Search

Your search keyword '"conserved water molecule"' showing total 2 results
Start Over Descriptor "conserved water molecule"
2 results on '"conserved water molecule"'

1. Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study

Author

Soumita Mukherjee, Utpal Adhikari, Sujit S. Panja, Tapasendra Adhikary, and Subrata Dasgupta

Subjects
Express Communication, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), viruses, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030303 biophysics, medicine.disease_cause, 03 medical and health sciences, Structural Biology, medicine, Humans, Protease Inhibitors, Molecular Biology, Coronavirus, 0303 health sciences, SARS-CoV-2, Chemistry, conserved water molecule, COVID-19, virus diseases, Hydroxychloroquine, General Medicine, Virology, COVID-19 Drug Treatment, Molecular Docking Simulation, catalytic triad, Research Article, Peptide Hydrolases, medicine.drug
Abstract

The spread of novel coronavirus strain, Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) causes Coronavirus disease (COVID-19) has now spread worldwide and effecting the entire human race. The viral genetic material is transcripted and replicated by 3 C-like protease, as a result, it is an important drug target for COVID-19. Hydroxychloroquine (HCQ) report promising results against this drug target so, we perform molecular docking followed by MD-simulation studies of HCQ and modelled some ligand (Mod-I and Mod-II) molecules with SARS-CoV-2-main protease which reveals the structural organization of the active site residues and presence of a conserve water-mediated catalytic triad that helps in the recognition of Mod-I/II ligand molecules. The study may be helpful to gain a detailed structural insight on the presence of water-mediated catalytic triad which could be useful for inhibitor modelling. Communicated by Ramaswamy H. Sarma

Published
2020
Full Text
View/download PDF

2. CONSERVED WATER MOLECULES IN X-RAY STRUCTURES HIGHLIGHT THE ROLE OF WATER IN INTRAMOLECULAR AND INTERMOLECULAR INTERACTIONS.

Author

AKSIANOV, EVGENIY, ZANEGINA, OLGA, GRISHIN, ALEXANDER, SPIRIN, SERGEY, KARYAGINA, ANNA, and ALEXEEVSKI, ANDREI

Subjects
*BIOMOLECULES, *NUCLEIC acids, *EXTRACHROMOSOMAL DNA, *DNA, *PROTEIN analysis, *PHYSIOLOGY
Abstract

Water molecules immobilized on a protein or DNA surface are known to play an important role in intramolecular and intermolecular interactions. Comparative analysis of related three-dimensional (3D) structures allows to predict the locations of such water molecules on the protein surface. We have developed and implemented the algorithm WLAKE detecting "conserved" water molecules, i.e. those located in almost the same positions in a set of superimposed structures of related proteins or macromolecular complexes. The problem is reduced to finding maximal cliques in a certain graph. Despite exponential algorithm complexity, the program works appropriately fast for dozens of superimposed structures. WLAKE was used to predict functionally significant water molecules in enzyme active sites (transketolases) as well as in intermolecular (ETS–DNA complexes) and intramolecular (thiol–disulfide interchange protein) interactions. The program is available online at . [ABSTRACT FROM AUTHOR]

Published
2008
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results