Department of Biochemistry and Molecular Biophysics

Author: Conrad Weiland

2024 News / All News

Congratulations to Jeramia Ory for being selected as a member of the WASHU Academy of Educators!

Jeramia Ory Congratulations to Jeramia Ory’s selection as a new member of the Washington University School of Medicine Academy of Educators! This achievement acknowledges significant contributions to education and recognizes their valuable place as a central contributor to the education mission of the School of Medicine.

The Academy of Educators received many applications for membership in the Academy. Each application was reviewed by one external and two internal peer reviewers. Ory’s application, letter(s) of support, CV and supporting documentation were scored by these three peers using our specific standards and criteria for membership, as delineated in the application review matrix. (more…)

All Research / Janetka Lab

Spotlight on Research – Janetka Lab

The Janetka Lab specializes in the rational design, chemical synthesis and drug development of small molecule therapeutics. Our group uses a combination of medicinal chemistry, chemical biology, and biochemistry to investigate and validate new therapeutic targets. We utilize computational tools to improve inhibitors based on X-ray structures followed by optimizing compounds for drug-like properties. We work closely with biology collaborators to evaluate compounds for their biological activity in vitro and efficacy in animal models of disease. The ultimate goal of our work is the clinical development of innovative drugs. The lab currently works on inhibitors of various enzymes, receptors, and lectins (carbohydrate binding proteins) as new treatments for viral, bacterial, and parasitic infections as well as anticancer therapeutics to prevent metastasis.

All Research / Ghanbarpour Lab

Spotlight on Research – Ghanbarpour Lab

The Ghanbarpour Lab studies the breakdown of proteins in bacteria and human mitochondria by ATP-dependent AAA proteases and their cognate modulators. AAA proteases are crucial for removing unneeded or aberrant proteins, ensuring cellular health and shaping the proteome for specific cellular functions.
The selection of proteins for degradation is a sophisticated process, influenced by accessory modulators called adaptor proteins. Despite the importance of this mechanism and the role of adaptor proteins in protein degradation, the molecular details of these processes remain largely unknown.
Our research aims to decode the intricate mechanisms behind protease specificity and how adaptor proteins tailor these actions. We employ a multidisciplinary approach that combines in vitro reconstitution and biochemistry, structural biology (cryo-EM, cryo-ET, and crystallography), cellular assays, and pulse-labeled mass spectrometry to monitor degradation.
Our long-term goal is to enable the development of new therapeutics that can manipulate these protease-adaptor interactions, offering new ways to treat human diseases and fight bacterial infections.

All Research / Li Lab

Spotlight on Research – Li Lab

The Li Lab studies the structure and function of integral membrane proteins, with a focus on ones that are important for hematologic and cardiovascular systems. We use a variety of structural biology, biochemistry, cell biology and mass spectrometry techniques to understand the structural mechanism of these membrane proteins. Structural insights give us a novel angle to elucidate the actions of these proteins in cellular settings. Deep understanding of protein structure and function often has implications significant for human disease. In addition, these proteins provide challenges that motivate us to develop new structural and biochemical methods broadly applicable to membrane biology.

All Publications / Garcia Publications

An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications

Richard M Searfoss, Rashmi Karki, Zongtao Lin, Faith Robison & Benjamin A Garcia (2023). “An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications” J Am Soc Mass Spectrom. 2023 Nov 1;34(11):2508-2517. doi: 10.1021/jasms.3c00223. Epub 2023 Oct 18. (Abstract)

All Publications / Garcia Publications

SWAMNA: a comprehensive platform for analysis of nucleic acid modifications

Yixuan Xie, Francisca N. De Luna Vitorino, Ye Chen, Joanna K. Lempiäinen, Chenfeng Zhao, Robert T. Steinbock, Zongtao Lin, Xingyu Liu, Emily Zahn, Arabella L. Garcia, Matthew D. Weitzmancd & Benjamin A Garcia (2023). “SWAMNA: a comprehensive platform for analysis of nucleic acid modifications” Chem Commun. 2023, 59(83):12499-12502. (Abstract)

All Publications / Garcia Publications

Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation

Peder J Lund, Leah A Gates, Marylene Leboeuf, Sarah A Smith, Lillian Chau, Mariana Lopes, Elliot S Friedman, Yedidya Saiman, Min Soo Kim, Clarissa A Shoffler, Christopher Petucci, C David Allis, Gary D Wu & Benjamin A Garcia (2022). “Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation” Cell Rep. 2022 Dec 13;41(11):111809. doi: 10.1016/j.celrep.2022.111809. (Abstract)

All Publications / Garcia Publications

Permethylation of Ribonucleosides Provides Enhanced Mass Spectrometry Quantification of Post-Transcriptional RNA Modifications

Yixuan Xie, Kevin A Janssen, Alessandro Scacchetti, Elizabeth G Porter, Zongtao Lin, Roberto Bonasio & Benjamin A Garcia (2022). “Permethylation of Ribonucleosides Provides Enhanced Mass Spectrometry Quantification of Post-Transcriptional RNA Modifications” Anal Chem. 2022 May 24;94(20):7246-7254. doi: 10.1021/acs.analchem.2c00471. Epub 2022 May 12. (Abstract)

All Publications / Garcia Publications

Epigenomic Reordering Induced by Polycomb Loss Drives Oncogenesis but Leads to Therapeutic Vulnerabilities in Malignant Peripheral Nerve Sheath Tumors

John B Wojcik, Dylan M Marchione, Simone Sidoli, Anissa Djedid, Amanda Lisby, Jacek Majewski & Benjamin A Garcia (2019). “Epigenomic Reordering Induced by Polycomb Loss Drives Oncogenesis but Leads to Therapeutic Vulnerabilities in Malignant Peripheral Nerve Sheath Tumors” Cancer Res. 2019 Jul 1;79(13):3205-3219. doi: 10.1158/0008-5472.CAN-18-3704. Epub 2019 Mar 21. (Abstract)

All Publications / Garcia Publications

One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry

Simone Sidoli, Yekaterina Kori, Mariana Lopes, Zuo-Fei Yuan, Hee Jong Kim, Katarzyna Kulej, Kevin A Janssen, Laura M Agosto, Julia Pinheiro Chagas da Cunha, Andrew J Andrews & Benjamin A Garcia (2019). “One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry” Genome Res. 2019 Jun;29(6):978-987. doi: 10.1101/gr.247353.118. Epub 2019 May 23. (Abstract)