Zobrazeno 1 - 10
of 10
pro vyhledávání: '"Helena W. Qi"'
Publikováno v:
Chemical Science. 12:1147-1162
Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computation
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c630aa3b80763ba360129811d183c8ff
https://doi.org/10.1039/d0sc05084a
https://doi.org/10.1039/d0sc05084a
Autor:
Helena W. Qi, Heather J. Kulik
Publikováno v:
Journal of Chemical Information and Modeling. 59:2199-2211
We investigate unexpectedly short non-covalent distances (85% of the sum of van der Waals radii) in X-ray crystal structures of proteins. We curate over 11 000 high-quality protein crystal structures and an ultra-high-resolution (1.2 Å or better) su
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4226a737f70fe7762eb69deeb2ce6471
https://doi.org/10.1021/acs.jcim.9b00144
https://doi.org/10.1021/acs.jcim.9b00144
Publikováno v:
PLoS ONE, Vol 9, Iss 6, p e98618 (2014)
Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, othe
Externí odkaz:
https://doaj.org/article/14109fb2cd384b44a1a5cf8f64e82ea1
Autor:
Dae Hee Yun, Byung Kook Lim, Heather J. Kulik, Ji Wang, Matthew P. Frosch, Xin Jin, Gabrielle T. Drummond, Hidde L. Ploegh, Shih-Chi Chen, Matthias C. Truttmann, Chang Ho Sohn, Ritchie Chen, Margaret McCue, Nicholas B. Evans, Wendy Trieu, Todd R. Golub, Taeyun Ku, Heejin Choi, Kwanghun Chung, Varoth Lilascharoen, Young Gyun Park, Hayeon Caitlyn Oak, Helena W. Qi
Publikováno v:
Nature Biotechnology. 37:73-83
Understanding complex biological systems requires the system-wide characterization of both molecular and cellular features. Existing methods for spatial mapping of biomolecules in intact tissues suffer from information loss caused by degradation and
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6abea34454e117ea51eb8d3791146d36
https://doi.org/10.1038/nbt.4281
https://doi.org/10.1038/nbt.4281
Biosynthetic enzyme complexes selectively catalyze challenging chemical transformations, including alkane functionalization (e.g., halogenation of threonine, Thr, by non-heme iron SyrB2). However, the role of complex formation in enabling reactivity
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8274f990300a300213dc41e7766a0cf4
https://doi.org/10.26434/chemrxiv.7234058
https://doi.org/10.26434/chemrxiv.7234058
Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2c96cf3d271b012ab2a051ffc61d14f6
https://doi.org/10.26434/chemrxiv.7130795
https://doi.org/10.26434/chemrxiv.7130795
Autor:
Helena W. Qi, Heather J. Kulik
Publikováno v:
Journal of Chemical Information and Modeling. 59:3609-3610
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::fa0c1994e4f2983c926d123e0234407b
https://doi.org/10.1021/acs.jcim.9b00606
https://doi.org/10.1021/acs.jcim.9b00606
Publikováno v:
The Journal of Physical Chemistry A. 117:4486-4499
This work presents a new fragment method, the electrostatically embedded many-body expansion of the nonlocal energy (EE-MB-NE), and shows that it, along with the previously proposed electrostatically embedded many-body expansion of the correlation en
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e78f08c2552c765ef85ee7fd3e3b52b4
https://doi.org/10.1021/jp401463f
https://doi.org/10.1021/jp401463f
Publikováno v:
Journal of Chemical Theory and Computation. 9:995-1006
The binding energies and relative conformational energies of five configurations of the water 16-mer are computed using 61 levels of density functional (DF) theory, 12 methods combining DF theory with molecular mechanics damped dispersion (DF-MM), se
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2a56f25787f788e93652897d12bae607
https://doi.org/10.1021/ct300848z
https://doi.org/10.1021/ct300848z
Publikováno v:
The journal of physical chemistry. A. 119(24)
The directed depolymerization of lignin biopolymers is of utmost relevance for the valorization or commercialization of biomass fuels. We present a computational and theoretical screening approach to identify potential cleavage pathways and resulting
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7b2d30f9911215d0ff5c59788f53d357
https://pubmed.ncbi.nlm.nih.gov/26001164
https://pubmed.ncbi.nlm.nih.gov/26001164