JACS 2016

A joint structural refinement against NMR data and X-ray diffraction patterns offers unique opportunities to detect differences in the conformation of biomolecules between the solution and the crystal states. Read More

ChemComm

An integrated approach which combines in-cell NMR spectroscopy with optical and X-ray fluorescence microscopy was developed to describe the intracellular maturation state of human Cu,Zn-SOD1.  Read More

NCB N terminal

Structural and biophysical evidences define the early steps of iron-sulfur protein maturation in the cytosol, demonstrating that  glutaredoxin-3 passes [2Fe-2S] clusters to anamorsin during a protein-protein interaction mediated by their N-terminal domains.  Read More 

nature chemistry

Dynamic nuclear polarization (DNP) in liquid solutions can enhance 13C NMR signals at magnetic fields of 3 T and room temperature up to three orders of magnitude. Read More  Highlighted in Angewandte Chemie

CERM research on covers

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High relaxivity Gd(III)-DNA gold nanostars: investigation of shape effects on proton relaxation, ACS nano, 9, 3385–3396, 2015 Exploring regions of conformational space occupied by two-domain proteins, J.Phys.Chem.B, 118, 10576-10587, 2014  

 

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NMR of Biomolecules

Towards Mechanistic Systems Biology

Bertini I, McGreevy KS, Parigi G (Eds.), Wiley-VCH, 2012

  

 

 

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NMR is one of the most powerful methods for studying the structure, dynamics, and interactions of biomolecules. This book provides a broad overview of the possibilities afforded by NMR and is especially geared towards students and newcomers to the field, providing not only background and practical tips, but also a forward looking view on the future of NMR in systems biology. The book includes an overview of biomolecular structure before identifying what NMR can teach us about the structure and dynamics of biomolecules and addresses a series of relevant topics in NMR-driven biological research: the role of NMR in the study of the structure and dynamics of biomolecular interactions, NMR in drug discovery, solid-state NMR, frontiers in NMR spectroscopy, and computational aspects.

Key features: 

  • Explores the role of NMR techniques in Systems Biology
  • Includes section on Computational Aspects
  • Includes protocols and troubleshooting sections
  • Provides perspectives on future developments
  • 

Contents:

Part One -  Introduction
1 NMR and its Place in Mechanistic Systems Biology - Ivano Bertini, Kathleen S. McGreevy, and Giacomo Parigi  
2 Structure of Biomolecules: Fundamentals   
2.1 Structural Features of Proteins - Lucia Banci and Francesca Cantini  
2.2 Nucleic Acids - Mirko Cevec, Hendrik R.A. Jonker, Senada Nozinovic, Christian Richter, and Harald Schwalbe  
3 What Can be Learned About the Structure and Dynamics of Biomolecules from NMR   
3.1 Proteins Studied by NMR - Lucio Ferella, Antonio Rosato, and Paola Turano
3.2 Nucleic Acids Studied by NMR - Janez Plavec
Part Two - Role of NMR in the Study of the Structure and Dynamics of Biomolecules   
4 Determination of Protein Structure and Dynamics - Lucio Ferella, Antonio Rosato, and Paola Turano
5 DNA - Janez Plavec
6 RNA - Richard Stefl and Vladimir Sklenar  
7 Intrinsically Disordered Proteins - Isabella C. Felli, Roberta Pierattelli, and Peter Tompa
8 Paramagnetic Molecules - Ivano Bertini, Claudio Luchinat, and Giacomo Parigi  
Part Three -  Role of NMR in the Study of the Structure and Dynamics of Biomolecular Interactions  
9 NMR Methodologies for the Analysis of Protein–Protein Interactions - Tobias Madl and Michael Sattler  
10 Metal-Mediated Interactions - Simone Ciofi-Baffoni  
11 Protein–Paramagnetic Protein Interactions - Peter H.J. Keizers, Yoshitaka Hiruma, and Marcellus Ubbink  
12 Protein–RNA Interactions - Vijayalaxmi Manoharan, Jose Manuel Perez-Canadillas, and Andres Ramos  
13 Protein–DNA Interactions - Lidija Kovacic and Rolf Boelens  
Part Four -  NMR in Drug Discovery   
14 High-Throughput Screening and Fragment-Based Design: General Considerations for Lead Discovery and Optimization - Maurizio Pellecchia  
15 Ligand-Observed NMR in Fragment-Based Approaches - Pawel Sledz, Chris Abell, and Alessio Ciulli  
16 Interactions of Metallodrugs with DNA - Hong-Ke Liu and Peter J. Sadler  
17 RNA as a Drug Target - Jan-Peter Ferner, Elke Duchardt Ferner, Jörg Rinnenthal, Janina Buck, Jens Wöhnert, and Harald Schwalbe  
18 Fluorine NMR Spectroscopy for Biochemical Screening in Drug Discovery - Claudio Dalvit  
19 NMR of Peptides - Johannes G. Beck, Andreas O. Frank, and Horst Kessler  
Part Five -  Solid-State NMR  
20 Biomolecular Solid-State NMR/Basics - Emeline Barbet-Massin and Guido Pintacuda  
21 Protein Dynamics in the Solid State - Jozef R. Lewandowski and Lyndon Emsley  
22 Microcrystalline Proteins – An Ideal Benchmark for Methodology Development - W. Trent Franks, Barth-Jan van Rossum, Benjamin Bardiaux, Enrico Ravera, Giacomo Parigi, Claudio Luchinat, and Hartmut Oschkinat  
23 Structural Studies of Protein Fibrils by Solid-State NMR - Anja Böckmann and Beat H. Meier  
24 Solid-State NMR on Membrane Proteins: Methods and Applications - A.A. Cukkemane, M. Renault, and M. Baldus  
Part Six -  Frontiers in NMR Spectroscopy  
25 Dynamic Nuclear Polarization - Thomas F. Prisner  
26 13C Direct Detection NMR - Isabella C. Felli and Roberta Pierattelli  
27 Speeding Up Multidimensional NMR Data Acquisition - Bernhard Brutscher, Dominique Marion, and Lucio Frydman  
28 Metabolomics - Leonardo Tenori  
29 In-Cell Protein NMR Spectroscopy - David S. Burz, David Cowburn, Kaushik Dutta, and Alexander Shekhtman  
30 Structural Investigation of Cell-Free Expressed Membrane Proteins - Solmaz Sobhanifar, Sina Reckel, Frank Löhr, Frank Bernhard, and Volker Dötsch  
Part Seven -  Computational Aspects  
31 Grid Computing - Antonio Rosato  
32 Protein–Protein Docking with HADDOCK  - Christophe Schmitz, Adrien S.J. Melquiond, Sjoerd J. de Vries, Ezgi Karaca, Marc van Dijk, Panagiotis L. Kastritis, and Alexandre M.J.J. Bonvin  
33 Automated Protein Structure Determination Methods - Paul Guerry and Torsten Herrmann  
34 NMR Structure Determination of Protein–Ligand Complexes - Ulrich Schieborr, Sridhar Sreeramulu, and Harald Schwalbe  
35 Small Angle X-Ray Scattering/Small Angle Neutron Scattering as Methods Complementary to NMR - M.V. Petoukhov and D.I. Svergun  

From Chapter 1:

“Mechanistic Systems Biology has the potential to become an important field within biology. With the term “mechanistic,” we can imagine a play whose plot is represented by a biochemical pathway. From our seats in the audience, we can see the three-dimensional structures of the biomolecular actors as they interact with one another in various scenes. In real terms, we can achieve an atomic-level, three-dimensional view of proteins interacting with one another or with DNA/RNA to achieve a biochemical result. Observing three-dimensional structures allows one to better understand the biomolecule, and provides a further means to intervene and monitor its function. (…) NMR has a primary role within this framework. It can provide a biomolecule’s structure and can monitor its interactions in a mechanistic frame. Both thermodynamic and kinetic information on the interactions between biomolecules can be obtained, thus providing a powerful tool for the modeling of the system.”

Figures and Tables of the book

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