Applications of MSMs

Gregory R. Bowman@drGregBowman

Associate ProfessorDept. of Biochemistry & Molecular Biophysics

Washington University School of Medicine

Bowman et al. Springer 2014.Knoverek et al. Trends Biochem Sci 2018.

Ensembles, energy landscapes, and Markov state models (MSMs)

Folding@home: A globally distributed computer

foldingathome.org

Computer simulations capture proteins’ moving parts

Bowman and Geissler. PNAS 2012Bowman et al. PNAS 2015

Bowman. J Comput Chem 2016.Bowman et al. J Phys Chem B 2014.

Active site

Computer simulations capture proteins’ moving parts

Cryptic pocketformation

Bowman and Geissler. PNAS 2012Bowman et al. PNAS 2015

Bowman. J Comput Chem 2016.Bowman et al. J Phys Chem B 2014.

Active site

Boltzmann docking has revealed new allosteric modulators

Hart et al. Nature Commun 2016.Hart et al. PLoS ONE 2017.

The IID of Ebola VP35 is essential for immune evasion

Leung et al. Nat Struct Mol Biol 2010.

The IID of Ebola VP35 is an ‘undruggable’ target

Blunt end-bindinginterface

Backbone-bindinginterface

Leung et al. Nat Struct Mol Biol 2010.

Extracting useful information from simulations poses its own challenges

Exposons analysisPorter et al. Biophys J 2019.

Enspara softwarePorter et al. JCP 2019.

Exposons identify sites of potentially functionally-relevant dynamics

Cruz et al. bioRxiv 2020.

Exposons identify sites of potentially functionally-relevant dynamics

Cruz et al. bioRxiv 2020.

Exposons uncover a cryptic pocket

Cruz et al. bioRxiv 2020.

The pocket is potentially druggable

Cruz et al. bioRxiv 2020.

Opening of the cryptic pocket disrupts the RNA-binding interface

H231S272

F239

K339

R322

Cruz et al. bioRxiv 2020.

Thiol labeling experiments report on the solvent exposure of cysteines

C307C247

C275

C326

Cruz et al. bioRxiv 2020.

Thiol labeling experiments corroborate the predicted cryptic pocket

C307C247

C275

C326

C307

C326

C247

Cruz et al. bioRxiv 2020.

A fluorescence polarization (FP) assay for monitoring RNA binding

Cruz et al. bioRxiv 2020.

A fluorescence polarization (FP) assay for monitoring RNA binding

Cruz et al. bioRxiv 2020.

The FP assay detects RNA binding

Cruz et al. bioRxiv 2020.

The FP assay reports on both binding modes

Cruz et al. bioRxiv 2020.

Thiol labeling allosterically disruptsblunt end binding

Cruz et al. bioRxiv 2020.

SARS-CoV-2/COVID-19

Folding@home has grown tremendously in response to COVID-19

Zimmerman et al. bioRxiv 2020.

Reaching the exascale

Zimmerman et al. bioRxiv 2020.

SARS-CoV-2/COVID-19

The ferocious COVID-19 Demogorgon

Zimmerman et al. bioRxiv 2020.

The ferocious COVID-19 Demogorgon

Zimmerman et al. bioRxiv 2020.

With help from a million friends, you can do a lot in parallel

• Spike• Nucleoprotein• NSP3 PL-protease domain• NSP5• NSP7• NSP9• NSP10• NSP12• NSP13• NSP14• NSP15• NSP16

Are you simulating monomers or dimers/complexes? Including

post-translational modifications or not?

YES!

Plentiful cryptic pockets

Zimmerman et al. bioRxiv 2020.

Searching for a patent-free drug with the COVID Moonshot

Vince Voelz, Temple UniversityJohn Chodera, MSKCC

Conclusions

Our simulations and analysis can reveal unexpected but functionally-relevant conformational changes

Our models are predictive, enabling the design of subsequent experimental tests

We can pivot rapidly to address emerging health threats

Thanks!

Folding@home

Conclusions

Our simulations and analysis can reveal unexpected but functionally-relevant conformational changes

Our models are predictive, enabling the design of subsequent experimental tests

We can pivot rapidly to address emerging health threats