Education and Training
B.A. Carleton College
Postdoctoral Training, UCSF, U. Washington
Tel: (518) 276-3185
Fax: (518) 276-2344
Office: Science Center Rm. 3C07
Rensselaer Polytechnic Institute
110 8th Street
Troy, NY 12180
Bioinformatics, protein folding, protein design; computational biology
My lab studies protein folding and design. Understanding the pathway of protein folding may be the key to better algorithms for protein design. We are focusing our protein design work on green fluorescent protein (GFP), with the goal of understanding its folding and its dynamics, and to harness its intrinsic reporting ability to create programmable fluorescent biosensors, capable of specifically detecting peptides and proteins. We develop software that runs on massively parallel clusters such as CCNI. We synthesize and screen computationally designed molecules in the lab using molecular biological techniques, and then subject the proteins to biophysical analysis and X-ray crystallography.
See my homepage for more information.
Huang Y-M, & Bystroff C. (2012) Exploring objective functions and cross-terms in the optimization of an energy function for protein design. ACM BCB 2012. Orlando FL, Oct 7, 2012. (in press)
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. (in press)
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.
Paredes DI, Watters KE, Pitman DJ, Bystroff C, & Dordick JS (2011) Comparative Void-Volume Analysis of Psychrophilic and Mesophilic Enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility BMC Structural Biology 11(1):42
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.
Salem S, Zaki MJ, Bystroff C (2009) Iterative non-sequential protein structural alignment. J Bioinform Comput Biol 7(3):571-96
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
Huang Y-M & Bystroff C. (2009). Specific complementation and reconstitution of flourescence from a circularly permuted, truncated green fluoresent protein. Biochemistry 48(5):929-40.
Buck P. & Bystroff C. (2008) Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field Proteins: Structure, Function and Bioinformatics 76(2):331-342.
Bystroff C. & Webb-Robertson, B.J. (2008) Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure BMC Bioinformatics 9:429 (10 October 2008)