Supercomputers and Spider Webs Uncover Bone Regeneration’s Secrets

Dentistry Today
Image courtesy of Davoud Ebrahimi, MIT.


Image courtesy of Davoud Ebrahimi, MIT.

Spider webs may offer clues to osteoregeneration, or how bones repair themselves. According to research conducted by Tufts University, the Massachusetts Institute of Technology (MIT), and Nottingham Trent University, genes that initiate biomineralization could be activated in human stem cells. The researchers achieved these results with engineered silk derived from the dragline of golden orb weaver spider webs, which they combined with silica.

The study used the Stampede supercomputer at the Texas Advanced Supercomputing Center at the University of Texas at Austin and the Comet supercomputer at the San Diego Supercomputer Center at the University of California San Diego through an allocation from the eXtreme Science and Engineering Discovery Environment (XSEDE), funding by the National Science Foundation.

The supercomputers helped scientists model how the cell membrane protein receptor called integrin folds and activates the intracellular pathways that lead to bone formation. The research will help larger efforts to treat bone growth diseases such as osteoporosis or calcific aortic valve disease.

“This work demonstrates a direct link between silk-silica-based biomaterials and intracellular pathways leading to osteogenesis,” said study coauthor Zaira Martín-Moldes, a postdoctoral scholar at the Kaplan Lab at Tufts University. “The hybrid material promoted the differentiation of human mesenchymal stem cells, the progenitor cells from the bone marrow, to osteoblasts as an indicator of osteogenesis, or bone-like tissue formation.”

Silk has been shown to be a suitable scaffold for tissue regeneration, due to its mechanical properties, Martín-Moldes said. It’s biodegradable, biocompatible, and fine-tunable through bioengineering modifications. The researchers at Tufts University modified the genetic sequence of silk from golden orb weaver spiders and fused the silica-promoting peptide R5 derived from a gene of the diatom Cylindrotheca fusiformis silaffin.

“We would love to generate a model that helps us predict and modulate these responses both in terms of preventing the mineralization and also to promote it,” said Martín-Moldes.

“High-performance supercomputing simulations are utilized along with experimental approaches to develop a model for the integrin activation, which is the first step in the bone formation process,” said study coauthor Davoud Ebrahimi, a postdoctoral associate at the Laboratory for Atomistic and Molecular Mechanics at MIT.

Integrin embeds itself in the cell membrane and mediates signals between the inside and the outside of cells. In its dormant state, the head unit sticking out of the membrane is bent over like a nodding sleeper. This inactive state prevents cellular adhesion. In its activated state, the head unit straightens out and is available for chemical binding at its exposed ligand region.

“Sampling different states of the conformation of the integrins in contact with silicified or non-silicified surfaces could predict activation of the pathway,” said Ebrahimi.

Sampling the folding of proteins remains a classically computationally expensive problem, despite recent and large efforts in developing new algorithms. The derived silk-silica chimera the researchers weighed around 40 kilodaltons, a unit that quantifies mass on an atomic or molecular scale.

“In this research, what we did in order to reduce the computational costs, we have only modeled the head piece of the protein, which is getting in contact with the surface that we’re modeling,” said Ebrahimi. “But again, it’s a big system to simulate and can’t be done on an ordinary system or ordinary computers.” 

The MIT computational team at MIT used the Gromacs molecular dynamics package, software for chemical simulation available on both the Stampede and Comet supercomputers. The researchers could perform those large simulations by having access to the XSEDE computational clusters. Computation combined with experimentation helped advance the work in developing a model of osteoregeneration. 

“We propose a mechanism in our work that starts with the silica-silk surface activating a specific cell membrane protein receptor, in this case integrin αVβ3,” said Martín-Moldes. 

This activation triggers a cascade in the cell through three mitogen-activated protein kinsase pathways, the main one being the c-Jun N-terminal kinase cascade. Other factors also are involved in this process, such as Runx2, the main transcription factor related to osteogenesis. According to the study, the control system did not show any response, and neither did the blockage of integrin using an antibody, confirming its involvement in the process.

“Another important outcome was the correlation between the amount of silica deposited in the film and the level of induction of the genes that we analyzed,” said Martín-Moldes. “These factors also provide an important feature to control in future material design for bone-forming biomaterials.” 

The researchers are building a pathway to generate biomaterials that could be used in the future, with the mineralization being a critical process. The final goal is to develop models that help design the biomaterials to optimize the bone regeneration process, when the bone is required to regenerate or to minimize it when bone formation needs to be reduced. These results also help advance the research and may be useful in larger efforts to treat and cure bone diseases.

“We could help in curing disease related to bone formation, such as calcific aortic valve disease or osteoporosis, which we need to know the pathway to control the amount of bone formed, to either reduce it or increase it,” said Ebrahimi. 

The study, “Intracellular Pathways Involved in Bone Regeneration Triggered by Recombinant Silk-Silica Chimeras,” was published by Advanced Functional Materials.

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