ArticleBiophysical journal2008
Molecular dynamics simulation of the neuroglobin crystal: comparison with the simulation in solution.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- gmXtal: Cooking Crystals with GROMACS.The protein journal · 2024Article
- Structural and (Pseudo-)Enzymatic Properties of Neuroglobin: Its Possible Role in Neuroprotection.Cells · 2021Review
- The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Proximal and distal control for ligand binding in neuroglobin: role of the CD loop and evidence for His64 gating.Scientific reports · 2019Article
- Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations.Biophysical journal · 2019Article
- Impact of A90P, F106L and H64V mutations on neuroglobin stability and ligand binding kinetics.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2019Article
- Dynamic features of carboxy cytoglobin distal mutants investigated by molecular dynamics simulations.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2016Article
- Article
- Effects of distal mutation on the dynamic properties of carboxycytoglobin: a molecular dynamics simulation study.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2013Article
- Polymorphism of the epidermal growth factor receptor extracellular ligand binding domain: the dimer interface depends on domain stabilization.Biochemistry · 2011Article
- Molecular dynamics simulation of a carboxy murine neuroglobin mutated on the proximal side: heme displacement and concomitant rearrangement in loop regions.Journal of molecular modeling · 2010Article
- Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose.Biophysical journal · 2009Article
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4 authors.
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Abstract
Neuroglobin (Ngb) is a monomeric protein that, despite the small sequence similarity with other globins, displays the typical globin fold. In the absence of exogenous ligands, the ferric and the ferrous forms of Ngb are both hexacoordinated to the distal and proximal histidines. In the ferrous form, oxygen, nitric oxide or carbon monoxide can displace the distal histidine, yielding a reversible adduct. Crystallographic data show that the binding of an exogenous ligand is associated to structural changes involving heme sliding and a topological reorganization of the internal cavities. Molecular dynamics (MD) simulations in solution show that the heme oscillates between two positions, much as the ones observed in the crystal structure, although the occupancy is different. The simulations also suggest that ligand binding in solution can affect the flexibility and conformation of residues connecting the C and D helices, referred to as the CD corner, which is coupled to the configuration adopted by the distal histidine. In this study, we report the results of 30 ns MD simulations of CO-bound Ngb in the crystal. Our goal was to compare the protein dynamical behavior in the crystal with the results supplied by the previous MD simulation of CO-bound Ngb in solution and the x-ray experimental data. The results show that the different environments (crystal or solution) affect the dynamics of the heme group and of the CD corner.
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