scholarly journals Towards Computationally Guided Design and Engineering of a Neisseria meningitidis Serogroup W Capsule Polymerase with Altered Substrate Specificity

Processes ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 2192
Author(s):  
Subhadra Paudel ◽  
James Wachira ◽  
Pumtiwitt C. McCarthy
Keyword(s):  
Sialic Acid ◽  
Metal Ions ◽  
Neisseria Meningitidis ◽  
Heavy Metal Contamination ◽  
Wastewater Treatment Plants ◽  
Binding Capacity ◽  
Binding Pocket ◽  
Health Concern ◽  
Rational Approach ◽  
Active Site Residues

Heavy metal contamination of drinking water is a public health concern that requires the development of more efficient bioremediation techniques. Absorption technologies, including biosorption, provide opportunities for improvements to increase the diversity of target metal ions and overall binding capacity. Microorganisms are a key component in wastewater treatment plants, and they naturally bind metal ions through surface macromolecules but with limited capacity. The long-term goal of this work is to engineer capsule polymerases to synthesize molecules with novel functionalities. In previously published work, we showed that the Neisseria meningitidis serogroup W (NmW) galactose–sialic acid (Gal–NeuNAc) heteropolysaccharide binds lead ions effectively, thereby demonstrating the potential for its use in environmental decontamination applications. In this study, computational analysis of the NmW capsule polymerase galactosyltransferase (GT) domain was used to gain insight into how the enzyme could be modified to enable the synthesis of N-acetylgalactosamine–sialic acid (GalNAc–NeuNAc) heteropolysaccharide. Various computational approaches, including molecular modeling with I-TASSER and molecular dynamics (MD) simulations with NAMD, were utilized to identify key amino acid residues in the substrate binding pocket of the GT domain that may be key to conferring UDP-GalNAc specificity. Through these combined strategies and using BshA, a UDP-GlcNAc transferase, as a structural template, several NmW active site residues were identified as mutational targets to accommodate the proposed N-acetyl group in UDP-GalNAc. Thus, a rational approach for potentially conferring new properties to bacterial capsular polysaccharides is demonstrated.

scholarly journals Towards Computationally Guided Design and Engineering of a Neisseria Meningitidis Serogroup W Capsule Polymerase with Altered Substrate Specificity

2021 ◽  
Author(s):  
Subhadra Paudel ◽  
James Wachira ◽  
Pumtiwitt C. McCarthy
Keyword(s):  
Sialic Acid ◽  
Metal Ions ◽  
Neisseria Meningitidis ◽  
Capsular Polysaccharide ◽  
Heavy Metal Contamination ◽  
Wastewater Treatment Plants ◽  
Binding Capacity ◽  
Health Concern ◽  
Rational Approach ◽  
Active Site Residues

Heavy metal contamination of drinking water is a public health concern that requires the development of more efficient bioremediation techniques. Absorption technologies, including biosorption, provide opportunities for improvements to increase the diversity of metal ions removed and overall binding capacity. Microorganisms are a key component in wastewater treatment plants and they naturally bind metal ions through surface macromolecules but with limited capacity. The long-term goal of this work is to engineer capsule polymerases to synthesize molecules with novel functionalities. In previously published work, we showed that the Neisseria meningitidis serogroup W (NmW) galactose-sialic acid (Gal—NeuNAc) heteropolysaccharide binds lead effectively, thereby demonstrating the potential for using this capsular polysaccharide in environmental decontamination applications. In this study, computational analysis of the NmW capsule polymerase galactosyltransferase (GT) domain was used to gain insight into how the enzyme could be modified to enable the synthesis N-acetylgalactosamine-sialic acid (GalNAc—NeuNAc) heteropolysaccharide. Various computational approaches, including molecular modeling with I-TASSER and molecular dynamics simulations (MD) with NAMD, were utilized to identify key amino acid residues in the substrate binding pocket of the GT domain that may be key to conferring UDP-GalNAc specificity. Through these combined strategies and using BshA, a UDP-GlcNAc transferase, as a structural template, several NmW active site residues were identified as mutational targets to accommodate the proposed N-acetyl group in UDP-GalNAc. Thus, a rational approach for potentially conferring new properties to bacterial capsular polysaccharides is demonstrated.

Application of Molecular Docking for the Development of Improved HIV-1 Reverse Transcriptase Inhibitors

2020 ◽  
Vol 16 ◽  
Author(s):  
Arash Soltani ◽  
Seyed Isaac Hashemy ◽  
Farnaz Zahedi Avval ◽  
Houshang Rafatpanah ◽  
Seyed Abdolrahim Rezaee ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Binding Capacity ◽  
Binding Pocket ◽  
Ligand Docking ◽  
Binding Modes ◽  
Wild Type ◽  
Parent Molecule ◽  
Discovery Studio ◽  
Approved Drugs ◽  
Hiv 1

Introoduction: Inhibition of the reverse transcriptase (RT) enzyme of human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. Then the parent molecule and derivatives were docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in druglikeness screening by Swiss-ADME or in docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to -58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using fragment-based approach.

scholarly journals Mutations That Affect the Tropism of DA and GDVII Strains of Theiler's Virus In Vitro Influence Sialic Acid Binding and Pathogenicity

2002 ◽  
Vol 76 (16) ◽  
pp. 8138-8147 ◽  
Author(s):  
Karima Jnaoui ◽  
Muriel Minet ◽  
Thomas Michiels
Keyword(s):  
Sialic Acid ◽  
Demyelinating Disease ◽  
Binding Capacity ◽  
Single Amino Acid ◽  
Sialic Acid Binding ◽  
Encephalomyelitis Virus ◽  
The Central Nervous System ◽  
Different Strains ◽  
Single Amino Acid Mutation

ABSTRACT Theiler's murine encephalomyelitis virus (TMEV) is a natural pathogen of the mouse. The different strains of TMEV are divided into two subgroups according to the pathology they provoke. The neurovirulent strains GDVII and FA induce an acute fatal encephalitis, while persistent strains, like DA and BeAn, cause a chronic demyelinating disease associated with viral persistence in the central nervous system. Different receptor usage was proposed to account for most of the phenotype difference between neurovirulent and persistent strains. Persistent but not neurovirulent strains were shown to bind sialic acid. We characterized DA and GDVII derivatives adapted to grow on CHO-K1 cells. Expression of glycosaminoglycans did not influence infection of CHO-K1 cells by parental and adapted viruses. Mutations resulting from adaptation of DA and GDVII to CHO-K1 cells notably mapped to the well-characterized VP1 CD and VP2 EF loops of the capsid. Adaptation of the DA virus to CHO-K1 cells correlated with decreased sialic acid usage for entry. In contrast, adaptation of the GDVII virus to CHO-K1 cells correlated with the appearance of a weak sialic acid usage for entry. The sialic acid binding capacity of the GDVII variant resulted from a single amino acid mutation (VP1-51, Asn→Ser) located out of the sialic acid binding region defined for virus DA. Mutations affecting tropism in vitro and sialic acid binding dramatically affected the persistence and neurovirulence of the viruses.

Study of Flocculation Mechanisms by Observing Effects of a Complexing Agent on Activated Sludge Properties

1991 ◽  
Vol 24 (7) ◽  
pp. 21-28 ◽  
Author(s):  
L. Eriksson ◽  
B. Alm
Keyword(s):  
Activated Sludge ◽  
Metal Ions ◽  
Electrostatic Interactions ◽  
Wastewater Treatment Plants ◽  
Sedimentation Velocity ◽  
Complexing Agent ◽  
Extracellular Polymers ◽  
Filtration Resistance ◽  
Polyvalent Metal ◽  
Sludge Properties

Electrostatic interactions between bacterial surfaces, extracellular polymers (ECP) and polyvalent metal ions are important in activated sludge flocculation. An indirect study of these mechanisms was done by adding different concentrations of EDTA to activated sludge samples from 6 Swedish wastewater treatment plants. The effects on sludge properties were studied with sedimentation and filtration tests as well as analysis of released extracellular polymers. EDTA had a significant effect on sedimentation velocity in all investigated sludges. This shows that charged polymers are important for the properties of the floc surfaces and in building up the sludge macroflocs. The effect on filtration resistance where the bulk properties of the primary flocs are more important varied considerably for the different sludges. Thus, both electrostatic and other interactions are involved to a varying extent in building up the primary flocs in the sludges investigated. Variations in sedimentation velocity, residual turbidity, filtration resistance and release of ECP with variations in EDTA concentrations could be explained by effects of polyvalent metal ions on ECP binding and conformation.

scholarly journals Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase

2011 ◽  
Vol 92 (7) ◽  
pp. 1607-1616 ◽  
Author(s):  
Ji-Hye Lee ◽  
Intekhab Alam ◽  
Kang Rok Han ◽  
Sunyoung Cho ◽  
Sungho Shin ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Crystal Structures ◽  
Active Site ◽  
Metal Ion ◽  
Health Concern ◽  
Murine Norovirus ◽  
Active Site Residues ◽  
Rna Dependent Rna Polymerase ◽  
Close Proximity ◽  
Functional Features

Norovirus is one of the leading agents of gastroenteritis and is a major public health concern. In this study, the crystal structures of recombinant RNA-dependent RNA polymerase (RdRp) from murine norovirus-1 (MNV-1) and its complex with 5-fluorouracil (5FU) were determined at 2.5 Å resolution. Crystals with C2 symmetry revealed a dimer with half a dimer in the asymmetrical unit, and the protein exists predominantly as a monomer in solution, in equilibrium with a smaller population of dimers, trimers and hexamers. MNV-1 RdRp exhibited polymerization activity with a right-hand fold typical of polynucleotide polymerases. The metal ion modelled in close proximity to the active site was found to be coordinated tetrahedrally to the carboxyl groups of aspartate clusters. The orientation of 5FU observed in three molecules in the asymmetrical unit was found to be slightly different, but it was stabilized by a network of favourable interactions with the conserved active-site residues Arg185, Asp245, Asp346, Asp347 and Arg395. The information gained on the structural and functional features of MNV-1 RdRp will be helpful in understanding replication of norovirus and in designing novel therapeutic agents against this important pathogen.

scholarly journals Use of Spilopelia senegalensis as a Biomonitor of Heavy Metal Contamination from Mining Activities in Riyadh (Saudi Arabia)

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1046 ◽  
Author(s):  
Ahmed M. Almalki ◽  
Jamaan Ajarem ◽  
Ahmed A. Allam ◽  
Hamed A. El-Serehy ◽  
Saleh N. Maodaa ◽  
...  
Keyword(s):  
Environmental Pollution ◽  
Human Health ◽  
Heavy Metal Contamination ◽  
Tissue Injury ◽  
Health Concern ◽  
Mining Activities ◽  
Mining Site ◽  
Liver And Kidney ◽  
Copper Zinc ◽  
Arsenic Copper

Environmental pollution with heavy metals (HMs) is of serious ecological and public health concern worldwide. Mining is one of the main sources of HMs and can impact the environment, species diversity, and human health. This study assessed the value of Spilopelia senegalensis as a biomonitor of environmental contamination with metal(loid)s caused by mining activities. S. senegalensis was collected from a gold mining site and a reference site, and metal(loid)s and biochemical parameters were determined. Lead, cadmium, mercury, vanadium, arsenic, copper, zinc, and iron were significantly increased in the liver, kidney, and lung of S. senegalensis from the mining site. Serum transaminases, alkaline phosphatase, creatinine, and urea were significantly elevated in S. senegalensis from the mining site. Lipid peroxidation and nitric oxide were increased, whereas glutathione and antioxidant enzymes were diminished in the liver and kidney of S. senegalensis from the mining site. In addition, multiple histological alterations were observed in the liver, kidney, and lung of S. senegalensis. In conclusion, mining activities provoke the accumulation of metal(loid)s, oxidative stress, and tissue injury in S. senegalensis. Therefore, S. senegalensis is a valuable biomonitor of environmental pollution caused by mining activities and could be utilized in epidemiological avian studies of human health.

scholarly journals Moderately Neutralizing Epitopes in Nonfunctional Regions Dominate the Antibody Response toPlasmodium falciparumEBA-140

2019 ◽  
Vol 87 (4) ◽  
Author(s):  
Nichole D. Salinas ◽  
May M. Paing ◽  
Jagat Adhikari ◽  
Michael L. Gross ◽  
Niraj Tolia
Keyword(s):  
Immune Response ◽  
Sialic Acid ◽  
Neutralizing Antibodies ◽  
Fold Increase ◽  
Binding Pocket ◽  
Content Type ◽  
Tight Junction Formation ◽  
Sialic Acid Binding ◽  
Erythrocyte Binding ◽  
Region Ii

ABSTRACTPlasmodium falciparumerythrocyte-binding antigen 140 (EBA-140) plays a role in tight junction formation during parasite invasion of red blood cells and is a potential vaccine candidate for malaria. Individuals in areas where malaria is endemic possess EBA-140-specific antibodies, and individuals with high antibody titers to this protein have a lower rate of reinfection by parasites. The red blood cell binding segment of EBA-140 is comprised of two Duffy-binding-like domains, called F1 and F2, that together create region II. The sialic acid-binding pocket of F1 is essential for binding, whereas the sialic acid-binding pocket in F2 appears dispensable. Here, we show that immunization of mice with the complete region II results in poorly neutralizing antibodies. In contrast, immunization of mice with the functionally relevant F1 domain of region II results in antibodies that confer a 2-fold increase in parasite neutralization compared to that of the F2 domain. Epitope mapping of diverse F1 and F2 monoclonal antibodies revealed that the functionally relevant F1 sialic acid-binding pocket is a privileged site inaccessible to antibodies, that the F2 sialic acid-binding pocket contains a nonneutralizing epitope, and that two additional epitopes reside in F1 on the opposite face from the sialic acid-binding pocket. These studies indicate that focusing the immune response to the functionally important F1 sialic acid binding pocket improves the protective immune response of EBA-140. These results have implications for improving future vaccine designs and emphasize the importance of structural vaccinology for malaria.

scholarly journals Structure of the regulatory domain of the LysR family regulator NMB2055 (MetR-like protein) fromNeisseria meningitidis

2012 ◽  
Vol 68 (7) ◽  
pp. 730-737 ◽  
Author(s):  
Sarah Sainsbury ◽  
Jingshan Ren ◽  
Nigel J. Saunders ◽  
David I. Stuart ◽  
Raymond J. Owens
Keyword(s):  
Crystal Structure ◽  
Transcription Factors ◽  
Neisseria Meningitidis ◽  
Disulfide Bond ◽  
Binding Pocket ◽  
Cysteine Residues ◽  
Regulatory Domain ◽  
High Degree ◽  
Effector Binding ◽  
Lysr Family

The crystal structure of the regulatory domain of NMB2055, a putative MetR regulator fromNeisseria meningitidis, is reported at 2.5 Å resolution. The structure revealed that there is a disulfide bond inside the predicted effector-binding pocket of the regulatory domain. Mutation of the cysteines (Cys103 and Cys106) that form the disulfide bond to serines resulted in significant changes to the structure of the effector pocket. Taken together with the high degree of conservation of these cysteine residues within MetR-related transcription factors, it is suggested that the Cys103 and Cys106 residues play an important role in the function of MetR regulators.

Sign in / Sign up

Export Citation Format

Share Document