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Ligand Binding in Enzyme Systems 2.0
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Ligand Binding in Enzyme Systems 2.0

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

Deadline for manuscript submissions: closed (10 November 2022) | Viewed by 2604

Special Issue Editor

Prof. Dr. Francesco Malatesta

E-Mail Website
Guest Editor
Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
Interests: bioenergetics; biophysics; chemical biology; enzymology kinetics; molecular medicine; protein chemistry; structural biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

From a chemical point of view, the primary event in most biological processes is a second-order reaction, i.e., the reversible binding of a ligand to a specific target (protein, receptor, nucleic acid, or enzyme). In general, the binding dynamics may involve induced-fit or conformational selection mechanisms. In the world of enzymes, ligand binding, unlike substrate binding, offers additional levels of complexity, whereby the enzyme may be regulated by feedback, product, and allosteric positive and negative modulation, or may acquire new enzymatic activities or novel biological functions, as in moonlighting enzymes.

This Special Issue concentrates on the role of ligand binding to enzymes at the onset of the perturbation triggered by the ligand, both from thermodynamic and kinetic viewpoints. Original research articles and up-to-date reviews on these and related topics are welcome in this Special Issue.

Prof. Dr. Francesco Malatesta
Guest Editor

Manuscript Submission Information

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Keywords

  • enzyme
  • ligand binding
  • allosteric enzymes
  • allostery
  • enzyme regulation
  • enzyme inhibition
  • moonlighting enzymes
  • steady-state kinetics
  • pre-steady-state kinetics
  • stopped-flow spectroscopy

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Published Papers (1 paper)

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Research

18 pages, 4660 KiB  
Article
New Insights into the Determinants of Specificity in Human Type I Arginase: Generation of a Mutant That Is Only Active with Agmatine as Substrate
by María-Soledad Orellana, Gonzalo A. Jaña, Maximiliano Figueroa, José Martínez-Oyanedel, Fabiola E. Medina, Estefanía Tarifeño-Saldivia, Marcell Gatica, María Ángeles García-Robles, Nelson Carvajal and Elena Uribe
Int. J. Mol. Sci. 2022, 23(12), 6438; https://doi.org/10.3390/ijms23126438 - 9 Jun 2022
Cited by 2 | Viewed by 2088
Abstract
Arginase catalyzes the hydrolysis of L-arginine into L-ornithine and urea. This enzyme has several analogies with agmatinase, which catalyzes the hydrolysis of agmatine into putrescine and urea. However, this contrasts with the highlighted specificity that each one presents for their respective substrate. A [...] Read more.
Arginase catalyzes the hydrolysis of L-arginine into L-ornithine and urea. This enzyme has several analogies with agmatinase, which catalyzes the hydrolysis of agmatine into putrescine and urea. However, this contrasts with the highlighted specificity that each one presents for their respective substrate. A comparison of available crystal structures for arginases reveals an important difference in the extension of two loops located in the entrance of the active site. The first, denominated loop A (I129-L140) contains the residues that interact with the alpha carboxyl group or arginine of arginase, and the loop B (D181-P184) contains the residues that interact with the alpha amino group of arginine. In this work, to determine the importance of these loops in the specificity of arginase, single, double, and triple arginase mutants in these loops were constructed, as well as chimeras between type I human arginase and E. coli agmatinase. In previous studies, the substitution of N130D in arginase (in loop A) generated a species capable of hydrolyzing arginine and agmatine. Now, the specificity of arginase is completely altered, generating a chimeric species that is only active with agmatine as a substrate, by substituting I129T, N130Y, and T131A together with the elimination of residues P132, L133, and T134. In addition, Quantum Mechanic/Molecular Mechanic (QM/MM) calculations were carried out to study the accommodation of the substrates in in the active site of this chimera. With these results it is concluded that this loop is decisive to discriminate the type of substrate susceptible to be hydrolyzed by arginase. Evidence was also obtained to define the loop B as a structural determinant for substrate affinity. Concretely, the double mutation D181T and V182E generate an enzyme with an essentially unaltered kcat value, but with a significantly increased Km value for arginine and a significant decrease in affinity for its product ornithine. Full article
(This article belongs to the Special Issue Ligand Binding in Enzyme Systems 2.0)
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