Special Issue "Enzyme Catalysis"

A special issue of Catalysts (ISSN 2073-4344).

Deadline for manuscript submissions: closed (31 March 2016)

Special Issue Editor

Guest Editor
Dr. David D. Boehr

Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
Website | E-Mail
Phone: +1-814-863-8605
Fax: +1-814-863-0618
Interests: enzymes; protein biophysics; allostery; protein engineering; NMR; microbiology

Special Issue Information

Dear Colleagues,

Enzymes are the catalysts that speed up and control biological reactions. Life would not be possible without the action of enzymes. Our understanding of enzymes has helped to facilitate drug discovery, and the development of new enzymes has application in a broad range of disciplines, including synthetic biology, industrial chemical processes, and materials science. Mechanistic information continues to develop from traditional physical organic chemistry tools, and newer methodologies are providing insight into the macromolecular machinery of enzymes.

This Special Issue will highlight our mechanistic and structural understanding of enzymes, and how that information is being leveraged towards the development of new catalysts. We are also interested in highlighting how enzyme technology is impacting a wide variety of fields from medicine to chemical industry.

Dr. David D. Boehr
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). 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

  • Mechanistic enzymology
  • Structural biology
  • Protein biophysics
  • Protein engineering
  • Synthetic biology
  • Enzyme technology
  • Enzyme applications

Published Papers (15 papers)

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Research

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Open AccessFeature PaperArticle Controlling Active Site Loop Dynamics in the (β/α)8 Barrel Enzyme Indole-3-Glycerol Phosphate Synthase
Catalysts 2016, 6(9), 129; doi:10.3390/catal6090129
Received: 9 June 2016 / Revised: 5 August 2016 / Accepted: 22 August 2016 / Published: 26 August 2016
Cited by 2 | PDF Full-text (2127 KB) | HTML Full-text | XML Full-text
Abstract
The β1α1 loop in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) is important for substrate binding, product release and chemical catalysis. IGPS catalyzes the ring closure of the substrate 1-(o-carboxyphenylamine)-1-dexoyribulose 5-phosphate to form indole-3-glycerol phosphate, involving distinct decarboxylation and dehydration
[...] Read more.
The β1α1 loop in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) is important for substrate binding, product release and chemical catalysis. IGPS catalyzes the ring closure of the substrate 1-(o-carboxyphenylamine)-1-dexoyribulose 5-phosphate to form indole-3-glycerol phosphate, involving distinct decarboxylation and dehydration steps. The ring closure step is rate-determining in the thermophilic Sulfolobus sulfataricus enzyme (ssIGPS) at high temperatures. The β1α1 loop is especially important in the dehydration step as it houses the general acid Lys53. We propose that loop dynamics are governed by competing interactions on the N- and C-terminal sides of the loop. We had previously shown that disrupting interactions with the N-terminal side of the loop through the N90A substitution decreases catalytic efficiency, slows down the dehydration step and quenches loop dynamics on the picosecond to millisecond timescales. Here, we show that disrupting interactions on the C-terminal side of the loop through the R64A/D65A substitutions likewise decreases catalytic efficiency, slows down the dehydration step and quenches loop dynamics. Interestingly, the triple substitution R64A/D65A/N90A leads to new μs–ms timescale loop dynamics and makes the ring-closure step rate-determining once again. These results are consistent with a model in which the β1α1 loop is maintained in a structurally dynamic state by these competing interactions, which is important for the dehydration step of catalysis. Competing interactions in other enzymes may likewise keep their loops and other structural elements appropriately mobile. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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Open AccessCommunication Mechanism-Guided Discovery of an Esterase Scaffold with Promiscuous Amidase Activity
Catalysts 2016, 6(6), 90; doi:10.3390/catal6060090
Received: 29 March 2016 / Revised: 23 May 2016 / Accepted: 9 June 2016 / Published: 18 June 2016
Cited by 1 | PDF Full-text (1529 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The discovery and generation of biocatalysts with extended catalytic versatilities are of immense relevance in both chemistry and biotechnology. An enhanced atomistic understanding of enzyme promiscuity, a mechanism through which living systems acquire novel catalytic functions and specificities by evolution, would thus be
[...] Read more.
The discovery and generation of biocatalysts with extended catalytic versatilities are of immense relevance in both chemistry and biotechnology. An enhanced atomistic understanding of enzyme promiscuity, a mechanism through which living systems acquire novel catalytic functions and specificities by evolution, would thus be of central interest. Using esterase-catalyzed amide bond hydrolysis as a model system, we pursued a simplistic in silico discovery program aiming for the identification of enzymes with an internal backbone hydrogen bond acceptor that could act as a reaction specificity shifter in hydrolytic enzymes. Focusing on stabilization of the rate limiting transition state of nitrogen inversion, our mechanism-guided approach predicted that the acyl hydrolase patatin of the α/β phospholipase fold would display reaction promiscuity. Experimental analysis confirmed previously unknown high amidase over esterase activity displayed by the first described esterase machinery with a protein backbone hydrogen bond acceptor to the reacting NH-group of amides. The present work highlights the importance of a fundamental understanding of enzymatic reactions and its potential for predicting enzyme scaffolds displaying alternative chemistries amenable to further evolution by enzyme engineering. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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Open AccessArticle Solvent-Free Lipase-Catalyzed Synthesis of Technical-Grade Sugar Esters and Evaluation of Their Physicochemical and Bioactive Properties
Catalysts 2016, 6(6), 78; doi:10.3390/catal6060078
Received: 24 March 2016 / Revised: 6 May 2016 / Accepted: 17 May 2016 / Published: 30 May 2016
Cited by 5 | PDF Full-text (1585 KB) | HTML Full-text | XML Full-text
Abstract
Technical-grade oleic acid esters of sucrose and fructose were prepared using solvent-free biocatalysis at 65 °C, without any downstream purification applied, and their physicochemical and bioactivity-related properties were evaluated and compared to a commercially available sucrose laurate emulsifier. To increase the conversion of
[...] Read more.
Technical-grade oleic acid esters of sucrose and fructose were prepared using solvent-free biocatalysis at 65 °C, without any downstream purification applied, and their physicochemical and bioactivity-related properties were evaluated and compared to a commercially available sucrose laurate emulsifier. To increase the conversion of sucrose and fructose oleate, prepared previously using solvent-free lipase-catalyzed esterification catalyzed by Rhizomucor miehei lipase (81% and 83% ester, respectively), the enzymatic reaction conditions was continued using CaSO4 to control the reactor’s air headspace and a lipase (from Candida antarctica B) with a hydrophobic immobilization matrix to provide an ultralow water activity, and high-pressure homogenation, to form metastable suspensions of 2.0–3.3 micron sized saccharide particles in liquid-phase reaction media. These measures led to increased ester content of 89% and 96% for reactions involving sucrose and fructose, respectively. The monoester content among the esters decreased from 90% to <70% due to differences in regioselectivity between the lipases. The resultant technical-grade sucrose and fructose lowered the surface tension to <30 mN/m, and possessed excellent emulsification capability and stability over 36 h using hexadecane and dodecane as oils, comparable to that of sucrose laurate and Tween® 80). The technical-grade sugar esters, particularly fructose oleate, more effectively inhibited gram-positive foodborne pathogens (Lactobacillus plantarum, Pediococcus pentosaceus and Bacillus subtilis). Furthermore, all three sugar esters displayed antitumor activity, particularly the two sucrose esters. This study demonstrates the importance of controlling the biocatalysts’ water activity to achieve high conversion, the impact of a lipase’s regioselectivity in dictating product distribution, and the use of solvent-free biocatalysis to important biobased surfactants useful in foods, cosmetics, personal care products, and medicine. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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Open AccessArticle Preparation of Cross-Linked Glucoamylase Aggregates Immobilization by Using Dextrin and Xanthan Gum as Protecting Agents
Catalysts 2016, 6(6), 77; doi:10.3390/catal6060077
Received: 24 March 2016 / Revised: 17 May 2016 / Accepted: 20 May 2016 / Published: 25 May 2016
Cited by 2 | PDF Full-text (1750 KB) | HTML Full-text | XML Full-text
Abstract
In this paper glucoamylase from Aspergillus niger was immobilized by using a modified version of cross-linked enzyme aggregates (CLEA). The co-aggregates were cross-linked with glutaraldehyde; meanwhile dextrin and xanthan gum as protecting agents were added, which provides high affinity with the enzyme molecules.
[...] Read more.
In this paper glucoamylase from Aspergillus niger was immobilized by using a modified version of cross-linked enzyme aggregates (CLEA). The co-aggregates were cross-linked with glutaraldehyde; meanwhile dextrin and xanthan gum as protecting agents were added, which provides high affinity with the enzyme molecules. The immobilized glucoamylase was stable over a broad range of pH (3.0–8.0) and temperature (55–75 °C); dependence shows more catalytic activity than a free enzyme. The thermostability, kinetic behavior, and first-order inactivation rate constant (ki) were investigated. The two types of protector made the immobilized glucoamylase more robust than the free form. Both of the immobilized enzymes have excellent recyclability, retaining over 45% of the relative activity after 24 runs. In addition, immobilized enzymes reduced only 40% of the initial activity after three months by the storability measure, indicating high activity. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
Open AccessArticle Cloning, Expression and Characterization of a Novel Fructosyltransferase from Aspergillus oryzae ZZ-01 for the Synthesis of Sucrose 6-Acetate
Catalysts 2016, 6(5), 67; doi:10.3390/catal6050067
Received: 26 March 2016 / Revised: 18 April 2016 / Accepted: 4 May 2016 / Published: 9 May 2016
Cited by 1 | PDF Full-text (2497 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A 1521 bp gene encoding for a novel fructosyltransferase from Aspergillus oryzae ZZ-01 (AoFT) has been amplified by RACE and TAIL PCR, and functionally overexpressed in Escherichia coli BL 21-CodonPlus (DE3)-RIL. The recombinant A. oryzae ZZ-01 fructosyltransferases (r-AoFT) was
[...] Read more.
A 1521 bp gene encoding for a novel fructosyltransferase from Aspergillus oryzae ZZ-01 (AoFT) has been amplified by RACE and TAIL PCR, and functionally overexpressed in Escherichia coli BL 21-CodonPlus (DE3)-RIL. The recombinant A. oryzae ZZ-01 fructosyltransferases (r-AoFT) was purified to homogeneity after Ni-NTA affinity and Superdex-200 gel filtration chromatography. SDS-PAGE analysis of the purified r-AoFT revealed a single protein band with an apparent molecular mass of 60.0 kDa. The r-AoFT enzyme exhibited its optimal activity at 55 °C and pH 5.5, and maintained about 63% of its activity even after 60 min of treatment at 60 °C. The addition of Mg2+ led to an increase in the activity of r-AoFT, whereas Zn2+, Cu2+ and Ni2+ led to a reduction in its activity. Six site-directed mutants of r-AoFT (D39A, D164A, E216A, N38L, S99A and Y282A) were constructed and characterized biochemically. The N38L, S99A and Y282A mutants had lower Km and higher Vmax values than the wild-type enzyme, highlighting their higher binding affinity for the substrates. These results therefore suggest that r-AoFT could be used for the enzymatic synthesis of Suc6A from sucrose and glucose 6-acetate. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
Open AccessArticle Immobilization of Genetically-Modified d-Amino Acid Oxidase and Catalase on Carbon Nanotubes to Improve the Catalytic Efficiency
Catalysts 2016, 6(5), 66; doi:10.3390/catal6050066
Received: 24 March 2016 / Revised: 24 April 2016 / Accepted: 28 April 2016 / Published: 9 May 2016
Cited by 1 | PDF Full-text (4963 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
d-amino acid oxidase (DAAO) and catalase (CAT) have been genetically modified by fusing them to an elastin-like polypeptide (ELP). ELP-DAAO and ELP-CAT have been separately immobilized on multi-walled carbon nanotubes (MWNTs). It has been found that the secondary structures of the enzymes
[...] Read more.
d-amino acid oxidase (DAAO) and catalase (CAT) have been genetically modified by fusing them to an elastin-like polypeptide (ELP). ELP-DAAO and ELP-CAT have been separately immobilized on multi-walled carbon nanotubes (MWNTs). It has been found that the secondary structures of the enzymes have been preserved. ELP-DAAO catalyzed the oxidative deamination of d-alanine, and H2O2 was evolved continuously. When the MWNT-supported enzymes were used together, the generated hydrogen peroxide of ELP-DAAO could be decomposed in situ. The catalytic efficiency of the two immobilized enzymes was more than five times greater than that of free ELP-DAAO when the ratio of immobilized ELP-CAT to immobilized ELP-DAAO was larger than 1:1. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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Open AccessArticle The Use of Biobased Surfactant Obtained by Enzymatic Syntheses for Wax Deposition Inhibition and Drag Reduction in Crude Oil Pipelines
Catalysts 2016, 6(5), 61; doi:10.3390/catal6050061
Received: 30 January 2016 / Revised: 6 April 2016 / Accepted: 20 April 2016 / Published: 26 April 2016
Cited by 3 | PDF Full-text (3419 KB) | HTML Full-text | XML Full-text
Abstract
Crude oil plays an important role in providing the energy supply of the world, and pipelines have long been recognized as the safest and most efficient means of transporting oil and its products. However, the transportation process also faces the challenges of asphaltene-paraffin
[...] Read more.
Crude oil plays an important role in providing the energy supply of the world, and pipelines have long been recognized as the safest and most efficient means of transporting oil and its products. However, the transportation process also faces the challenges of asphaltene-paraffin structural interactions, pipeline pressure losses and energy consumption. In order to determine the role of drag-reducing surfactant additives in the transportation of crude oils, experiments of wax deposition inhibition and drag reduction of different oil in pipelines with a biobased surfactant obtained by enzymatic syntheses were carried out. The results indicated that heavy oil transportation in the pipeline is remarkably enhanced by creating stable oil-in-water (O/W) emulsion with the surfactant additive. The wax appearance temperature (WAT) and pour point were modified, and the formation of a space-filling network of interlocking wax crystals was prevented at low temperature by adding a small concentration of the surfactant additive. A maximum viscosity reduction of 70% and a drag reduction of 40% for light crude oil flows in pipelines were obtained with the surfactant additive at a concentration of 100 mg/L. Furthermore, a successful field application of the drag-reducing surfactant in a light crude oil pipeline in Daqing Oilfield was demonstrated. Hence, the use of biobased surfactant obtained by enzymatic syntheses in oil transportation is a potential method to address the current challenges, which could result in a significant energy savings and a considerable reduction of the operating cost. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
Open AccessArticle Structural and Biochemical Characterization of a Cyanobacterial PP2C Phosphatase Reveals Insights into Catalytic Mechanism and Substrate Recognition
Catalysts 2016, 6(5), 60; doi:10.3390/catal6050060
Received: 26 February 2016 / Revised: 19 April 2016 / Accepted: 20 April 2016 / Published: 26 April 2016
PDF Full-text (1324 KB) | HTML Full-text | XML Full-text
Abstract
PP2C-type phosphatases play roles in signal transduction pathways related to abiotic stress. The cyanobacterial PP2C-type phosphatase tPphA specifically dephosphorylates the PII protein, which is a key regulator in cyanobacteria adapting to nitrogen-deficient environments. Previous studies have shown that residue His39 of tPphA is
[...] Read more.
PP2C-type phosphatases play roles in signal transduction pathways related to abiotic stress. The cyanobacterial PP2C-type phosphatase tPphA specifically dephosphorylates the PII protein, which is a key regulator in cyanobacteria adapting to nitrogen-deficient environments. Previous studies have shown that residue His39 of tPphA is critical for the enzyme’s recognition of the PII protein; however, the manner in which this residue determines tPphA substrate specificity is unknown. Here, we solved the crystal structure of H39A, a tPphA variant. The structure revealed that the mutation of residue His39 to alanine changes the conformation and the flexibility of the loop in which residue His39 is located, and these changes affect the substrate specificity of tPphA. Moreover, previous studies have assumed that the FLAP subdomain and the third metal (M3) of tPphA could mutually influence each other to regulate PP2C catalytic activity and substrate specificity. However, despite the variable conformations adopted by the FLAP subdomain, the position of M3 was consistent in the tPphA structure. These results indicate that the FLAP subdomain does not influence M3 and vice versa. In addition, a small screen of tPphA inhibitors was performed. Sanguinarine and Ni2+ were found to be the most effective inhibitors among the assayed chemicals. Finally, the dimeric form of tPphA was stabilized by cross-linkers and still exhibited catalytic activity towards p-nitrophenyl phosphate. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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Open AccessArticle Heterogeneous Asymmetric Oxidation Catalysis Using Hemophore HasApf. Application in the Chemoenzymatic Deracemization of sec-Alcohols with Sodium Borohydride
Catalysts 2016, 6(3), 38; doi:10.3390/catal6030038
Received: 24 December 2015 / Revised: 26 January 2016 / Accepted: 23 February 2016 / Published: 8 March 2016
Cited by 1 | PDF Full-text (4053 KB) | HTML Full-text | XML Full-text
Abstract
This study aims to demonstrate the coordination of oxygen regarding the hemophore HasApf expressed by Escherichia coli cells, which appears to create an unlikely oxygen-activating system in HasA due to the already-coordinated iron. In the asymmetric oxidation of rac-1-(6-methoxynaphthalen-2-yl)ethanol (rac-1)
[...] Read more.
This study aims to demonstrate the coordination of oxygen regarding the hemophore HasApf expressed by Escherichia coli cells, which appears to create an unlikely oxygen-activating system in HasA due to the already-coordinated iron. In the asymmetric oxidation of rac-1-(6-methoxynaphthalen-2-yl)ethanol (rac-1) using dissolved oxygen, the signals at g-values of 2.8, 2.22, and 1.72 in the electron spin resonance (ESR) spectra disappeared in conjunction with the promotion of oxoferric (FeIII−O–O) species in the distal site. These results suggest that the iron of porphyrin/Fe may be oxidized in water, leading to exhibition of greater asymmetric oxidation activity in the promotion of oxoferryl (FeIV=O) species. A ketone (~50% chemical yield) produced from (R)-(−)-sec-alcohol can be desymmetrized by NaBH4 in aqueous medium at 40 °C (>99% enantiomer excess, ee, >90% chemical yield) in the absence of NAD(P). Therefore, HasA can be regenerated via successive asymmetric catalytic events through an incorporated iron electron-transfer system in the presence of oxygen: FeII + O2 → FeIII−O–O → FeIV=O (oxidizing rac-1) → FeII + H2O. This process is similar to a Fenton reaction. The use of a HasA-catalytic system with an incorporated redox cofactor for asymmetric oxidation overcomes the apparent difficulties in working with pure dehydrogenase enzyme/redox cofactor systems for biotransformations. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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Open AccessArticle Characterization of a Metagenome-Derived β-Glucosidase and Its Application in Conversion of Polydatin to Resveratrol
Catalysts 2016, 6(3), 35; doi:10.3390/catal6030035
Received: 8 December 2015 / Revised: 25 January 2016 / Accepted: 19 February 2016 / Published: 1 March 2016
Cited by 2 | PDF Full-text (1983 KB) | HTML Full-text | XML Full-text
Abstract
For the beneficial pharmacological properties of resveratrol, there is increasingly interest in enzymatic conversion of polydatin to resveratrol. The metagenomic technique provides an effective strategy for mining novel polydatin-hydrolysis enzymes from uncultured microorganisms. In this study, a metagenomic library of mangrove soil was
[...] Read more.
For the beneficial pharmacological properties of resveratrol, there is increasingly interest in enzymatic conversion of polydatin to resveratrol. The metagenomic technique provides an effective strategy for mining novel polydatin-hydrolysis enzymes from uncultured microorganisms. In this study, a metagenomic library of mangrove soil was constructed and a novel β-glucosidase gene MlBgl was isolated. The deduced amino acid sequences of MlBgl showed the highest identity of 64% with predicted β-glucosidase in the GenBank database. The gene was cloned and overexpressed in Escherichia coli BL21(DE3). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) assay demonstrated the purified recombinant β-glucosidase r-MlBgl with a molecular weight approximately of 71 kDa. The optimal pH and temperature of purified recombinant r-MlBgl were 7.0 and 40 °C, respectively. r-MlBgl could hydrolyze polydatin effectively. The kcat and kcat/Km values for polydatin were 989 s−1 and 1476 mM−1·s−1, respectively. These properties suggest that -r-MlBgl has potential application in the enzymatic conversion of polydatin to resveratrol for further study. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
Open AccessArticle Production of Resveratrol by Piceid Deglycosylation Using Cellulase
Catalysts 2016, 6(3), 32; doi:10.3390/catal6030032
Received: 15 December 2015 / Revised: 4 February 2016 / Accepted: 16 February 2016 / Published: 24 February 2016
PDF Full-text (1554 KB) | HTML Full-text | XML Full-text
Abstract
Resveratrol is a dietary polyphenolic compound widely used in medicine, food, and cosmetic products. The glycoside form of resveratrol, piceid, is also present in several plant materials but is less bioavailable. In this study, enzymatic transformation of piceid into resveratrol using inexpensive cellulase
[...] Read more.
Resveratrol is a dietary polyphenolic compound widely used in medicine, food, and cosmetic products. The glycoside form of resveratrol, piceid, is also present in several plant materials but is less bioavailable. In this study, enzymatic transformation of piceid into resveratrol using inexpensive cellulase was investigated. Response surface methodology was used to evaluate the effect of reaction parameters, including reaction temperature, reaction time, enzyme amount and pH. The optimal conditions for biotransformation of piceid to resveratrol are: a reaction temperature of 50 °C, reaction time of 4.75 h, enzyme amount of 2.5 fungal β-glucanase (FBG) units and pH of 4.3. In addition, the extracts from Polygonum cuspidatum root contained high amounts of piceid were treated with cellulase in order to deglycosylation that increased resveratrol yield. After treatment, the resveratrol yield significantly increased from 2.72 to 9.49 mg/g, while the piceid contents decreased from 8.60 to 0 mg/g. The result provides an efficient method to convert piceid in the extracts of P. cuspidatum root into resveratrol by cellulase. Full article
(This article belongs to the Special Issue Enzyme Catalysis)

Review

Jump to: Research

Open AccessReview Nature Inspired Solutions for Polymers: Will Cutinase Enzymes Make Polyesters and Polyamides Greener?
Catalysts 2016, 6(12), 205; doi:10.3390/catal6120205
Received: 31 October 2016 / Revised: 26 November 2016 / Accepted: 7 December 2016 / Published: 13 December 2016
Cited by 5 | PDF Full-text (2357 KB) | HTML Full-text | XML Full-text
Abstract
The polymer and plastic sectors are under the urge of mitigating their environmental impact. The need for novel and more benign catalysts for polyester synthesis or targeted functionalization led, in recent years, to an increasing interest towards cutinases due to their natural ability
[...] Read more.
The polymer and plastic sectors are under the urge of mitigating their environmental impact. The need for novel and more benign catalysts for polyester synthesis or targeted functionalization led, in recent years, to an increasing interest towards cutinases due to their natural ability to hydrolyze ester bonds in cutin, a natural polymer. In this review, the most recent advances in the synthesis and hydrolysis of various classes of polyesters and polyamides are discussed with a critical focus on the actual perspectives of applying enzymatic technologies for practical industrial purposes. More specifically, cutinase enzymes are compared to lipases and, in particular, to lipase B from Candida antarctica, the biocatalyst most widely employed in polymer chemistry so far. Computational and bioinformatics studies suggest that the natural role of cutinases in attacking natural polymers confer some essential features for processing also synthetic polyesters and polyamides. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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Open AccessFeature PaperReview Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools
Catalysts 2016, 6(6), 82; doi:10.3390/catal6060082
Received: 12 April 2016 / Revised: 13 May 2016 / Accepted: 23 May 2016 / Published: 31 May 2016
Cited by 1 | PDF Full-text (8095 KB) | HTML Full-text | XML Full-text
Abstract
This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations
[...] Read more.
This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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Open AccessFeature PaperReview Role of Conformational Motions in Enzyme Function: Selected Methodologies and Case Studies
Catalysts 2016, 6(6), 81; doi:10.3390/catal6060081
Received: 5 April 2016 / Revised: 11 May 2016 / Accepted: 20 May 2016 / Published: 27 May 2016
Cited by 3 | PDF Full-text (5290 KB) | HTML Full-text | XML Full-text
Abstract
It is now common knowledge that enzymes are mobile entities relying on complex atomic-scale dynamics and coordinated conformational events for proper ligand recognition and catalysis. However, the exact role of protein dynamics in enzyme function remains either poorly understood or difficult to interpret.
[...] Read more.
It is now common knowledge that enzymes are mobile entities relying on complex atomic-scale dynamics and coordinated conformational events for proper ligand recognition and catalysis. However, the exact role of protein dynamics in enzyme function remains either poorly understood or difficult to interpret. This mini-review intends to reconcile biophysical observations and biological significance by first describing a number of common experimental and computational methodologies employed to characterize atomic-scale residue motions on various timescales in enzymes, and second by illustrating how the knowledge of these motions can be used to describe the functional behavior of enzymes and even act upon it. Two biologically relevant examples will be highlighted, namely the HIV-1 protease and DNA polymerase β enzyme systems. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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Open AccessReview Enzyme Stability and Activity in Non-Aqueous Reaction Systems: A Mini Review
Catalysts 2016, 6(2), 32; doi:10.3390/catal6020032
Received: 14 December 2015 / Revised: 19 January 2016 / Accepted: 21 January 2016 / Published: 22 February 2016
Cited by 14 | PDF Full-text (249 KB) | HTML Full-text | XML Full-text
Abstract
Enormous interest in biocatalysis in non-aqueous phase has recently been triggered due to the merits of good enantioselectivity, reverse thermodynamic equilibrium, and no water-dependent side reactions. It has been demonstrated that enzyme has high activity and stability in non-aqueous media, and the variation
[...] Read more.
Enormous interest in biocatalysis in non-aqueous phase has recently been triggered due to the merits of good enantioselectivity, reverse thermodynamic equilibrium, and no water-dependent side reactions. It has been demonstrated that enzyme has high activity and stability in non-aqueous media, and the variation of enzyme activity is attributed to its conformational modifications. This review comprehensively addresses the stability and activity of the intact enzymes in various non-aqueous systems, such as organic solvents, ionic liquids, sub-/super-critical fluids and their combined mixtures. It has been revealed that critical factors such as Log P, functional groups and the molecular structures of the solvents define the microenvironment surrounding the enzyme molecule and affect enzyme tertiary and secondary structure, influencing enzyme catalytic properties. Therefore, it is of high importance for biocatalysis in non-aqueous media to elucidate the links between the microenvironment surrounding enzyme surface and its stability and activity. In fact, a better understanding of the correlation between different non-aqueous environments and enzyme structure, stability and activity can contribute to identifying the most suitable reaction medium for a given biotransformation. Full article
(This article belongs to the Special Issue Enzyme Catalysis)
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