- Research Overview
- Chemical Biology and Medicinal Chemistry
- Chemical Biology and Medicinal Chemistry Overview
- Discovering Enzyme Substrates and Functions
- Discovering Protein Ligands to Probe and Alter Function
- Discovering Enzyme Activators
- Analyzing Mechanisms of Drug Resistance via Chemical Biology
- Analyzing Enzyme Conformational Dynamics, Substrate Binding, and Catalysis
- Effective Drug Targeting of Pathogens via Medicinal Chemistry
- Computational Chemistry and Biology
- Computational Chemistry and Biology Overview
- Modeling protein regulation via allostery and post-translational modifications
- Visualizing and integrating bioinformatics and biomolecular data
- Modeling membrane permeation to optimize pharmacokinetics
- Determining enzyme function by predicting substrate specificity
- Physical Biology
- Protein and Cellular Engineering
- Protein and Cellular Engineering Overview
- Monitoring enzyme activity and disease biomarkers
- Generating human proteome antibodies via phage display and directed evolution
- Globally analyzing and dissecting apoptosis
- Proximity tagging of protein-protein interactions
- Investigating cellular interactions in tissues
- Creating fluorescent probes targeting the genome and key bio-pathways
- De novo design of catalytic and membrane proteins
- Probing and modulating membrane proteins
Probing and modulating membrane proteins
Examples of our research and methods include
Developing peptides to bind transmembrane domains
Department scientists have computationally designed membrane-spanning helical peptides that recognize and bind to the membrane-embedded helices of transmembrane proteins with high sequence specificity.
The method, dubbed computed helical anti-membrane protein, or CHAMP, selects a backbone geometry to complement target helices based on structural databases of known helix pairs in transmembrane proteins. Then it further selects for the best adjusted fit (re-packing) between amino acid side chains at the interface of the CHAMP-generated and target helix. (In the membrane environment it is hypothesized that precise geometric complementarity is especially crucial for binding selectivity and affinity. But it should also be possible to extend this method to helix associations involving polar side chains, which have also been found to drive the association of model transmembrane peptides).
Our applications of such protein engineering include
Targeting transmembrane domains of platelet receptors
The CHAMP method has been tested by targeting the very similar (homologous) transmembrane domains of two closely related types of membrane receptors in platelets, circulating cell fragments that play a key role in blood clotting. The targeted receptors, called integrins, have a large extracellular domain, transmembrane helices, and a short cytoplasmic domain. They induce platelets to stick to one another or to matrix proteins, thus contributing to clotting.
It was determined that the CHAMP peptides were able to:
- Assume an alpha helical shape and insert themselves into and across phospholipid bilayers that comprise cell membranes, like those of human red blood cells such as platelets, without lysing them.
- Selectively interact with their target integrins, even when they were outnumbered several hundred-fold by homologous isoforms.
- Induce integrin activation and thus platelet and/or platelet-matrix adhesion in assays using mammalian cells—as well as in models such as detergent micelles.
- Help confirm that, in their resting state, the heterodimer integrins’ transmembrane helices interact. It is when they are disassociated, as with competing CHAMP peptide binding, that integrins become active.
Such modulation of the transmembrane domains of integrins has potential therapeutic applications in safer reduction of pathological clotting leading to heart attack and stroke. It could also reduce scarring of blood vessels in the kidney (glomeruli) that can contribute to end-stage renal disease. Glomerulosclerosis can be caused by a type of integrin that upregulates collagen synthesis, thus its inhibition reduces glomerular injury.