Volume 10, Issue 3 | Summer 2025

Science Feature

From Snapshots to Dynamics: A Peek Through the Lens of a Computational Microscope

By Fabrizio Marinelli, PhD

In one of our ongoing projects, we are using advanced computational techniques and high-performance resources to investigate the mechanisms of multidrug transport in the small multidrug resistance (SMR) family—membrane proteins that expel a broad range of drugs and toxins across bacterial membranes, contributing to antimicrobial resistance. Our lab focuses on understanding substrate promiscuity in two prototypical SMR subtypes. Their small size and variable specificity make them ideal models for studying promiscuous drug transport.
These transporters operate by dynamically cycling between distinct conformational states, intermittently exposing substrates to either side of the membrane. Capturing this dynamic behavior is crucial for understanding substrate specificity, which cannot be explained by static binding affinities alone. Because no single method can fully capture both structural and dynamic aspects, we employ an integrative approach combining experimental data with advanced molecular dynamics simulations.

To overcome the limitations of conventional MD in accessing slow functional transitions, we have developed a first-of-its-kind computational framework that uses machine learning to accelerate sampling. This has enabled us to simulate transitions on timescales approaching seconds—a significant milestone. Applying this framework to SMR transporters has revealed novel structural intermediates and early mechanistic insights into how these proteins recognize and translocate substrates.

Collaborative work with Randy Stockbridge’s lab, using single-molecule experiments, supports our key finding: substrate recognition is determined not merely by binding to the open conformation, but from occlusion of the access pathway following correct substrate binding. We are now expanding our framework using AI-driven techniques to integrate simulation data with diverse experimental methods—including smFRET, EPR, HDX, EM, and NMR—to obtain deeper molecular insights into how multidrug transporters catalyze drug efflux and achieve broad substrate promiscuity. Our goal is to predict drug resistance.
 

Figure 1. Role and mechanism of drug transporters via machine learning integrated simulations and experiments.

Graduate Student Q&A

Learn about the students in our Biophysics Graduate Program.

Research Interests: Over the past five years, my research has focused on the structural investigation of proteins required for lipopolysaccharide (LPS) shuttling from the inner to outer membrane of gram-negative bacteria. LPS provides a physiochemical barrier against a variety of antimicrobial compounds, and proper localization of LPS to the outer membrane is essential for bacterial viability. Therefore, structural investigation of the LPS transport (Lpt) system will lay the groundwork for targeted approaches to inhibit or hinder outer membrane biogenesis. I specifically study the inner membrane component of the Lpt system, LptB2FG. This protein complex is an ATP-binding cassette transporter and is the driving force of the Lpt system, extracting LPS from the inner membrane and providing energy to push the glycolipid through the rest of the Lpt system.

Since the start of my research career at UW-Parkside, I have been especially interested in protein structural biology and the mechanisms that facilitate function, making the Klug lab an ideal fit for my interests. Our lab primarily uses site-directed spin labeling EPR spectroscopy to investigate biophysical and structural properties of proteins.  Most recently, we have been closely collaborating with Dr. Fabrizio Marinelli from our department to conduct molecular dynamics simulations. These simulations on LptB2FGC will use our experimental EPR data to bias the simulations and obtain dynamic structural information that is relevant for proper function.

Future Plans: After completing my PhD, I plan to remain in the Klug Lab as a postdoctoral researcher for a short period while I explore career opportunities in the greater Milwaukee and Madison area. During my time as a graduate student, I discovered a strong interest in scientific communication, particularly in writing research manuscripts. This has led me to consider a career in scientific writing, though I remain open to a range of opportunities in industry where I can apply my skills and research experience.

Fun Fact: I love getting into mosh pits at concerts. One time, a guitarist jumped off the stage mid-song, and I was kicked in the head. This did not discourage me from jumping right back in. 

Biophysics Alumni: Where Are They Now?

Department News

Welcome

• William Brown (Postdoctoral Researcher, Marinelli lab)
• Yaqiang Wang (Assistant Professor)

Farewell

• Laura Borst (Business Operations Coordinator)
• Jennifer Gavina (Research Technologist I, Zielonka lab)
• Akansha Sharma (Postdoctoral Fellow, Sidabras lab)
• Tim Thelaner (Engineer II)
• Joey Wehrley (Engineering Technician III, Sidabras lab)

Congratulations

• Mona Al-Gizawiy received a one-year, $50,000 Imagine More award from the Neuroscience Research Center for her proposal titled "Does the novel antineoplastic compound, gallium maltolate, cause neurologic dysfunction? – Multimodal assessment."
• Patrick Brennan, Julian Grosskopf, Alex Garces, and Michael Lerch published an article in Current Opinion in Structural Biology. 
• Gang Cheng, Micael Hardy, Jimmy Feix, and Balaraman Kalyanaram published an article in Scientific Reports.
• Alex Garces successfully defended his dissertation, titled "Elucidating Structural Features of GPCR Signaling with Novel EPR Technologies," for his PhD (advisor: Michael T. Lerch, PhD).
• Alex Garces was awarded a Department of Biophysics Postdoctoral Fellowship to conduct research in Dr. Mike Lerch's laboratory.
• Alex Garces, Richard Mett, Candice Klug, Jason Sidabras, and Michael Lerch published an article in Protein Science.
• Neil Hogg was promoted to the position of Senior Associate Dean - Academic Affairs of the School of Graduate Studies.
• Jason Sidabras was awarded a five-year $1.75 million multi-PI U01AI189427, titled "A Unique Device to Measure Radiation Dose and Homogeneity of Exposure Following a Large-Scale Ionizing Radiation Event," from NIH/NIAID. The other PI is Harold Swartz from Clin EPR LLC.
• Karol Subczynski published an article in Biomolecules.
• Nick Wood, Alyssa Kraft, Kyung Shin, Gopinath Tata, & Francesca Marassi published an article in Proceedings of the National Academy of Sciences of the United States of America.
• Jacek Zielonka published an article in International Journal of Molecular Sciences. 

Welcome, Dr. Wang

Schmainda Lab Receives American Society of Neuroradiology Awards

Melissa Prah and co-authors Kathleen Schmainda and Max Krucoff in Neurosurgery received the prestigious ASNR25 Adult Brain Outstanding Project Award for their presentation titled "Fractional tumor burden accurately predicts histologic diagnosis."

Additionally, Kathleen Schmainda, Melissa Prah, and Max Krucoff in Neurosurgery received an ASNR Merit Award in recognition of their educational poster exhibit titled "Delta T1 (dT1) Maps for the Determination of Ablation Extent After Laser Interstitial Thermal Therapy (LITT)."

Biophysics Featured in Afternoon Tea

Biophysics was featured in the July 1, 2025, issue of Afternoon Tea with Dr. Costakos. This feature highlighted some of our preclinical work in oncology, research toward a potential therapeutic avenue for Parkinson's disease, recent findings supporting structure-based drug design optimization of new antibiotics, new perspectives for antibiotic development, a new high-pressure EPR system technology, and the PLUBMED collaborative.

Second Annual James S. Hyde, PhD, Memorial Lecture

The Second Annual James S. Hyde, PhD, Memorial Lecture took place on May 19, and featured a presentation, titled "Spectroscopic Probes of Protein Structural Dynamics, Thanks to Jim Hyde!," by guest lecturer David D. Thomas, PhD. Thanks to all who helped set up the event! And to all who attended!

Pictured (left to right): Francesca Marassi, Candice Klug, David Thomas

In Memoriam - Claire Kennedy, PhD

Sister Mary Claire Kennedy passed away on May 23, 2025, at the age of 96 years. Claire retired from her scientific career in 2001 as professor of biochemistry here at MCW. Her office and lab were physically located in the Biophysics space as part of the National Biomedical EPR Center, and we here in the department knew her well. She worked closely with National Academy of Science member Professor Helmut Beinert and had moved from UW-Madison to MCW when Helmut was recruited here in 1985. As eminent as he was in the fields of enzymology and metalloprotein biochemistry, it has been said that the true gem of that hire was Claire. She was a gifted scientist and educator and a strong supporter of trainees in science. She was also known for her writing and editing and was often referred to as the “comma lady.” During her time at MCW, she was also a visiting scholar at the University of Konstanz with Peter Kroneck, a frequent visitor to the EPR Center. After retiring from science, Claire returned to religious service at the Sisters of St. Joseph in Erie, PA, as their Social Justice Coordinator. While her time in Wisconsin was only a small piece of her long and well-lived life, she made a big impact on many of us in the scientific community, both locally and internationally. The world is a better place because of her, and she will be missed!

The obituary for Sister Mary Claire Kennedy is available online.

Candice S. Klug

Please Join Us

Tim Thelaner, Engineer II in the Department of Biophysics, is retiring on August 1. In celebration of his service to MCW, we will be hosting a come-and-go open house in the Biophysics Conference Room (MFRC 2063) from 2-3 pm on Friday, August 1.

Stop by to chat with Tim and wish him a happy retirement. We hope to see you there!

Featured Pet

Biophysics News is a quarterly MCW departmental newsletter aimed at enhancing departmental engagement through information and good news sharing. Do you have information you’d like to share—news, events, photos, a photo of your pet? Send it to Lydia.

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