Computational design of specific binding proteins using Leave-One-Out The goal of this research is to be able to design a receptor protein for any protein target. Furthermore, we propose that the binding event will be signaled by the appearance of enzyme activity or fluorescence. The novel binding proteins will be able to sense and report the presence of a specific protein or peptide in a mixture of others, allowing the detection of disease agents or other proteins of interest both in vivo and in vitro. The new approach takes advantage of protein folding pathways. When proteins fold, they do so in a specified order of events, and the events can be predicted based on the structure of the protein. When a protein finishes folding, its activity is immediately turned on. If we leave out one small piece of the protein so that the folding cannot finish, then the protein sits in an inactive state ntil the missing piece appears. Using this Leave-One- Out strategy, partially folded proteins become sensors for their missing pieces. Using computational design algorithms, a new amino acid sequence can be substituted for the left out piece. This new sequence can be from anthrax, avian flu, a cancer cell marker or any other protein. Computational substitution of the amino acids surrounding this new sequence is made possible using massively parallel computing clusters and grid computing, and by dividing the design task into numerous smaller tasks based on what is known about protein folding and energy calculations. The final design is a protein that wraps around the target peptide, specifically identifying it by its complementary shape. Green fluorescent protein has been the subject of the first leave-one-out design studies and has yielded specific binding proteins that glow only when the target peptide is present.

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Computational design of specific binding proteins using Leave-One-Out The results of this research could revolutionize protein diagnostics, replacing monoclonal antibodies as the current best means of specific protein identification. Computationally designed specific binding proteins could be used as protein therapeutics, biosensors, proteomic arrays, fluorescent probes, protein purification affinity agents, and many other applications.

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National Institute of General Medical Sciences (NIGMS)
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Macromolecular Structure and Function D Study Section (MSFD)
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Preusch, Peter
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Rensselaer Polytechnic Institute
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Schenkelberg, Christian D; Bystroff, Christopher (2016) Protein backbone ensemble generation explores the local structural space of unseen natural homologs. Bioinformatics 32:1454-61
Shirke, Abhijit N; Basore, Danielle; Butterfoss, Glenn L et al. (2016) Toward rational thermostabilization of Aspergillus oryzae cutinase: Insights into catalytic and structural stability. Proteins 84:60-72
Shirke, Abhijit N; Basore, Danielle; Holton, Samantha et al. (2016) Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics. Appl Microbiol Biotechnol 100:4435-46
Schenkelberg, Christian D; Bystroff, Christopher (2015) InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite. Bioinformatics 31:4023-5
Huang, Yao-Ming; Banerjee, Shounak; Crone, Donna E et al. (2015) Toward Computationally Designed Self-Reporting Biosensors Using Leave-One-Out Green Fluorescent Protein. Biochemistry 54:6263-73
Pitman, Derek J; Banerjee, Shounak; Macari, Stephen J et al. (2015) Exploring the folding pathway of green fluorescent protein through disulfide engineering. Protein Sci 24:341-53
Rosenman, David J; Huang, Yao-ming; Xia, Ke et al. (2014) Green-lighting green fluorescent protein: faster and more efficient folding by eliminating a cis-trans peptide isomerization event. Protein Sci 23:400-10
Pitman, Derek J; Schenkelberg, Christian D; Huang, Yao-Ming et al. (2014) Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design. Bioinformatics 30:1138-1145
Xia, Yan; DiPrimio, Nina; Keppel, Theodore R et al. (2013) The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation. J Am Chem Soc 135:18840-9
Huang, Yao-Ming; Bystroff, Christopher (2013) Expanded explorations into the optimization of an energy function for protein design. IEEE/ACM Trans Comput Biol Bioinform 10:1176-87

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