Ray, Sreejana Tillo, Desiree Ufot, Aniekanabasi Assad, Nima Durell, Stewart Vinson, Charles
Published in
Biochemistry
In mammalian cells, 5-methylcytosine (5mC) occurs in genomic double-stranded DNA (dsDNA) and is enzymatically oxidized to 5-hydroxymethylcytosine (5hmC), then to 5-formylcytosine (5fC), and finally to 5-carboxylcytosine (5caC). These cytosine modifications are enriched in regulatory regions of the genome. The effect of these oxidative products on f...
Cui, Jennifer Y Zhang, Fuming Nierzwicki, Lukasz Palermo, Giulia Linhardt, Robert J Lisi, George P
Published in
Biochemistry
Granulocyte macrophage colony stimulating factor (GMCSF) is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is known to interact with other clinically important molecules, such as heparin, suggesting that endogenous and administered GMCSF has the potential to modulate orthogonal treatment outcomes. Thus, molecular level chara...
Thakur, Abhishek Somai, Shruti Yue, Kun Ippolito, Nicole Pagan, Dianne Xiong, Jingyuan Ellis, Holly R Acevedo, Orlando
Published in
Biochemistry
Substrate-induced conformational changes present in alkanesulfonate monooxygenase (SsuD) are crucial to catalysis and lead to distinct interactions between a dynamic loop region and the active site. Accelerated molecular dynamics (aMD) simulations have been carried out to examine this potential correlation by studying wild-type SsuD and variant enz...
Zhao, Weitong Liang, Yong Yan, Xiaowen Yang, Limin Wang, Qiuquan
Published in
Biochemistry
A pathogenic bacterium has its own mechanisms for not only pathogenic attack but also exogenous invasion defense, in which the bacterial cell wall is the front line of attack and defense. We developed a biochemical lanthanide-encoding approach to quantify the uncanonical d-amino acid (d-X) that was edited in a small proportion into the terminal acy...
Prentice, Erica J Hicks, Joanna Ballerstedt, Hendrik Blank, Lars M Liáng, Liyı N L Schipper, Louis A Arcus, Vickery L
Published in
Biochemistry
The temperature dependence of biological rates at different scales (from individual enzymes to isolated organisms to ecosystem processes such as soil respiration and photosynthesis) is the subject of much historical and contemporary research. The precise relationship between the temperature dependence of enzyme rates and those at larger scales is n...
Cross, Thomas J. Takahashi, Gemma R. Diessner, Elizabeth M. Crosby, Marquise G. Farahmand, Vesta Zhuang, Shannon Butts, Carter T. Martin, Rachel W.
Published in
Biochemistry
The SARS-CoV-2 main protease (M pro ) is essential to viral replication and cleaves highly specific substrate sequences, making it an obvious target for inhibitor design. However, as for any virus, SARS-CoV-2 is subject to constant neutral drift and selection pressure, with new M pro mutations arising over time. Identification and structural charac...
Ste Marie, Emma J Wehrle, Robert J Haupt, Daniel J Wood, Neil B van der Vliet, Albert Previs, Michael J Masterson, Douglas S Hondal, Robert J
Published in
Biochemistry
Yoshii, Tatsuyuki Tahara, Kai Suzuki, Sachio Hatano, Yuka Kuwata, Keiko Tsukiji, Shinya
Published in
Biochemistry
The ability to chemically introduce lipid modifications to specific intracellular protein targets would enable the conditional control of protein localization and activity in living cells. We recently developed a chemical-genetic approach in which an engineered SNAP-tag fusion protein can be rapidly relocated and anchored from the cytoplasm to the ...
Paço, Lorela Zarate-Perez, Francisco Clouser, Amanda F Atkins, William M Hackett, John C
Published in
Biochemistry
Aromatase (CYP19A1) catalyzes the synthesis of estrogens from androgens and is an invaluable target of pharmacotherapy for estrogen-dependent cancers. CYP19A1 is also one of the most primordial human CYPs and, to the extent that its fundamental dynamics are conserved, is highly relevant to understanding those of the more recently evolved and promis...
Doh, Julia K Tobin, Savannah J Beatty, Kimberly E
Published in
Biochemistry
Microscopy allows researchers to interrogate proteins within a cellular context. To deliver protein-specific contrast, we developed a new class of genetically encoded peptide tags called versatile interacting peptide (VIP) tags. VIP tags deliver a reporter to a target protein via the formation of a heterodimer between the peptide tag and an exogeno...
