Book Chapter10.1385/1-59259-809-9:353
Automated NMR structure calculation with CYANA.
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TL;DR: This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA.
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Abstract: This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columns from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY cross-peaks and the three-dimensional structure of the protein in solution can be calculated automatically with CYANA.
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Citations
Hydrogen exchange study on the hydroxyl groups of serine and threonine residues in proteins and structure refinement using NOE restraints with polar side-chain groups
TL;DR: The methods for monitoring the hydrogen exchange rates of the OH groups of serine (Ser) and threonine (Thr) residues in an 18.2 kDa protein, EPPIb, are extended and the usefulness of NOE restraints with slowly exchanging OH protons for refining the protein structure is demonstrated.
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Solution structure of the rat P2X4 receptor head domain involved in inhibitory metal binding.
TL;DR: NMR analysis showed that the head domain possessed the same fold as in the zebrafish P2X4 receptor previously determined by crystallography, and the inhibitory, divalent, metal ion binding sites were determined by NMR techniques.
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Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A
Jordi Juárez-Jiménez,Arun A. Gupta,Gogulan Karunanithy,Antonia S. J. S. Mey,Charis Georgiou,Harris Ioannidis,Alessio De Simone,Paul N. Barlow,Alison N. Hulme,Malcolm D. Walkinshaw,Andrew Baldwin,Julien Michel +11 more
TL;DR: A novel combination of accelerated MD (aMD) simulations and Markov state modelling (MSM) to explore functionally relevant, but sparsely populated conformational states with millisecond lifetimes in silico has tremendous promise for the design of dynamic protein free energy landscapes for both protein engineering and drug discovery.
Structural analysis of the UBA domain of x-linked inhibitor of apoptosis protein reveals different surfaces for ubiquitin-binding and self-association
Man-Kit Tse,Sin Kam Hui,Yinhua Yang,Si-Tao Yin,Hong-Yu Hu,Bing Zou,Benjamin Chun Yu Wong,Kong-Hung Sze +7 more
TL;DR: The notion that XIAP-UBA uses different surfaces for ubiquitin-binding and self-association provides a plausible model to explain the reported selectivity of XIAP in binding polyubiquitin chains with different linkages.
Structural and Biochemical Characterization of NarE, an Iron-containing ADP-ribosyltransferase from Neisseria meningitidis
Christian Koehler,Ludovic Carlier,Daniele Veggi,Enrico Balducci,Frederica Di Marcello,Mario Ferrer-Navarro,Mariagrazzia Pizza,Xavier Daura,Xavier Daura,Marco Soriani,Rolf Boelens,Alexandre M. J. J. Bonvin +11 more
TL;DR: This study combines structural and functional features of NarE providing for the first time a characterization of an iron-dependent ADPRT, which shows structural homology to other ADPRTs.
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