When bacteria break down cellulose, they first anchor themselves to the substrate’s surface using carbohydrate binding proteins and enzymes. But understanding just how sticky that bond is has been a challenge for scientists, and it matters because it will help the development of new nanomaterials, potentially improving biofuel production and global carbon cycling, and identifying new and better drug targets.
A recent study in the Proceedings of the National Academy of Sciences explains the underlying molecular rules that control that stickiness, using computational simulations performed at Los Alamos National Laboratory.
The study examines the molecular interactions between a carbohydrate binding module (CBM) protein and its binding substrate, cellulose. Cellulose is the most abundant organic compound on Earth that is naturally decomposed by microorganisms, and hence it plays a central role in the global carbon cycle. It is a type of plant fiber polymer made of repeating glucose sugars and has industrial uses for textiles, cellophane, paperboard and paper, in addition to serving as renewable feedstock to produce biofuels and biochemicals.
However, scientists still have a limited understanding of how microorganisms such as bacteria conduct this breakdown, so their starting point was to analyze the phase where the bacteria first anchor themselves to the substrate surface using cellulosomes, which are extracellular complex carbohydrate binding proteins and multiple enzymes. Understanding this sticky problem will enable scientists to engineer more efficient enzymes and microbes that decompose cellulose into sugars for biofuels production such as ethanol, biodiesel, green diesel or biogas.
How they did it
The research team studied a specific CBM protein that enables bacterial multi-enzyme machinery such as cellulosome, in action like a gecko sticking its feet to a wall, to anchor tightly to cellulose surfaces and then the researchers changed the engineered protein’s surface ‘stickiness,’ as measured using a new toolkit to monitor cellulose decomposition activity.
Computational simulations were carried out by the Laboratory’s Cesar López and Gnana Gnanakaran, providing a framework to understand and interpret the findings from this analytical kit.
“The atomistic simulations explain the underlying molecular rules that govern the CBM protein stickiness towards cellulose surfaces. Also, these calculations showed how modifications to key residues could alter the association to cellulose, either by affecting the stability of CBM or modifying the interactions with the cellulose surface,” said Gnanakaran.
The project was supported by the National Science Foundation (NSF) Division of Chemical, Bioengineering, Environmental and Transport Systems. Co-authors on the study include Edward Contrada, Jonathan Ash, Atharv Kulkarni, Ki-Bum Lee, Jinho Yoon, Hyeon-Yeol Cho of Rutgers University and researchers from the National Renewable Energy Laboratory (John Yarbrough) and Los Alamos National Laboratory’s Cesar López and Sandrasegaram (Gnana) Gnanakaran.