MGMS Lecture Tour – Dr. Rommie Amaro

All MGMS Seminars are free of charge and open to all.
Please register below to attend this event.

The MGMS was formed in 1981 to bring together scientists working in different fields of study—such as chemistry, physics, biology, mathematics and computer science—who have a common interest in computational molecular modelling and molecular graphics. One of our activities is to organize MGMS Lecture Tours to highlight cutting-edge research in the field.

2022 MGMS Lecture Tour:
Dr. Rommie Amaro

Dr. Rommie Amaro

We are pleased to announce that Dr. Rommie Amaro from the Department of Chemistry and Biochemistry, University of California, San Diego will be giving a virtual MGMS Lecture Tour lecture titled, “In situ dynamics reveal unseen vulnerabilities of viral glycoproteins”, and it will be held via Zoom.

Please register below to attend, connection zoom details will be sent shortly before the event.

Friday, October 21st, 2022

“In situ dynamics reveal unseen vulnerabilities of viral glycoproteins”

Rommie Amaro1

1Department of Chemistry and Biochemistry, University of California, San Diego

Viral glycoproteins are important targets for vaccine and drug design. I will discuss our efforts to provide never-before-seen views of these amazing molecular machines, for both SARS-CoV-2 and influenza. For the latter, we investigated the dynamics of influenza glycoproteins in a crowded protein environment through mesoscale all-atom molecular dynamics simulations of two evolutionary-linked glycosylated influenza A whole-virion models. Our simulations reveal and kinetically characterize three main molecular motions of influenza glycoproteins: NA head tilting, HA ectodomain tilting, and HA head breathing. From an immunogenic point of view, the glycoproteins’ accentuated conformational plasticity observed in our simulations has unveiled their full vulnerabilities, exposing epitopes that otherwise would not be accessible or would be sterically occluded. Our work therefore highlights the importance of exploring and characterizing in situ dynamics of proteins in their native, crowded environments.

About Rommie Amaro
Dr. Rommie Amaro is a native of the south side of Chicago and earned her bachelor’s degree in chemical engineering with high distinction from the University of Illinois at Urbana-Champaign in 1999. After graduating, she joined Kraft Foods, Inc. as an Associate Research Engineer in Glenview, Illinois, working mainly on Philadelphia Cream Cheese productivity and commercialization projects. After two years of working with condensed matter, she returned to Urbana to attend graduate school in Chemistry.
Dr. Amaro earned her Ph.D. in chemistry in the lab of Professor Zan Luthey-Schulten, where she worked mainly on computational methods to reconstruct free energy profiles from non-equilibrium pulling experiments of ammonia conduction through a beta-barrel protein involved in histidine biosynthesis and studying mechanisms of allosteric regulation in proteins. While a graduate student, she also worked closely with the National Institutes of Health (NIH) Resource for Macromolecular Modeling and Bioinformatics, led by Professor Klaus Schulten, where she helped develop a series of workshops that have now been taught worldwide.
After earning her Ph.D., Dr. Amaro went on to receive a NIH Kirschstein-National Research Service Award (NRSA) postdoctoral fellowship and worked under the tutelage of the Howard Hughes Medical Investigator and National Academy of Sciences member, Professor J. Andrew McCammon at University of California, San Diego (UCSD).
In 2009, Dr. Amaro started her independent research career in the Deparments of Pharmaceutical Sciences, Computer Science, and Chemistry at the University of California, Irvine. In 2010 she was selected as an NIH New Innovator for her work developing cutting-edge computational methods to help discover new drugs. The following year, she received the Presidential Early Career Award for Scientists and Engineers. In 2012, Dr. Amaro opened her lab at UCSD in the Department of Chemistry and Biochemistry.
Research in the Amaro Lab is broadly concerned with the development and application of state-of-the-art computational methods to address outstanding questions in drug discovery and molecular-level biophysics. Her lab focuses mainly on targeting neglected diseases, Chlamydia, influenza, and cancer, and works closely with experimental collaborators to catalyze the discovery of new potential therapeutic agents. The Amaro Lab is also keenly interested in developing new multiscale simulation methods and novel modeling paradigms that scale from the level of atoms to whole cells, and beyond.

You can read more about Dr Amaro’s research interests here


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Past MGMS Lecture Tours

2021 Prof. Graham Richards
University of Oxford, zoom talk recording
2020 Professor Rebecca Wade
Heidelberg University (ZMBH), zoom talk recording
2018 Dr. David Glowacki,
University of Bristol, UK
2015 Professor Dr Gisbert Schneider,
ETH Zurich, Switzerland
2014 Prof. Arthur J. Olson,
The Scripps Research Institute, La Jolla, California, USA
2012 Prof. Modesto Orozco,
Group Leader, Molecular Modelling and Bioinformatics, Institute for Research in Biomedicine (IRB Barcelona)
2011 Prof. Tim Clark,
Friedrich-Alexander-University Erlangen- Nurnberg, Germany, and
Centre for Molecular Design, University of Portsmouth