Engineering non-conserved salt bridges in GH11 xylanase from Bacillus pumilus SSP34 for improved thermal stability: an in-silico evaluation

2021 ◽  
pp. 1-13
Author(s):  
Sagar Krishna Bhat ◽  
Kavya Purushothaman ◽  
Appu Rao Gopala Rao Appu Rao ◽  
K. Ramachandra Kini
Keyword(s):  
Thermal Stability ◽  
In Silico ◽  
Bacillus Pumilus ◽  
Salt Bridges

scholarly journals Protein Thermal Stability Enhancement by Designing Salt Bridges: A Combined Computational and Experimental Study

PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e112751 ◽  
Author(s):  
Chi-Wen Lee ◽  
Hsiu-Jung Wang ◽  
Jenn-Kang Hwang ◽  
Ching-Ping Tseng
Keyword(s):  
Thermal Stability ◽  
Experimental Study ◽  
Salt Bridges ◽  
Protein Thermal Stability ◽  
Stability Enhancement

In silico and in vitro Approaches to Elucidate the Thermal Stability of Human UDP-glucuronosyltransferase (UGT) 1A9

2009 ◽  
Vol 24 (3) ◽  
pp. 235-244 ◽  
Author(s):  
Ryoichi Fujiwara ◽  
Miki Nakajima ◽  
Tetsunori Yamamoto ◽  
Hidemi Nagao ◽  
Tsuyoshi Yokoi
Keyword(s):  
Thermal Stability ◽  
In Silico ◽  
Udp Glucuronosyltransferase ◽  
Thermal Stability Of

scholarly journals In Silico Investigation of pH-Dependence of Prolactin and Human Growth Hormone Binding to Human Prolactin Receptor

2013 ◽  
Vol 13 (1) ◽  
pp. 207-222 ◽  
Author(s):  
Lin Wang ◽  
Shawn Witham ◽  
Zhe Zhang ◽  
Lin Li ◽  
Michael Hodsdon ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Human Growth Hormone ◽  
In Silico ◽  
Ph Dependence ◽  
Prolactin Receptor ◽  
Human Growth ◽  
Chemical Mechanism ◽  
Salt Bridges ◽  
Histidine Residues ◽  
Human Prolactin

AbstractExperimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that the main reason for pH-dependence of the binding of hPRL-hPRLr-ECD is a number of salt-bridges across the interface of the complex, while no salt-bridges are formed in the hGH-hPRlr-ECD. Specifically, most of the salt-bridges involve histidine residues and this is the reason for the pH-dependence across a physiological range of pH. The analysis not only revealed the molecular mechanism of the pH-dependence of the hPRL-hPRLr-ECD, but also provided critical insight into the underlying physic-chemical mechanism.

scholarly journals In Silico Analysis of Glucose Oxidase from Aspergillus niger: Potential Cysteine Mutation Sites for Enhancing Protein Stability

2021 ◽  
Vol 8 (11) ◽  
pp. 188
Author(s):  
Sirawit Ittisoponpisan ◽  
Itthipon Jeerapan
Keyword(s):  
Thermal Stability ◽  
Aspergillus Niger ◽  
Glucose Oxidase ◽  
Disulfide Bond ◽  
In Silico ◽  
Disulfide Bonds ◽  
Grand Challenge ◽  
Analysis Tool ◽  
Bond Quality ◽  
Protein Database

Glucose oxidase (GOx) holds considerable advantages for various applications. Nevertheless, the thermal instability of the enzyme remains a grand challenge, impeding the success in applications outside the well-controlled laboratories, particularly in practical bioelectronics. Many strategies to modify GOx to achieve better thermal stability have been proposed. However, modification of this enzyme by adding extra disulfide bonds is yet to be explored. This work describes the in silico bioengineering of GOx from Aspergillus niger by judiciously analyzing characteristics of disulfide bonds found in the Top8000 protein database, then scanning for amino acid residue pairs that are suitable to be replaced with cysteines in order to establish disulfide bonds. Next, we predicted and assessed the mutant GOx models in terms of disulfide bond quality (bond length and α angles), functional impact by means of residue conservation, and structural impact as indicated by Gibbs free energy. We found eight putative residue pairs that can be engineered to form disulfide bonds. Five of these are located in less conserved regions and, therefore, are unlikely to have a deleterious impact on functionality. Finally, two mutations, Pro149Cys and His158Cys, showed potential for stabilizing the protein structure as confirmed by a structure-based stability analysis tool. The findings in this study highlight the opportunity of using disulfide bond modification as a new alternative technique to enhance the thermal stability of GOx.

scholarly journals DISEÑO DE PLÁSMIDOS PARA LA EXPRESIÓN DEL CYND EN ARABIDOPSIS THALIANA VÍA AGROBACTERIUM TUMEFACIENS

Biotempo ◽  
1970 ◽  
Vol 14 (2) ◽  
Author(s):  
Miguel Montero ◽  
Andrea Cuba ◽  
Bryan Canal ◽  
Claudia De los Ríos ◽  
Roberto Pineda
Keyword(s):  
Arabidopsis Thaliana ◽  
Agrobacterium Tumefaciens ◽  
In Silico ◽  
Bacillus Pumilus

El cianuro, usado por las industrias mineras, es un compuesto tóxico que afecta principalmente a la metaloenzima c oxidasa en los seres vivos, enzima esencial para la respiración celular; por lo que la inhibición de esta enzima bloquea la fosforilación oxidativa, provocando la muerte celular. Ante ello, métodos biológicos como la fi torremediación proporcionan una alternativa para reducir o degradar contaminantes como el cianuro; sin embargo, esta técnica requeriría plantas que toleren altas concentraciones del metal en el suelo. Por otro lado, algunos microorganismos tienen una alta capacidad de desintoxicación de cianuro debido a una serie de vías metabólicas, como es el caso del Bacillus pumilus Meyer and Gottheil 1901, que presenta la cianidasa CynD que permite la degradación del cianuro a ácido fórmico y amonio. Por ello, el presente trabajo tiene como objetivo el diseño de plásmidos para la expresión de CynD en una planta modelo como la Arabidopsis thaliana (L.), Heynh. vía Agrobacterium tumefaciens (Smith & Townsend, 1907) Conn, 1942 con el fin de sentar las bases para evaluar si el CynD de B. pumilus le podría conferir a las plantas la facultad de crecer en presencia de cianuro y ayudar a su degradación. Para lo cual, se hizo uso de herramientas de la bioinformática, logrando diseñar un vector de clonación (pUCCynD), insertando in silico la secuencia del CynD en el polilinker del plásmido pUC18, entre las enzimas EcoRi (5’GAATTC - 3’CTTAAG) y BamHi (5’GGATCC-3’CCTAGG) del sitio múltiple de restricción y también un vector de transformación (pBCynD), insertando in silico la secuencia del CynD en el polilinker del plásmido pBI121, entre las enzimas ScaI (5’GAGCTC - 3’CTCGAG) y BamHI (5’GGATCC - 3’CCTAGG).

Molecular dynamics on laccase from Trametes versicolor to examine thermal stability induced by salt bridges

2019 ◽  
Vol 517 ◽  
pp. 253-264 ◽  
Author(s):  
Leonardo David Herrera-Zúñiga ◽  
Cesar Millán-Pacheco ◽  
Gustavo Viniegra-González ◽  
Elba Villegas ◽  
Leticia Arregui ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Trametes Versicolor ◽  
Salt Bridges

scholarly journals Antibacterial effects assessment on some livestock pathogens, thermal stability and proposing a probable reason for different levels of activity of thanatin

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ali Javadmanesh ◽  
Elyas Mohammadi ◽  
Zahra Mousavi ◽  
Marjan Azghandi ◽  
Abass Tanhaiean
Keyword(s):  
Escherichia Coli ◽  
Thermal Stability ◽  
Pseudomonas Aeruginosa ◽  
Minimum Inhibitory Concentration ◽  
In Silico ◽  
Inhibitory Concentration ◽  
Farm Animals ◽  
Probable Reason ◽  
Thermal Stability Of

AbstractThere is a continuing need to prevent the increasing use of common antibiotic and find the replacement to combat the drug/antibiotic resistant bacteria such as antimicrobial peptides (AMPs) such as thanatin peptide. In this study, recombinant thanatin peptide was expressed in the HEK293 cell line. Then the antimicrobial properties of this peptide on some poultry and farm animal’s pathogen strains were assessed. The thermal-stability of thanatin was predicted in various temperatures through in silico analysis. Afterwards, according to Minimum Inhibitory Concentration (MIC) results, Escherichia coli and Pseudomonas aeruginosa were chosen to test the hypothesis of LptA/LptD–thanatin interaction, computationally. Relative amino acid sequences and crystallography structures were retrieved and missed tertiary structures were predicted. The interaction of thanatin with LptA and LptD of Escherichia coli and Pseudomonas aeruginosa were analyzed subsequently. The antibacterial activity of thanatin peptide was evaluated between 6.25 and 100 μg/mL using minimum inhibitory concentration. Also, the amounts of minimum bactericidal concentrations (MBC) were between 12.5 and 200 μg/mL. The bioinformatics analysis followed by the in vitro assessment, demonstrated that thanatin would be thermally stable in the body temperature of poultry and farm animals. Thanatin could penetrate to the outer membrane domain of LptD in Escherichia coli and it could block the transition path of this protein while the entrance of LptD in Pseudomonas aeruginosa was blocked for thanatin by extra residues in comparison with Escherichia coli LptD. In addition, the quality of interaction, with regard to the number and distance of interactions which leads to higher binding energy for thanatin and LptD of Escherichia coli was much better than Pseudomonas aeruginosa. But the site and quality of interaction for thanatin and LptA was almost the same for Escherichia coli and Pseudomonas aeruginosa. Accordingly, thanatin can prevent the assembly of LptA periplasmic bridge in both pathogens. The antibacterial and thermal stability of the thanatin peptide suggested that thanatin peptide might serve as a natural alternative instead of common antibiotics in the veterinary medicine. The outcome of this in silico study supports the MIC results. Therefore, a probable reason for different level of activity of thanatin against Escherichia coli and Pseudomonas aeruginosa might be the quality of LptA/LptD–thanatin interaction.

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