Zobrazeno 1 - 10
of 84
pro vyhledávání: '"Karissa Y Sanbonmatsu"'
Publikováno v:
PLoS Computational Biology, Vol 16, Iss 11, p e1008293 (2020)
Molecular Dynamics (MD) simulations seek to provide atomic-level insights into conformationally dynamic biological systems at experimentally relevant time resolutions, such as those afforded by single-molecule fluorescence measurements. However, limi
Externí odkaz:
https://doaj.org/article/db0e0fee946d461b8734df83c9cbea39
Autor:
Susmita Roy, Heiko Lammert, Ryan L Hayes, Bin Chen, Regan LeBlanc, T Kwaku Dayie, José N Onuchic, Karissa Y Sanbonmatsu
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 3, p e1005406 (2017)
Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecula
Externí odkaz:
https://doaj.org/article/8ab6a05fea3742f2b2caaf5cc33b1883
Autor:
Vrinda Venu, Cullen Roth, Samantha H. Adikari, Eric M. Small, Shawn R. Starkenburg, Karissa Y. Sanbonmatsu, Christina R. Steadman
Publikováno v:
Communications Biology, Vol 7, Iss 1, Pp 1-17 (2024)
Abstract The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To
Externí odkaz:
https://doaj.org/article/1f9c4b86b9b745debf3baf5aa53f6f3d
Autor:
Nan Li, Scott P Hennelly, Chris J Stubben, Sofiya Micheva-Viteva, Bin Hu, Yulin Shou, Momchilo Vuyisich, Chang-Shung Tung, Patrick S Chain, Karissa Y Sanbonmatsu, Elizabeth Hong-Geller
Publikováno v:
PLoS ONE, Vol 11, Iss 12, p e0168915 (2016)
Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that ar
Externí odkaz:
https://doaj.org/article/1b1d0df5ef2e4076a5d3ec9b25a8299d
Publikováno v:
PLoS Computational Biology, Vol 9, Iss 3, p e1003003 (2013)
Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project
Externí odkaz:
https://doaj.org/article/fd135dfba03a404f8ad2759009f9c4a5
Autor:
Cullen Roth, Vrinda Venu, Vanessa Job, Nicholas Lubbers, Karissa Y. Sanbonmatsu, Christina R. Steadman, Shawn R. Starkenburg
Publikováno v:
BMC Bioinformatics, Vol 24, Iss 1, Pp 1-22 (2023)
Abstract Background Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between
Externí odkaz:
https://doaj.org/article/3cb6da81502f4e049ace1245f25c75d3
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-15 (2023)
Abstract Accurate protein synthesis is determined by the two-subunit ribosome’s capacity to selectively incorporate cognate aminoacyl-tRNA for each mRNA codon. The molecular basis of tRNA selection accuracy, and how fidelity can be affected by anti
Externí odkaz:
https://doaj.org/article/a5e0703efe69456b8f8e549d1ab39eb7
Autor:
Jacob C. Miner, Paul W. Fenimore, William M. Fischer, Benjamin H. McMahon, Karissa Y. Sanbonmatsu, Chang-Shung Tung
Publikováno v:
Current Research in Structural Biology. 4:220-230
SARS-CoV-2 is the virus responsible for the COVID-19 pandemic and catastrophic, worldwide health and economic impacts. The spike protein on the viral surface is responsible for viral entry into the host cell. The binding of spike protein to the host
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a4e2c2558626fb5e2bedcadaf524909e
https://doi.org/10.1016/j.crstbi.2022.06.004
https://doi.org/10.1016/j.crstbi.2022.06.004
Autor:
Karissa Y. Sanbonmatsu
Publikováno v:
Mammalian Genome
While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d435c642af2c5ffe5be8813eae53f289
http://europepmc.org/articles/PMC8509902
http://europepmc.org/articles/PMC8509902
Autor:
Wataru Nishima, Dylan Girodat, Mikael Holm, Emily J Rundlet, Jose L Alejo, Kara Fischer, Scott C Blanchard, Karissa Y Sanbonmatsu
Publikováno v:
Nucleic Acids Res
Translocation of messenger RNA (mRNA) and transfer RNA (tRNA) substrates through the ribosome during protein synthesis, an exemplar of directional molecular movement in biology, entails a complex interplay of conformational, compositional, and chemic
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c003ca8e4a001aea2d8bef962d4aff9c
https://europepmc.org/articles/PMC9371933/
https://europepmc.org/articles/PMC9371933/
