Project Title

Deconstruction of Cellulosic Biomass: CpHMD Simulations of Cel7B

PI

Dr. C Mark Maupin

Email

cmmaupin@mines.edu

Department

Chemical & Biological Engineering

Project summary

This project focuses on the hypothesis that protonation states of active site residues and pH dependent protein fluctuations play a key role in the enzymatic degradation of cellulose by the endocellulase enzyme Cel7B. To evaluate this hypothesis, we propose using constant pH molecular dynamics (CpHMD) simulations on three enzyme systems over a pH range of 3 to 8. The use of CpHMD will reveal time dependent protein fluctuations and dynamical interactions crucial to protein functionality. Furthermore, CpHMD allows pH to be set as an external parameter and for the protonation states of certain amino acids to change in response to the dynamic electrostatic environment. This provides valuable information on proton transfer coupled with other pH dependent fluctuations and dynamic interactions. The information gained from CpHMD simulations is not easily accessible to experimentalists, and is crucial to future efforts in bio-engineering enhanced cellulase enzymes.

Commercial software

AMBER 12

Gaussian09

Open Source software

None