biochemistry, bioinformatics, biosensors, protein folding, protein design, population
My lab studies the folding and design of proteins, enzymes, vaccine antigens, and biosensors. When I came here in 1999, I was a bioinformaticist and my lab worked exclusively in computational biology. Since then, we have evolved into a mostly experimental lab, with a little computation still mixed in. Our early work included algorithm development in protein structural bioinformatics, including structure prediction, contact map prediction, local structure prediction, hidden Markov models, sequence alignment, molecular surface area calculation, torsion space molecular dynamics, simplified representations for molecular dynamics, bioinformatics-driven force fields, structure-based alignment, and models for folding pathways. We proposed the "phone cord effect" to explain superhelicity in alpha helical crossovers. Starting about ten years ago, we began doing experimental work on green fluorescent protein (GFP) with the help of molecular biologist Prof. Donna E. Crone. We created a non-circularly permuted "re-wired" GFP, a permuted and truncated "leave-one-out" GFP, a variant that folds faster and more efficiently, and a GFP-base biosensor. We inserted strategically-placed disulfides to test specific hypotheses for the folding pathway of GFP and reasoned out the presence of two specific folding intermediates. More recently we are studying the formation of the fluorescent chromophore and the dependence of GFP fluorescence on specific residues and on thermodynamic stability. The principle thrust of the lab is to develop the leave-one-out (LOO) method for GFP-based biosensors. By combining computational design and high throughput screening, we find sets of mutations that complement a specific bound peptide and allow the truncated LOO-GFP to fold and glow only in the presence of a target protein which has been unfolded to expose that sequence. A biosensor for detection of H5N1 influenza virus hemagglutinin was published in 2015. We are collaborating on the development of a sensor for dengue virus and zika. We are also engaged in collaborative efforts to develop better enzymes, design new biosensors, and to develop new protein-based vaccines. Specifically, we are at work developing a vaccine for dengue, and a contraceptive vaccine targeting sperm-specific antigens. And we continue to develop algorithmic tools for protein design, including a graphical interface for the Rosetta package, called InteractiveRosetta. This work was made possible by our collaborators, the Center for Computational Innovation (CCI), and Center for Biotechnology and Interdisciplinary Sciences (CBIS), and by grants from the NSF, NIH, and Rosetta Commons.
BA. Carleton College, Northfield MN.
Ph.D. University of California, San Diego
- Shirke AN, Basore D, Holton S, Su A, Baugh E, Butterfoss GL, Makhatadze G, Bystroff C, Gross RA. (2016) Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics. Applied microbiology and biotechnology. 2016 Jan 13:1-2
- Schenkelberg CD, Bystroff C. (2016) Protein backbone ensemble generation explores the local structural space of unseen natural homologs. Bioinformatics. 2016 Jan 18:btw001.
- Huang Y-M, Banerjee S, Crone DE, Buck PM, Schenkelberg CD, Pitman DJ & Bystroff C. (2015) Computationally designed biosensors based on leave-one-out green fluorescent protein. Biochemistry 54(40):6263-73.
- Shirke AN, Basore D, Butterfoss GL, Bonneau R, Bystroff C, Gross RA (2015) Thermostabilization of Aspergillus oryzae Cutinase using Rational Design Approach. Proteins, Structure, Function and Bioinformatics 84(1), 60-72 abstract
- Schenkelberg CD, & Bystroff C. (2015) InteractiveROSETTA: A client graphical user interface for the Py-Rosetta and Rosetta protein modeling suite. Bioinformatics btv492.
- Pitman DJ, Banerjee S, Macari S, Castaldi C, Crone DE, & Bystroff C. (2015) Exploring the folding pathway of green fluorescent protein through disulfide engineering. Protein Science 24:341-353
- Pitman DJ, Schenkelberg CD, Huang Y-M, DiTursi D, Teets FD & Bystroff C. (2014) Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design. Bioinformatics.
- Rosenman DJ, Huang Y-M, Xia K, Fraser K, Jones VE, Lamberson CM, Van Roey P & Bystroff C. (2014) Green-lighting Green Fluorescent Protein: Faster and more efficient folding by eliminating a cis-trans peptide isomerization event. Protein Science 23(4):400-410.
- Huang Y-M, & Bystroff C. (2013) Expanded Explorations into the Optimization of an Energy Function for Protein Design. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 26 Sept. 2013. IEEE computer Society Digital Library. IEEE Computer Society
- Ramakrishnan V, Srinivasan S, Salem SM, Zaki MJ , Matthews SJ, Colon W, & Bystroff C. (2012) GeoFold: Topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability. Proteins 80(3):920-934.
- Crone DE, Huang Y-M, Pitman DJ, Schenkelberg C, Fraser K, Macari S, & Bystroff C. (2012) GFP-based Biosensors State of the Art in Biosensors / Book 1 ISBN 980-953-307-669-5.
- Huang Y-M, Nayak S, Bystroff C. (2011) Quantitative in vivo solubility and reconstitution of truncated circular permutants of green fluorescent protein. Protein Science 20(11):1775-80
- Buck PM & Bystroff C (2011) Constraining Local Structure Using Rigid Body Dynamics Can Speed Up Folding By Promoting Structural Polarization Of The Folding Pathway Protein Science 20(6):959-969
- Reeder PJ, Huang Y-M, Dordick JS & Bystroff C. (2010) A Rewired Green Fluorescent Protein: Folding and Function in a Nonsequential, Noncircular GFP Permutant. Biochemistry 49(51), 10773-10779.
- Salem SM, Zaki MJ, Bystroff C. (2010) FlexSnap: Flexible Non-Sequential Protein Structure Alignment. Algorithms for Molecular Biology Jan 4;5(1):12.
- Cole B & Bystroff C. (2009) Alpha helical crossovers favor right-handed supersecondary structures by a kinetic trapping mechanism. The phone cord effect in protein folding. Protein Science 18(8) 1602 - 1608