CAREER: In Silico Single-Molecule Force Spectroscopy

Auburn University, Auburn AL

Investigators

Abstract

This award is funded in part under the American Rescue Plan Act of 2021 (Public Law 117-2). Other funding was provided by the Molecular Biophysics Program in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and by the Established Program to Stimulate Competitive Research (EPSCoR). Since the stone age, humans know that mechanical forces can be used to bend and break materials. Young children intuitively shape playdough, unaware that they are controlling shear-forces when deciding to tear or pinch the material, where the direction of applied force defines their effects. However, the outcomes of applied mechanical forces become much less intuitive if we zoom into biomolecules. In fact, chemistry at shear forces is quite intriguing, with relatively soft bonds becoming very strong depending on how force is applied to them. Such intriguing behavior is crucial for the inner workings of all cells, where proteins are often under the influence of mechanical forces. Frequently, the directionality and amplitude of these forces can regulate biological activities. In this project, the researchers are not only investigating the intriguing behavior of proteins that are mechanoactive, that is, that react differently depending on the forces applied on them, but also developing computational tools that make it possible to study them with atomic detail. Particularly, mechanoactive proteins that are found in the surface of both good and bad bacteria will be investigated to elucidate how they become extremally resilient to shear forces and allow infections to take place within our bodies. Additionally, new immersive technologies will be developed to observe these proteins under shear-force load, powering the “Immersive Biophysics on the Road” program, where tools and knowledge developed in this project will tour Alabama to showcase STEM. An inflatable projection dome will then be used to teach the molecular mechanisms of life. The long-term goal of this project is to characterize, with atomic and sub-atomic resolution, the protein:protein interactions responsible for the remarkable mechanostability of extracellular protein complexes. The central hypothesis of this project is that evolution has created geometrical artifices that are used by different proteins to become stronger when under mechanical stress, and also modular and flexible when needed. This hypothesis is based on preliminary work that has shown a simple geometric mechanism responsible for mechanostability, but that is challenging to be achieved at the molecular level. Here, the rationale is that understanding the molecular details at play will allow for the manipulation of mechanostability; for guiding the development of molecules that can inhibit adhesion processes; and for proposing the development of biotechnology tools that could profit from the mechanostability of these proteins. These goals will be achieved by: 1. developing bioinformatic tools to resurrect cellulosomal proteins ancestors to understand how mechanostability evolved; 2. Investigating the mechanism by which staph bacteria form highly-stable bonds to the human extra-cellular matrix. Particularly, this project will employ a combination of classical molecular dynamics, hybrid quantum/classical calculations, and dimensionality reduction methods, in order to characterize sub-atomic properties of proteins under mechanical stress. Additionally, new molecular dynamics methods for analysis and visualization will be made easier by implementing them into graphical user interfaces. Most of the new implementations will be made into QwikMD, which will incorporate new methods for structure prediction based on artificial intelligence, as well as new immersive visualization renderings, which will allow for the use of portable planetarium-like domes and virtual reality headsets for science outreach. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.