scholarly journals Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application

Crystals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 597 ◽  
Author(s):  
Changsuk Oh ◽  
T. Doohun Kim ◽  
Kyeong Kyu Kim
Keyword(s):  
Acyl Chain ◽  
Data Bank ◽  
Industrial Applications ◽  
Head Group ◽  
Carboxylic Ester ◽  
Site Structure ◽  
Domains Of Life ◽  
Carboxylic Esters ◽  
Hydrolysis Of ◽  
Ester Hydrolases

Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from 52 genera and metagenome have been reported. In this review, we categorize these structures based on catalytic machinery, structure and substrate specificity to provide a comprehensive understanding of the bacterial CEHs. CEHs use Ser, Asp or water as a nucleophile to drive diverse catalytic machinery. The α/β/α sandwich architecture is most frequently found in CEHs, but 3-solenoid, β-barrel, up-down bundle, α/β/β/α 4-layer sandwich, 6 or 7 propeller and α/β barrel architectures are also found in these CEHs. Most are substrate-specific to various esters with types of head group and lengths of the acyl chain, but some CEHs exhibit peptidase or lactamase activities. CEHs are widely used in industrial applications, and are the objects of research in structure- or mutation-based protein engineering. Structural studies of CEHs are still necessary for understanding their biological roles, identifying their structure-based functions and structure-based engineering and their potential industrial applications.

scholarly journals A corynecaterium glutamicum expression system for glycoside hydrolase analysis

2021 ◽  
Author(s):  
Hirak Saxena
Keyword(s):  
Expression System ◽  
Lysosomal Storage Diseases ◽  
Industrial Applications ◽  
Glycoside Hydrolases ◽  
Cellulosic Biomass ◽  
Lysosomal Storage ◽  
Cellular Functions ◽  
Domains Of Life ◽  
Hydrolysis Of ◽  
Structure And Activity

The biological hydrolysis of glycosidic linkages in complex sugars is facilitated by glycoside hydrolases. These enzymes are ubiquitous across all domains of life, playing significant roles in important biological processes like the degradation of cellulosic biomass, viral pathogenesis, antibacterial defense, and normal cellular functions. The potential industrial applications of highly efficient glycoside hydrolases, as well as the fact that a number of lysosomal storage diseases have been attributed to deficiencies in these enzymes 43, 22, merits further study into their structure and activity. For this reason, a handful of novel glycoside hydrolases from Cellulomonas fimi, a Gram-positive Actinobacteria known for its ability to degrade cellulose 39, will be cloned, expressed and biochemically analyzed.

scholarly journals A corynecaterium glutamicum expression system for glycoside hydrolase analysis

2021 ◽  
Author(s):  
Hirak Saxena
Keyword(s):  
Expression System ◽  
Lysosomal Storage Diseases ◽  
Industrial Applications ◽  
Glycoside Hydrolases ◽  
Cellulosic Biomass ◽  
Lysosomal Storage ◽  
Cellular Functions ◽  
Domains Of Life ◽  
Hydrolysis Of ◽  
Structure And Activity

The biological hydrolysis of glycosidic linkages in complex sugars is facilitated by glycoside hydrolases. These enzymes are ubiquitous across all domains of life, playing significant roles in important biological processes like the degradation of cellulosic biomass, viral pathogenesis, antibacterial defense, and normal cellular functions. The potential industrial applications of highly efficient glycoside hydrolases, as well as the fact that a number of lysosomal storage diseases have been attributed to deficiencies in these enzymes 43, 22, merits further study into their structure and activity. For this reason, a handful of novel glycoside hydrolases from Cellulomonas fimi, a Gram-positive Actinobacteria known for its ability to degrade cellulose 39, will be cloned, expressed and biochemically analyzed.

Mechanisms of Drug Solubilization by Polar Lipids in Biorelevant Media

2020 ◽  
Author(s):  
Vladimir Katev ◽  
Zahari Vinarov ◽  
Slavka S. Tcholakova
Keyword(s):  
Chain Length ◽  
Acyl Chain ◽  
Polar Lipids ◽  
Superior Performance ◽  
Head Group ◽  
Formulation Development ◽  
Biorelevant Media ◽  
Drug Solubilization ◽  
Colloidal Aggregates ◽  
Class 1

Despite the widespread use of lipid excipients in both academic research and oral formulation development, rational selection guidelines are still missing. In the current study, we aimed to establish a link between the molecular structure of commonly used polar lipids and drug solubilization in biorelevant media. We studied the effect of 26 polar lipids of the fatty acid, phospholipid or monoglyceride type on the solubilization of fenofibrate in a two-stage <i>in vitro</i> GI tract model. The main trends were checked also with progesterone and danazol.<br>Based on their fenofibrate solubilization efficiency, the polar lipids can be grouped in 3 main classes. Class 1 substances (n = 5) provide biggest enhancement of drug solubilization (>10-fold) and are composed only by unsaturated compounds. Class 2 materials (n = 10) have an intermediate effect (3-10 fold increase) and are composed primarily (80 %) of saturated compounds. Class 3 materials (n = 11) have very low or no effect on drug solubilization and are entirely composed of saturated compounds.<br>The observed behaviour of the polar lipids was rationalized by using two classical physicochemical parameters: the acyl chain phase transition temperature (<i>T</i><sub>m</sub>) and the critical micellar concentration (CMC). Hence, the superior performance of class 1 polar lipids was explained by the double bonds in their acyl chains, which: (1) significantly decrease <i>T</i><sub>m</sub>, allowing these C18 lipids to form colloidal aggregates and (2) prevent tight packing of the molecules in the aggregates, resulting in bigger volume available for drug solubilization. Long-chain (C18) saturated polar lipids had no significant effect on drug solubilization because their <i>T</i><sub>m</sub> was much higher than the temperature of the experiment (<i>T</i> = 37 C) and, therefore, their association in colloidal aggregates was limited. On the other end of the spectrum, the short chain octanoic acid manifested a high CMC (50 mM), which had to be exceeded in order to enhance drug solubilization. When these two parameters were satisfied (C > CMC, <i>T</i><sub>m</sub> < <i>T</i><sub>exp</sub>), the increase of the polar lipid chain length increased the drug solubilization capacity (similarly to classical surfactants), due to the decreased CMC and bigger volume available for solubilization.<br>The hydrophilic head group also has a dramatic impact on the drug solubilization enhancement, with polar lipids performance decreasing in the order: choline phospholipids > monoglycerides > fatty acids.<br>As both the acyl chain length and the head group type are structural features of the polar lipids, and not of the solubilized drugs, the impact of <i>T</i><sub>m</sub> and CMC on solubilization by polar lipids should hold true for a wide variety of hydrophobic molecules. The obtained mechanistic insights can guide rational drug formulation development and thus support modern drug discovery pipelines.<br>

Mechanisms of Drug Solubilization by Polar Lipids in Biorelevant Media

2020 ◽  
Author(s):  
Vladimir Katev ◽  
Zahari Vinarov ◽  
Slavka S. Tcholakova
Keyword(s):  
Chain Length ◽  
Acyl Chain ◽  
Polar Lipids ◽  
Superior Performance ◽  
Head Group ◽  
Formulation Development ◽  
Biorelevant Media ◽  
Drug Solubilization ◽  
Colloidal Aggregates ◽  
Class 1

Despite the widespread use of lipid excipients in both academic research and oral formulation development, rational selection guidelines are still missing. In the current study, we aimed to establish a link between the molecular structure of commonly used polar lipids and drug solubilization in biorelevant media. We studied the effect of 26 polar lipids of the fatty acid, phospholipid or monoglyceride type on the solubilization of fenofibrate in a two-stage <i>in vitro</i> GI tract model. The main trends were checked also with progesterone and danazol.<br>Based on their fenofibrate solubilization efficiency, the polar lipids can be grouped in 3 main classes. Class 1 substances (n = 5) provide biggest enhancement of drug solubilization (>10-fold) and are composed only by unsaturated compounds. Class 2 materials (n = 10) have an intermediate effect (3-10 fold increase) and are composed primarily (80 %) of saturated compounds. Class 3 materials (n = 11) have very low or no effect on drug solubilization and are entirely composed of saturated compounds.<br>The observed behaviour of the polar lipids was rationalized by using two classical physicochemical parameters: the acyl chain phase transition temperature (<i>T</i><sub>m</sub>) and the critical micellar concentration (CMC). Hence, the superior performance of class 1 polar lipids was explained by the double bonds in their acyl chains, which: (1) significantly decrease <i>T</i><sub>m</sub>, allowing these C18 lipids to form colloidal aggregates and (2) prevent tight packing of the molecules in the aggregates, resulting in bigger volume available for drug solubilization. Long-chain (C18) saturated polar lipids had no significant effect on drug solubilization because their <i>T</i><sub>m</sub> was much higher than the temperature of the experiment (<i>T</i> = 37 C) and, therefore, their association in colloidal aggregates was limited. On the other end of the spectrum, the short chain octanoic acid manifested a high CMC (50 mM), which had to be exceeded in order to enhance drug solubilization. When these two parameters were satisfied (C > CMC, <i>T</i><sub>m</sub> < <i>T</i><sub>exp</sub>), the increase of the polar lipid chain length increased the drug solubilization capacity (similarly to classical surfactants), due to the decreased CMC and bigger volume available for solubilization.<br>The hydrophilic head group also has a dramatic impact on the drug solubilization enhancement, with polar lipids performance decreasing in the order: choline phospholipids > monoglycerides > fatty acids.<br>As both the acyl chain length and the head group type are structural features of the polar lipids, and not of the solubilized drugs, the impact of <i>T</i><sub>m</sub> and CMC on solubilization by polar lipids should hold true for a wide variety of hydrophobic molecules. The obtained mechanistic insights can guide rational drug formulation development and thus support modern drug discovery pipelines.<br>

scholarly journals A computer-based approach for developing linamarase inhibitory agents

2020 ◽  
Vol 5 (7) ◽  
Author(s):  
Lucas Paul ◽  
Celestin N. Mudogo ◽  
Kelvin M. Mtei ◽  
Revocatus L. Machunda ◽  
Fidele Ntie-Kang
Keyword(s):  
Structure Elucidation ◽  
Three Dimensional ◽  
Data Bank ◽  
Competitive Inhibitor ◽  
Industrial Applications ◽  
Dimensional Structure ◽  
Full Understanding ◽  
The Poor ◽  
Computer Based ◽  
Inhibitory Agents

AbstractCassava is a strategic crop, especially for developing countries. However, the presence of cyanogenic compounds in cassava products limits the proper nutrients utilization. Due to the poor availability of structure discovery and elucidation in the Protein Data Bank is limiting the full understanding of the enzyme, how to inhibit it and applications in different fields. There is a need to solve the three-dimensional structure (3-D) of linamarase from cassava. The structural elucidation will allow the development of a competitive inhibitor and various industrial applications of the enzyme. The goal of this review is to summarize and present the available 3-D modeling structure of linamarase enzyme using different computational strategies. This approach could help in determining the structure of linamarase and later guide the structure elucidation in silico and experimentally.

scholarly journals Metabolic engineering strategy for synthetizing trans-4-hydroxy-l-proline in microorganisms

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhenyu Zhang ◽  
Pengfu Liu ◽  
Weike Su ◽  
Huawei Zhang ◽  
Wenqian Xu ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Biosynthetic Pathway ◽  
Industrial Applications ◽  
Microbial Cell Factories ◽  
Important Amino Acid ◽  
Cell Factories ◽  
Complex Process ◽  
Engineering Strategy ◽  
Hydrolysis Of ◽  
New Strategies

AbstractTrans-4-hydroxy-l-proline is an important amino acid that is widely used in medicinal and industrial applications, particularly as a valuable chiral building block for the organic synthesis of pharmaceuticals. Traditionally, trans-4-hydroxy-l-proline is produced by the acidic hydrolysis of collagen, but this process has serious drawbacks, such as low productivity, a complex process and heavy environmental pollution. Presently, trans-4-hydroxy-l-proline is mainly produced via fermentative production by microorganisms. Some recently published advances in metabolic engineering have been used to effectively construct microbial cell factories that have improved the trans-4-hydroxy-l-proline biosynthetic pathway. To probe the potential of microorganisms for trans-4-hydroxy-l-proline production, new strategies and tools must be proposed. In this review, we provide a comprehensive understanding of trans-4-hydroxy-l-proline, including its biosynthetic pathway, proline hydroxylases and production by metabolic engineering, with a focus on improving its production.

Interactions of the Antimicrobial Peptide Maculatin 1.1 and Analogues with Phospholipid Bilayers

2011 ◽  
Vol 64 (6) ◽  
pp. 798 ◽  
Author(s):  
David I. Fernandez ◽  
Marc-Antoine Sani ◽  
Frances Separovic
Keyword(s):  
Antimicrobial Peptide ◽  
Solid State Nmr ◽  
Acyl Chain ◽  
Head Group ◽  
Group Interactions ◽  
Bacterial Membranes ◽  
Helical Content ◽  
Lipid System ◽  
Acyl Chains ◽  
Mixed Bilayer

The interactions of the antimicrobial peptide, maculatin 1.1 (GLFGVLAKVAAHVVPAIAEHF-NH2) and two analogues, with model phospholipid membranes have been studied using solid-state NMR and circular dichroism spectroscopy. Maculatin 1.1 and the P15G and P15A analogues displayed minimal secondary structure in water, but with zwitterionic dimyristoylphosphatidylcholine (DMPC) vesicles displayed a significant increase in α-helical content. In mixed phospholipid vesicles of DMPC and anionic dimyristoylphosphatidylglycerol (DMPG), each peptide was highly structured with ~80% α-helical content. In DMPC vesicles, the native peptide displayed moderate head group interaction and significant perturbation of the lipid acyl chains. In DMPC/DMPG vesicles, maculatin 1.1 promoted formation of a DMPG-enriched phase and moderately increased disorder towards acyl chain ends of DMPC in the mixed bilayer. Both analogues showed reduced phospholipid head group interactions with DMPC but displayed significant interactions with the mixed lipid system. These effects support the preferential activity of these antimicrobial peptides for bacterial membranes.

scholarly journals Properties of a new fungal b-galactosidase with potential application in the dairy industry

1999 ◽  
Vol 30 (3) ◽  
pp. 265-271 ◽  
Author(s):  
Rubens Cruz ◽  
Vinícius D'Arcádia Cruz ◽  
Juliana Gisele Belote ◽  
Marcelo de Oliveira Khenayfes ◽  
Claudia Dorta ◽  
...  
Keyword(s):  
Hydrolytic Activity ◽  
Industrial Applications ◽  
Transferase Activity ◽  
Optimum Temperature ◽  
Milk Whey ◽  
Beneficial Effects ◽  
Optimum Ph ◽  
Semi Solid ◽  
Good Productivity ◽  
Hydrolysis Of

<FONT FACE="Symbol">b</font>-Galactosidase or <FONT FACE="Symbol">b</font>-D-galactoside-galactohydrolase (EC. 3.2.1.23) is an important enzyme industrially used for the hydrolysis of lactose from milk and milk whey for several applications. Lately, the importance of this enzyme was enhanced by its galactosyltransferase activity, which is responsible for the synthesis of transgalactosylated oligosaccharides (TOS) that act as functional foods, with several beneficial effects on consumers. Penicillium simplicissimum, a strain isolated from soil, when grown in semi-solid medium showed good productivity of <FONT FACE="Symbol">b</font>-galactosidase with galactosyltransferase activity. The optimum pH for hydrolysis was in the 4.04.6 range and the optimum pH for galactosyltransferase activity was in the 6.07.0 range. The optimum temperature for hydrolysis and transferase activity was 55-60°C and 50°C, respectively, and the enzyme showed high thermostability for the hydrolytic activity. The enzyme showed a potential for several industrial applications such as removal of 67% of the lactose from milk and 84% of the lactose from milk whey when incubated at their original pH (4.5 and 6.34, respectively) under optimum temperature conditions. When incubated with a 40% lactose solution in 150 mM McIlvaine buffer, pH 4.5, at 55°C the enzyme converted 86.5% of the lactose to its component monosaccharides. When incubated with a 60% lactose solution in the same buffer but at pH 6.5 and 50°C, the enzyme can synthetize up to 30.5% TOS, with 39.5% lactose and 30% monosaccharides remaining in the preparation.

scholarly journals Structural Characterization of Natural Yeast Phosphatidylcholine and Bacterial Phosphatidylglycerol Lipid Multilayers by Neutron Diffraction

2021 ◽  
Vol 9 ◽  
Author(s):  
Alessandra Luchini ◽  
Giacomo Corucci ◽  
Krishna Chaithanya Batchu ◽  
Valerie Laux ◽  
Michael Haertlein ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Acyl Chain ◽  
Model Systems ◽  
Head Group ◽  
Single Class ◽  
Lipid Mixtures ◽  
Chain Composition ◽  
Acyl Chain Composition ◽  
The Impact

Eukaryotic and prokaryotic cell membranes are difficult to characterize directly with biophysical methods. Membrane model systems, that include fewer molecular species, are therefore often used to reproduce their fundamental chemical and physical properties. In this context, natural lipid mixtures directly extracted from cells are a valuable resource to produce advanced models of biological membranes for biophysical investigations and for the development of drug testing platforms. In this study we focused on single phospholipid classes, i.e. Pichia pastoris phosphatidylcholine (PC) and Escherichia coli phosphatidylglycerol (PG) lipids. These lipids were characterized by a different distribution of their respective acyl chain lengths and number of unsaturations. We produced both hydrogenous and deuterated lipid mixtures. Neutron diffraction experiments at different relative humidities were performed to characterize multilayers from these lipids and investigate the impact of the acyl chain composition on the structural organization. The novelty of this work resides in the use of natural extracts with a single class head-group and a mixture of chain compositions coming from yeast or bacterial cells. The characterization of the PC and PG multilayers showed that, as a consequence of the heterogeneity of their acyl chain composition, different lamellar phases are formed.

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