Probing Protein Mechanics with Probing Protein Mechanics with Molecular Dynamics Simulations and Molecular Dynamics Simulations and SingleSingle--Molecule ExperimentsMolecule Experiments
PRAC: The Computational Microscope PI: Emad Tajkhorshid Co-PIs: Rafael C. Bernardi, John E. Stone, and James C. Phillips
Rafael C. Bernardi Theoretical and Computational Biophysics Group NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana, IL
[email protected] www.ks.uiuc.edu/~rcbernardi What are we doing in Illinois?
Development of NAMD & VMD: • Available for Free; • One of the Most used Software in US Super Computer Centers;
Over 700 publications;
Prof. Emad Tajkhorshid Prof. Zan Luthey-Schulten Prof. Klaus Schulten Over 120k citations;
NIH Center for Macromolecular Modeling and Bioinformatics NSF Center for the Physics of Living Cells
Rafael C. Bernardi www.ks.uiuc.edu/~rcbernardi Probing Protein Mechanics with Molecular Dynamics Simulations and Single-Molecule Experiments
in silico (Steered Molecular Dynamics) in vitro (AFM-based SMFS)
Prof. Klaus Schulten Prof. Hermann Gaub Beckman Institute LMU Munich, Germany University of Illinois
Prof. Zaida Luthey-Schulten Prof. Michael Nash Department of Chemistry University of Basel, Switzerland University of Illinois
NIH Center for Macromolecular Modeling and Bioinformatics NCSA Blue Waters Supercomputer Combining in silico and in vitro Experiments Unraveling Molecular Mechanisms of Extreme Mechanostability in Proteins
Experimental Setup Computational Setup in vitro in silico Single-Molecule Force a Dockerins c Spectroscopy (SMFS) Steered Molecular X AFM Dynamics (SMD) Cohesins Coh ScaC cantilever Atomic Force Enzymes PEG
ScaA Microscope (AFM) CBM ScaE Coh Doc ScaB X Doc Protein Complex of Interest XMod
XMod-Doc:Coh XMod Force Xyn CttA CBM CBM X PEG Glass
R. flavefaciens Extension Cellulosic substrate ScaE surface b Rafael C. Bernardi www.ks.uiuc.edu/~rcbernardi
X-module Cohesin Dockerin Extreme Mechanostability in Bacterial Proteins
Cellulosomes Adhesins
Rafael C. Bernardi www.ks.uiuc.edu/~rcbernardi Cellulosomes are Used by Some Bacteria to Digest Plant Fiber
Cellulosomal organisms often live in a turbulent environment.
How Mechanically Stable are Cellulosomes?
RC Bernardi, et. al. Enhanced sampling techniques in molecular dynamics simulations of biological systems. BBA, 2015
Rafael C. Bernardi www.ks.uiuc.edu/~rcbernardi CohE:CttA
PDBid:4IU3
R. flavefaciens Rafael C. Bernardi www.ks.uiuc.edu/~rcbernardi Strongest Non-Covalent Bond Ever Found
Molecular Finger Trap Puzzle
KD = 20 nM About the same as a typical antibody–antigen
Rupture Under Force = 600-750 pN Antibody-antigen rupture at only ~60 pN
About half the rupture force of a covalent gold-thiol bond
C Schoeler, KH Malinowska, RC Bernardi, et. al. Ultrastable cellulosome-adhesion complex tightens under load. Nature Communications, 2014 C Schoeler, RC Bernardi, et. al. Mapping mechanical force propagation through biomolecular complexes. Nano Letters, 2015 M Scheurer, P Rodenkirch, M Siggel, RC Bernardi, et. al. PyContact: Rapid, customizable, and visual analysis of noncovalent interactions in MD simulations. Biophysical Journal, 2018 Rafael C. Bernardi www.ks.uiuc.edu/~rcbernardi Can we use simulations to engineer modified cellulosomal proteins?
Rafael C. Bernardi www.ks.uiuc.edu/~rcbernardi Are the cohesins in a scaffold different?
Bridging Cohesins are Stronger than Hanging Cohesins. Proposed by Valbuena, et. al. PNAS 2009