Natural methods of protein stabilization: thermostable biocatalysts

2007 ◽  
Vol 35 (6) ◽  
pp. 1558-1563 ◽  
Author(s):  
J.A. Littlechild ◽  
J. Guy ◽  
S. Connelly ◽  
L. Mallett ◽  
S. Waddell ◽  
...  
Keyword(s):  
Alcohol Dehydrogenase ◽  
Three Dimensional ◽  
Biochemical Properties ◽  
Protein Stabilization ◽  
Detailed Knowledge ◽  
Reaction Conditions ◽  
Fine Chemical ◽  
Pharmaceutical Industries ◽  
Hyperthermophilic Organisms

Enzymes that are naturally found in thermophilic and hyperthermophilic organisms are being used as robust biocatalysts in the fine chemical and pharmaceutical industries. They have important use in these industries due to their increased stability which is often required during commercial reaction conditions. The approach used in these studies is to learn how nature has managed to stabilize these proteins using a detailed knowledge of their biochemical properties and three-dimensional structures. This is illustrated with several different classes of enzyme that have been studied at Exeter. These include alcohol dehydrogenase, aminoacylase, pyroglutamyl carboxypeptidase, γ-lactamase, dehalogenase and lysophospholipase.

scholarly journals Cures from the ends of the earth: Novel thermostable enzymes and the pharmaceutical industry

2005 ◽  
Vol 27 (1) ◽  
pp. 27-29 ◽  
Author(s):  
Jenny Littlechild
Keyword(s):  
Pharmaceutical Industry ◽  
Biochemical Properties ◽  
Thermostable Enzymes ◽  
Fine Chemical ◽  
Commercial Use ◽  
The Earth ◽  
Pharmaceutical Industries ◽  
Hyperthermophilic Organisms

Enzymes that are found naturally in thermophilic and hyperthermophilic organisms are being used as robust biocatalysts in the fine-chemical and pharmaceutical industries. Knowledge of their biochemical properties and three-dimeasional structures has proved invaluable in understanding their mechanism and in optimizing their commercial use.

scholarly journals Cyclodextrin-preferring glycoside hydrolases: properties and applications

Amylase ◽  
2021 ◽  
Vol 5 (1) ◽  
pp. 23-37
Author(s):  
Iqra Aroob ◽  
Nasir Ahmad ◽  
Naeem Rashid
Keyword(s):  
Substrate Specificity ◽  
Three Dimensional ◽  
Distinct Group ◽  
Structural Features ◽  
Biochemical Properties ◽  
Glycoside Hydrolases ◽  
Cazy Database ◽  
Potential Applications ◽  
Pharmaceutical Industries ◽  
Hydrolyzing Enzymes

Abstract Cyclodextrin-hydrolyzing enzymes are widespread in bacteria and archaea where they play their roles in carbohydrates metabolism. They were previously characterized as cyclodextrinases, neopullulanases and maltogenic amylases. In the Carbohydrate-Active enZyme (CAZy) database, most of these enzymes are grouped into the GH13_20 subfamily of the α-amylase family GH13. Here, we have summarized the information available on the substrate specificity, structural features, physiological roles and applications of cyclodextrin-preferring glycoside hydrolases. These enzymes form a distinct group in the α-amylase family. Members of this distinct group possess an extra extension at the N-terminus, which causes a modification of the active site geometry thus making these enzymes more specific for smaller molecules like cyclodextrins than for macromolecules such as starches or pullulan. Multi-substrate specificity, hydrolytic as well as transglycosylation activities make these enzymes attractive for applications in the food and pharmaceutical industries. We have tried here to collect information available on their biochemical properties, three-dimensional structures, physiological roles and potential applications.

scholarly journals A Novel Pseudomonas geniculata AGE Family Epimerase/Isomerase and Its Application in d-Mannose Synthesis

Foods ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1809
Author(s):  
Zhanzhi Liu ◽  
Ying Li ◽  
Jing Wu ◽  
Sheng Chen
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Optimal Temperature ◽  
Reaction Conditions ◽  
Enzymatic Production ◽  
Physiological Properties ◽  
Potential Applications ◽  
Kinetics Of ◽  
Optimal Reaction ◽  
Gene Age

d-mannose has exhibited excellent physiological properties in the food, pharmaceutical, and feed industries. Therefore, emerging attention has been applied to enzymatic production of d-mannose due to its advantage over chemical synthesis. The gene age of N-acetyl-d-glucosamine 2-epimerase family epimerase/isomerase (AGEase) derived from Pseudomonas geniculata was amplified, and the recombinant P. geniculata AGEase was characterized. The optimal temperature and pH of P. geniculata AGEase were 60 °C and 7.5, respectively. The Km, kcat, and kcat/Km of P. geniculata AGEase for d-mannose were 49.2 ± 8.5 mM, 476.3 ± 4.0 s−1, and 9.7 ± 0.5 s−1·mM−1, respectively. The recombinant P. geniculata AGEase was classified into the YihS enzyme subfamily in the AGE enzyme family by analyzing its substrate specificity and active center of the three-dimensional (3D) structure. Further studies on the kinetics of different substrates showed that the P. geniculata AGEase belongs to the d-mannose isomerase of the YihS enzyme. The P. geniculata AGEase catalyzed the synthesis of d-mannose with d-fructose as a substrate, and the conversion rate was as high as 39.3% with the d-mannose yield of 78.6 g·L−1 under optimal reaction conditions of 200 g·L−1d-fructose and 2.5 U·mL−1P. geniculata AGEase. This novel P. geniculata AGEase has potential applications in the industrial production of d-mannose.

scholarly journals Towards a Novel Computer-Aided Optimization of Microreactors: Techno-Economic Evaluation of an Immobilized Enzyme System

Symmetry ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 524
Author(s):  
Philip Pietrek ◽  
Manfred Kraut ◽  
Roland Dittmeyer
Keyword(s):  
Magnetic Beads ◽  
Glucose Dehydrogenase ◽  
Packed Bed ◽  
Detailed Knowledge ◽  
Reaction Conditions ◽  
Flow Reactors ◽  
Continuous Flow Reactors ◽  
Enzyme Cascades ◽  
And Control ◽  
Physical And Chemical

Immobilized multi-enzyme cascades are increasingly used in microfluidic devices. In particular, their application in continuous flow reactors shows great potential, utilizing the benefits of reusability and control of the reaction conditions. However, capitalizing on this potential is challenging and requires detailed knowledge of the investigated system. Here, we show the application of computational methods for optimization with multi-level reactor design (MLRD) methodology based on the underlying physical and chemical processes. We optimize a stereoselective reduction of a diketone catalyzed by ketoreductase (Gre2) and Nicotinamidadenindinukleotidphosphat (NADPH) cofactor regeneration with glucose dehydrogenase (GDH). Both enzymes are separately immobilized on magnetic beads forming a packed bed within the microreactor. We derive optimal reactor feed concentrations and enzyme ratios for enhanced performance and a basic economic model in order to maximize the techno-economic performance (TEP) for the first reduction of 5-nitrononane-2,8-dione.

scholarly journals Pyrrolidine in Drug Discovery: A Versatile Scaffold for Novel Biologically Active Compounds

2021 ◽  
Vol 379 (5) ◽  
Author(s):  
Giovanna Li Petri ◽  
Maria Valeria Raimondi ◽  
Virginia Spanò ◽  
Ralph Holl ◽  
Paola Barraja ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Binding Mode ◽  
Biologically Active ◽  
Bioactive Molecules ◽  
Biological Profile ◽  
Pyrrolidine Ring ◽  
Reaction Conditions ◽  
Drug Candidates ◽  
Steric Factors ◽  
Proline Derivatives

AbstractThe five-membered pyrrolidine ring is one of the nitrogen heterocycles used widely by medicinal chemists to obtain compounds for the treatment of human diseases. The great interest in this saturated scaffold is enhanced by (1) the possibility to efficiently explore the pharmacophore space due to sp3-hybridization, (2) the contribution to the stereochemistry of the molecule, (3) and the increased three-dimensional (3D) coverage due to the non-planarity of the ring—a phenomenon called “pseudorotation”. In this review, we report bioactive molecules with target selectivity characterized by the pyrrolidine ring and its derivatives, including pyrrolizines, pyrrolidine-2-one, pyrrolidine-2,5-diones and prolinol described in the literature from 2015 to date. After a comparison of the physicochemical parameters of pyrrolidine with the parent aromatic pyrrole and cyclopentane, we investigate the influence of steric factors on biological activity, also describing the structure–activity relationship (SAR) of the studied compounds. To aid the reader’s approach to reading the manuscript, we have planned the review on the basis of the synthetic strategies used: (1) ring construction from different cyclic or acyclic precursors, reporting the synthesis and the reaction conditions, or (2) functionalization of preformed pyrrolidine rings, e.g., proline derivatives. Since one of the most significant features of the pyrrolidine ring is the stereogenicity of carbons, we highlight how the different stereoisomers and the spatial orientation of substituents can lead to a different biological profile of drug candidates, due to the different binding mode to enantioselective proteins. We believe that this work can guide medicinal chemists to the best approach in the design of new pyrrolidine compounds with different biological profiles.

The Three-Dimensional Surface Topographic Characterisation of Diamond Grinding Wheels

2010 ◽  
Vol 126-128 ◽  
pp. 690-695
Author(s):  
David Lee Butler
Keyword(s):  
Measurement Techniques ◽  
Three Dimensional ◽  
Surface Measurement ◽  
Grinding Wheel ◽  
Profile Measurement ◽  
Detailed Knowledge ◽  
Grinding Wheels ◽  
Diamond Grinding ◽  
Insight Into ◽  
Dimensional Surface

Surface measurement using three-dimensional stylus instruments is a relatively new technique that offers numerous advantages over more traditional profilometry methods. The information generated is, unlike profile measurement, less subjective and more statistical providing additional insight into the surface structure. One application of surface measurement that has encountered problems when using the profilometry method is that of grinding wheel characterisation. The wheel surface texture (topography) and the conditions under which it is generated have a profound effect upon the grinding performance as characterised by the grinding forces, power consumption, temperature, and surface integrity of components. A detailed knowledge of the nature of the topography of the grinding wheel would provide further insight into surface interactions between the wheel and workpiece as well as enabling improved control of the grinding process in general. In this paper four diamond grinding wheels of 91 and 181 micron grit size were subjected to differing dressing conditions to produce varying final wheel topographies. Three-dimensional surface measurement techniques were employed to quantitatively characterise the topographic change and provide an aerial estimation of the number of cutting grains. The results demonstrate that the techniques can distinguish between a worn and dressed wheel. In addition, the parametric values generated from the various surfaces can aid the user in determining when re-dressing is required.

scholarly journals Basin Depth Mapping Beneath Wellington City Based on Residual Gravity Anomalies

2021 ◽  
Author(s):  
◽  
Alistair Stronach
Keyword(s):  
Gravity Anomaly ◽  
Sedimentary Basin ◽  
Gravity Data ◽  
Three Dimensional ◽  
Maximum Amplitude ◽  
Central Business District ◽  
Gravity Anomalies ◽  
Depth Map ◽  
Capital City ◽  
Detailed Knowledge

<p><b>New Zealand’s capital city of Wellington lies in an area of high seismic risk, which is further increased by the sedimentary basin beneath the Central Business District (CBD). Ground motion data and damage patterns from the 2013 Cook Strait and 2016 Kaikōura earthquakes indicate that two- and three-dimensional amplification effects due to the Wellington sedimentary basin may be significant. These effects are not currently accounted for in the New Zealand Building Code. In order for this to be done, three-dimensional simulations of earthquake shaking need to be undertaken, which requires detailed knowledge of basin geometry. This is currently lacking, primarily because of a dearth of deep boreholes in the CBD area, particularly in Thorndon and Pipitea where sediment depths are estimated to be greatest.</b></p> <p>A new basin depth map for the Wellington CBD has been created by conducting a gravity survey using a modern Scintrex CG-6 gravity meter. Across the study area, 519 new high precision gravity measurements were made and a residual anomaly map created, showing a maximum amplitude anomaly of -6.2 mGal with uncertainties better than ±0.1 mGal. Thirteen two-dimensional geological profiles were modelled to fit the anomalies, then combined with existing borehole constraints to construct the basin depth map. </p> <p>Results indicate on average greater depths than in existing models, particularly in Pipitea where depths are interpreted to be as great as 450 m, a difference of 250 m. Within 1 km of shore depths are interpreted to increase further, to 600 m. The recently discovered basin bounding Aotea Fault is resolved in the gravity data, where the basement is offset by up to 13 m, gravity anomaly gradients up to 8 mGal/km are observed, and possible multiple fault strands identified. A secondary strand of the Wellington Fault is also identified in the north of Pipitea, where gravity anomaly gradients up to 18 mGal/km are observed.</p>

scholarly journals Additive Manufacturing of Biopolymers for Tissue Engineering and Regenerative Medicine: An Overview, Potential Applications, Advancements, and Trends

2021 ◽  
Vol 2021 ◽  
pp. 1-20 ◽  
Author(s):  
Dhinakaran Veeman ◽  
M. Swapna Sai ◽  
P. Sureshkumar ◽  
T. Jagadeesha ◽  
L. Natrayan ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Additive Manufacturing ◽  
3D Printing ◽  
Regenerative Medicine ◽  
Tissue Regeneration ◽  
Three Dimensional ◽  
Porous Scaffolds ◽  
Wide Range ◽  
Potential Applications ◽  
Pharmaceutical Industries

As a technique of producing fabric engineering scaffolds, three-dimensional (3D) printing has tremendous possibilities. 3D printing applications are restricted to a wide range of biomaterials in the field of regenerative medicine and tissue engineering. Due to their biocompatibility, bioactiveness, and biodegradability, biopolymers such as collagen, alginate, silk fibroin, chitosan, alginate, cellulose, and starch are used in a variety of fields, including the food, biomedical, regeneration, agriculture, packaging, and pharmaceutical industries. The benefits of producing 3D-printed scaffolds are many, including the capacity to produce complicated geometries, porosity, and multicell coculture and to take growth factors into account. In particular, the additional production of biopolymers offers new options to produce 3D structures and materials with specialised patterns and properties. In the realm of tissue engineering and regenerative medicine (TERM), important progress has been accomplished; now, several state-of-the-art techniques are used to produce porous scaffolds for organ or tissue regeneration to be suited for tissue technology. Natural biopolymeric materials are often better suited for designing and manufacturing healing equipment than temporary implants and tissue regeneration materials owing to its appropriate properties and biocompatibility. The review focuses on the additive manufacturing of biopolymers with significant changes, advancements, trends, and developments in regenerative medicine and tissue engineering with potential applications.

scholarly journals Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers

2021 ◽  
Author(s):  
Klara Markova ◽  
Antonin Kunka ◽  
Klaudia Chmelova ◽  
Martin Havlasek ◽  
Petra Babkova ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Design ◽  
Energy Landscape ◽  
Single Point ◽  
Three Dimensional ◽  
Protein Stabilization ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Folding Energy

<p>The functionality of a protein depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric α/β-hydrolase enzyme (<i>T</i><sub>m</sub> = 73.5°C; Δ<i>T</i><sub>m</sub> > 23°C) affected the protein folding energy landscape. Introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded catalytically active domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations target cryptic hinge regions and newly introduced secondary interfaces, where they make extensive non-covalent interactions between the intertwined misfolded protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from SAXS and crosslinking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain-swapping occurs exclusively <i>in vivo</i>. Our findings uncovered hidden protein-folding consequences of computational protein design, which need to be taken into account when applying a rational stabilization to proteins of biological and pharmaceutical interest.</p>

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