Exploring cryo-electron microscopy with molecular dynamics
Integrating single particle cryo-electron microscopy (EM) and molecular dynamics (MD) has made a paradigm shift to the field of structural biology in order to determine both structure and function of biomolecules.
In this review article, we present a current overview of integrative modeling in a post resolution revolution era in cryo-EM. With the advancement in detector technology, a wide range of computational methods – both physics based and using machine learning – have been developed to determine high resolution structures of proteins in diverse biological systems such as plants, bacteria and viruses. Some of these computational methods include molecular dynamics flexible fitting (MDFF), cross-correlation driven molecular dynamics (CDMD), Cryo-BIFE, MultiMap and many more as listed under Table 1 of the review.
Significance and Impact
In addition to the methods, the review tabulates (Table 2) some of the recent exemplary examples where integrative modeling methods have been adopted to determine a high-resolution map and model of biological systems critical to human health. Such recent examples include the high-resolution structure of the Chimpanzee Adenovirus (ChAdOx1) Oxford-AstraZeneca COVID-19 vaccine at 3.07 Å and the spike protein structure of the coronavirus (SARS-COV-2) at 3.46 Å, to name a few.
Our collaborators from Abhishek Singharoy's group at Arizona State University and Josh Vermaas’s lab at the MSU-DOE Plant Research Laboratory were invited by Biochemical Society Transactions to work on a special issue of the journal focusing on computational biology, molecular dynamics and structural biology. Although we recognize that there are different experimental and computational methods in the field of structural biology, in this review we focus on the success of integrating cryo-EM and molecular dynamics, as we anticipate that this will be the future of experimental and computational structural biology.
This work was funded in part by the US Department of Energy, Office of Basic Energy Sciences.
Jianping Hu, professor at the MSU-DOE Plant Research Laboratory (PRL) and the Department of Plant Biology, received a $900,000 grant from the National Science Foundation (NSF) to study the motility of cellular energy organelles, peroxisomes and mitochondria in particular, along the cytoskeleton in Arabidopsis thaliana.
As our planet’s climate continues to be unpredictable, understanding how plants respond to adverse environmental conditions becomes essential. Improving crop productivity will be vital to feed the nine billion people estimated to be alive in 2050.
Grad student Philip Engelgau and postdoc Peipei Wang have been awarded the 2022 Anton Lang Memorial Award at a ceremony which took place on Monday, April 25, 2022. This year’s lecture was given by Professor Emeritus Govindjee from the University of Illinois at Urbana-Champaign.