Molecular modeling extends knowledge of biopolymeric materials

Computational molecular dynamics simulation produces promising results with cellulose and advances research in glass ceramics and soft condensed matter

Diego Freire | Agência FAPESP – At the Center for Computational Engineering and Sciences (CCES), one of the Research, Innovation and Dissemination Centers (RIDCs) funded by FAPESP, modeling based on molecular dynamics simulation has led to a better understanding of biopolymers – materials like cellulose, hemicellulose or lignin – and how they are structured in plant cell walls.

Possible applications of the technique to research in glass ceramics and soft condensed matter were shared by researchers from institutions in São Paulo State and California during FAPESP Week UC Davis in Brazil, hosted by FAPESP and the University of California, Davis (UC Davis), on May 12-13, 2015, in São Paulo City.

The research done at CCES as part of FAPESP’s Bioenergy Research Program (BIOEN) to produce second-generation bioethanol, was presented by Munir Salomao Skaf, who runs CCES and is a professor at the University of Campinas’s Chemistry Institute (IQ-UNICAMP) in São Paulo State.

“Molecular modeling helps us compute and determine the movements of every atom in the molecular system,” Skaf told Agência FAPESP. “The simulation mimics the system’s physiology, protein, polymer, solvent, ions, and so on. Detailed knowledge of these particles obtained by using the high-performance computational resources at CCES enables us to study and understand how they interact.”

The most recent findings include the identification of factors that determine the thermostability and thermophilicity of certain enzymes involved in the process of hydrolysis.

Research conducted by Rodrigo Leandro Silveira at IQ-UNICAMP with support from FAPESP set out to discover why cellobiose, a product of cellulose hydrolysis, inhibits cellobiohydrolases, which are precisely the enzymes that catalyze hydrolysis.

“The enzymes attack the cellulose fibers, break down the cellulose chains and generate small molecules called cellobioses, which are a product of this reaction. As the reaction continues, the concentration of cellobioses increases and they start to inhibit enzyme activity, which eventually stops,” Skaf said.

This happens because as soon as the enzyme completes hydrolysis, it binds with the cellobiose, which is trapped where it is produced and blocks the channel.

“In fact we found that a specific amino acid residue is responsible for binding the cellobiose in the enzyme cavity and preventing it from being released into the medium. We also found that the enzyme attacks new substrates that haven’t been hydrolyzed,” he said.

According to Skaf, the research suggests genetic modification could lead to an enzyme that is catalytically efficient and less inhibited by the product of its own reaction.

In other research Erica Teixeira Prates, also supported by FAPESP, studied endoglucanases, modular enzymes with one module responsible for the reaction and others for binding with the substrate so that they “stick” to the cell wall fibers of the cellulose and promote contact between the catalytic domain and its target.

Performed in collaboration with Igor Polikarpov and his team at the University of São Paulo’s São Carlos Institute of Physics (IFSC-USP), the research showed how the enzyme used alternative mechanisms to bind to the cellulose.

“This enzyme is an endoglucanase from a microorganism that has evolved other mechanisms to perform this role of binding to the substrate,” Skaf said.

The group also obtained promising results in a study of the thermodynamic forces that maintain cell wall cohesion, identifying the influence of the different types of hemicellulose on cellulose fibrils.


CCES conducts research involving molecular modeling in partnership with biophysicists who specialize in protein structure, crystallographers and molecular biologists. In particular, its researchers collaborate with Polikarpov and the National Bioethanol Science &Technology Laboratory (CTBE).

While the biologists isolate proteins and determine their crystallographic structure via static images of each atom’s position, molecular biologists and enzymologists perform enzymatic assays to understand how enzymes interact with substrates such as different types of cellulose and other polysaccharides.

“On one hand you have the protein structure and on the other biological assays showing how the protein goes about breaking down the biomass. The research provides a bridge between static structure and biological behavior,” Skaf said.

Information about enzyme structure and data from enzymatic assays are used to produce short films of molecular pathways showing how the atoms move.

CCES’s high-performance computational resources capture millions of frames displaying the pathways, which are analyzed to see how protein and substrate bind, for example, what keeps substrates in the right position for hydrolysis, which residues interact most, and how enzyme structure changes over time, among other things.

“We observe and analyze these processes to correlate them with their biological behavior in enzyme assays, in natural processes when fungi and bacteria break down organic matter in nature, or in industrial processes where these enzymes are used to break down biomass and convert it into smaller sugars fermented to ethanol or converted into other higher value-added chemicals in what’s known as biorefining,” Skaf explained.

Glass ceramics

For Alexandra Navrotsky, UC Davis Interim Dean and a researcher in mathematical and physical sciences, the molecular dynamics simulations developed at CCES could be used in research on many different materials.

“The techniques are basically the same,” she told Agência FAPESP. “After all, we’re talking about matter made up of atoms and molecules. If we know how they interact, we can compute these processes, the forces exerted on the atoms and molecules, and their movements. Then we can track the paths of atoms in any system. Brazil’s successful experiments in this direction can and should be multiplied.”

Navrotsky’s presentation to FAPESP Week UC Davis in Brazil focused on her research with soft condensed matter, especially calorimetric studies of micelle systems and other related materials.

The Center for Research, Teaching, and Innovation in Glass (CeRTEV), one of the Research, Innovation & Diffusion Centers (RIDCs) supported by FAPESP, also presented some of its findings at the event.

“We set out to understand the correlations between the complex molecular structure of glass, which as a non-crystalline material has randomly oriented atoms, and dynamic processes such as viscous flow or fluidity and structural relaxation. We’re also interested in how the structure of glass changes when heated to a certain temperature. Our foremost interest is crystallization, because it leads to glass ceramics and possible commercial applications of these polycrystalline materials,” said Edgar Dutra Zanotto, who heads CeRTEV and is a professor in the Department of Materials Engineering at the Federal University of São Carlos (UFSCar) in São Paulo State.

Glass ceramics are produced by controlled crystallization of glass. Among the commercial applications presented by Zanotto were false teeth indistinguishable from the real thing and bulletproof transparent materials that look like glass but are polycrystalline and hence far harder and stronger.

Other applications of glass ceramics include architectural materials rendered to look like marble and granite, and bioactive ossicular implants for ear, hand or cheek bones.

“These biovitroceramic materials are much more biocompatible and bioactive than titanium, for example,” Zanotto said. “When they come into contact with blood plasma, saliva, sweat and other body fluids, they automatically form a layer of carbonate hydroxyapatite and bind to the cartilage and bone. So they can perform functions that can’t be performed by titanium.”

For Zanotto the discussions that took place during FAPESP Week UC Davis should lead to partnerships between researchers in São Paulo and California to extend the scope of their work.

“Our studies can benefit from the data and thermodynamic measurements compiled by colleagues at UC Davis,” he said. “Alexandra Navrotsky, one of the leading experts on fluid and glass thermodynamics, and her group can benefit from dynamic process simulations and experimental data obtained by our group to enhance their understanding of the processes studied at UC Davis.”