Biology subjects

Linsky, T. W.

Publications and source records attributed to Linsky, T. W..

2 recordsLinked to original sources

bioRxiv2021

Sampling of Structure and Sequence Space of Small Protein Folds

Nature only samples a small fraction in sequence space, yet many more amino acid combinations can fold into stable proteins. Furthermore, small structural variations in a single fold, which may only be a few amino acids different from the next homolog, define their molecular function. Hence, to design proteins with novel molecular functionalities, such as molecular recognition, methods to control and sample shape diversity are necessary. To explore this space, we developed and experimentally validated a computational platform that can design a wide variety of small protein folds while sampling high shape diversity. We designed and evaluated about 30,000 de novo protein designs of 7 different folds. Among these designs, about 6,200 stable proteins were identified, with predicted structures having first-of-its-kind minimalized thioredoxin. Obtained data revealed more protein folding rules, such as helix connecting loops, which were in nature. Beyond providing a resource database for protein engineering, our data presents a large training data set for machine learning. We developed a high-accuracy classifier to predict the stability of our designed proteins. The methods and the wide range of new protein shapes provide a basis for the design of new protein function without compromising stability.

bioengineering↗

bioRxiv2020

De novo design of ACE2 protein decoys to neutralize SARS-CoV-2

There is an urgent need for the ability to rapidly develop effective countermeasures for emerging biological threats, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a generalized computational design strategy to rapidly engineer de novo proteins that precisely recapitulate the protein surface targeted by biological agents, like viruses, to gain entry into cells. The designed proteins act as decoys that block cellular entry and aim to be resilient to viral mutational escape. Using our novel platform, in less than ten weeks, we engineered, validated, and optimized de novo protein decoys of human angiotensin-converting enzyme 2 (hACE2), the membrane-associated protein that SARS-CoV-2 exploits to infect cells. Our optimized designs are hyperstable de novo proteins ([~]18-37 kDa), have high affinity for the SARS-CoV-2 receptor binding domain (RBD) and can potently inhibit the virus infection and replication in vitro. Future refinements to our strategy can enable the rapid development of other therapeutic de novo protein decoys, not limited to neutralizing viruses, but to combat any agent that explicitly interacts with cell surface proteins to cause disease.

biochemistry↗