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Title: Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose

Abstract

The processive cycle of the bacterial cellulose synthase (Bcs) includes the addition of a single glucose moiety to the end of a growing cellulose chain followed by the translocation of the nascent chain across the plasma membrane. The mechanism of this translocation and its precise location within the processive cycle are not well understood. In particular, the molecular details of how a polymer (cellulose) whose basic structural unit is a dimer (cellobiose) can be constructed by adding one monomer (glucose) at a time are yet to be elucidated. Here, we have utilized molecular dynamics simulations and free energy calculations to the shed light on these questions. We find that translocation forward by one glucose unit is quite favorable energetically, giving a free energy stabilization of greater than 10 kcal mol-1. In addition, there is only a small barrier to translocation, implying that translocation is not rate limiting within the Bcs processive cycle (given experimental rates for cellulose synthesis in vitro). Perhaps most significantly, our results also indicate that steric constraints at the transmembrane tunnel entrance regulate the dimeric structure of cellulose. Namely, when a glucose molecule is added to the cellulose chain in the same orientation as the acceptor glucose,more » the terminal glucose freely rotates upon forward motion, thus suggesting a regulatory mechanism for the dimeric structure of cellulose. We characterize both the conserved and non-conserved enzyme-polysaccharide interactions that drive translocation, and find that 20 of the 25 residues that strongly interact with the translocating cellulose chain in the simulations are well conserved, mostly with polar or aromatic side chains. Our results also allow for a dynamical analysis of the role of the so-called 'finger helix' in cellulose translocation that has been observed structurally. Taken together, these findings aid in the elucidation of the translocation steps of the Bcs processive cycle and may be widely relevant to polysaccharide synthesizing or degrading enzymes that couple catalysis with chain translocation.« less

Authors:
 [1];  [1];  [1];  [2];  [1]
  1. National Renewable Energy Lab. (NREL), Golden, CO (United States)
  2. Univ. of Virginia, Charlottesville, VA (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1250687
Report Number(s):
NREL/JA-5100-65894
Journal ID: ISSN 2041-6520; CSHCBM
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Accepted Manuscript
Journal Name:
Chemical Science
Additional Journal Information:
Journal Volume: 7; Journal Issue: 5; Related Information: Chemical Science; Journal ID: ISSN 2041-6520
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; bacterial cellulose synthase (Bcs); translocation; processive cycle; molecular dynamics simulations

Citation Formats

Knott, Brandon C., Crowley, Michael F., Himmel, Michael E., Zimmer, Jochen, and Beckham, Gregg T. Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose. United States: N. p., 2016. Web. doi:10.1039/C5SC04558D.
Knott, Brandon C., Crowley, Michael F., Himmel, Michael E., Zimmer, Jochen, & Beckham, Gregg T. Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose. United States. doi:10.1039/C5SC04558D.
Knott, Brandon C., Crowley, Michael F., Himmel, Michael E., Zimmer, Jochen, and Beckham, Gregg T. Fri . "Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose". United States. doi:10.1039/C5SC04558D. https://www.osti.gov/servlets/purl/1250687.
@article{osti_1250687,
title = {Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose},
author = {Knott, Brandon C. and Crowley, Michael F. and Himmel, Michael E. and Zimmer, Jochen and Beckham, Gregg T.},
abstractNote = {The processive cycle of the bacterial cellulose synthase (Bcs) includes the addition of a single glucose moiety to the end of a growing cellulose chain followed by the translocation of the nascent chain across the plasma membrane. The mechanism of this translocation and its precise location within the processive cycle are not well understood. In particular, the molecular details of how a polymer (cellulose) whose basic structural unit is a dimer (cellobiose) can be constructed by adding one monomer (glucose) at a time are yet to be elucidated. Here, we have utilized molecular dynamics simulations and free energy calculations to the shed light on these questions. We find that translocation forward by one glucose unit is quite favorable energetically, giving a free energy stabilization of greater than 10 kcal mol-1. In addition, there is only a small barrier to translocation, implying that translocation is not rate limiting within the Bcs processive cycle (given experimental rates for cellulose synthesis in vitro). Perhaps most significantly, our results also indicate that steric constraints at the transmembrane tunnel entrance regulate the dimeric structure of cellulose. Namely, when a glucose molecule is added to the cellulose chain in the same orientation as the acceptor glucose, the terminal glucose freely rotates upon forward motion, thus suggesting a regulatory mechanism for the dimeric structure of cellulose. We characterize both the conserved and non-conserved enzyme-polysaccharide interactions that drive translocation, and find that 20 of the 25 residues that strongly interact with the translocating cellulose chain in the simulations are well conserved, mostly with polar or aromatic side chains. Our results also allow for a dynamical analysis of the role of the so-called 'finger helix' in cellulose translocation that has been observed structurally. Taken together, these findings aid in the elucidation of the translocation steps of the Bcs processive cycle and may be widely relevant to polysaccharide synthesizing or degrading enzymes that couple catalysis with chain translocation.},
doi = {10.1039/C5SC04558D},
journal = {Chemical Science},
number = 5,
volume = 7,
place = {United States},
year = {2016},
month = {1}
}

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Works referenced in this record:

Cellulose biosynthesis in Acetobacter xylinum: visualization of the site of synthesis and direct measurement of the in vivo process.
journal, December 1976

  • Brown, R. M.; Willison, J. H.; Richardson, C. L.
  • Proceedings of the National Academy of Sciences, Vol. 73, Issue 12
  • DOI: 10.1073/pnas.73.12.4565

CHARMM-GUI: A web-based graphical user interface for CHARMM
journal, March 2008

  • Jo, Sunhwan; Kim, Taehoon; Iyer, Vidyashankara G.
  • Journal of Computational Chemistry, Vol. 29, Issue 11
  • DOI: 10.1002/jcc.20945

Cell-wall carbohydrates and their modification as a resource for biofuels
journal, May 2008


Crystallographic snapshot of cellulose synthesis and membrane translocation
journal, December 2012

  • Morgan, Jacob L. W.; Strumillo, Joanna; Zimmer, Jochen
  • Nature, Vol. 493, Issue 7431
  • DOI: 10.1038/nature11744

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP
journal, April 2014

  • Morgan, Jacob L. W.; McNamara, Joshua T.; Zimmer, Jochen
  • Nature Structural & Molecular Biology, Vol. 21, Issue 5
  • DOI: 10.1038/nsmb.2803

Cellulose as an Architectural Element in Spatially Structured Escherichia coli Biofilms
journal, October 2013

  • Serra, D. O.; Richter, A. M.; Hengge, R.
  • Journal of Bacteriology, Vol. 195, Issue 24
  • DOI: 10.1128/JB.00946-13

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
journal, October 1992

  • Kumar, Shankar; Rosenberg, John M.; Bouzida, Djamal
  • Journal of Computational Chemistry, Vol. 13, Issue 8
  • DOI: 10.1002/jcc.540130812

How Cellulose Elongates—A QM/MM Study of the Molecular Mechanism of Cellulose Polymerization in Bacterial CESA
journal, April 2015

  • Yang, Hui; Zimmer, Jochen; Yingling, Yaroslava G.
  • The Journal of Physical Chemistry B, Vol. 119, Issue 22
  • DOI: 10.1021/acs.jpcb.5b01433

Molecular biology of cellulose production in bacteria
journal, May 2002


A Molecular Description of Cellulose Biosynthesis
journal, June 2015


Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
journal, September 2007


BcsA and BcsB form the catalytically active core of bacterial cellulose synthase sufficient for in vitro cellulose synthesis
journal, October 2013

  • Omadjela, O.; Narahari, A.; Strumillo, J.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 44
  • DOI: 10.1073/pnas.1314063110

Catalytic Mechanism of Glycosyltransferases:  Hybrid Quantum Mechanical/Molecular Mechanical Study of the Inverting N -Acetylglucosaminyltransferase I
journal, December 2006

  • Kozmon, Stanislav; Tvaroška, Igor
  • Journal of the American Chemical Society, Vol. 128, Issue 51
  • DOI: 10.1021/ja065944o

Carbohydrate–Protein Interactions That Drive Processive Polysaccharide Translocation in Enzymes Revealed from a Computational Study of Cellobiohydrolase Processivity
journal, June 2014

  • Knott, Brandon C.; Crowley, Michael F.; Himmel, Michael E.
  • Journal of the American Chemical Society, Vol. 136, Issue 24
  • DOI: 10.1021/ja504074g

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations
journal, August 2014

  • Wu, Emilia L.; Cheng, Xi; Jo, Sunhwan
  • Journal of Computational Chemistry, Vol. 35, Issue 27
  • DOI: 10.1002/jcc.23702

Protein-Induced Membrane Curvature Investigated through Molecular Dynamics Flexible Fitting
journal, July 2009


Cellulose biogenesis: Polymerization and crystallization are coupled processes in Acetobacter xylinum
journal, November 1980

  • Benziman, M.; Haigler, C. H.; Brown, R. M.
  • Proceedings of the National Academy of Sciences, Vol. 77, Issue 11
  • DOI: 10.1073/pnas.77.11.6678

Localization of c-di-GMP-Binding Protein with the Linear Terminal Complexes of Acetobacter xylinum
journal, October 2001


Cellulose Synthesis in Higher Plants
journal, November 2006


A structural basis for processivity
journal, September 2001

  • Breyer, Wendy A.; Matthews, Brian W.
  • Protein Science, Vol. 10, Issue 9
  • DOI: 10.1110/ps.10301

CHARMM: The biomolecular simulation program
journal, July 2009

  • Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
  • Journal of Computational Chemistry, Vol. 30, Issue 10
  • DOI: 10.1002/jcc.21287

CELLULOSE BIOSYNTHESIS: Exciting Times for A Difficult Field of Study
journal, June 1999


Carbohydrate–Aromatic Interactions
journal, June 2012

  • Asensio, Juan Luis; Ardá, Ana; Cañada, Francisco Javier
  • Accounts of Chemical Research, Vol. 46, Issue 4
  • DOI: 10.1021/ar300024d

Alteration of in vivo cellulose ribbon assembly by carboxymethylcellulose and other cellulose derivatives
journal, July 1982


QM/MM distortion energies in di- and oligosaccharides complexed with proteins
journal, January 2001

  • French, Alfred D.; Johnson, Glenn P.; Kelterer, Anne-Marie
  • International Journal of Quantum Chemistry, Vol. 84, Issue 4
  • DOI: 10.1002/qua.1111

Sum of the Parts: Composition and Architecture of the Bacterial Extracellular Matrix
journal, November 2013

  • McCrate, Oscar A.; Zhou, Xiaoxue; Reichhardt, Courtney
  • Journal of Molecular Biology, Vol. 425, Issue 22
  • DOI: 10.1016/j.jmb.2013.06.022

Accumulation of a Novel Glycolipid and a Betaine Lipid in Cells of Rhodobacter sphaeroides Grown under Phosphate Limitation
journal, February 1995

  • Benning, C.; Huang, Z. H.; Gage, D. A.
  • Archives of Biochemistry and Biophysics, Vol. 317, Issue 1
  • DOI: 10.1006/abbi.1995.1141

Structural and Energetic Basis of Carbohydrate–Aromatic Packing Interactions in Proteins
journal, June 2013

  • Chen, Wentao; Enck, Sebastian; Price, Joshua L.
  • Journal of the American Chemical Society, Vol. 135, Issue 26
  • DOI: 10.1021/ja4040472

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
journal, July 2009


Hybrid Quantum Mechanical/Molecular Mechanical Investigation of the β-1,4-Galactosyltransferase-I Mechanism
journal, August 2009

  • Krupička, Martin; Tvaroška, Igor
  • The Journal of Physical Chemistry B, Vol. 113, Issue 32
  • DOI: 10.1021/jp904716t