273 Topics in Current Chemistry

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2 273 Topics in Current Chemistry Editorial Board: V. Balzani A. de Meijere K. N. Houk H. Kessler J.-M. Lehn S. V. Ley S. L. Schreiber J. Thiem B. M. Trost F. Vögtle H. Yamamoto

3 Topics in Current Chemistry Recently Published and Forthcoming Volumes STM and AFM Studies on (Bio)molecular Systems: Unravelling the Nanoworld Volume Editor: Samori, P. Vol. 285, 2008 Amplification of Chirality Volume Editor: Soai, K. Vol. 284, 2008 Anthracycline Chemistry and Biology II Mode of Action, Clinical Aspects and New Drugs Volume Editor: Krohn, K. Vol. 283, 2008 Anthracycline Chemistry and Biology I Biological Occurence and Biosynthesis, Synthesis and Chemistry Volume Editor: Krohn, K. Vol. 282, 2008 Photochemistry and Photophysics of Coordination Compounds II Volume Editors: Balzani, V., Campagna, S. Vol. 281, 2007 Photochemistry and Photophysics of Coordination Compounds I Volume Editors: Balzani, V., Campagna, S. Vol. 280, 2007 Metal Catalyzed Reductive C C Bond Formation A Departure from Preformed Organometallic Reagents VolumeEditor:Krische,M.J. Vol. 279, 2007 Combinatorial Chemistry on Solid Supports Volume Editor: Bräse, S. Vol. 278, 2007 Creative Chemical Sensor Systems Volume Editor: Schrader, T. Vol. 277, 2007 In situ NMR Methods in Catalysis Volume Editors: Bargon, J., Kuhn, L. T. Vol. 276, 2007 Sulfur-Mediated Rearrangements II Volume Editor: Schaumann, E. Vol. 275, 2007 Sulfur-Mediated Rearrangements I Volume Editor: Schaumann, E. Vol. 274, 2007 Bioactive Conformation II Volume Editor: Peters, T. Vol. 273, 2007 Bioactive Conformation I Volume Editor: Peters, T. Vol. 272, 2007 Biomineralization II Mineralization Using Synthetic Polymers and Templates Volume Editor: Naka, K. Vol. 271, 2007 Biomineralization I Crystallization and Self-Organization Process Volume Editor: Naka, K. Vol. 270, 2007

4 Bioactive Conformation II Volume Editor: Thomas Peters With contributions by S. Afonin A. S. Arseniev T. Arvinte J. L. Asensio A. Bastida M. J. J. Blommers E. V. Bocharov V. Dötsch U. H. N. Dürr M. Geiser W. Jahnke V. Jayalakshmi J. Jiménez-Barbero M. A. Johnson N. R. Krishna K. V. Pavlov T. Peters B. M. Pinto C. Rademacher P. Ramage J. Salgado H. Sparrer A. Strauss A. S. Ulrich P. Wadhwani 123

5 The series Topics in Current Chemistry presents critical reviews of the present and future trends in modern chemical research. The scope of coverage includes all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the nonspecialist reader, whether at the university or in industry, a comprehensive overview of an area where new insights are emerging that are of interest to a larger scientific audience. As a rule, contributions are specially commissioned. The editors and publishers will, however, always be pleased to receive suggestions and supplementary information. Papers are accepted for Topics in Current Chemistry in English. In references Topics in Current Chemistry is abbreviated Top Curr Chem and is cited as a journal. Visit the TCC content at springerlink.com ISBN e-isbn DOI / Topics in Current Chemistry ISSN Library of Congress Control Number: c 2008 Springer-Verlag Berlin Heidelberg This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover design: WMXDesign GmbH, Heidelberg Typesetting and Production: le-tex publishing services ohg, Leipzig Printed on acid-free paper springer.com

6 Volume Editor Prof. Dr. Thomas Peters Universität Lübeck Inst. Chemie Ratzeburger Allee Lübeck Editorial Board Prof. Vincenzo Balzani Dipartimento di Chimica G. Ciamician University of Bologna via Selmi Bologna, Italy vincenzo.balzani@unibo.it Prof. Dr. Armin de Meijere Institut für Organische Chemie der Georg-August-Universität Tammanstr Göttingen, Germany ameijer1@uni-goettingen.de Prof. Dr. Kendall N. Houk University of California Department of Chemistry and Biochemistry 405 Hilgard Avenue Los Angeles, CA USA houk@chem.ucla.edu Prof. Dr. Horst Kessler Institut für Organische Chemie TU München Lichtenbergstraße Garching, Germany kessler@ch.tum.de Prof. Jean-Marie Lehn ISIS 8, allée Gaspard Monge BP Strasbourg Cedex, France lehn@isis.u-strasbg.fr Prof. Steven V. Ley University Chemical Laboratory Lensfield Road Cambridge CB2 1EW Great Britain Svl1000@cus.cam.ac.uk Prof. Stuart L. Schreiber Chemical Laboratories Harvard University 12 Oxford Street Cambridge, MA USA sls@slsiris.harvard.edu Prof. Dr. Joachim Thiem Institut für Organische Chemie Universität Hamburg Martin-Luther-King-Platz Hamburg, Germany thiem@chemie.uni-hamburg.de

7 VI Prof. Barry M. Trost Department of Chemistry Stanford University Stanford, CA USA Prof. Dr. F. Vögtle Kekulé-Institut für Organische Chemie und Biochemie der Universität Bonn Gerhard-Domagk-Str Bonn, Germany voegtle@uni-bonn.de Prof. Dr. Hisashi Yamamoto Department of Chemistry The University of Chicago 5735 South Ellis Avenue Chicago, IL USA yamamoto@uchicago.edu Editorial Board

8 Topics in Current Chemistry Also Available Electronically For all customers who have a standing order to Topics in Current Chemistry, we offer the electronic version via SpringerLink free of charge. Please contact your librarian who can receive a password or free access to the full articles by registering at: springerlink.com If you do not have a subscription, you can still view the tables of contents of the volumes and the abstract of each article by going to the SpringerLink Homepage, clicking on Browse by Online Libraries, then Chemical Sciences, and finally choose Topics in Current Chemistry. You will find information about the Editorial Board AimsandScope Instructions for Authors SampleContribution at springer.com using the search function. Color figures are published in full color within the electronic version on SpringerLink.

9 Preface Specific binding of a ligand to a receptor is a key step in a variety of biological processes, such as immune reactions, enzyme cascades, or intracellular transport processes. The ligand receptor terminology implies that the receptor molecule is significantly larger than the ligand, and the term bioactive conformation usually characterizes the conformation of a ligand when it is bound to a receptor. In a more general sense, bioactive conformation applies to any molecule in a biologically relevant bound state regardless of size considerations. Most of the contributions to this book address ligands that are much smaller than their receptors. X-ray crystallography and high resolution NMR spectroscopy are the two main experimental techniques used to study bioactive conformations. Therefore, the two volumes of this book cover approaches that use either of the two techniques, or a combination thereof. The combination of X-ray crystallography and NMR spectroscopy is particularly useful when a crystal structure of a receptor protein, but not of the receptor protein ligand complex, is available. A number of experimental techniques to analyze the bioactive conformation of a ligand with NMR are based on the observation of the resonance signals of the free ligand that is in exchange with the bound ligand. Several chapters focus on such approaches that range from classical transferred NOE experiments, to transferred dipolar couplings, to STD (saturation transfer difference) NMR techniques. In cases where tight binding in the sub-nanomolar range prevents the analysis of the bioactive conformation via free ligand signals, the ligand protein complex has to be analyzed with protein NMR-based techniques or by crystallography. Since this area has been the subject of many reviews and monographs it will not be covered here in particular detail. As a unifying theme, all contributions target the question of how molecular recognition of biologically active molecules is achieved on the atomic scale. Depending on the research topic the results from these studies have a strong impact not only in basic research but also in several fields of application ranging from pharmaceutical applications to the use of biomolecules as, for example, cryoprotectants. Almost all contributions to the two volumes highlight the fact that ligand protein complexes cannot be treated as static ensembles. On both sides, the ligand and the receptor side, dynamic processes contribute to the molecular recognition. In this sense it is hoped that these two volumes of Bioactive Confor-

10 X Preface mation will sensitize us for the need to invent and develop more experimental techniques to study the dynamic aspects of bioactive conformations. Lübeck, December 2007 Thomas Peters

11 Contents NMR-Based Strategies to Elucidate Bioactive Conformations of Weakly Binding Ligands M.J.J.Blommers A.Strauss M.Geiser P.Ramage H.Sparrer W.Jahnke... 1 Quantitative Analysis of STD-NMR Spectra of Reversibly Forming Ligand Receptor Complexes N.R.Krishna V.Jayalakshmi Structural and Functional Studies of Peptide Carbohydrate Mimicry M.A.Johnson B.M.Pinto Studies on the Conformational Features of Neomycin-B and its Molecular Recognition by RNA and Bacterial Defense Proteins J.L.Asensio A.Bastida J.Jiménez-Barbero Solid State NMR Structure Analysis of the Antimicrobial Peptide Gramicidin S in Lipid Membranes: Concentration-Dependent Re-alignment and Self-Assembly as a β-barrel S. Afonin U. H. N. Dürr P. Wadhwani J. Salgado A. S. Ulrich Modulation of the Bioactive Conformation of Transforming Growth Factor β: Possible Implications of Cation Binding for Biological Function E.V.Bocharov K.V.Pavlov M.J.J.Blommers T.Arvinte A.S.Arseniev Molecular Recognition of Ligands by Native Viruses and Virus-Like Particles as Studied by NMR Experiments C.Rademacher T.Peters

12 XII Contents Investigation of Proteins in Living Bacteria with In-Cell NMR Experiments V.Dötsch Author Index Volumes Subject Index

13 Contents of Volume 272 Bioactive Conformation I Volume Editor: Peters, T. ISBN: Spatial Screening for the Identification of the Bioactive Conformation of Integrin Ligands T. Weide A. Modlinger H. Kessler Dynamics and Thermodynamics of Ligand Protein Interactions S. W. Homans The Fibroblast Growth Factor (FGF) FGF Receptor Complex: Progress Towards the Physiological State N. J. Harmer Characterization of Interactions Between Misfolding Proteins and Molecular Chaperones by NMR Spectroscopy B. Reif S. Narayanan NMR Analysis of Bioprotective Sugars: Sucrose and Oligomeric (1 2)-α-d-glucopyranosyl- (1 2)-β-d-fructofuranosides D. Fischer A. Geyer Residual Dipolar Couplings Report on the Active Conformation of Rhodopsin-Bound Protein Fragments B. W. Koenig Glycosyltransferase Structure and Function B. Schuman J. A. Alfaro S. V. Evans Exploiting Ligand and Receptor Adaptability in Rational Drug Design Using Dynamics and Structure-Based Strategies S. R. LaPlante

14 Top Curr Chem (2008) 273: 1 14 DOI /128_2007_16 Springer-Verlag Berlin Heidelberg Published online: 23 April 2008 NMR-Based Strategies to Elucidate Bioactive Conformations of Weakly Binding Ligands Marcel J. J. Blommers ( ) Andre Strauss Martin Geiser Paul Ramage Helmut Sparrer Wolfgang Jahnke Novartis Institutes for BioMedical Research, Discovery Technologies, 4002 Basel, Switzerland marcel_jj.blommers@novartis.com 1 Transferred Cross-Correlated Relaxation Theory Applications Strategy for the Structure Determination of a Weakly Bound Peptide BiologicalContext NMRStudies Measurement of the Torsion Angle ψ Measurement of the Torsion Angle φ StructureCalculations Conclusion and Outlook References Abstract Key processes in molecular biology are regulated by interactions between biomolecules. Protein protein and protein ligand interactions, e.g., in signal transduction pathways, rely on the subtle interactions between atoms at the binding interface of the involved molecules. Because biomolecules often have many interacting partners, these interactions are not necessarily strong. The study of molecular recognition gives insight into the complex network of signaling in life and is the basis of structure-based drug design. In the situation where the interaction is weak, one of the traditional methods that can be applied to obtain structural information (internuclear distances) of the bound ligand is the so-called transferred NOE (trnoe) method. Recently, it became possible to use transferred cross-correlated relaxation (trccr) to directly measure dihedral angles. The combined use of these two techniques significantly improves the precision of the structure determination of ligands weakly bound to macromolecules. The application of these techniques will be discussed in detail for a peptide derived from IKKβ bound to the protein NEMO that plays an important role in the NFκB pathway. Keywords Cross-correlated relaxation IKKβ NEMO NMR trccr trnoe Abbreviations CCR Cross-correlated relaxation CSA Chemical shift anisotropy

15 2 M.J.J. Blommers et al. IKK IκB kinase NBD NEMO binding domain NEMO NFκB essential modulator NOE Nuclear Overhauser effect RDC Residual dipolar coupling SAR Structure activity relationship trccr Transferred CCR trnoe Transferred NOE 1 Transferred Cross-Correlated Relaxation 1.1 Theory Since the discovery of the nuclear Overhauser effect (NOE) [1, 2] and scalar couplingconstants[3,4]decadesago,nmr-derivedstructurecalculationsof biomolecules largely depended on measurement of these two parameters [5]. Presently, new NMR observables, like residual dipolar couplings (RDC) [6] and cross-correlated relaxation (CCR) rates [7] have become popular in conjunction with structure determination. Application of RDC provides a way to obtain long-range restraints and therefore has an impact on the resolution of biomolecular structures studied by solution-state NMR. Measurement of CCR-rates is also broadly applicable for isotopically labelled molecules and gives new direction to the design of experiments to determine the structure of biomolecules by NMR spectroscopy. The information extracted from CCR rates not only improves the resolution of NMR structures, but is also indispensable when applied to weakly binding ligands [8, 9] that are measured in the presence of the receptor using an excess of ligand. In these cases, J-coupling constants cannot be used to derive torsion angles. Alternatively, CCR-rates and RDCs provide new ways to obtain information on molecular dynamics. Herein, we will focus on CCR (for the application of transferred RDCs see the Bioactive Conformation I contribution by B.W. Koenig [54]). Measurement of cross-correlated relaxation has been described for homonuclear cases [10, 11], and is widely used in solid-state NMR [12 14]. It is the availability of isotopically labelled biomolecules and its application to solution-state NMR that makes the method so interesting. The first application of CCR in solution-state NMR with a 15 N, 13 Clabelledprotein,wasthe determination of the torsion angle ψ in the small protein rhodniin [7]. This torsion angle is difficult to obtain by traditional methods. CCR can easily be explained in a simplified form: all coherences between nuclearspins,thatfinallygiverisetonmrsignals,relax(decay)withacertain rate, and eventually disappear. In dipolar relaxation, the relaxation of a spin is mediated by the fluctuating electromagnetic field caused by adjacent