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The Consortium of Molecular Design at BYU provides cutting edge interdisciplinary research opportunities for students to push the envelope for protein engineering and drug discovery.

We use close collaboration between laboratories at BYU in Physics, Chemistry, Computer Science, LifeSciences, and Engineering to tackle these challenging topics from all angles.

We actively seek industrial collaboration and support for our efforts and are excited to explore mutually beneficial application of all state-of-the-art technologies to revolutionize molecular design.


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Selected Publications

Atomic models of proteins built by homology modeling or from low-resolution experimental data may contain considerable local errors. The refinement success of molecular dynamics simulations is usually limited by both force field accuracy and by the substantial width of the conformational distribution at physiological temperatures. We propose a method to overcome both these problems by coupling homologous replicas during a molecular dynamics simulation, which narrows the conformational distribution, and smoothens and even improves the energy landscape by adding evolutionary information.
A novel protein refinement protocol is presented which utilizes molecular dynamics (MD) simulations of an ensemble of adaptively restrained homologous replicas. This approach adds evolutionary information to the force field and reduces random conformational fluctuations by coupling of several replicas. It is shown that this protocol refines the majority of models from the CASP11 refinement category and that larger conformational changes of the starting structure are possible than with current state of the art methods. The performance of this protocol in the CASP11 experiment is discussed. We found that the quality of the refined model is correlated with the structural variance of the coupled replicas, which therefore provides a good estimator of model quality. Furthermore, some remarkable refinement results are discussed in detail.
Corbyn Kubalek, Spencer Gardiner, William Heaps, Kristina M. McCammon, Sam Talcott, Matthew Argyle, Bradley C. Bundy, and Dennis Della Corte

Glycosylation is the most common post-translational modification in the human proteome, with over half of all human proteins bearing covalently attached glycans. These glycan structures direct protein folding through ER quality control machinery, shield polypeptides from proteolytic degradation, regulate circulatory half-life via the asialoglycoprotein receptor, and serve as molecular signals for immune recognition and intracellular trafficking. For biopharmaceuticals, which constitute a rapidly growing share of approved drugs, glycan profiles are critical quality attributes that directly determine clinical efficacy and safety. Yet achieving the correct glycosylation on a therapeutic protein remains one of the field’s central challenges, as glycan biosynthesis is non-template-driven and highly sensitive to expression system and manufacturing conditions. This review connects the biological functions of glycosylation to the practical strategies of glycoengineering, examining how sequence design, expression system selection, and downstream enzymatic remodeling are used to optimize therapeutic glycoproteins. Clinical case studies spanning monoclonal antibodies, cytokines, and enzyme replacement therapies illustrate how glycan engineering translates into improved patient outcomes. We conclude by surveying emerging technologies poised to make precisely glycosylated therapeutics more accessible.