ArticleJournal of computer-aided molecular design2015
Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.
Article in Journal of computer-aided molecular design, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Conformational dynamics of adenylate kinase in crystals.Structural dynamics (Melville, N.Y.) · 2024Article
- LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories.Journal of chemical information and modeling · 2023Article
- Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics.Nature catalysis · 2019Article
- Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles.The journal of physical chemistry. B · 2018Article
- The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer.Frontiers in molecular biosciences · 2016Article
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Authors and funding
3 authors.
Funding
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Abstract
Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.
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