Zobrazeno 1 - 10
of 188
pro vyhledávání: '"James S. Fraser"'
Publikováno v:
IUCrJ, Vol 11, Iss 4, Pp 494-501 (2024)
In the folded state, biomolecules exchange between multiple conformational states crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules
Externí odkaz:
https://doaj.org/article/0b2b761acf384d09b28475fb4cdafe9d
Autor:
Jingyou Rao, Ruiqi Xin, Christian Macdonald, Matthew K. Howard, Gabriella O. Estevam, Sook Wah Yee, Mingsen Wang, James S. Fraser, Willow Coyote-Maestas, Harold Pimentel
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-22 (2024)
Abstract Deep mutational scanning (DMS) measures the effects of thousands of genetic variants in a protein simultaneously. The small sample size renders classical statistical methods ineffective. For example, p-values cannot be correctly calibrated w
Externí odkaz:
https://doaj.org/article/f2997b4bc0bd45f1b3bfee9e093dce6c
Autor:
Christian B. Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James S. Fraser, Willow Coyote-Maestas
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-19 (2023)
Abstract Insertions and deletions (indels) enable evolution and cause disease. Due to technical challenges, indels are left out of most mutational scans, limiting our understanding of them in disease, biology, and evolution. We develop a low cost and
Externí odkaz:
https://doaj.org/article/11399c52db2f4426b21268f10cf7d139
Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico
Autor:
Aron Broom, Rojo V. Rakotoharisoa, Michael C. Thompson, Niayesh Zarifi, Erin Nguyen, Nurzhan Mukhametzhanov, Lin Liu, James S. Fraser, Roberto A. Chica
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-10 (2020)
Kemp eliminases are artificial enzymes that catalyze the concerted deprotonation and ring-opening of benzisoxazoles. Here, the authors use room-temperature X-ray crystallography to investigate changes to the conformational ensemble of the Kemp elimin
Externí odkaz:
https://doaj.org/article/7439f4de0efc41d198a2176b909a8ff0
Autor:
Alexander M. Wolff, Iris D. Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T. Biel, Sergio Carbajo, Aina E. Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D. Koralek, Minoru Kubo, Tomas S. Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M. Thompson, Henry van den Bedem, Rahel A. Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sebastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
Publikováno v:
IUCrJ, Vol 7, Iss 2, Pp 306-323 (2020)
Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful me
Externí odkaz:
https://doaj.org/article/6e6b471c98104285badfe50aab472279
Autor:
Renee Otten, Lin Liu, Lillian R. Kenner, Michael W. Clarkson, David Mavor, Dan S. Tawfik, Dorothee Kern, James S. Fraser
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-11 (2018)
A key challenge in the field of protein design and evolution is to understand the mechanisms by which directed evolution is improving enzymes. Here the authors combine different biophysical methods and give mechanistic insights into how directed evol
Externí odkaz:
https://doaj.org/article/92e5d2150eec485a8a3eef20778b77f0
Autor:
Adam R. Offenbacher, Shenshen Hu, Erin M. Poss, Cody A. M. Carr, Alexander D. Scouras, Daniil M. Prigozhin, Anthony T. Iavarone, Ali Palla, Tom Alber, James S. Fraser, Judith P. Klinman
Publikováno v:
ACS Central Science, Vol 3, Iss 6, Pp 570-579 (2017)
Externí odkaz:
https://doaj.org/article/9e694d41cae949cb94870565b513e6ae
Publikováno v:
Structural Dynamics, Vol 6, Iss 6, Pp 064704-064704-11 (2019)
To gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2 × 2 × 2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study colle
Externí odkaz:
https://doaj.org/article/92a613ca992c4753babeb7183254ebed
Autor:
Nilanjana Chatterjee, Evangelos Pazarentzos, Manasi K. Mayekar, Philippe Gui, David V. Allegakoen, Gorjan Hrustanovic, Victor Olivas, Luping Lin, Erik Verschueren, Jeffrey R. Johnson, Matan Hofree, Jenny J. Yan, Billy W. Newton, John V. Dollen, Charles H. Earnshaw, Jennifer Flanagan, Elton Chan, Saurabh Asthana, Trey Ideker, Wei Wu, Junji Suzuki, Benjamin A. Barad, Yuriy Kirichok, James S. Fraser, William A. Weiss, Nevan J. Krogan, Asmin Tulpule, Amit J. Sabnis, Trever G. Bivona
Publikováno v:
Cell Reports, Vol 28, Iss 9, Pp 2317-2330.e8 (2019)
Summary: Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a tumor suppressor and bi-functional lipid and protein phosphatase. We report that the metabolic regulator pyruvate dehydrogenase kinase1 (PDHK1) is a synthetic-essential gene
Externí odkaz:
https://doaj.org/article/83f131016a464f1dbca868c93b137b5a
Autor:
Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M. J. J. Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung-I Chang, Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove, Sean Crosson, Sirano Dhe-Paganon, Enrico Di Cera, Catherine L. Drennan, Michael J. Eck, Brandt F. Eichman, Qing R. Fan, Adrian R. Ferré-D'Amaré, J. Christopher Fromme, K. Christopher Garcia, Rachelle Gaudet, Peng Gong, Stephen C. Harrison, Ekaterina E. Heldwein, Zongchao Jia, Robert J. Keenan, Andrew C. Kruse, Marc Kvansakul, Jason S. McLellan, Yorgo Modis, Yunsun Nam, Zbyszek Otwinowski, Emil F. Pai, Pedro José Barbosa Pereira, Carlo Petosa, C. S. Raman, Tom A. Rapoport, Antonina Roll-Mecak, Michael K. Rosen, Gabby Rudenko, Joseph Schlessinger, Thomas U. Schwartz, Yousif Shamoo, Holger Sondermann, Yizhi J. Tao, Niraj H. Tolia, Oleg V. Tsodikov, Kenneth D. Westover, Hao Wu, Ian Foster, James S. Fraser, Filipe R. N C. Maia, Tamir Gonen, Tom Kirchhausen, Kay Diederichs, Mercè Crosas, Piotr Sliz
Publikováno v:
Nature Communications, Vol 7, Iss 1, Pp 1-12 (2016)
The validation and analysis of X-ray crystallographic data is essential for reproducibility and the development of crystallographic methods. Here, the authors describe a repository for crystallographic datasets and demonstrate some of the ways it cou
Externí odkaz:
https://doaj.org/article/72383da3679147f9a2668c703d709d2e