ArticleeLife2018
Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size.
Article in eLife, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
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- Chemical Mechanism of Allosteric and Asymmetric Dark Reversion in a Bacterial Phytochrome Uncovered by Cryo-EM.Journal of the American Chemical Society · 2025Article
- Structural mechanisms behind the neutralisation of long-chain α-neurotoxins by broadly neutralising VCommunications chemistry · 2025Article
- Orally delivered toxin-binding protein protects against diarrhoea in a murine cholera model.Nature communications · 2025Article
- A single mutation in dairy cow-associated H5N1 viruses increases receptor binding breadth.Nature communications · 2024Article
- Analysis of the Dynamics of a Complex, Multipathway Reaction: Insulin Dimer Dissociation.The journal of physical chemistry. B · 2024Article
- Fit-for-purpose heterodivalent single-domain antibody for gastrointestinal targeting of toxin B from Clostridium difficile.Protein science : a publication of the Protein Society · 2024Article
- Optimal Molecular Dynamics System Size for Increased Precision and Efficiency for Epoxy Materials.The journal of physical chemistry. B · 2024Article
- The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.Journal of chemical theory and computation · 2024Article
- Defining the cross-reactivity between peanut allergens Ara h 2 and Ara h 6 using monoclonal antibodies.Clinical and experimental immunology · 2024Article
- Evaluating sheep hemoglobins with MD simulations as an animal model for sickle cell disease.Scientific reports · 2024Article
- Phage display assisted discovery of a pH-dependent anti-α-cobratoxin antibody from a natural variable domain library.Protein science : a publication of the Protein Society · 2023Article
- Structural basis of epitope selectivity and potent protection from malaria by PfCSP antibody L9.Nature communications · 2023Article
- Structural Characterization of Nanobodies during Germline Maturation.Biomolecules · 2023Article
- Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs.Journal of chemical information and modeling · 2022Article
- Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.Journal of chemical theory and computation · 2022Article
- Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR.International journal of molecular sciences · 2022Article
- Cross-Correlated Motions in Azidolysozyme.Molecules (Basel, Switzerland) · 2022Article
- Dynamics of camel and human hemoglobin revealed by molecular simulations.Scientific reports · 2022Article
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Abstract
Recent molecular dynamics (MD) simulations of human hemoglobin (Hb) give results in disagreement with experiment. Although it is known that the unliganded (T[Formula: see text]) and liganded (R[Formula: see text]) tetramers are stable in solution, the published MD simulations of T[Formula: see text] undergo a rapid quaternary transition to an R-like structure. We show that T[Formula: see text] is stable only when the periodic solvent box contains ten times more water molecules than the standard size for such simulations. The results suggest that such a large box is required for the hydrophobic effect, which stabilizes the T[Formula: see text] tetramer, to be manifested. Even in the largest box, T[Formula: see text] is not stable unless His146 is protonated, providing an atomistic validation of the Perutz model. The possibility that extra large boxes are required to obtain meaningful results will have to be considered in evaluating existing and future simulations of a wide range of systems.
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