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Chemistry Guest Seminars

Recruiting Seminars 2021

Wednesday January 27, 3:30-4:30, ZOOMlin

High-Speed Atomic Force Microscopy: A Forceful and Dynamic Tool for Visualizing Membrane Proteins at Work

Yi-Chih Lin

Postdoctoral Researcher

Weill Cornell Medicine

PhD, Univ. of Pennsylvania, 2017

Simon Scheuring Lab

Abstract: The advent of high-speed atomic force microscopy (HS-AFM) has opened a new era in molecular biophysics for watching single bio-molecules in action at the membrane at high spatial-temporal resolution: Membrane protein diffusion, assembly, structural dynamics, and conformational changes now could be directly visualized and studied. Further developments in environmental control (temperature, force, light, and buffer conditions) and fast-scanning submodes expand HS-AFM's applicability to study biomolecular dynamics spanning from seconds to microseconds in different biochemical conditions. This talk will exemplify HS-AFM's power for the quantitative analysis of function-related structural dynamics on membrane proteins. The first part of my talk will focus on the discovery of conformational changes in mechanosensitive Piezo1 ion channel in response to the force application, which mediates the force-detection in many eukaryotic cells. I will then discuss the physiological role of the Ca2+-triggered membrane-binding protein Annexin-V during the membrane repairing processes when cell injuries. The newfound understanding of membrane proteins' structure-function relationship could shed light on novel strategies to develop drug treatments currently not readily available.


Publications (Google Scholar Citations)

ORCID:  https://orcid.org/0000-0002-6498-215X

Author Metrics

h-index: 13  Total Articles: 21  Total Citations: 643 (Web of Science, Jan. 2021)

h-index: 13  Total Citations: 703  (Google Scholar Citations, Jan. 2021)

Monday, January 25, 3:30-4:30, ZOOMgeri

Photocatalytic Proximity Labeling

Jacob Geri

Postdoctoral Fellow

Princeton University

PhD, Michigan, 2018 (Nathaniel Szymczak)

Dave Macmillan Group

Abstract:  The spatial relationships between biomolecules define the structure of life. Consequently, new technologies that can reveal these relationships with increased precision deepen our understanding of biology and create avenues of inquiry which would be otherwise unavailable. Proximity-based labeling, in which chemically reactive tags are generated at a protein of interest and then label nearby biomolecules for MS-based identification, is a conceptually powerful way to leverage spatial relationships between proteins to discover protein-biomolecule interactions. Widely used proximity labeling technologies currently use enzymatically generated electrophilic biotin-AMP and phenoxyl radicals as reactive tags, which can undergo long-range diffusion in water and have limited spatial resolution. After an overview of my graduate work in inorganic chemistry and organic methodology, I will describe the development of a new, higher resolution proximity labeling approach which instead uses more reactive biotin-carbene species incapable of diffusion through water, termed µMap. This technology uses antibodies conjugated to iridium-based photocatalysts to catalytically activate diazirines via Dexter energy transfer, converting them to carbenes which crosslink only to proteins that are adjacent to the antibody binding target. This technique was then used to label proteins colocalized with a variety of receptors on the surface of live lymphocytes, such as PD-L1, CD45, and CD300A, and was capable of distinguishing between receptor interactomes which could not be disentangled using traditional phenoxyl radical proximity labeling. Using small molecule probes in place of antibodies, the tight labeling radius enabled efficient chemoproteomic target ID and the identification of amino acids adjacent to their binding sites. This photocatalytic proximity labeling strategy is highly general, and represents a new level of spatial resolution in the discovery of protein-protein interactions. 


Publications (Google Scholar Citations)

Author Metrics

h-index: 7  Total Articles: 12  Total Citations: 281 (Web of Science, Jan. 2021)

h-index: 8  Total Citations: 344  (Google Scholar Citations, Jan. 2021)

Wednesday, January 20, 3:30-4:30, ZOOMogata

Finding the clues for disease: Nanoscale to microscale materials for advancing protein detection technologies

Alana F. Ogata

Postdoctoral Fellow

Harvard University, Brigham & Women's Hospital

PhD, UC Irvine 2018 (Reg Penner)

David Walt Lab

Abstract: The field of bioanalytical sensors for protein detection has progressed immensely over the past decade, resulting in research tools that directly impact our understanding of human diseases. Dr. Ogata’s seminar will focus on her PhD and postdoctoral research, which has focused on the development of novel bioanalytical technologies for disease diagnostics. During her PhD at UC Irvine, Dr. Ogata developed simple and rapid sensors for the detection of proteins using electrochemical methods and pioneered the “virus bioresistor” , a sensor platform that continues to be developed for the detection of bladder cancer markers in urine. As a postdoctoral fellow at UC Irvine, Dr. Ogata studied the formation mechanisms of biological-synthetic nanomaterials using cryogenic transmission electron microscopy. The use of cryoTEM enabled the direct observation of several precursor phases that play an important role in crystal formation and protein encapsulation. Currently, Dr. Ogata is a postdoctoral fellow at the Brigham and Women’s hospital working on the development of ultrasensitive protein assays using single-molecule array technology. In collaboration with clinicians, she recently developed an ultrasensitive assay for the detection of SARS-CoV-2 antigens in the blood of COVID-19 patients. These viral antigens show correlation with disease severity and respiratory failure, and the assays are currently being developed as a prognosis tool for doctors in the intensive care unit.


Publications (Google Scholar Citations)

Author Metrics

h-index: 8  Total Articles: 18  Total Citations: 224 (Web of Science, Dec. 2020)

h-index: 9  Total Citations: 304 (Google Scholar Citations, Dec. 2020)

Wednesday, January 13, 3:30-4:30, ZOOMnewberry

Chemical and Cellular Determinants of Functional Protein Structures

Robert W. Newberry

Postdoctoral Scholar (Pharmaceutical Chemistry)

UC San Francisco

PhD, Wisconsin, 2016 (Ronald Raines)

Profile

I am broadly interested in how the intrinsic, chemical properties and features of proteins bias them toward specific structures, particularly the amyloid state implicated in many neurodegenerative disorders. My work integrates approaches and perspectives from the fields of biophysics and chemical biology to dissect the determinants of folding and misfolding in proteins linked to human diseases like Alzheimer's or Parkinson's. Understanding what makes proteins susceptible or resistant to misfolding will inform strategies for targeted intervention.  


Publications (Profile)

Publications (Google Scholar Citations)

ORCID:  https://orcid.org/0000-0002-2020-2641

Author Metrics

h-index: 12  Total Articles: 16  Total Citations: 684  (Web of Science, Dec. 2020)

h-index: 14  Total Citations:  888  (Google Scholar Citations, Dec. 2020)

Monday, January 11, 3:30-4:30, ZOOMcallmann

Co-Opting Nature’s Own Molecules for Targeted Cancer Therapy: Supramolecular Chemistry using Peptides, Lipids, and Nucleic Acids

Cassandra Callmann

American Cancer Society Postdoctoral Fellow

Northwestern University

PhD, UC San Diego, 2018 (Nathan Gianneschi)

Profile

Chad Mirkin Group

Bio:  Following the completion of her B.S. in Biochemistry (2012) at West Chester University, Cassandra earned both her M.S. (2014) and Ph.D. (2018) in Chemistry at the University of California, San Diego under the guidance of Prof. Nathan Gianneschi. At UC San Diego, she elucidated fundamental molecular design parameters for the synthesis of biohybrid materials that site-specifically interact with proteins, cells, and tissues with high affinity. Her graduate work was supported by fellowships from the Inamori Foundation, the ARCS Foundation, and the Cancer Researchers in Nanotechnology program (NIH R25T). Cassandra was recognized for her thesis research with an Outstanding Dissertation Award from the UC San Diego Department of Chemistry and Biochemistry in 2018. She is currently an American Cancer Society Postdoctoral Fellow in Prof. Chad Mirkin's research group at Northwestern University (previously: Eden & Steven Romick IIN Fellow at Northwestern University). At Northwestern, her research has revealed that the chemical composition of vaccine components, coupled with their the three-dimensional nanoscale arrangement, determines their physical stability and release kinetics in biological media, which in turn dictates the kinetics of cellular signaling and overall immunotherapeutic function. For her work as an early career researcher, Cassandra was selected as a 2019 CAS Future Leader by the Chemical Abstracts Service of the American Chemical Society. 


Publications (Profile)

Publications (Google Scholar Citations)

ORCID:  https://orcid.org/0000-0003-1561-3240

Author Metrics

h-index: 6  Total Articles: 12  Total Citations: 488 (Web of Science, Dec. 2020)

h-index: 7  Total Citations: 793  (Google Scholar Citations, Dec. 2020)

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