Recent advances in understanding the mechanism of action of CBH I cellulase through advanced MD simulations

Ross C. Walker, Mark R. Nimlos, Michael F. Crowley, John W. Brady, James F. Matthews, Linghao Zhong, Charles L. Brooks, Michael E. Himmel

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

With the depletion of fossil fuels and related increases in oil price, bio fuels become ever more attractive as an alternative source of energy. The production of ethanol from lignocellulose has been identified as a vital step in reducing our nation's dependence on foreign oil. The enzymatic conversion of cellulose to glucose for use in fermentation offers an attractive solution for large scale bio ethanol production. However, the turnover rates of natural cellulases are too low to be commercially viable. A detailed understanding of the mechanisms of action of these cellulases would offer the possibility for improving their efficiency and ultimately reducing bio ethanol production costs while at the same time unlocking an abundant and renewable feed stock. Due to the insolubility of cellulose one of the most promising families of cellulases are the processive enzymes which successively hydrolyze linkages in a single chain. We have employed a range of advanced molecular dynamics techniques, including umbrella sampling, targeted MD and replica exchange, to gain insight into the mechanism of action of the CBH I cellulase enzyme (Cel7A) from T. reesei. By focusing on individual domains of the enzyme we have been able to isolate specific properties of this enzyme including insights into how the binding domain identifies the cellulose substrate and subsequently a broken cellulose strand as well as how the energetic potential within the catalytic tunnel varies as a function of the chain position. We present here recent results from these simulations including the identification of a potential induced fit mechanism between the binding module and the cellulose substrate.

Original languageEnglish (US)
Title of host publicationAmerican Chemical Society - 235th National Meeting, Abstracts of Scientific Papers
StatePublished - Dec 1 2008
Event235th National Meeting of the American Chemical Society, ACS 2008 - New Orleans, LA, United States
Duration: Apr 6 2008Apr 10 2008

Publication series

NameACS National Meeting Book of Abstracts
ISSN (Print)0065-7727

Other

Other235th National Meeting of the American Chemical Society, ACS 2008
CountryUnited States
CityNew Orleans, LA
Period4/6/084/10/08

Fingerprint

Cellulase
Cellulose
Cellulases
Enzymes
Ethanol
Oils
Substrates
Fossil fuels
Fermentation
Glucose
Molecular dynamics
Tunnels
Solubility
Sampling
Costs

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Chemical Engineering(all)

Cite this

Walker, R. C., Nimlos, M. R., Crowley, M. F., Brady, J. W., Matthews, J. F., Zhong, L., ... Himmel, M. E. (2008). Recent advances in understanding the mechanism of action of CBH I cellulase through advanced MD simulations. In American Chemical Society - 235th National Meeting, Abstracts of Scientific Papers (ACS National Meeting Book of Abstracts).
Walker, Ross C. ; Nimlos, Mark R. ; Crowley, Michael F. ; Brady, John W. ; Matthews, James F. ; Zhong, Linghao ; Brooks, Charles L. ; Himmel, Michael E. / Recent advances in understanding the mechanism of action of CBH I cellulase through advanced MD simulations. American Chemical Society - 235th National Meeting, Abstracts of Scientific Papers. 2008. (ACS National Meeting Book of Abstracts).
@inproceedings{baba27e80e7f4d21ac587a3ccf2693a4,
title = "Recent advances in understanding the mechanism of action of CBH I cellulase through advanced MD simulations",
abstract = "With the depletion of fossil fuels and related increases in oil price, bio fuels become ever more attractive as an alternative source of energy. The production of ethanol from lignocellulose has been identified as a vital step in reducing our nation's dependence on foreign oil. The enzymatic conversion of cellulose to glucose for use in fermentation offers an attractive solution for large scale bio ethanol production. However, the turnover rates of natural cellulases are too low to be commercially viable. A detailed understanding of the mechanisms of action of these cellulases would offer the possibility for improving their efficiency and ultimately reducing bio ethanol production costs while at the same time unlocking an abundant and renewable feed stock. Due to the insolubility of cellulose one of the most promising families of cellulases are the processive enzymes which successively hydrolyze linkages in a single chain. We have employed a range of advanced molecular dynamics techniques, including umbrella sampling, targeted MD and replica exchange, to gain insight into the mechanism of action of the CBH I cellulase enzyme (Cel7A) from T. reesei. By focusing on individual domains of the enzyme we have been able to isolate specific properties of this enzyme including insights into how the binding domain identifies the cellulose substrate and subsequently a broken cellulose strand as well as how the energetic potential within the catalytic tunnel varies as a function of the chain position. We present here recent results from these simulations including the identification of a potential induced fit mechanism between the binding module and the cellulose substrate.",
author = "Walker, {Ross C.} and Nimlos, {Mark R.} and Crowley, {Michael F.} and Brady, {John W.} and Matthews, {James F.} and Linghao Zhong and Brooks, {Charles L.} and Himmel, {Michael E.}",
year = "2008",
month = "12",
day = "1",
language = "English (US)",
isbn = "9780841269859",
series = "ACS National Meeting Book of Abstracts",
booktitle = "American Chemical Society - 235th National Meeting, Abstracts of Scientific Papers",

}

Walker, RC, Nimlos, MR, Crowley, MF, Brady, JW, Matthews, JF, Zhong, L, Brooks, CL & Himmel, ME 2008, Recent advances in understanding the mechanism of action of CBH I cellulase through advanced MD simulations. in American Chemical Society - 235th National Meeting, Abstracts of Scientific Papers. ACS National Meeting Book of Abstracts, 235th National Meeting of the American Chemical Society, ACS 2008, New Orleans, LA, United States, 4/6/08.

Recent advances in understanding the mechanism of action of CBH I cellulase through advanced MD simulations. / Walker, Ross C.; Nimlos, Mark R.; Crowley, Michael F.; Brady, John W.; Matthews, James F.; Zhong, Linghao; Brooks, Charles L.; Himmel, Michael E.

American Chemical Society - 235th National Meeting, Abstracts of Scientific Papers. 2008. (ACS National Meeting Book of Abstracts).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

TY - GEN

T1 - Recent advances in understanding the mechanism of action of CBH I cellulase through advanced MD simulations

AU - Walker, Ross C.

AU - Nimlos, Mark R.

AU - Crowley, Michael F.

AU - Brady, John W.

AU - Matthews, James F.

AU - Zhong, Linghao

AU - Brooks, Charles L.

AU - Himmel, Michael E.

PY - 2008/12/1

Y1 - 2008/12/1

N2 - With the depletion of fossil fuels and related increases in oil price, bio fuels become ever more attractive as an alternative source of energy. The production of ethanol from lignocellulose has been identified as a vital step in reducing our nation's dependence on foreign oil. The enzymatic conversion of cellulose to glucose for use in fermentation offers an attractive solution for large scale bio ethanol production. However, the turnover rates of natural cellulases are too low to be commercially viable. A detailed understanding of the mechanisms of action of these cellulases would offer the possibility for improving their efficiency and ultimately reducing bio ethanol production costs while at the same time unlocking an abundant and renewable feed stock. Due to the insolubility of cellulose one of the most promising families of cellulases are the processive enzymes which successively hydrolyze linkages in a single chain. We have employed a range of advanced molecular dynamics techniques, including umbrella sampling, targeted MD and replica exchange, to gain insight into the mechanism of action of the CBH I cellulase enzyme (Cel7A) from T. reesei. By focusing on individual domains of the enzyme we have been able to isolate specific properties of this enzyme including insights into how the binding domain identifies the cellulose substrate and subsequently a broken cellulose strand as well as how the energetic potential within the catalytic tunnel varies as a function of the chain position. We present here recent results from these simulations including the identification of a potential induced fit mechanism between the binding module and the cellulose substrate.

AB - With the depletion of fossil fuels and related increases in oil price, bio fuels become ever more attractive as an alternative source of energy. The production of ethanol from lignocellulose has been identified as a vital step in reducing our nation's dependence on foreign oil. The enzymatic conversion of cellulose to glucose for use in fermentation offers an attractive solution for large scale bio ethanol production. However, the turnover rates of natural cellulases are too low to be commercially viable. A detailed understanding of the mechanisms of action of these cellulases would offer the possibility for improving their efficiency and ultimately reducing bio ethanol production costs while at the same time unlocking an abundant and renewable feed stock. Due to the insolubility of cellulose one of the most promising families of cellulases are the processive enzymes which successively hydrolyze linkages in a single chain. We have employed a range of advanced molecular dynamics techniques, including umbrella sampling, targeted MD and replica exchange, to gain insight into the mechanism of action of the CBH I cellulase enzyme (Cel7A) from T. reesei. By focusing on individual domains of the enzyme we have been able to isolate specific properties of this enzyme including insights into how the binding domain identifies the cellulose substrate and subsequently a broken cellulose strand as well as how the energetic potential within the catalytic tunnel varies as a function of the chain position. We present here recent results from these simulations including the identification of a potential induced fit mechanism between the binding module and the cellulose substrate.

UR - http://www.scopus.com/inward/record.url?scp=77955640641&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77955640641&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:77955640641

SN - 9780841269859

T3 - ACS National Meeting Book of Abstracts

BT - American Chemical Society - 235th National Meeting, Abstracts of Scientific Papers

ER -

Walker RC, Nimlos MR, Crowley MF, Brady JW, Matthews JF, Zhong L et al. Recent advances in understanding the mechanism of action of CBH I cellulase through advanced MD simulations. In American Chemical Society - 235th National Meeting, Abstracts of Scientific Papers. 2008. (ACS National Meeting Book of Abstracts).