Guide for determination of protein structural ensembles by combining cryo-EM data with metadynamics.
Zacharias Faidon BrotzakisPublished in: FEBS open bio (2022)
Metadynamics electron microscopy metaInference (MEMMI) is an integrative structural biology method that enables a rapid and accurate characterization of protein structural dynamics at the atomic level and the error in the cryo-EM experimental data, even in cases where conformations are separated by high energy barriers. It achieves this by incorporating (a) cryo-electron microscopy electron density maps with (b) metadynamic-enhanced-sampling molecular dynamics. Here, I showcase the setup and analysis protocol of MEMMI, used to discover the atomistic structural ensemble and error in the cryo-EM electron density map of the fuzzy coat of IAPP, a fibril implicated in type II diabetes.
Keyphrases
- electron microscopy
- molecular dynamics
- electronic health record
- type diabetes
- density functional theory
- randomized controlled trial
- cardiovascular disease
- big data
- high resolution
- binding protein
- molecular dynamics simulations
- amino acid
- mass spectrometry
- convolutional neural network
- skeletal muscle
- glycemic control
- solid phase extraction
- liquid chromatography
- insulin resistance
- network analysis
- sensitive detection
- loop mediated isothermal amplification