We are biophysicists, chemists, biologists, and computer scientists, who address pressing questions in mechanisms of the cell signaling in health and disease. We develop multiscale computational methods and workflows by combining frameworks of molecular dynamics, quantum chemistry, and molecular evolution with multi-resolution experimental data. Current emphasis is on plasma membrane cell signaling, protein dynamics in complex environments, and functional lipids in membrane-associated phenomena.
Research Highlights
Majority of findings were achieved and/or verified in collaboration with experimental colleagues, including M. Gruebele, C. Rienstra, M. Burke, K. Hristova, J. Morrissey, and K. Zhang, among others.
Transmembrane signaling proteins: receptor tyrosine kinases
- Funding: PI: NIH-R01 GM141298 2021/25, co-Is: Hristova & Zhang
- Candidate structures of previously invisible RTK TM dimer structures (in progress)
- Mutations play in EphA4 oligomerization and signaling (J. Biol. Chem, 2021)
- Key side chains in binding of RTK TrkA juxtamembrane domain to membrane (JPCB, 2019)
Functional lipid signatures & membrane-active agents
- Funding: PI: NCSA CDDR (2021/23), co-I Kindratenko; co-I: NIH-tR01 GM123455 (2016/23), PIs: Rienstra, Morrissey, Tajkhoshid
- Cholesterol coupled dynamics in membrane (JACS, 2023)
- Dynamic structure of anionic PS lipids shaped by Ca2+ in signaling (Biochem., 2018)
- Contributed to capturing structure of the functional amphotericin B (AmB) – ergosterol sponge and development of safe AmB variant (Nature, 2023)
- Structure of the functional AmB sponge (Nat. Str. Mol. Biol., 2021)
In silico cell: dynamics in the crowd
- Funding: key contributor: NSF 2205665 (2022/26), NIH-R01GM093318 (2017/21), PI: Gruebele
- Perspective review article (JPCB, 2023)
- In-cell dynamics of ATP (JPCL, 2022)
- Folding dynamics of diverse topologies – protein B (Prot. Sci., 2023) & WW domain (JPCB, 2020)
- Protein-protein interactions are transient – a sign of quinary structure (JPCL, 2019)
Mechanisms of fast protein folding
- Funding: key contributor: NSF 2205665 (2022/26), NIH-R01GM093318 (2017/21), PI: Gruebele
- Small ubiquitous osmolyte TMAO protects proteins (Biophys. J., 2023)
- Formation of a dry molten globule by a fast-folding protein (PNAS, 2019)
- Differences in local and global probes of folding (JPCL, 2016)
- Trap state explored by a fast-folding protein (PNAS, 2015)
LATEST NEWS
- Kevin Cheng wins 2023 BPS Student Research Achievement Award! https://t.co/JNv6p1tzUc
- Three new PhD students join the lab! We welcome Sepehr Alaeen (Biophysics, co-advised with Martin Gruebele), Aigaran Bala Raman (Chemical & Biomolecular Engineering, co-advised with Baron Peters) & Shashank Shastry (Biophysics)!
- Kevin Cheng awarded the GRC Board of Trustees Carl Storm Underrepresented Minority (CSURM) Fellowship
- Mayank Boob wins 2022 Protein Society Symposium Best Poster Award.