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Blueprints of Enzymatic Function and Structure in Biocatalysis
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Blueprints of Enzymatic Function and Structure in Biocatalysis

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

Deadline for manuscript submissions: 20 March 2026 | Viewed by 5964

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,

In this Special Issue of the International Journal of Molecular Sciences, entitled "Blueprints of Enzymatic Function and Structure in Biocatalysis", we delve into the intricate relationship between enzyme structure, kinetics, and thermodynamics in the realm of biocatalysis. Enzymes, as nature's catalysts, play a vital role in accelerating biochemical reactions, and a deeper understanding of their structural and thermodynamic blueprints is essential for innovations in synthetic biology, pharmaceuticals, and industrial applications. This Special Issue aims to present cutting-edge research on enzyme engineering, mechanistic pathways, and the kinetic and thermodynamic principles that govern enzyme efficiency, shedding light on the design of more effective and sustainable biocatalysts.

Prof. Dr. Francesco Malatesta
Guest Editor

Manuscript Submission Information

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Keywords

  • enzyme
  • biocatalysis
  • enzyme structure
  • enzyme kinetics and thermodynamics
  • enzyme engineering
  • synthetic biology applications
  • sustainable biocatalyst design

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Published Papers (2 papers)

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Research

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23 pages, 6905 KB  
Article
The Functional State of Thermoplasma acidophilum Pyruvate Kinase Relies on an Extra Carboxyl-Terminal Sequence
by Leticia Ramírez-Silva, Héctor Riveros-Rosas, Gloria Hernández-Alcántara, José J. García-Trejo, Alicia Vega-Segura, Martin González-Andrade, A. Jessica Díaz-Salazar and Guillermo Salcedo-Barrientos
Int. J. Mol. Sci. 2025, 26(17), 8410; https://doi.org/10.3390/ijms26178410 - 29 Aug 2025
Viewed by 1099
Abstract
Phylogenetic studies of the pyruvate kinase family reveal two clusters: the K+-dependent and -independent enzymes. Thermoplasma acidophilum pyruvate kinase belongs to the latter but possesses the conserved signature of those K+-dependent. Recently, we found two distinct ways for these [...] Read more.
Phylogenetic studies of the pyruvate kinase family reveal two clusters: the K+-dependent and -independent enzymes. Thermoplasma acidophilum pyruvate kinase belongs to the latter but possesses the conserved signature of those K+-dependent. Recently, we found two distinct ways for these groups to catalyze. It is interesting to elucidate how the T. acidophilum enzyme achieves its active conformation. A structural model of this enzyme revealed the presence of an extra C-terminal sequence (ECTS). To understand its role, an enzyme lacking this sequence from T. acidophilum was constructed. We then compared the kinetic parameters, far-UV CD spectra, thermal stability, molecular dynamics simulations, and oligomeric states of both the wild-type and truncated enzymes. We found that the truncated enzyme is aggregated and almost inactive, with residual 20% of the total interactions, and it exhibits a soluble fraction of smaller oligomeric states than the wild-type enzyme. These findings suggest that ECTS plays a crucial role in maintaining its active tetrameric state. This sequence is the first reported in an archaeal pyruvate kinase and is also found in other archaea and bacteria. Phylogenetic analysis of ECTS in pyruvate kinases exhibits a sparse distribution that might be explained if ECTS represents an ancient domain prone to loss. Full article
(This article belongs to the Special Issue Blueprints of Enzymatic Function and Structure in Biocatalysis)
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Review

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18 pages, 3334 KB  
Review
Exploiting Silica-Binding and Silica-Forming Proteins as Versatile Tools for One-Step Enzyme Immobilization on Siliceous Materials
by Gyun Taek Lim and Byung Hoon Jo
Int. J. Mol. Sci. 2025, 26(3), 1304; https://doi.org/10.3390/ijms26031304 - 3 Feb 2025
Cited by 7 | Viewed by 4379
Abstract
Enzyme immobilization has emerged as an essential technique in industrial applications of enzymes. Silica (SiO2) serves as a prominent support material for enzyme immobilization. Recent advancements have led to the development of various silica-binding proteins (SBPs) and silica-forming proteins (SFPs) that [...] Read more.
Enzyme immobilization has emerged as an essential technique in industrial applications of enzymes. Silica (SiO2) serves as a prominent support material for enzyme immobilization. Recent advancements have led to the development of various silica-binding proteins (SBPs) and silica-forming proteins (SFPs) that are invaluable tools in immobilizing enzymes on siliceous materials in a fast and simple manner. SBPs facilitate the immobilization of enzymes with controlled orientation on silica surfaces, while SFPs enable the biomimetic synthesis and encapsulation of enzymes within silica particles. In this review, we explore recent advances in the use of SBPs and SFPs in enzyme applications. We provide a comprehensive overview of their mechanisms and sequence characteristics relevant to enzyme immobilization. Additionally, we summarize the recombinant production and immobilization procedures for enzymes with SBPs or SFPs. We then categorize the available SBPs and SFPs into naturally occurring and artificially engineered types, presenting recent examples that demonstrate their utilization in enzyme immobilization. Our review highlights the strengths and limitations of various SBPs and SFPs and sheds light on future directions for the development of tailor-made biocatalytic silica. Full article
(This article belongs to the Special Issue Blueprints of Enzymatic Function and Structure in Biocatalysis)
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