Written by Richard Wu
David Baker, the University of Washington
The Coming of Age of De Novo Protein Design
Life on Earth depends on proteins. Proteins are large molecules assembled from building blocks, called amino acids, and are produced through a folding process that results in a complex three-dimensional structure, like origami. There are many different amino acids, each with particular properties such as size and charge, and the sequence of amino acids in a protein determines its structure and function.
However, given the complexity of proteins, it is difficult to predict protein structures from amino acid sequences alone. David Baker from the University of Washington is studying protein-folding and designing algorithms to predict protein structures. His laboratory has harnessed artificial intelligence to develop RoseTTAFold, a software tool that computes protein structures from amino acid sequences. From there, they have also worked on software approaches to generate new amino acid sequences which could fold into desired protein structures.
Baker’s research has led to the design of various artificial proteins that can block the flu and COVID-19 viruses, prevent the formation of Alzheimer’s disease-associated proteins, harvest sunlight for energy, produce light, and self-assemble into geometrically-shaped nanostructures. The design of artificial proteins is an exciting step forward in science, with the potential to transform numerous fields ranging from medicine to energy.
Ebru Demir, Sabanci University
Self-Assembling Peptide Nanofiber Hydrogel as 3D Scaffolds for Corneal Stromal Cells
Severe damage to the cornea of the eye, which can lead to visual impairment or blindness, is often treated with corneal transplantation. However, corneal transplantation is limited by donor tissue availability.
One alternative to corneal transplantation is tissue engineering. Ebru Demir from Sabanxci University has been investigating the use of peptide-based hydrogels as scaffolds for corneal tissue engineering. These hydrogels are gel-like materials containing water, similar to gelatin, and are synthesized from peptide materials, which are made from the same building blocks as proteins.
Demir’s experiments show that the peptide-based hydrogels are biocompatible, have similar transparency to natural corneal tissue, and are strong enough to support corneal cell and blood vessel regeneration. These properties make the peptide-based hydrogels a good candidate material for use in corneal tissue scaffolds.
Through this work, Demir and colleagues demonstrate how materials research can help advance the field of tissue engineering, thereby making steps toward improving human health and well-being.
Mohamed Soliman, De Montfort University and Cairo University
Antimicrobial Activity of β-Sheet Forming Ultra-Short De Novo Ionic-Complementary Peptides Towards Wound Infections
A significant problem facing medicine today is the rise of bacterial resistance to antibiotics. To address this public health challenge, Mohamed Soliman, from De Montfort University and Cairo University, is researching the antimicrobial properties of peptide-based hydrogels. Peptide materials are made from the same building blocks as proteins, and hydrogels are gel-like materials that contain water, similar to gelatin. These peptide-based hydrogel materials can kill bacteria by puncturing bacterial cell membranes, and yet are biocompatible and biodegradable.
Soliman and colleagues have found that their peptide-based hydrogels were effective at killing multiple infectious bacteria species, including P. aeruginosa, A. baumannii, E. coli, and K. Pneumoniae. These findings are promising and suggest that antimicrobial peptide-based hydrogels could soon help save lives.