 papers)

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Research

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16 pages, 14151 KiB

Open AccessArticle

Biochemical and Biophysical Characterization of Recombinant Human 3-Phosphoglycerate Dehydrogenase

by Giulia Murtas, Giorgia Letizia Marcone, Alessio Peracchi, Erika Zangelmi and Loredano Pollegioni

Int. J. Mol. Sci. 2021, 22(8), 4231; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22084231 - 19 Apr 2021

Cited by 10 | Viewed by 2780

Abstract

The human enzyme D-3-phosphoglycerate dehydrogenase (hPHGDH) catalyzes the reversible dehydrogenation of 3-phosphoglycerate (3PG) into 3-phosphohydroxypyruvate (PHP) using the NAD⁺/NADH redox cofactor, the first step in the phosphorylated pathway producing L-serine. We focused on the full-length enzyme that was produced in fairly large amounts in E. coli cells; the effect of pH, temperature and ligands on hPHGDH activity was studied. The forward reaction was investigated on 3PG and alternative carboxylic acids by employing two coupled assays, both removing the product PHP; 3PG was by far the best substrate in the forward direction. Both PHP and α-ketoglutarate were efficiently reduced by hPHGDH and NADH in the reverse direction, indicating substrate competition under physiological conditions. Notably, neither PHP nor L-serine inhibited hPHGDH, nor did glycine and D-serine, the coagonists of NMDA receptors related to L-serine metabolism. The investigation of NADH and phosphate binding highlights the presence in solution of different conformations and/or oligomeric states of the enzyme. Elucidating the biochemical properties of hPHGDH will enable the identification of novel approaches to modulate L-serine levels and thus to reduce cancer progression and treat neurological disorders. Full article

(This article belongs to the Special Issue Structure–Function Relationship in Proteins Correlated with the Insurgence of Diseases)

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Other

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9 pages, 1311 KiB

Open AccessPerspective

More Is Always Better Than One: The N-Terminal Domain of the Spike Protein as Another Emerging Target for Hampering the SARS-CoV-2 Attachment to Host Cells

by Sonia Di Gaetano, Domenica Capasso, Pietro Delre, Luciano Pirone, Michele Saviano, Emilia Pedone and Giuseppe Felice Mangiatordi

Int. J. Mol. Sci. 2021, 22(12), 6462; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22126462 - 16 Jun 2021

Cited by 13 | Viewed by 2748

Abstract

Although the approved vaccines are proving to be of utmost importance in containing the Coronavirus disease 2019 (COVID-19) threat, they will hardly be resolutive as new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, a single-stranded RNA virus) variants might be insensitive to the immune response they induce. In this scenario, developing an effective therapy is still a dire need. Different targets for therapeutic antibodies and diagnostics have been identified, among which the SARS-CoV-2 spike (S) glycoprotein, particularly its receptor-binding domain, has been defined as crucial. In this context, we aim to focus attention also on the role played by the S N-terminal domain (S1-NTD) in the virus attachment, already recognized as a valuable target for neutralizing antibodies, in particular, building on a cavity mapping indicating the presence of two druggable pockets and on the recent literature hypothesizing the presence of a ganglioside-binding domain. In this perspective, we aim at proposing S1-NTD as a putative target for designing small molecules hopefully able to hamper the SARS-CoV-2 attachment to host cells. Full article

(This article belongs to the Special Issue Structure–Function Relationship in Proteins Correlated with the Insurgence of Diseases)

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