Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations.

PubWeight™: 1.40‹?› | Rank: Top 5%

🔗 View Article (PMC 2665887)

Published in J Am Chem Soc on April 08, 2009

Authors

Rommie E Amaro1, Xiaolin Cheng, Ivaylo Ivanov, Dong Xu, J Andrew McCammon

Author Affiliations

1: Department of Chemistry & Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093-0365, USA. ramaro@mccammon.ucsd.edu

Articles citing this

Structural and functional characterization of neuraminidase-like molecule N10 derived from bat influenza A virus. Proc Natl Acad Sci U S A (2012) 1.35

Structural and functional analysis of laninamivir and its octanoate prodrug reveals group specific mechanisms for influenza NA inhibition. PLoS Pathog (2011) 1.25

Improving pandemic influenza risk assessment. Elife (2014) 1.20

Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases. PLoS Comput Biol (2010) 1.11

Novel sialic acid derivatives lock open the 150-loop of an influenza A virus group-1 sialidase. Nat Commun (2010) 1.08

Emerging methods for ensemble-based virtual screening. Curr Top Med Chem (2010) 1.08

Neuraminidase inhibitor sensitivity and receptor-binding specificity of Cambodian clade 1 highly pathogenic H5N1 influenza virus. Antimicrob Agents Chemother (2011) 1.06

Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy. Proteins (2010) 1.04

Influenza neuraminidase operates via a nucleophilic mechanism and can be targeted by covalent inhibitors. Nat Commun (2013) 0.98

Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective. J Am Chem Soc (2009) 0.97

Multidrug-resistant pandemic (H1N1) 2009 infection in immunocompetent child. Emerg Infect Dis (2011) 0.94

Structural basis for a class of nanomolar influenza A neuraminidase inhibitors. Sci Rep (2013) 0.88

Scoring ensembles of docked protein:ligand interactions for virtual lead optimization. J Chem Inf Model (2009) 0.87

A strategy for reducing gross errors in the generalized Born models of implicit solvation. J Chem Phys (2011) 0.87

Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations. PLoS One (2013) 0.86

Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications. J Chem Theory Comput (2013) 0.86

Interface dynamics explain assembly dependency of influenza neuraminidase catalytic activity. J Biomol Struct Dyn (2013) 0.86

Improving the description of salt bridge strength and geometry in a Generalized Born model. J Mol Graph Model (2010) 0.84

Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J (2015) 0.83

Reduced susceptibility to all neuraminidase inhibitors of influenza H1N1 viruses with haemagglutinin mutations and mutations in non-conserved residues of the neuraminidase. J Antimicrob Chemother (2013) 0.82

Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study. J Comput Aided Mol Des (2013) 0.81

Computer-guided approach to access the anti-influenza activity of licorice constituents. J Nat Prod (2013) 0.80

Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase. PLoS Comput Biol (2012) 0.80

Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase. J Mol Genet Med (2012) 0.80

Introducing Charge Hydration Asymmetry into the Generalized Born Model. J Chem Theory Comput (2014) 0.78

Molecular dynamics analysis of antibody recognition and escape by human H1N1 influenza hemagglutinin. Biophys J (2015) 0.76

Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI). J Comput Chem (2015) 0.76

Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review. Biomed Res Int (2015) 0.76

Locking the 150-cavity open: in silico design and verification of influenza neuraminidase inhibitors. PLoS One (2013) 0.75

Discovery and Characterization of Diazenylaryl Sulfonic Acids as Inhibitors of Viral and Bacterial Neuraminidases. Front Microbiol (2017) 0.75

Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism. J Mol Model (2011) 0.75

The significance of naturally occurring neuraminidase quasispecies of H5N1 avian influenza virus on resistance to oseltamivir: a point of concern. J Gen Virol (2016) 0.75

Molecular-level simulation of pandemic influenza glycoproteins. Methods Mol Biol (2012) 0.75

Computer-based de novo designs of tripeptides as novel neuraminidase inhibitors. Int J Mol Sci (2010) 0.75

Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design. PLoS Comput Biol (2016) 0.75

Equilibrium and folding simulations of NS4B H2 in pure water and water/2,2,2-trifluoroethanol mixed solvent: examination of solvation models. J Mol Model (2013) 0.75

Articles cited by this

Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci (1994) 31.96

The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84

Development and testing of a general amber force field. J Comput Chem (2004) 23.29

Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res (2004) 11.53

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res (2000) 10.78

Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins (2004) 9.15

Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature (1993) 8.62

Avian flu: isolation of drug-resistant H5N1 virus. Nature (2005) 6.66

Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem (2000) 6.55

The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature (2006) 6.00

Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 A resolution. Nature (1983) 5.56

All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc (2002) 4.99

Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers (2001) 4.68

Neuraminidase sequence analysis and susceptibilities of influenza virus clinical isolates to zanamivir and oseltamivir. Antimicrob Agents Chemother (2003) 3.90

Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity. J Am Chem Soc (1997) 3.69

Selection of influenza virus mutants in experimentally infected volunteers treated with oseltamivir. J Infect Dis (2001) 3.69

The GROMOS software for biomolecular simulation: GROMOS05. J Comput Chem (2005) 3.36

Antiviral agents active against influenza A viruses. Nat Rev Drug Discov (2006) 3.12

Influenza virus carrying neuraminidase with reduced sensitivity to oseltamivir carboxylate has altered properties in vitro and is compromised for infectivity and replicative ability in vivo. Antiviral Res (2002) 3.07

BCX-1812 (RWJ-270201): discovery of a novel, highly potent, orally active, and selective influenza neuraminidase inhibitor through structure-based drug design. J Med Chem (2000) 2.74

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J (2004) 2.69

Reversible peptide folding in solution by molecular dynamics simulation. J Mol Biol (1998) 2.48

Comparison of the activities of zanamivir, oseltamivir, and RWJ-270201 against clinical isolates of influenza virus and neuraminidase inhibitor-resistant variants. Antimicrob Agents Chemother (2001) 2.46

Comparison of efficacies of RWJ-270201, zanamivir, and oseltamivir against H5N1, H9N2, and other avian influenza viruses. Antimicrob Agents Chemother (2001) 2.21

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14

Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69

Three-dimensional structure of neuraminidase of subtype N9 from an avian influenza virus. Proteins (1987) 1.69

Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc (2007) 1.65

Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. J Med Chem (2007) 1.63

Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci U S A (2002) 1.56

A computational study of nucleosomal DNA flexibility. Biophys J (2006) 1.42

Identification of substrate binding sites in enzymes by computational solvent mapping. J Mol Biol (2003) 1.37

Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. J Med Chem (2003) 1.15

Activity of the neuraminidase inhibitor A-315675 against oseltamivir-resistant influenza neuraminidases of N1 and N2 subtypes. Antiviral Res (2007) 1.12

Optimal charges in lead progression: a structure-based neuraminidase case study. J Med Chem (2006) 0.91

A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase. J Comput Aided Mol Des (1996) 0.87

Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: application to influenza neuraminidase. J Mol Graph Model (2005) 0.83

Articles by these authors

Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res (2004) 11.53

Molecular dynamics simulations of biomolecules. Nat Struct Biol (2002) 7.68

Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J (2004) 6.67

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys (2004) 5.00

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78

Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics (2006) 4.44

Long-term monitoring shows hepatitis B virus resistance to entecavir in nucleoside-naïve patients is rare through 5 years of therapy. Hepatology (2009) 4.00

Enhanced computer vision with Microsoft Kinect sensor: a review. IEEE Trans Cybern (2013) 3.75

Slug antagonizes p53-mediated apoptosis of hematopoietic progenitors by repressing puma. Cell (2005) 3.73

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput (2012) 3.40

Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res (2007) 3.40

Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18

Graph embedding and extensions: a general framework for dimensionality reduction. IEEE Trans Pattern Anal Mach Intell (2007) 3.06

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J (2004) 2.69

Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc (2002) 2.58

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52

Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (2006) 2.49

B lymphocyte stimulator overexpression in patients with systemic lupus erythematosus: longitudinal observations. Arthritis Rheum (2003) 2.47

Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem (2004) 2.43

An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J (2010) 2.41

HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci (2004) 2.34

Visualization of nitric oxide in living cells by a copper-based fluorescent probe. Nat Chem Biol (2006) 2.33

Local production of B lymphocyte stimulator protein and APRIL in arthritic joints of patients with inflammatory arthritis. Arthritis Rheum (2003) 2.21

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16

Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc Natl Acad Sci U S A (2006) 2.15

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14

Generalized Born model with a simple, robust molecular volume correction. J Chem Theory Comput (2007) 2.10

Discovery of a novel binding trench in HIV integrase. J Med Chem (2004) 2.09

A novel switch region regulates H-ras membrane orientation and signal output. EMBO J (2008) 2.06

Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc (2004) 2.00

Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys (2007) 1.93

Molecular dynamics simulations and drug discovery. BMC Biol (2011) 1.91

Understanding the unique characteristics of suicide in China: national psychological autopsy study. Biomed Environ Sci (2005) 1.90

Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. J Med Chem (2007) 1.84

Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics (2002) 1.81

Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence. J Biol Chem (2004) 1.81

Microarray analysis of chitin elicitation in Arabidopsis thaliana. Mol Plant Pathol (2002) 1.80

Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. Epigenetics (2012) 1.80

The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers (2003) 1.80

POVME: an algorithm for measuring binding-pocket volumes. J Mol Graph Model (2010) 1.75

Epidermal growth factor-like domain 7 protects endothelial cells from hyperoxia-induced cell death. Am J Physiol Lung Cell Mol Physiol (2007) 1.75

Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure (2008) 1.75

Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques (2004) 1.74

Application of the level-set method to the implicit solvation of nonpolar molecules. J Chem Phys (2007) 1.73

Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proc Natl Acad Sci U S A (2008) 1.73

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res (2013) 1.72

Photoaffinity isolation and identification of proteins in cancer cell extracts that bind to platinum-modified DNA. Chembiochem (2009) 1.71

Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucleic Acids Res (2004) 1.71

Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69

Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A (2012) 1.69

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol (2009) 1.67

A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A (2005) 1.66

Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc (2007) 1.65

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput (2012) 1.65

Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol (2006) 1.65

Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol (2005) 1.64

Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model (2008) 1.64

Water in cavity-ligand recognition. J Am Chem Soc (2010) 1.63

Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc (2002) 1.63

Exploring global motions and correlations in the ribosome. Biophys J (2005) 1.62

Efficacy of entecavir in chronic hepatitis B patients with mildly elevated alanine aminotransferase and biopsy-proven histological damage. Hepatology (2010) 1.61

Long-term treatment with entecavir induces reversal of advanced fibrosis or cirrhosis in patients with chronic hepatitis B. Clin Gastroenterol Hepatol (2010) 1.60

Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc (2009) 1.55

Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Mol Cell Proteomics (2010) 1.55

Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics (2007) 1.53

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J Chem Theory Comput (2008) 1.52

How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study. J Am Chem Soc (2005) 1.51

Control of cation permeation through the nicotinic receptor channel. PLoS Comput Biol (2008) 1.51

No supernovae associated with two long-duration gamma-ray bursts. Nature (2006) 1.47

CUBIC: identification of regulatory binding sites through data clustering. J Bioinform Comput Biol (2003) 1.47

catena-Poly[[bis(thiocyanato-kappa N)cadmium(II)]-di-mu-thiourea-kappa(4)S:S]. Acta Crystallogr C (2002) 1.45

SNP discovery by high-throughput sequencing in soybean. BMC Genomics (2010) 1.45

Electrostatic free energy and its variations in implicit solvent models. J Phys Chem B (2008) 1.45

How Can Hydrophobic Association Be Enthalpy Driven? J Chem Theory Comput (2010) 1.44

Implementation of Accelerated Molecular Dynamics in NAMD. Comput Sci Discov (2011) 1.44

Preoperative rosuvastatin protects patients with coronary artery disease undergoing noncardiac surgery. Cardiology (2015) 1.43

Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys (2007) 1.43

The physical basis of microtubule structure and stability. Protein Sci (2003) 1.43

MUFOLD: A new solution for protein 3D structure prediction. Proteins (2010) 1.42

Single feature polymorphism discovery in rice. PLoS One (2007) 1.42

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys J (2006) 1.42

Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A (2013) 1.41

SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol (2010) 1.40

Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics (2010) 1.39

Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol (2010) 1.38

Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment. J Biol Chem (2005) 1.37

The influence of macromolecular crowding on HIV-1 protease internal dynamics. J Am Chem Soc (2006) 1.37

Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res (2006) 1.37

Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J (2004) 1.35

Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys Chem Chem Phys (2011) 1.35

PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics (2008) 1.35

Computational identification of protein methylation sites through bi-profile Bayes feature extraction. PLoS One (2009) 1.34

Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A (2012) 1.33

BAFF overexpression and accelerated glomerular disease in mice with an incomplete genetic predisposition to systemic lupus erythematosus. Arthritis Rheum (2005) 1.33

Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J Chem Phys (2005) 1.31

P3DB: a plant protein phosphorylation database. Nucleic Acids Res (2008) 1.31