scholarly journals Homology Modeling of Bifunctional Enzyme Alanine Racemase from Taibaiella Chishuiensis

2020 ◽  
Vol 17 (03) ◽  
pp. 607-620
Author(s):  
Gulsanga lemar ◽  
Farid Ahmad Danish Far
Keyword(s):  
Homology Modeling ◽  
Alanine Racemase ◽  
Bifunctional Enzyme

scholarly journals Enzymatic and Structural Characterization of Alanine Racemase from Enterococcus faecium by Kinetic and Computational Studies

2021 ◽  
Vol 18 (1) ◽  
pp. 3-12
Author(s):  
Arie Van Wieren ◽  
Emma Bouchard ◽  
Sudipta Majumdar
Keyword(s):  
Steady State ◽  
Homology Modeling ◽  
Enterococcus Faecium ◽  
Catalytic Efficiency ◽  
Homology Model ◽  
Alanine Racemase ◽  
Active Site Residues ◽  
Ph Optimum ◽  
Vancomycin Resistant Enterococci ◽  
Vancomycin Resistant

The surge in vancomycin-resistant enterococci (VRE) strains poses a serious threat to public and clinical health. VRE strains are the leading cause of multi-drug resistant enterococcal infections and are commonly acquired from medical devices. Therefore, it is essential to discover new antibacterial targets and drugs for this pathogen. Alanine racemase could be a valuable drug target due to its crucial role in E. faecium survival. Alr from E. faecium (EF_Alr) was heterologously produced and purified from E. coli., and the steady-state kinetic constants were determined at different pH values. Using a coupled reaction with L-alanine dehydrogenase, rate of production of NADH was measured at 340 nm to observe EF_Alr activity in the D- to L-alanine direction. The highest catalytic efficiency, 8.61 ± 0.5 s-1 mM-1, was found at pH 9. Additionally, the tentative active site residues, Lys40 and Tyr268, for the alanine racemization reaction were assigned by homology modeling and sequence comparison studies. Using UCSF Chimera, the structure of the EF_Alr homology model was superimposed and compared to the crystal structure of Alr from E. faecalis. KEYWORDS: Alanine Racemase; Enterococcus faecium; Vancomycin-Resistant Enterococci; Homology Modeling; pH Optimum; Kinetic Characterization; SWISS-MODEL Server; Steady-State Kinetics

Identifying redox-sensitive extra-chloroplastic enzymes by homology modeling

2000 ◽  
Vol 110 (3) ◽  
pp. 296-302
Author(s):  
Louise E. Anderson ◽  
Alex Dong Li ◽  
Elizabeth H. Muslin ◽  
Marianne Schiffer ◽  
Fred J. Stevens
Keyword(s):  
Homology Modeling

Unveiling the Accuracy of Homology Modeling to Elucidate the Structure of GPCRs-HIV Co-receptor-CCR5 as a Case Study

2018 ◽  
Vol 15 (10) ◽  
pp. 1068-1078
Author(s):  
Vadivelu Aanand ◽  
Rajendran Anitha ◽  
Somarathinam Kanagasabai ◽  
Gunalan Seshan ◽  
Changdev G. Gadhe ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Receptor Ccr5

LegumeDB: Development of Legume Medicinal Plant Database and Comparative Molecular Evolutionary Analysis of matK Proteins of Legumes and Mangroves

2019 ◽  
Vol 15 (4) ◽  
pp. 353-362
Author(s):  
Sambhaji B. Thakar ◽  
Maruti J. Dhanavade ◽  
Kailas D. Sonawane
Keyword(s):  
Phylogenetic Analysis ◽  
Medicinal Plants ◽  
Homology Modeling ◽  
Sequence Alignment ◽  
Vigna Unguiculata ◽  
Multiple Sequence Alignment ◽  
Legume Species ◽  
Mangrove Species ◽  
Multiple Sequence ◽  
Thespesia Populnea

Background: Legume plants are known for their rich medicinal and nutritional values. Large amount of medicinal information of various legume plants have been dispersed in the form of text. Objective: It is essential to design and construct a legume medicinal plants database, which integrate respective classes of legumes and include knowledge regarding medicinal applications along with their protein/enzyme sequences. Methods: The design and development of Legume Medicinal Plants Database (LegumeDB) has been done by using Microsoft Structure Query Language Server 2017. DBMS was used as back end and ASP.Net was used to lay out front end operations. VB.Net was used as arranged program for coding. Multiple sequence alignment, phylogenetic analysis and homology modeling techniques were also used. Results: This database includes information of 50 Legume medicinal species, which might be helpful to explore the information for researchers. Further, maturase K (matK) protein sequences of legumes and mangroves were retrieved from NCBI for multiple sequence alignment and phylogenetic analysis to understand evolutionary lineage between legumes and mangroves. Homology modeling technique was used to determine three-dimensional structure of matK from Legume species i.e. Vigna unguiculata using matK of mangrove species, Thespesia populnea as a template. The matK sequence analysis results indicate the conserved residues among legume and mangrove species. Conclusion: Phylogenetic analysis revealed closeness between legume species Vigna unguiculata and mangrove species Thespesia populnea to each other, indicating their similarity and origin from common ancestor. Thus, these studies might be helpful to understand evolutionary relationship between legumes and mangroves. : LegumeDB availability: http://legumedatabase.co.in

Homology Modeling Inspired Synthesis of 5-HT2A Receptor Inhibitors: A Diazepine Analogue of the Atypical Antipsychotic JL13

2017 ◽  
Vol 17 (3) ◽  
Author(s):  
Enrico Mongeau ◽  
Gengyang Yuan ◽  
Zachary Minden ◽  
Scott Waldron ◽  
Raymond Booth ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Atypical Antipsychotic

scholarly journals Mechanism-based inactivation of alanine racemase by 3-halovinylglycines.

1991 ◽  
Vol 266 (32) ◽  
pp. 21657-21665 ◽  
Author(s):  
N.A. Thornberry ◽  
H.G. Bull ◽  
D. Taub ◽  
K.E. Wilson ◽  
G. Giménez-Gallego ◽  
...  
Keyword(s):  
Alanine Racemase

scholarly journals PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL

2012 ◽  
Vol 13 (Suppl 4) ◽  
pp. S2 ◽  
Author(s):  
Emanuele Bramucci ◽  
Alessandro Paiardini ◽  
Francesco Bossa ◽  
Stefano Pascarella
Keyword(s):  
Homology Modeling ◽  
Sequence Similarity ◽  
Sequence Structure ◽  
Multiple Sequence ◽  
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