Molecular dynamics study of Pseudomonas aeruginosa lectin-II complexed with monosaccharides

Proteins
Navnit Kumar MishraJaroslav Koca

Abstract

We present the results of a series of 10-ns molecular dynamics simulations on Pseudomonas aeruginosa lectin-II (PA-IIL) and its complexes with four different monosaccharides. We compare the saccharide-free, saccharide-occupied, and saccharide- and ion-free forms of the lectin. The results are coupled with analysis of the water density map and calcium coordination. The water density pattern around the binding site in the free lectin molecular dynamics was fitted with that in the X-ray and with the hydroxyl groups of the monosaccharide within the lectin/monosaccharide complexes and the best ligand was predicted based on the best fit. Interestingly, the water density pattern around the binding site in the uncomplexed lectin exactly fitted the O2, O3, and O4 hydroxyl groups of the fucose complex with the lectin. This observation could lead to a hypothesis that the replacement of these three water molecules from the binding site by the monosaccharide decreases the entropy of the complex and increases the entropy of the water molecules, which favors the binding. It suggests that the high density peaks of the solvent around the binding site in the free protein could be the tool to predict hydroxyl group orientation of the sugar in the...Continue Reading

References

Dec 1, 1993·Proteins·A AmadeiH J Berendsen
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jul 18, 2001·Journal of the American Chemical Society·F JalilehvandM Sandström
Dec 6, 2001·Journal of the American Chemical Society·C ClarkeG J Boons
Mar 28, 1996·Chemical Reviews·Raymond A. Dwek
Feb 19, 2002·Chemical Reviews·Halina Lis, Nathan Sharon
Jul 24, 2003·Journal of Molecular Biology·Marc BaadenMark S P Sansom
Aug 12, 2003·Journal of Molecular Biology·Remy LorisLode Wyns
Jan 13, 2004·Advances in Experimental Medicine and Biology·Philippe Roussel, Geneviève Lamblin
Apr 23, 2004·Acta Crystallographica. Section D, Biological Crystallography·Marjorie M Harding
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Nov 20, 2004·Annals of Oncology : Official Journal of the European Society for Medical Oncology·P SchöffskiUNKNOWN European Organization for Research and Treatment of Cancer New Drug Development Group
Dec 9, 2004·Chemical Reviews·Raz Jelinek, Sofiya Kolusheva
Jun 11, 2005·The Journal of Chemical Physics·Sau Lawrence LeeJeffrey R Errington
Apr 28, 2006·Angewandte Chemie·Joseph C ManimalaJeffrey C Gildersleeve
May 16, 2006·Acta Crystallographica. Section D, Biological Crystallography·Marjorie M Harding

❮ Previous
Next ❯

Citations

Apr 7, 2010·Cellular and Molecular Life Sciences : CMLS·Martin Frank, Siegfried Schloissnig
Apr 23, 2010·The Journal of Biological Chemistry·Alessandra NurissoAnne Imberty
Aug 17, 2012·The Journal of Chemical Physics·Madhurima Jana, Sanjoy Bandyopadhyay
Oct 17, 2009·Journal of Theoretical Biology·Sandeep K Kushwaha, Madhvi Shakya
Aug 12, 2014·Current Opinion in Structural Biology·Oliver C Grant, Robert J Woods
May 5, 2011·Biophysical Journal·Ignacia Echeverria, L Mario Amzel
Apr 19, 2011·Chembiochem : a European Journal of Chemical Biology·Virginia RoldósJesús Jiménez-Barbero

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.