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Enzyme Structure Function Stability

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 (30 December 2023) | Viewed by 15070

Special Issue Editors


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Guest Editor
School of Biotechnology and Biomolecular Sciences (BABS), The University of New South Wales (UNSW), Sydney, NSW 2052, Australia
Interests: biocatalysis; biotechnology; medical biotechnology; bacteriophage-mediated biocontrol; glutathione biochemistry

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Guest Editor
School of Biotechnology and Biomolecular Sciences (BABS), The University of New South Wales (UNSW), Sydney, NSW 2052, Australia
Interests: protein structure function stability; enzyme biotechnology; protein bioinformatics; biochemical analysis and biotechniques; protein chemical modification; extremophilic enzymes

Special Issue Information

Dear Colleagues,

Proteins are central to all vital functions in biological systems. Enzymes are biocatalytic proteins that increase the rate of metabolic reactions to sustain life under environmental and physiological conditions. Due to their high substrate specificity and tremendous acceleration over non-catalysed reactions, enzymes have potential and real applications in the diverse fields of medical, industrial, agriculture and environmental biotechnologies. Enzymes also play key roles in aetiology of many diseases, which has led to an ever-expanding effort to identify efficacious inhibitors.  In order to exploit their full potential, the sequence-structure-function-stability relationship of an enzyme needs to be comprehensively elucidated.  This requires the development and application of novel cutting-edge technologies to study and resolve all aspects of enzyme kinetics.

In this special issue we will discuss current research on the structure-function-stability relationship in enzymes of medical, environmental and industrial importance. We are also interested in advanced tools such as cryo-electron microscopy for protein structure elucidation, ab initio protein structure prediction, single molecule enzymology, high-throughput microfluidic enzyme kinetics and any other novel methods that are topical and have potential to contribute towards understanding and optimizing structure-function in proteins. With the current on-going COVID-19 pandemic, articles on the viral enzymes are also welcomed. Due to industrial and environmental applications, topics dealing with the polyextremophilic enzymes are also solicited.  Kindly note that as IJMS focus is on molecular science, pure clinical studies will not suitable. However, clinical submissions that involve the introduction and discussion of biomolecular mechanisms are welcome. We are open to all types of articles including research, review and opinion.

Dr. Wallace Bridge
Dr. Khawar Sohail Siddiqui
Guest Editors

Manuscript Submission Information

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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

  • enzyme structure
  • enzyme function
  • enzyme stability
  • protein/enzyme analysis tools
  • COVID-19 viral enzymes
  • polyextremophilic enzymes
  • enzyme biotechnology
  • Ab initio protein structure prediction
  • cryo-electron microscopy
  • single molecule enzymology
  • high-throughput microfluidic enzyme kinetics

Published Papers (9 papers)

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Research

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17 pages, 3694 KiB  
Article
Immp2l Enhances the Structure and Function of Mitochondrial Gpd2 Dehydrogenase
by Raymond A. Clarke, Hemna Govindaraju, Martina Beretta, Ellen Olzomer, Adam J. Lawther, Adam K. Walker, Zhiming Fang, Valsamma Eapen, Tzipi Cohen Hyams, Murray Killingsworth, Wallace Bridge, Nigel Turner and Khawar Sohail Siddiqui
Int. J. Mol. Sci. 2024, 25(2), 990; https://doi.org/10.3390/ijms25020990 - 12 Jan 2024
Viewed by 821
Abstract
‘Inner mitochondrial membrane peptidase 2 like’ (IMMP2L) is a nuclear-encoded mitochondrial peptidase that has been conserved through evolutionary history, as has its target enzyme, ‘mitochondrial glycerol phosphate dehydrogenase 2′ (GPD2). IMMP2L is known to cleave the mitochondrial transit peptide from GPD2 and another [...] Read more.
‘Inner mitochondrial membrane peptidase 2 like’ (IMMP2L) is a nuclear-encoded mitochondrial peptidase that has been conserved through evolutionary history, as has its target enzyme, ‘mitochondrial glycerol phosphate dehydrogenase 2′ (GPD2). IMMP2L is known to cleave the mitochondrial transit peptide from GPD2 and another nuclear-encoded mitochondrial respiratory-related protein, cytochrome C1 (CYC1). However, it is not known whether IMMP2L peptidase activates or alters the activity or respiratory-related functions of GPD2 or CYC1. Previous investigations found compelling evidence of behavioural change in the Immp2lKD−/− KO mouse, and in this study, EchoMRI analysis found that the organs of the Immp2lKD−/− KO mouse were smaller and that the KO mouse had significantly less lean mass and overall body weight compared with wildtype littermates (p < 0.05). Moreover, all organs analysed from the Immp2lKD−/− KO had lower relative levels of mitochondrial reactive oxygen species (mitoROS). The kidneys of the Immp2lKD−/− KO mouse displayed the greatest decrease in mitoROS levels that were over 50% less compared with wildtype litter mates. Mitochondrial respiration was also lowest in the kidney of the Immp2lKD−/− KO mouse compared with other tissues when using succinate as the respiratory substrate, whereas respiration was similar to the wildtype when glutamate was used as the substrate. When glycerol-3-phosphate (G3P) was used as the substrate for Gpd2, we observed ~20% and ~7% respective decreases in respiration in female and male Immp2lKD−/− KO mice over time. Together, these findings indicate that the respiratory-related functions of mGpd2 and Cyc1 have been compromised to different degrees in different tissues and genders of the Immp2lKD−/− KO mouse. Structural analyses using AlphaFold2-Multimer further predicted that the interaction between Cyc1 and mitochondrial-encoded cytochrome b (Cyb) in Complex III had been altered, as had the homodimeric structure of the mGpd2 enzyme within the inner mitochondrial membrane of the Immp2lKD−/− KO mouse. mGpd2 functions as an integral component of the glycerol phosphate shuttle (GPS), which positively regulates both mitochondrial respiration and glycolysis. Interestingly, we found that nonmitochondrial respiration (NMR) was also dramatically lowered in the Immp2lKD−/− KO mouse. Primary mouse embryonic fibroblast (MEF) cell lines derived from the Immp2lKD−/− KO mouse displayed a ~27% decrease in total respiration, comprising a ~50% decrease in NMR and a ~12% decrease in total mitochondrial respiration, where the latter was consistent with the cumulative decreases in substrate-specific mediated mitochondrial respiration reported here. This study is the first to report the role of Immp2l in enhancing Gpd2 structure and function, mitochondrial respiration, nonmitochondrial respiration, organ size and homeostasis. Full article
(This article belongs to the Special Issue Enzyme Structure Function Stability)
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14 pages, 3117 KiB  
Article
Improving the Thermostability of Thermomyces lanuginosus Lipase by Restricting the Flexibility of N-Terminus and C-Terminus Simultaneously via the 25-Loop Substitutions
by Xia Xiang, Enheng Zhu, Diao Xiong, Yin Wen, Yu Xing, Lirong Yue, Shuang He, Nanyu Han and Zunxi Huang
Int. J. Mol. Sci. 2023, 24(23), 16562; https://doi.org/10.3390/ijms242316562 - 21 Nov 2023
Viewed by 678
Abstract
(1) Lipases are catalysts widely applied in industrial fields. To sustain the harsh treatments in industries, optimizing lipase activities and thermal stability is necessary to reduce production loss. (2) The thermostability of Thermomyces lanuginosus lipase (TLL) was evaluated via B-factor analysis and consensus-sequence [...] Read more.
(1) Lipases are catalysts widely applied in industrial fields. To sustain the harsh treatments in industries, optimizing lipase activities and thermal stability is necessary to reduce production loss. (2) The thermostability of Thermomyces lanuginosus lipase (TLL) was evaluated via B-factor analysis and consensus-sequence substitutions. Five single-point variants (K24S, D27N, D27R, P29S, and A30P) with improved thermostability were constructed via site-directed mutagenesis. (3) The optimal reaction temperatures of all the five variants displayed 5 °C improvement compared with TLL. Four variants, except D27N, showed enhanced residual activities at 80 °C. The melting temperatures of three variants (D27R, P29S, and A30P) were significantly increased. The molecular dynamics simulations indicated that the 25-loop (residues 24–30) in the N-terminus of the five variants generated more hydrogen bonds with surrounding amino acids; hydrogen bond pair D254-I255 preserved in the C-terminus of the variants also contributes to the improved thermostability. Furthermore, the newly formed salt-bridge interaction (R27…E56) in D27R was identified as a crucial determinant for thermostability. (4) Our study discovered that substituting residues from the 25-loop will enhance the stability of the N-terminus and C-terminus simultaneously, restrict the most flexible regions of TLL, and result in improved thermostability. Full article
(This article belongs to the Special Issue Enzyme Structure Function Stability)
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17 pages, 3855 KiB  
Article
Overexpression of Both Human Sodium Iodide Symporter (NIS) and BRG1-Bromodomain Synergistically Enhances Radioiodine Sensitivity by Stabilizing p53 through NPM1 Expression
by Juri Na, Chul-Hee Lee, June-Key Chung and Hyewon Youn
Int. J. Mol. Sci. 2023, 24(3), 2761; https://doi.org/10.3390/ijms24032761 - 01 Feb 2023
Viewed by 2012
Abstract
Improved therapeutic strategies are required to minimize side effects associated with radioiodine gene therapy to avoid unnecessary damage to normal cells and radiation-induced secondary malignancies. We previously reported that codon-optimized sodium iodide symporter (oNIS) enhances absorption of I-131 and that the brahma-associated gene [...] Read more.
Improved therapeutic strategies are required to minimize side effects associated with radioiodine gene therapy to avoid unnecessary damage to normal cells and radiation-induced secondary malignancies. We previously reported that codon-optimized sodium iodide symporter (oNIS) enhances absorption of I-131 and that the brahma-associated gene 1 bromodomain (BRG1-BRD) causes inefficient DNA damage repair after high-energy X-ray therapy. To increase the therapeutic effect without applying excessive radiation, we considered the combination of oNIS and BRG1-BRD as gene therapy for the most effective radioiodine treatment. The antitumor effect of I-131 with oNIS or oNIS+BRD expression was examined by tumor xenograft models along with functional assays at the cellular level. The synergistic effect of both BRG1-BRD and oNIS gene overexpression resulted in more DNA double-strand breaks and led to reduced cell proliferation/survival rates after I-131 treatment, which was mediated by the p53/p21 pathway. We found increased p53, p21, and nucleophosmin 1 (NPM1) in oNIS- and BRD-expressing cells following I-131 treatment, even though the remaining levels of citrulline and protein arginine deiminase 4 (PAD4) were unchanged at the protein level. Full article
(This article belongs to the Special Issue Enzyme Structure Function Stability)
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17 pages, 3335 KiB  
Article
Thermofluor-Based Optimization Strategy for the Stabilization of Recombinant Human Soluble Catechol-O-Methyltransferase
by Ana M. Gonçalves, Augusto Q. Pedro, Diana M. Oliveira, Adriana E. Oliveira, Marino F. A. Santos, Márcia A. S. Correia, João A. Queiroz, Eugénia Gallardo, Maria J. Romão and Luís A. Passarinha
Int. J. Mol. Sci. 2022, 23(20), 12298; https://doi.org/10.3390/ijms232012298 - 14 Oct 2022
Cited by 2 | Viewed by 2017
Abstract
Catechol-O-methyltransferase (COMT) has been involved in a number of medical conditions including catechol-estrogen-induced cancers and a great range of cardiovascular and neurodegenerative diseases such as Parkinson’s disease. Currently, Parkinson’s disease treatment relies on a triple prophylaxis, involving dopamine replacement by levodopa, [...] Read more.
Catechol-O-methyltransferase (COMT) has been involved in a number of medical conditions including catechol-estrogen-induced cancers and a great range of cardiovascular and neurodegenerative diseases such as Parkinson’s disease. Currently, Parkinson’s disease treatment relies on a triple prophylaxis, involving dopamine replacement by levodopa, the use of aromatic L-amino acid decarboxylase inhibitors, and the use of COMT inhibitors. Typically, COMT is highly thermolabile, and its soluble isoform (SCOMT) loses biological activity within a short time span preventing further structural and functional trials. Herein, we characterized the thermal stability profile of lysate cells from Komagataella pastoris containing human recombinant SCOMT (hSCOMT) and enzyme-purified fractions (by Immobilized Metal Affinity Chromatography—IMAC) upon interaction with several buffers and additives by Thermal Shift Assay (TSA) and a biological activity assessment. Based on the obtained results, potential conditions able to increase the thermal stability of hSCOMT have been found through the analysis of melting temperature (Tm) variations. Moreover, the use of the ionic liquid 1-butyl-3-methylimidazolium chloride [C4mim]Cl (along with cysteine, trehalose, and glycerol) ensures complete protein solubilization as well as an increment in the protein Tm of approximately 10 °C. Thus, the developed formulation enhances hSCOMT stability with an increment in the percentage of activity recovery of 200% and 70% when the protein was stored at 4 °C and −80 °C, respectively, for 12 h. The formation of metanephrine over time confirmed that the enzyme showed twice the productivity in the presence of the additive. These outstanding achievements might pave the way for the development of future hSCOMT structural and biophysical studies, which are fundamental for the design of novel therapeutic molecules. Full article
(This article belongs to the Special Issue Enzyme Structure Function Stability)
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15 pages, 3649 KiB  
Article
A New Phospholipase D from Moritella sp. JT01: Biochemical Characterization, Crystallization and Application in the Synthesis of Phosphatidic Acid
by Fanghua Wang, Xuejing Mao, Fuli Deng, Ruiguo Cui, Lilang Li, Siyu Liu, Bo Yang, Dongming Lan and Yonghua Wang
Int. J. Mol. Sci. 2022, 23(19), 11633; https://doi.org/10.3390/ijms231911633 - 01 Oct 2022
Viewed by 1377
Abstract
A new phospholipase D from marine Moritella sp. JT01 (MsPLD) was recombinantly expressed and biochemically characterized. The optimal reaction temperature and pH of MsPLD were determined to be 35 °C and 8.0. MsPLD was stable at a temperature lower than 35 °C, and [...] Read more.
A new phospholipase D from marine Moritella sp. JT01 (MsPLD) was recombinantly expressed and biochemically characterized. The optimal reaction temperature and pH of MsPLD were determined to be 35 °C and 8.0. MsPLD was stable at a temperature lower than 35 °C, and the t1/2 at 4 °C was 41 days. The crystal structure of apo-MsPLD was resolved and the functions of a unique extra loop segment on the enzyme activity were characterized. The results indicated that a direct deletion or fastening of the extra loop segment by introducing disulfide bonds both resulted in a complete loss of its activity. The results of the maximum insertion pressure indicated that the deletion of the extra loop segment significantly decreased MsPLD’s interfacial binding properties to phospholipid monolayers. Finally, MsPLD was applied to the synthesis of phosphatidic acid by using a biphasic reaction system. Under optimal reaction conditions, the conversion rate of phosphatidic acid reached 86%. The present research provides a foundation for revealing the structural–functional relationship of this enzyme. Full article
(This article belongs to the Special Issue Enzyme Structure Function Stability)
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13 pages, 1663 KiB  
Article
Improving Both the Thermostability and Catalytic Efficiency of Phospholipase D from Moritella sp. JT01 through Disulfide Bond Engineering Strategy
by Lilang Li, Xuejing Mao, Fuli Deng, Yonghua Wang and Fanghua Wang
Int. J. Mol. Sci. 2022, 23(19), 11319; https://doi.org/10.3390/ijms231911319 - 26 Sep 2022
Cited by 3 | Viewed by 1433
Abstract
Mining of Phospholipase D (PLD) with high activity and stability has attracted strong interest for investigation. A novel PLD from marine Moritella sp. JT01 (MsPLD) was biochemically and structurally characterized in our previous study; however, the short half-life time (t1/2) [...] Read more.
Mining of Phospholipase D (PLD) with high activity and stability has attracted strong interest for investigation. A novel PLD from marine Moritella sp. JT01 (MsPLD) was biochemically and structurally characterized in our previous study; however, the short half-life time (t1/2) under its optimum reaction temperature seriously hampered its further applications. Herein, the disulfide bond engineering strategy was applied to improve its thermostability. Compared with wild-type MsPLD, mutant S148C-T206C/D225C-A328C with the addition of two disulfide bonds exhibited a 3.1-fold t1/2 at 35 °C and a 5.7 °C increase in melting temperature (Tm). Unexpectedly, its specific activity and catalytic efficiency (kcat/Km) also increased by 22.7% and 36.5%, respectively. The enhanced activity might be attributed to an increase in the activation entropy by displacing more water molecules by the transition state. The results of molecular dynamics simulations (MD) revealed that the introduction of double disulfide bonds rigidified the global structure of the mutant, which might cause the enhanced thermostability. Finally, the synthesis capacity of the mutant to synthesize phosphatidic acid (PA) was evaluated. The conversion rate of PA reached about 80% after 6 h reaction with wild-type MsPLD but reached 78% after 2 h with mutant S148C-T206C/D225C-A328C, which significantly reduced the time needed for the reaction to reach equilibrium. The present results pave the way for further application of MsPLD in the food and pharmaceutical industries. Full article
(This article belongs to the Special Issue Enzyme Structure Function Stability)
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18 pages, 2110 KiB  
Article
Kinetic Modeling, Thermodynamic Approach and Molecular Dynamics Simulation of Thermal Inactivation of Lipases from Burkholderia cepacia and Rhizomucor miehei
by Natividad Ortega, Laura Sáez, David Palacios and María D. Busto
Int. J. Mol. Sci. 2022, 23(12), 6828; https://doi.org/10.3390/ijms23126828 - 19 Jun 2022
Cited by 8 | Viewed by 2229
Abstract
The behavior against temperature and thermal stability of enzymes is a topic of importance for industrial biocatalysis. This study focuses on the kinetics and thermodynamics of the thermal inactivation of Lipase PS from B. cepacia and Palatase from R. miehei. Thermal inactivation [...] Read more.
The behavior against temperature and thermal stability of enzymes is a topic of importance for industrial biocatalysis. This study focuses on the kinetics and thermodynamics of the thermal inactivation of Lipase PS from B. cepacia and Palatase from R. miehei. Thermal inactivation was investigated using eight inactivation models at a temperature range of 40–70 °C. Kinetic modeling showed that the first-order model and Weibull distribution were the best equations to describe the residual activity of Lipase PS and Palatase, respectively. The results obtained from the kinetic parameters, decimal reduction time (D and tR), and temperature required (z and z’) indicated a higher thermal stability of Lipase PS compared to Palatase. The activation energy values (Ea) also indicated that higher energy was required to denature bacterial (34.8 kJ mol−1) than fungal (23.3 kJ mol−1) lipase. The thermodynamic inactivation parameters, Gibbs free energy (ΔG#), entropy (ΔS#), and enthalpy (ΔH#) were also determined. The results showed a ΔG# for Palatase (86.0–92.1 kJ mol−1) lower than for Lipase PS (98.6–104.9 kJ mol−1), and a negative entropic and positive enthalpic contribution for both lipases. A comparative molecular dynamics simulation and structural analysis at 40 °C and 70 °C were also performed. Full article
(This article belongs to the Special Issue Enzyme Structure Function Stability)
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Review

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38 pages, 26329 KiB  
Review
Lipoxygenases at the Intersection of Infection and Carcinogenesis
by Abdul-Saleem Amoah, Nikolay B. Pestov, Tatyana V. Korneenko, Igor A. Prokhorenko, Georgy F. Kurakin and Nickolai A. Barlev
Int. J. Mol. Sci. 2024, 25(7), 3961; https://doi.org/10.3390/ijms25073961 - 02 Apr 2024
Viewed by 680
Abstract
The persisting presence of opportunistic pathogens like Pseudomonas aeruginosa poses a significant threat to many immunocompromised cancer patients with pulmonary infections. This review highlights the complexity of interactions in the host’s defensive eicosanoid signaling network and its hijacking by pathogenic bacteria to their [...] Read more.
The persisting presence of opportunistic pathogens like Pseudomonas aeruginosa poses a significant threat to many immunocompromised cancer patients with pulmonary infections. This review highlights the complexity of interactions in the host’s defensive eicosanoid signaling network and its hijacking by pathogenic bacteria to their own advantage. Human lipoxygenases (ALOXs) and their mouse counterparts are integral elements of the innate immune system, mostly operating in the pro-inflammatory mode. Taking into account the indispensable role of inflammation in carcinogenesis, lipoxygenases have counteracting roles in this process. In addition to describing the structure-function of lipoxygenases in this review, we discuss their roles in such critical processes as cancer cell signaling, metastases, death of cancer and immune cells through ferroptosis, as well as the roles of ALOXs in carcinogenesis promoted by pathogenic infections. Finally, we discuss perspectives of novel oncotherapeutic approaches to harness lipoxygenase signaling in tumors. Full article
(This article belongs to the Special Issue Enzyme Structure Function Stability)
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16 pages, 9062 KiB  
Review
Evaluating Enzymatic Productivity—The Missing Link to Enzyme Utility
by Khawar Sohail Siddiqui, Haluk Ertan, Anne Poljak and Wallace J. Bridge
Int. J. Mol. Sci. 2022, 23(13), 6908; https://doi.org/10.3390/ijms23136908 - 21 Jun 2022
Cited by 18 | Viewed by 2544
Abstract
Kinetic productivity analysis is critical to the characterization of enzyme catalytic performance and capacity. However, productivity analysis has been largely overlooked in the published literature. Less than 0.01% of studies which report on enzyme characterization present productivity analysis, despite the fact that this [...] Read more.
Kinetic productivity analysis is critical to the characterization of enzyme catalytic performance and capacity. However, productivity analysis has been largely overlooked in the published literature. Less than 0.01% of studies which report on enzyme characterization present productivity analysis, despite the fact that this is the only measurement method that provides a reliable indicator of potential commercial utility. Here, we argue that reporting productivity data involving native, modified, and immobilized enzymes under different reaction conditions will be of immense value in optimizing enzymatic processes, with a view to accelerating biotechnological applications. With the use of examples from wide-ranging studies, we demonstrate that productivity is a measure of critical importance to the translational and commercial use of enzymes and processes that employ them. We conclude the review by suggesting steps to maximize the productivity of enzyme catalyzed reactions. Full article
(This article belongs to the Special Issue Enzyme Structure Function Stability)
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