Ivan Korendovych

Syracuse University

Date: Wednesday, June 15, 2022
Talk Time: 03:50 pm - 04:10 pm
Talk Title: Catalytic Peptide Assemblies Promote Carbon Dioxide Hydration with Efficiencies that Rival those of Native Carbonic Anhydrases

Metalloproteins are involved in all processes in the cell ranging from respiratory energy generation and signal transduction to metabolism. Such functional diversity is fulfilled by a relatively limited number of metal-containing cofactors that perform different functions depending on their interaction with the protein scaffold. Changes in protein tertiary and secondary structure upon allosteric ligand binding or changes in redox state can translate into subtle modifications of cofactor environment, leading to drastic alteration of the function. I seek to understand in molecular detail the interplay between protein scaffolds and metal cofactors that ultimately determine changes in protein function. Such understanding will have important medicinal, environmental and energy-related implications.

Hemoglobin's Role in the Innate Immune Response. Development of Protease Resistant Inhibitors of Hemoglobin-Toxin Interaction
Preserved for 500 million years of evolution, innate immune response is organism's first line of defense against various pathogens. Innate immunity relies on recognition of molecular patterns specific to all bacteria. While toll-like receptors are largely responsible for pathogen sensing, there is mounting evidence of involvement of oxygen transporting proteins in the initial steps of innate immune response. The goal of this project is to develop tools to regulate production of immunological reactive oxygen species, ROS, generation by hemoglobin. Bacterial endotoxins trigger hemoglobin-assisted production of ROS that destroy the pathogen directly and induce inflammation that turns on additional mechanisms of cell defense. The ROS production is caused by oxidation of the heme iron resulting from protein conformational change, illustrating the delicate interplay between cofactor binding, protein stability and function. I seek to understand the interaction of lipid toxins derived from both gram-positive, lipoteichoic acid, LTA, and gram-negative, lipopolysaccharides, LPS, organisms with hemoglobin and its role in ROS production and regulation. In addition to basic fundamental value, this research will help develop new strategies for treatment of methicillin resistant Staphylococcus aureus, MRSA, and cancer therapy, tumor necrosis factor activation by ROS.

Development of Biocompatible and Biodegradable Oxygen Activation Catalysts
Development of efficient catalysts for chemical transformations is the "Holy Grail" of chemistry. Nature has developed means to facilitate an enormous variety of chemical transformations with exceptional regio- and stereo-selectivity starting with simple starting reactants in the ultimately "green" solvent - water. My research program will focus on oxygen activation for hydrocarbon functionalization. Amazingly, nature achieved this goal using a handful of transition metals finely tuned to perform specific tasks by a protein scaffold. Mononuclear iron oxygenases, the most common class of such enzymes, frequently rely on one particular metal coordination fragment, the "2-His-1-carboxylate facial triad". This is a remarkable fact considering the diversity of function exhibited by these proteins. What are the factors that determine the type of reaction catalyzed by mononuclear iron oxygenases? How does the protein scaffold influence the function? What is responsible for functional switching? What is the role of the second coordination sphere? Solving these problems will provide us with new insights into protein function, better control of chemical transformations, and catalysts for new applications. I am interested in functional properties of the active site in isopenicillin N synthase, a representative iron oxygenase, and in designing simpler protein models to independently test and refine principles of binding of metals to protein scaffolds. All approaches work toward a detailed understanding of function of monoiron oxygenases at the molecular level. Combining the detailed knowledge of the structure and reaction mechanisms available for small molecule catalysts with computational tools for protein design will allow for development of efficient biocompatible and biodegradable catalysts of hydrocarbon hydroxylation and epoxidation.

Design of Switchable Enzymes for Metal Sensing
Metal sensing is important for a variety of applications ranging from metal tracking in living cells to detection of toxic metal ions in the environment. Protein-based sensors offer a number of advantages: they are biodegradable, biocompatible, and thus can be used in living cells, and most importantly, adaptable for a variety of different readout modes and metal ions. Additional benefits can be obtained by coupling metal ion binding to catalysis creating catalytically amplified sensors with exceptional sensitivity. I'm working on developing an enzymaticplatform for selective, catalytically amplified metal ion sensing. This will be accomplished by introducing a catalytic site into a switchable protein scaffold. Separation of the binding and the catalytic domains will allow for their independent development to improve both selectivity and sensitivity to the metal ion.

Previously we have shown that short de novo designed peptides can self-assemble into highly reactive amyloid-like catalysts for hydrolysis of activated esters. Subsequent work by many groups showed broad applicability of this approach to many different model transformations.

Here we set out to explore whether catalytic amyloids can replicate native activities of enzymes. We have rationally designed a series 9-residue peptides that self-assemble in the presence of zinc to promote CO2 hydration with kcat/KM of 6 x 105 M-1s-1 at pH 9.5 and 3 x 105 M-1s-1 at pH 8.

The latter value is at least 100-fold faster than any reported to date artificial catalysts of CO2 hydration. Moreover, given the low molecular weights of the peptides, the designed catalysts have specific activities that are on par with those of natural carbonic anhydrases.

To our knowledge, this is the first example of a model system matching enzymes in their own game. This is even more exciting considering that the functional complexity needed to promote efficient catalysis was achieved by supramolecular self-assembly of short peptides containing only natural amino acid residues. Unlike enzymes, catalytic amyloids are extremely robust and can be used under harsh conditions to help promote CO2 capture and fixation.

Ivan Korendovych, talk image 2

Ivan Korendovych
Ivan Korendovych, talk image 1
Ivan Korendovych, talk image 3
Ivan Korendovych, talk image 4