Student Publications
Shreyoshi Chakraborti
Mycolic Acid-like Lipids Act as Substrates for Mycobacterium marinum me1H
https://pubmed.ncbi.nlm.nih.gov/40978362/
Samruddhi Jewlikar
Probing the Signal Transduction Mechanism of the Light-Activated Adenylate Cyclase OaPAC Using Unnatural Amino Acid Mutagenesis
Kafi Belfon
Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate https://pubs.acs.org/doi/10.1021/acs.biochem.3c00640
Yu-Ching Chen
Uncovering the roles of Mycobacterium tuberculosis melH in redox and bioenergetic homeostasis: implications for antitubercular therapy https://journals.asm.org/doi/10.1128/msphere.00061-24
Miaomiao He
Regulation of NMDAR activation efficiency by environmental factors and subunit composition
http://dx.doi.org/10.1085/jgp.202413637
Brandon Irizarry
An electrostatic cluster guides Aβ40 fibril formation in sporadic and Dutch-type cerebral amyloid angiopathy https://www.sciencedirect.com/science/article/pii/S1047847724000327?via%3Dihub
Ian Outhwaite
Lucanthone, a Potential PPT1 Inhibitor, Perturbs Stemness, Reduces Tumor Microtube Formation, and Slows the Growth of Temozolomide-Resistant Gliomas In Vivo
https://www.sciencedirect.com/science/article/pii/S0022356524172254?via%3Dihub
Absence of ABL1 exon 2-encoded SH3 residues in BCR::ABL1 destabilizes the autoinhibited kinase conformation and confers resistance to asciminib
https://www.nature.com/articles/s41375-024-02353-0
Pavana Suresh
Linking insulin receptor activation to hydrophobic mismatch using transmembrane mutations https://www.cell.com/biophysj/fulltext/S0006-3495(23)01432-7
MαCD-based plasma membrane outer leaflet lipid exchange in mammalian cells to study insulin receptor activity https://www.sciencedirect.com/science/article/pii/S0076687924001228?via%3Dihub
Abhik Tambe
Interpretable deep learning reveals the role of an E-box motif in suppressing somatic hypermutation of AGCT motifs within human immunoglobulin variable regions
Kafi Belfon
Structure-Guided Discovery of N5-CAIR Mutase Inhibitors https://pubs.acs.org/doi/10.1021/acs.biochem.2c00705
Yu-Ching Chen
A Chemoproteomic Approach to Elucidate the Mechanism of Action of 6-Azasteroids with Unique Activity in Mycobacteria https://doi.org/10.1021/acsinfecdis.3c00296
Yong-Mi Choi
Structural insights into perilipin 3 membrane association in response to diacylglycerol accumulation https://www.nature.com/articles/s41467-023-38725-w
Miaomiao He
Activation of excitatory glycine NMDA receptors: At the mercy of a whimsical GluN1 subunit
http://dx.doi.org/10.1085/jgp.202313391
Two gates mediate NMDAR activity and are under subunit-specific regulation
http://dx.doi.org/10.1016/j.bpj.2022.11.1456
Samruddhi Jewlikar
Elucidating signal transduction pathway in light-activated adenylyl cyclase using unnatural amino acid mutagenesis
https://www.sciencedirect.com/science/article/pii/S0006349522027035?via%3Dihub
Ming-Hao Li
Interspecies Variation Affects Islet Amyloid Polypeptide Membrane Binding https://pubs.acs.org/doi/10.1021/acs.biochem.2c00470
Impact of Ca2+ on membrane catalyzed IAPP amyloid formation and IAPP induced vesicle leakage https://www.sciencedirect.com/science/article/pii/S0005273623000433
Forrest Bowling
Defining the proximal interaction networks of Arf GTPases reveals a mechanism for the regulation of PLD1 and PI4KB https://www.embopress.org/doi/full/10.15252/embj.2022110698
Yong-Mi Choi
Structure and Dynamics of Human Perilipin 3 Membrane Association https://faseb.onlinelibrary.wiley.com/doi/10.1096/fasebj.2022.36.S1.00R88
Measurement of neutral ceramidase activity in vitro and in vivo https://www.sciencedirect.com/science/article/abs/pii/S000326972200032X?via%3Dihub
Miaomiao He
Hidden intermediate states of NMDAR in synapse dynamics
http://dx.doi.org/10.1016/j.bpj.2021.11.2299
Ming-Hao Li
Analysis of Sheep and Goat IAPP Provides Insight into IAPP Amyloidogenicity and Cytotoxicity https://pubs.acs.org/doi/10.1021/acs.biochem.2c00470
Lauren Prentis
A molecular evolution algorithm for ligand design in DOCK https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.26993
Pavana Suresh
Effect of MαCD-mediated phospholipid exchange on plasma membrane ordered lipid domain stability https://www.cell.com/biophysj/fulltext/S0006-3495(21)02841-1
Alexandra Weinheimer
Extended DNA binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks https://doi.org/10.1016/j.jbc.2022.102268
Forrest Bowling
Structure and regulation of human phospholipase D https://www.sciencedirect.com/science/article/abs/pii/S2212492620300944?via%3Dihub
Brandon Irizarry
Human cerebral vascular amyloid contains both antiparallel and parallel in-register Aβ40 fibrils https://www.sciencedirect.com/science/article/pii/S0021925821010620?via%3Dihub
Ming-Hao Li
Preparation of Asymmetric Vesicles with Trapped CsCl Avoids Osmotic Imbalance, Non-Physiological External Solutions, and Minimizes Leakage https://pubs.acs.org/doi/10.1021/acs.langmuir.1c01971
The Fluorescent Dye 1,6-Diphenyl-1,3,5-hexatriene Binds to Amyloid Fibrils Formed by Human Amylin and Provides a New Probe of Amylin Amyloid Kinetics https://pubs.acs.org/doi/10.1021/acs.biochem.1c00328
Frank Mindlin
Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer https://www.sciencedirect.com/science/article/pii/S002228362030718X
Pavana Suresh
Loss of plasma membrane lipid asymmetry can induce ordered domain (raft) formation https://www.sciencedirect.com/science/article/pii/S0022227521001383?via%3Dihub
Using cyclodextrin-induced lipid substitution to study membrane lipid and ordered membrane domain (raft) function in cells https://www.sciencedirect.com/science/article/pii/S0005273621002224?via%3Dihub
Phospholipid exchange shows insulin receptor activity is supported by both the propensity to form wide bilayers and ordered raft domains https://www.sciencedirect.com/science/article/pii/S0021925821008127?via%3Dihub
Modulation of Insulin Receptor Activity Upon Plasma Membrane Sterol and Phospholipid Substitutions to Alter Lipid Domain Formation https://www.sciencedirect.com/science/article/pii/S0006349520329660?via%3Dihub
Forrest Bowling
Crystal structure of human PLD1 provides insight into activation by PI(4,5)P2 and RhoA https://www.nature.com/articles/s41589-020-0499-8
Yong-Mi Choi
Identification of Small-Molecule Inhibitors of Neutral Ceramidase (nCDase) via Target-Based High-Throughput Screening https://www.sciencedirect.com/science/article/pii/S247255522206659X?via%3Dihub
Valerie Khayyo
Crystal structure of a lipin/Pah phosphatidic acid phosphatase https://www.nature.com/articles/s41467-020-15124-z
Daeun Noh
Analysis of Amylin Consensus Sequences Suggests That Human Amylin Is Not Optimized to Minimize Amyloid Formation and Provides Clues to Factors That Modulate Amyloidogenicity https://pubs.acs.org/doi/10.1021/acschembio.9b01050
Analysis of Proline Substitutions Reveals the Plasticity and Sequence Sensitivity of Human IAPP Amyloidogenicity and Toxicity https://pubmed.ncbi.nlm.nih.gov/31922743/
Alexandra Weinheimer
SDE2 integrates into the TIMELESS-TIPIN complex to protect stalled replication forks https://www.nature.com/articles/s41467-020-19162-5
Frank Mindlin
Structure of the full-length Clostridium difficile toxin B https://www.nature.com/articles/s41594-019-0268-0
Daeun Noh
Analysis of Prairie Vole Amylin Reveals the Importance of the N-Terminus and Residue 22 in Amyloidogenicity and Cytotoxicity https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254015/
Lauren Prentis
FABP1 controls hepatic transport and biotransformation of Δ9-THC https://www.nature.com/articles/s41598-019-44108-3
Alexandra Weinheimer
Proteolytic Control of Genome Integrity at the Replication Fork https://pubmed.ncbi.nlm.nih.gov/31324531/
Conditional degradation of SDE2 by the Arg/N-End rule pathway regulates stress response at replication forks https://academic.oup.com/nar/article/47/8/3996/5304317
Bezalel Bacon
Bacterial haemoprotein sensors of NO: H-NOX and NosP https://www.sciencedirect.com/science/article/pii/S0065291117300048
Bacterial Heme-Based Sensors of Nitric Oxide. Antioxidants & Redox Signaling https://www.liebertpub.com/doi/full/10.1089/ars.2017.7235
Frank Mindlin
Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95 https://www.nature.com/articles/s41467-018-06133-0
Sanchez-Reyes OB, Cooke ALG, Tranter DB, Rashid D, Eilers M, Reeves PJ, Smith SO. Biophys J. 2017 Jun 6;112(11):2315-2326. doi: 10.1016/j.bpj.2017.04.051.
Chitrakar, I., Kim-Holzapfel, D.M., Zhou, W. and French, J.B. (2017) Higher Order Structures in Purine and Pyrimidine Metabolism. J. Struct. Biol. 197(3): 354-364.
WeberFishkin, S., Clark, R., Galanakis, D., Irizarry, B., Young, A. and Frame, M. (2017) Fibrinogen and its Soluble Fibrin as Mediators of Erythrocyte Aggregation. FASEB Abstract Number:677.6
Yasunori Noguchi(*), Zuanning Yuan(*), Lin Bai(*), Sarah Schneider, Bruce Stillman, Christian Speck, and Huilin Li Cryo-EM structure of Mcm2-7 double-hexamer on DNA suggests a lagging strand DNA extrusion model (2017)Proc. Natl. Acad. Sci. U S A. 114(45) * co-first author
Zuanning Yuan, Lin Bai, Alberto Riera, Jingchuan Sun, Bruce Stillman, Christian Speck, and Huilin Li Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1. (2017) Nature Structural & Molecular biology 24(3):316-324
Ante Tocilj, Kin Fan On, Zuanning Yuan, Jingchuan Sun, Elad Elkayam, Huilin Li, Bruce Stillman, Leemor Joshua-Tor Structure of the active form of human Origin Recognition Complex and its ATPase motor module (2017) eLife 6:e20818)
Roxana Georgescu*, Zuanning Yuan*, Lin Bai*, Ruda de Luna Almeida Santos, Jingchuan Sun, Dan Zhang, Olga Yurieva, Huilin Li and Michael E. O’Donnell Structure of Eukaryotic CMG Helicase at a Replication Fork and Implications to Replisome Architecture and Origin Initiation (2017) Proc. Natl. Acad. Sci. U S A. 113(48):13612-13617)* co-first author
Georgescu, R. , Yuan, Z., Bai, L., Santos, R.L.A., Sun, J., Zhang, D., Yurieva, O., Li, H., O’Donnell, M.E. (2017) Structure of CMG
helicase at a replication fork.Proc. Natl. Acad. Sci. U S A. 114 (5), E697-E706.
Santos, R.L.A., Bai, L., Singh, P.K., Murakami, N., Fan, H., Zhan, W., Zhu, Y., Jiang, X., Zhang,
K., Assker, J.P., Nathan, F.C., Li, H., Azzi, J., Lin, G. (2017) Structure of human
immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits
activated lymphocytes. Nature Communications 8(1):1692.
St Clair, J. R. S., Wang, Q., Li, G., & London, E. (2017). Preparation and Physical Properties of Asymmetric
Model Membrane Vesicles. In The Biophysics of Cell Membranes (pp. 1-27). Springer, Singapore.
Zhang, X., St. Clair, J. R., London, E., & Raleigh, D. P. (2017). Islet amyloid polypeptide membrane interactions:
Effects of membrane composition. Biochemistry, 56(2), 376-390.
Shek, R., Dattmore, D. A., Stives, D. P., Jackson, A. L., Chatfield, C. H., Hicks, K. A., and French, J. B. (2017) Structural and functional basis for targeting Campylobacter jejuni agmatine deiminase to overcome antibiotic resistance, Biochemistry 56, 6734-6742
Li, G., Kim, J., Huang, Z., Clair, J. R. S., Brown, D. A., & London, E. (2016). Efficient replacement of plasma membrane outer
leaflet phospholipids and sphingolipids in cells with exogenous lipids. Proc. Natl. Acad. Sci. U S A., 113(49), 14025-14030.
Zuanning Yuan, Lin Bai, Jingchuan Sun, Roxana Georgescu, Jun Liu, Michael E. O’Donnell, Huilin Li Structure of the eukaryotic replicative CMG helicase and pumpjack motion (2016) Nature Structural & Molecular Biology23(3):217-24
Yang, M., Lu, R., Guja, K. E., Wipperman, M. F., St. Clair, J. R., Bonds, A. C., ... & Sampson, N. S. (2015). Unraveling cholesterol catabolism in Mycobacterium tuberculosis: ChsE4-ChsE5 α2β2 acyl-CoA dehydrogenase initiates β-oxidation of 3-oxo-cholest-4-en-26-oyl CoA. ACS Infectious Diseases, 1(2), 110-125.
Chen YC, Wu YT, and Wei YH. (2015) Depletion of mitoferrins leads to mitochondrial dysfunction and impairment of adipogenic differentiation in 3T3-L1 preadipocytes. Free Radic Res. 49(11):1285-95.
Jingchuan Sun, Yi Shi, Roxana E Georgescu, Zuanning Yuan, Brian T Chait, Huilin Li &Michael E O’Donnell The architecture of a eukaryotic replisome (2015) Nature Structural & Molecular Biology.22(12):976-82
Matarlo, J. S., Evans, C. E., Sharma, I., Lavaud, L. J., Ngo, S. C., Shek, R., Rajashankar, K. R., French, J. B., Tan, D. S., and Tonge, P. J. (2015) Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents, Biochemistry 54, 6514