ArticleProteins2010
Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 54 citations in OpenAlex.
- Molecular dynamics study on the effect of the N1 neuraminidase double mutant G147R/H274Y on oseltamivir sensitivity.RSC advances · 2024Article
- Modulation of human-to-swine influenza a virus adaptation by the neuraminidase low-affinity calcium-binding pocket.Communications biology · 2024Article
- Binding mechanism of oseltamivir and influenza neuraminidase suggests perspectives for the design of new anti-influenza drugs.PLoS computational biology · 2022Article
- Mechanistic insights into the role of calcium in the allosteric regulation of the calmodulin-regulated death-associated protein kinase.Frontiers in molecular biosciences · 2022Article
- Article
- Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif.The Journal of chemical physics · 2021Article
- Closing the Gap: An Atomistic Structural and Functional Perspective of S. mansoni Universal Stress G4LZI3 Protein in Complex with Phenolic Compounds.Current drug discovery technologies · 2021Article
- Plasticity of the 340-Loop in Influenza Neuraminidase Offers New Insight for Antiviral Drug Development.International journal of molecular sciences · 2020Article
- Using AMBER18 for Relative Free Energy Calculations.Journal of chemical information and modeling · 2019Article
- Influenza Virus Neuraminidase Structure and Functions.Frontiers in microbiology · 2019Review
- Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- All-atom virus simulations.Current opinion in virology · 2018Review
- Identification of Residues That Affect Oligomerization and/or Enzymatic Activity of Influenza Virus H5N1 Neuraminidase Proteins.Journal of virology · 2016Article
- Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.Chemphyschem : a European journal of chemical physics and physical chemistry · 2015Article
- Nanobiological studies on drug design using molecular mechanic method.Advanced biomedical research · 2015Article
- Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review.BioMed research international · 2015Review
- Article
- Structure of influenza virus N7: the last piece of the neuraminidase "jigsaw" puzzle.Journal of virology · 2014Article
- Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.Journal of chemical information and modeling · 2013Article
- w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations.Journal of chemical theory and computation · 2013Article
Corrections and comments
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Authors and funding
6 authors at 5 institutions in 1 country.
Funding
Abstract
The highly pathogenic influenza strains H5N1 and H1N1 are currently treated with inhibitors of the viral surface protein neuraminidase (N1). Crystal structures of N1 indicate a conserved, high affinity calcium binding site located near the active site. The specific role of this calcium in the enzyme mechanism is unknown, though it has been shown to be important for enzymatic activity and thermostability. We report molecular dynamics (MD) simulations of calcium-bound and calcium-free N1 complexes with the inhibitor oseltamivir (marketed as the drug Tamiflu), independently using both the AMBER FF99SB and GROMOS96 force fields, to give structural insight into calcium stabilization of key framework residues. Y347, which demonstrates similar sampling patterns in the simulations of both force fields, is implicated as an important N1 residue that can "clamp" the ligand into a favorable binding pose. Free energy perturbation and thermodynamic integration calculations, using two different force fields, support the importance of Y347 and indicate a +3 to +5 kcal/mol change in the binding free energy of oseltamivir in the absence of calcium. With the important role of structure-based drug design for neuraminidase inhibitors and the growing literature on emerging strains and subtypes, inclusion of this calcium for active site stability is particularly crucial for computational efforts such as homology modeling, virtual screening, and free energy methods.
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Registered trials
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