Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human

Autor: Karol Szlachta, Ryan G. Thys, Naomi D. Atkin, Levi C. T. Pierce, Stefan Bekiranov, Yuh-Hwa Wang

Publikováno v: Genome Biology, Vol 19, Iss 1, Pp 1-19 (2018)

Abstract Background Alternative DNA secondary structures can arise from single-stranded DNA when duplex DNA is unwound during DNA processes such as transcription, resulting in the regulation or perturbation of these processes. We identify sites of hi

Externí odkaz: https://doaj.org/article/5ebe8266f4b44aac81a092a1bc50aa27

Theoretical Insights Reveal Novel Motions in Csk's SH3 Domain That Control Kinase Activation.

Autor: Sulyman Barkho, Levi C T Pierce, Sheng Li, Joseph A Adams, Patricia A Jennings

Publikováno v: PLoS ONE, Vol 10, Iss 6, p e0127724 (2015)

The Src family of tyrosine kinases (SFKs) regulate numerous aspects of cell growth and differentiation and are under the principal control of the C-terminal Src Kinase (Csk). Although Csk and SFKs share conserved kinase, SH2 and SH3 domains, they dif

Externí odkaz: https://doaj.org/article/f2d7a697c5cd4ff69d64605907f1bac5

DNA topoisomerases participate in fragility of the oncogene RET.

Autor: Laura W Dillon, Levi C T Pierce, Christine E Lehman, Yuri E Nikiforov, Yuh-Hwa Wang

Publikováno v: PLoS ONE, Vol 8, Iss 9, p e75741 (2013)

Fragile site breakage was previously shown to result in rearrangement of the RET oncogene, resembling the rearrangements found in thyroid cancer. Common fragile sites are specific regions of the genome with a high susceptibility to DNA breakage under

Externí odkaz: https://doaj.org/article/3d327dd1fed34847a33792d3489fa825

Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant

Autor: Rommie E. Amaro, Nathan Mih, Daniel J. Mermelstein, Victoria A. Feher, J. Andrew McCammon, Levi C. T. Pierce, Jamie M. Schiffer

Publikováno v: Biophysical journal, vol 116, iss 2

The atomic-level mechanisms that coordinate ligand release from protein pockets are only known for a handful of proteins. Here, we report results from accelerated molecular dynamics simulations for benzene dissociation from the buried cavity of the T

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0681d94169c91291244fac93afc922c
https://pubmed.ncbi.nlm.nih.gov/30606449

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Autor: Yuqing Deng, Edward Harder, Lingle Wang, Bruce J. Berne, Ramy Farid, Ron Wester, Richard A. Friesner, Levi C. T. Pierce, Teng-Yi Lin, Donna L. Romero, William L. Jorgensen, Mark L. Brewer, Murcko Mark A, Shaughnessy Robinson, Robert Abel, Jeremy R. Greenwood, Jennifer L. Knight, Thijs Beuming, Byungchan Kim, Goran Krilov, Leah L. Frye, Dmitry Lupyan, David L. Mobley, Wolfgang Damm, Yujie Wu, Thomas Steinbrecher, Craig E. Masse, Markus K. Dahlgren, Woody Sherman

Publikováno v: Journal of the American Chemical Society, vol 137, iss 7
Wang, L; Wu, Y; Deng, Y; Kim, B; Pierce, L; Krilov, G; et al.(2015). Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. Journal of the American Chemical Society, 137(7), 2695-2703. doi: 10.1021/ja512751q. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/5061663w

© 2015 American Chemical Society. Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over the past few decades, free-energy calculations have benefited from improved force fields and sampling algorithms, as well

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::773d1836a8ebda0977ca7d9384d08fcb
https://doi.org/10.1021/ja512751q