By Ivano Bertini, Kathleen S. McGreevy, Giacomo Parigi
NMR is among the strongest equipment for imaging of biomolecules. This ebook is the last word NMR consultant for researchers within the biomedical group and provides not just history and sensible assistance but in addition a ahead taking a look view at the way forward for NMR in platforms biology.Content:
Chapter 1 NMR and its position in Mechanistic platforms Biology (pages 1–5): Prof. Dr. Ivano Bertini, Kathleen S. McGreevy and Prof. Giacomo Parigi
Chapter 2 constitution of Biomolecules: basics (pages 7–32): Lucia Banci, Francesca Cantini, Mirko Cevec, Hendrik R. A. Jonker, Senada Nozinovic, Christian Richter and Harald Schwalbe
Chapter three What may be discovered concerning the constitution and Dynamics of Biomolecules from NMR (pages 33–50): Lucio Ferella, Antonio Rosato, Paola Turano and Janez Plavec
Chapter four decision of Protein constitution and Dynamics (pages 51–94): Lucio Ferella, Antonio Rosato and Paola Turano
Chapter five DNA (pages 96–116): Janez Plavec
Chapter 6 RNA (pages 118–135): Richard Stefl and Vladimir Sklenar
Chapter 7 Intrinsically Disordered Proteins (pages 136–152): Isabella C. Felli, Roberta Pierattelli and Peter Tompa
Chapter eight Paramagnetic Molecules (pages 154–171): Ivano Bertini, Claudio Luchinat and Giacomo Parigi
Chapter nine NMR Methodologies for the research of Protein–Protein Interactions (pages 173–194): Tobias Madl and Michael Sattler
Chapter 10 Metal?Mediated Interactions (pages 196–203): Simone Ciofi?Baffoni
Chapter eleven Protein–Paramagnetic Protein Interactions (pages 204–217): Peter H. J. Keizers, Yoshitaka Hiruma and Marcellus Ubbink
Chapter 12 Protein–RNA Interactions (pages 218–236): Vijayalaxmi Manoharan, Jose Manuel Perez?Canadillas and Andres Ramos
Chapter thirteen Protein–DNA Interactions (pages 238–252): Lidija Kovacic and Rolf Boelens
Chapter 14 High?Throughput Screening and Fragment?Based layout: basic concerns for Lead Discovery and Optimization (pages 253–263): Maurizio Pellecchia
Chapter 15 Ligand?Observed NMR in Fragment?Based techniques (pages 264–280): Pawel Sledz, Chris Abell and Alessio Ciulli
Chapter sixteen Interactions of Metallodrugs with DNA (pages 282–296): Hong?Ke Liu and Peter J. Sadler
Chapter 17 RNA as a Drug goal (pages 298–313): Jan?Peter Ferner, Elke Duchardt Ferner, Jorg Rinnenthal, Janina greenback, Jens Wohnert and Harald Schwalbe
Chapter 18 Fluorine NMR Spectroscopy for Biochemical Screening in Drug Discovery (pages 314–327): Claudio Dalvit
Chapter 19 NMR of Peptides (pages 328–344): Johannes G. Beck, Andreas O. Frank and Horst Kessler
Chapter 20 Biomolecular Solid?State NMR/Basics (pages 345–364): Emeline Barbet?Massin and Guido Pintacuda
Chapter 21 Protein Dynamics within the reliable country (pages 366–375): Jozef R. Lewandowski and Lyndon Emsley
Chapter 22 Microcrystalline Proteins – a fantastic Benchmark for method improvement (pages 376–392): W. Trent Franks, Barth?Jan van Rossum, Benjamin Bardiaux, Enrico Ravera, Giacomo Parigi, Claudio Luchinat and Hartmut Oschkinat
Chapter 23 Structural reviews of Protein Fibrils via Solid?State NMR (pages 394–405): Anja Bockmann and Beat H. Meier
Chapter 24 Solid?State NMR on Membrane Proteins: equipment and purposes (pages 406–417): A. A. Cukkemane, M. Renault and M. Baldus
Chapter 25 Dynamic Nuclear Polarization (pages 419–431): Thomas F. Prisner
Chapter 26 13C Direct Detection NMR (pages 432–443): Isabella C. Felli and Roberta Pierattelli
Chapter 27 dashing up Multidimensional NMR information Acquisition (pages 444–465): Bernhard Brutscher, Dominique Marion and Lucio Frydman
Chapter 28 Metabolomics (pages 466–477): Leonardo Tenori
Chapter 29 In?Cell Protein NMR Spectroscopy (pages 478–494): David S. Burz, David Cowburn, Kaushik Dutta and Alexander Shekhtman
Chapter 30 Structural research of Cell?Free Expressed Membrane Proteins (pages 496–508): Solmaz Sobhanifar, Sina Reckel, Frank Lohr, Frank Bernhard and Volker Dotsch
Chapter 31 Grid Computing (pages 509–518): Antonio Rosato
Chapter 32 Protein–Protein Docking with HADDOCK (pages 520–535): Christophe Schmitz, Adrien S. J. Melquiond, Sjoerd J. de Vries, Ezgi Karaca, Marc van Dijk, Panagiotis L. Kastritis and Alexandre M. J. J. Bonvin
Chapter 33 computerized Protein constitution decision tools (pages 536–546): Paul Guerry and Torsten Herrmann
Chapter 34 NMR constitution selection of Protein–Ligand Complexes (pages 548–561): Ulrich Schieborr, Sridhar Sreeramulu and Harald Schwalbe
Chapter 35 Small attitude X?Ray Scattering/Small attitude Neutron Scattering as equipment Complementary to NMR (pages 562–574): M. V. Petoukhov and D. I. Svergun
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Extra resources for NMR of Biomolecules: Towards Mechanistic Systems Biology
In both types of fold, the b-strands can interact in two ways. 7b). The side-chains of the hydrophobic residues point inside the barrel, where hydrophobic molecules can also be accommodated, while the hydrophilic residues point towards the solvent. Fig. 9 Example of b-barrel (a, PDB ID: 1PRN, membrane channel porin), b-sandwich (b, PDB ID: 1F6L, variable light chain dimer of antiferritin antibody) and six b-propeller types of fold (c). In the b-propeller the six motifs formed by four up-anddown antiparallel b-strands are shown with different colors.
One of the most common motifs is the helix–turn–helix . It is often related to speciﬁc binding sites such as DNA binding . When the stretch connecting the two helices is longer than a turn, the structural motif is called a helix–loop–helix; this motif can also be involved in DNA or calcium binding. The helix–loop–helix, in which the two helices are perpendicular, is also called an EF-hand motif . If the stretch connecting the two helices is instead only formed by two residues, the latter are orientated approximately perpendicular to the helical axes.
Another supersecondary structure, common for many proteins, is formed by a b-hairpin and an a-helix. The latter is tightly packed on one side of the sheet formed by the b-hairpin forming a left-handed a-helix–b-hairpin fold . While a b-hairpin produces an antiparallel arrangement of two consecutive b-strands, the b–a–b structural motif is formed by two parallel consecutive b-strands connected by an a-helix. Each secondary structure element is separated by loops that can vary in length. The a-helix is essentially parallel to the b-strands, but lies above the plane formed by the two b-strands (this motif is also called a right-handed b–a–b motif).