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
Citations
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60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle.
Christoph Leidig,Matthias Thoms,Iris Holdermann,Bettina Bradatsch,Otto Berninghausen,Gert Bange,Irmgard Sinning,Ed Hurt,Roland Beckmann +8 more
TL;DR: It is suggested that the 5S RNP performs a semicircular movement during 60S biogenesis to adopt its final position, fulfilling a chaperone-like function in guiding the flanking 25S rRNA helices of the central protuberance to their final topology.
Journal ArticleDOI
Defining a protective epitope on factor H binding protein, a key meningococcal virulence factor and vaccine antigen
Enrico Malito,Agnese Faleri,Paola Lo Surdo,Daniele Veggi,Giulietta Maruggi,Eva Grassi,Elena Cartocci,Isabella Bertoldi,Alessia Genovese,Laura Santini,Giacomo Romagnoli,Erica Borgogni,Sébastien Brier,Carla Lo Passo,Maria Domina,Flora Castellino,Franco Felici,Stijn van der Veen,Steven Johnson,Susan M. Lea,Christoph M. Tang,Mariagrazia Pizza,Silvana Savino,Nathalie Norais,Rino Rappuoli,Matthew J. Bottomley,Vega Masignani +26 more
TL;DR: Data show that linear epitope mapping techniques provide useful but incomplete descriptions of B-cell epitopes, indicating that increased efforts to fully characterize antigen–antibody interfaces are required to understand and design effective immunogens.
Journal ArticleDOI
Anti-obesity effects of GIPR antagonists alone and in combination with GLP-1R agonists in preclinical models
Elizabeth A. Killion,Jinghong Wang,Junming Yie,Stone D.-H. Shi,Darren L. Bates,Xiaoshan Min,Renee Komorowski,Todd Hager,Liying Deng,Larissa Atangan,Lu Shu Chen,Robert J.M. Kurzeja,Glenn Sivits,Joanne Lin,Qing Chen,Zhulun Wang,Stephen A. Thibault,Christina Abbott,Tina Meng,Brandon C. P. Clavette,Christopher Murawsky,Ian Foltz,James B. Rottman,Clarence Hale,Murielle M. Véniant,David Lloyd +25 more
TL;DR: Preclinical validation of a therapeutic approach to treat obesity with anti-GIPR antibodies is provided and it is found that weight loss in obese nonhuman primates (NHPs) using an anti-human GIPR antibody (hG IPR-Ab) is more pronounced than in mice.
Journal ArticleDOI
Observing cellulose biosynthesis and membrane translocation in crystallo
Jacob L. W. Morgan,Joshua T. McNamara,Michael Fischer,Jamie R. Rich,Hong-Ming Chen,Stephen G. Withers,Jochen Zimmer +6 more
TL;DR: Structural snapshots of a complete cellulose biosynthesis cycle are revealed, from substrate binding to polymer translocation, and substrate- and product-bound structures of BcsA provide the basis for substrate recognition and demonstrate the stepwise elongation of cellulose.
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The Molecular Mechanism of Substrate Engagement and Immunosuppressant Inhibition of Calcineurin
Simina Grigoriu,Rachel Bond,Pilar Cossio,Jennifer A. Chen,Nina Ly,Gerhard Hummer,Rebecca Page,Martha S. Cyert,Wolfgang Peti +8 more
TL;DR: Structural analyses show that a viral protein and immunosuppressant drugs inhibit theosphatase calcineurin by preventing substrate binding, and provide a model of a phosphatase engaged with its substrate.
References
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Phaser crystallographic software
Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
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