scholarly journals Characteristics, immobilization, and application of Candida rugosa lipase: a review

Food Research ◽  
2020 ◽  
Vol 4 (5) ◽  
pp. 1391-1401
Author(s):  
E. Subroto ◽  
R. Indiarto ◽  
A.D. Pangawikan ◽  
S. Huda ◽  
V.P. Yarlina
Keyword(s):  
Catalytic Mechanism ◽  
Candida Rugosa ◽  
Reaction System ◽  
Candida Rugosa Lipase ◽  
Nucleophilic Attack ◽  
Food Industries ◽  
Lipid Modifications ◽  
Catalytic Mechanisms ◽  
Lipase A ◽  
Α Helix

Candida rugosa lipase (CRL) is one of the lipases widely used in various food industries and studies, especially in linkage with the modification of lipids. This review discusses CRL, including CRL features (molecular biology, the structure of the enzyme protein, the flap/ lid), catalytic mechanisms and substrates specificity, CRL immobilization technologies, and various applications in lipid modifications. CRL has five isoenzymes, namely LIP1 - LIP5, then develops again into LIP1 - LIP8. However, LIP1 is the most commonly found isoenzymes. CRL has a structure similar to that of Geotricum candidum lipase, has a flap/ lid, which is an active side cover in the form of α-helix, which is relatively shorter than other lipases. The active site of the CRL consists of triads ser-209, His-449, and Glu-341, while the catalytic mechanism of the CRL is the same as the other lipases by the nucleophilic attack. CRL catalyzes triacylglycerol at all positions randomly and has hydrolysis and synthesis activities that are strongly affected by the presence of water in the reaction system. CRL can be used for various lipid modifications through hydrolysis, esterification, interesterification/transesterification, and alcoholysis/ glycerolysis reactions.

scholarly journals A QM/MM Study of Acylphosphatase Reveals the Nucleophilic-Attack and Ensuing Carbonyl-Assisted Catalytic Mechanisms

2020 ◽  
Author(s):  
zheng zhao ◽  
Phil bourne ◽  
Hao Hu ◽  
Huanyu Chu
Keyword(s):  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Catalytic Mechanism ◽  
Interaction Networks ◽  
Nucleophilic Attack ◽  
Reaction Coordinates ◽  
Transition State Stabilization ◽  
Catalytic Mechanisms ◽  
Energy Surfaces

Acylphosphatase is one of the vital enzymes in many organs/tissues to catalyze an acylphosphate molecule into carboxylate and phosphate. Here we use a combined <i>ab initio</i> QM/MM approach to reveal the catalytic mechanism of the benzoylphosphate-bound acylphosphatase system. Using a multi-dimensional reaction-coordinates-driving scheme, we obtained a detailed catalytic process including one nucleophilic-attack and then an ensuing carbonyl-shuttle catalytic mechanism by calculating two-dimensional potential energy surfaces. We also obtained an experiment-agreeable energy barrier and validated the role of the key amino acid Asn38. Additionally, we qualified the transition state stabilization strategy based on the amino acids-contributed interaction networks revealed in the enzymatic environment. This study provided usefule insights into the underlying catalytic mechanism to contribute to disease-involved research.

Molecular Modelling Studies on the Catalytic Mechanism of Candida Rugosa Lipase

1998 ◽  
Vol 4 (12) ◽  
pp. 395-404 ◽  
Author(s):  
Peter Monecke ◽  
Rudolf Friedemann ◽  
Stefan Naumann ◽  
Ren� Csuk
Keyword(s):  
Molecular Modelling ◽  
Catalytic Mechanism ◽  
Candida Rugosa ◽  
Candida Rugosa Lipase ◽  
Molecular Modelling Studies ◽  
Modelling Studies

scholarly journals Isolation of Candida rugosa lipase isoforms

2013 ◽  
Vol 67 (5) ◽  
pp. 703-706 ◽  
Author(s):  
Jovana Trbojevic ◽  
Aleksandra Dimitrijevic ◽  
Dusan Velickovic ◽  
Marija Gavrovic-Jankulovic ◽  
Nenad Milosavic
Keyword(s):  
Catalytic Mechanism ◽  
Candida Rugosa ◽  
Candida Rugosa Lipase ◽  
Post Translational Modifications ◽  
Fermentation Conditions ◽  
Advantages And Disadvantages ◽  
Isoelectric Points ◽  
Crude Preparation ◽  
Other Substances ◽  
Overall Performance

Convenient source of lipases for science and industry is yeast Candida rugosa. Crude preparation of Candida rugosa lipase (CRL) consists of several extracellular lipases. Isoenzyme profile depends on the culture or fermentation conditions. All isoforms are coded by lip pseudogene family; they are monomers of 534 amino acids and molecular weight of about 60 kDa. They share the same catalytic mechanism and interfacial mode of activation. Isoenzymes differ in isoelectric points, post-translational modifications, substrate specificity and hydrophobicity. The presence of different lipase isoforms and other substances (i. e. inhibitors) in crude preparation leads to lack of their productivity in biocatalytic reactions. Purification of specific isoform improves its overall performance and stability. This paper provides an overview of different methods for purification of CRL isoenzymes up to date, their advantages and disadvantages.

scholarly journals Alternative catalytic mechanisms driven by structural plasticity is an emerging theme in HAS-GTPases, Era and FeoB

2020 ◽  
Author(s):  
Sahil Batra ◽  
Ashok Kumar ◽  
Balaji Prakash
Keyword(s):  
Catalytic Mechanism ◽  
Structural Plasticity ◽  
Nucleophilic Attack ◽  
Hydrophobic Residue ◽  
Gtp Hydrolysis ◽  
Primary Mechanism ◽  
Transition State Analogue ◽  
Physiological Relevance ◽  
Underlying Basis ◽  
Catalytic Mechanisms

AbstractGTP hydrolysis is the underlying basis for functioning of ‘biological switches’ or GTPases. Extensively studied GTPases, Ras and EF-Tu, use a conserved Gln/His that facilitates the activation of attacking water for nucleophilic attack. However, this is insufficient to explain catalysis in Hydrophobic Amino acid Substituted (HAS)-GTPases that naturally possess a hydrophobic residue in lieu of Gln/His. We had previously reported a bridging water-chain mediated catalytic mechanism for HAS-GTPase FeoB; which utilizes two distantly-located but conserved glutamates. Curiously, mutating these does not abolish GTP hydrolysis. Similarly, in this study we report our observations on another HAS-GTPase Era, wherein the mutants of catalytically important residues continue to hydrolyze GTP. We attempt to rationalize these inquisitive observations on GTP hydrolysis by FeoB and Era mutants. We propose a general theory that appears common to at least three classes of GTPases, where ‘alternative mechanisms’ emerge when the primary mechanism is disrupted. Based on the analysis of crystal structures of FeoB and Era mutants, bound to the transition state analogue GDP.AlFx, this work suggests that in the absence of catalytically important residues, the active site waters in both FeoB and Era undergo re-arrangements, which in turn helps in sustaining GTP hydrolysis. Similar employment of alternative mechanisms was also suggested for the catalytic mutants of hGBP1. Importantly, such alternatives underscore the robustness of GTP hydrolysis mechanisms in these systems, and raise important questions regarding the need for persistent GTP hydrolysis and the physiological relevance of structural plasticity seen here.

Candida rugosa Lipase: A Traditional and Complex Biocatalyst

2006 ◽  
Vol 10 (10) ◽  
pp. 1053-1066 ◽  
Author(s):  
P. Dominguez de Maria ◽  
A. Alcantara ◽  
J. Carballeira ◽  
R. de la Casa ◽  
C. Garcia-Burgos ◽  
...  
Keyword(s):  
Candida Rugosa ◽  
Candida Rugosa Lipase ◽  
Lipase A

scholarly journals A QM/MM Study of Acylphosphatase Reveals the Nucleophilic-Attack and Ensuing Carbonyl-Assisted Catalytic Mechanisms

2020 ◽  
Author(s):  
zheng zhao ◽  
Phil bourne ◽  
Hao Hu ◽  
Huanyu Chu
Keyword(s):  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Catalytic Mechanism ◽  
Interaction Networks ◽  
Nucleophilic Attack ◽  
Reaction Coordinates ◽  
Transition State Stabilization ◽  
Catalytic Mechanisms ◽  
Energy Surfaces

Acylphosphatase is one of the vital enzymes in many organs/tissues to catalyze an acylphosphate molecule into carboxylate and phosphate. Here we use a combined <i>ab initio</i> QM/MM approach to reveal the catalytic mechanism of the benzoylphosphate-bound acylphosphatase system. Using a multi-dimensional reaction-coordinates-driving scheme, we obtained a detailed catalytic process including one nucleophilic-attack and then an ensuing carbonyl-shuttle catalytic mechanism by calculating two-dimensional potential energy surfaces. We also obtained an experiment-agreeable energy barrier and validated the role of the key amino acid Asn38. Additionally, we qualified the transition state stabilization strategy based on the amino acids-contributed interaction networks revealed in the enzymatic environment. This study provided usefule insights into the underlying catalytic mechanism to contribute to disease-involved research.

Arylboronic Acids in Self-condensation of Glucosamines Forming Deoxyfructosazine, Catalysts or Reagents?

2019 ◽  
Author(s):  
Meifeng Wang ◽  
Gan Zhu ◽  
Yiqun Li ◽  
Liuqun Gu
Keyword(s):  
Molecular Recognition ◽  
Boric Acid ◽  
Boronic Acid ◽  
Catalytic Mechanism ◽  
Organic Transformations ◽  
Food Industries ◽  
Arylboronic Acids ◽  
Excess Amount ◽  
Phenyl Boronic Acid ◽  
Boron Acid

Arylboronic acids were widely used as efficient catalysts in direct amide formation and other organic transformations. Surprisingly, reports on their use as catalysts in carbohydrates synthesis are very rare even though boron acid-diol complexation was extensively investigated in molecular recognition for saccharides and so on. Here we developed an efficient arylboronic acids catalyzed dimerization of glucosamines forming deoxyfructosazine which is important compound in pharmaceutical and food industries, against a commonly held belief that excess amount of phenyl boronic acid (or boric acid) is a must. A catalytic mechanism was also proposed and arylboronic acids instead of their boronates was identified as catalysts.

scholarly journals Functional dissection of the catalytic mechanism of mammalian RNA polymerase II

2005 ◽  
Vol 83 (4) ◽  
pp. 497-504 ◽  
Author(s):  
Benoit Coulombe ◽  
Marie-France Langelier
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Catalytic Mechanism ◽  
Mutational Analysis ◽  
Structural Elements ◽  
Catalytic Mechanisms ◽  
Rnap Ii ◽  
Affinity Peptide

High resolution X-ray crystal structures of multisubunit RNA polymerases (RNAP) have contributed to our understanding of transcriptional mechanisms. They also provided a powerful guide for the design of experiments aimed at further characterizing the molecular stages of the transcription reaction. Our laboratory used tandem-affinity peptide purification in native conditions to isolate human RNAP II variants that had site-specific mutations in structural elements located strategically within the enzyme's catalytic center. Both in vitro and in vivo analyses of these mutants revealed novel features of the catalytic mechanisms involving this enzyme.Key words: RNA polymerase II, transcriptional mechanisms, mutational analysis, mRNA synthesis.

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