PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
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TLDR
The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.Abstract:
Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.read more
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Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation.
Tariq Afroz,Eva-Maria Hock,Patrick Ernst,Chiara Foglieni,Melanie Jambeau,Larissa A. B. Gilhespy,Florent Laferrière,Zuzanna Maniecka,Andreas Plückthun,Peer R. E. Mittl,Paolo Paganetti,Frédéric H.-T. Allain,Magdalini Polymenidou +12 more
TL;DR: It is reported that physiological nuclear TDP-43 in mouse and human brain forms homo-oligomers that are resistant to cellular stress and mediated through its N-terminal domain, which forms functional and dynamic oligomers antagonizing pathologic aggregation.
Journal ArticleDOI
Elongation factor G bound to the ribosome in an intermediate state of translocation.
TL;DR: Comparison with the posttranslocational state suggests that interactions between the tRNA and L1 stalk are preserved throughout translocation and that these are probably an essential feature of translocation required for stabilization of the hybrid P/E state.
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Non-invasive intravital imaging of cellular differentiation with a bright red-excitable fluorescent protein
Jun Chu,Russell D. Haynes,Stéphane Y. Corbel,Pengpeng Li,Emilio Gonzalez-Gonzalez,John S Burg,Niloufar Ataie,Amy J. Lam,Paula J. Cranfill,Michelle A. Baird,Michael W. Davidson,Ho Leung Ng,Ho Leung Ng,K. Christopher Garcia,K. Christopher Garcia,Christopher H. Contag,Kang Shen,Kang Shen,Helen M. Blau,Michael Z. Lin +19 more
TL;DR: In this article, three new red-excitable monomeric fluorescent proteins obtained by structure-guided mutagenesis of mNeptune are described and used to visualize the differentiation of myoblasts into myocytes in living mice.
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Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformation
Tea Pemovska,Eric Johnson,Mika Kontro,Gretchen A. Repasky,Jeffrey H. Chen,Peter A. Wells,Ciarán N. Cronin,Michele McTigue,Olli Kallioniemi,Kimmo Porkka,Brion W. Murray,Krister Wennerberg +11 more
TL;DR: This study shows that wild-type proteins do not always sample the conformations available to disease-relevant mutant proteins and that comprehensive drug testing of patient-derived cells can identify unpredictable, clinically significant drug-repositioning opportunities.
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SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity
Tomonari Muramatsu,Chie Takemoto,Yong-Tae Kim,Hongfei Wang,Wataru Nishii,Takaho Terada,Mikako Shirouzu,Shigeyuki Yokoyama +7 more
TL;DR: Crystallography revealed that Phe at the P2 position changes the conformation of the substrate-binding pocket, and thereby creates the subsite for Pheat the P3′ position, which reveals a type of subsite cooperativity in 3CLpro.
References
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