Abstract
| I. | Introduction | 306 |
| II. | Supramolecular Structure Characterization | 308 |
| | A. A Protein Is Used as a “Hook” | 309 |
| | 1. Immuno‐Precipitation | 309 |
| | 2. Tagging with a Poly‐Histidine Sequence | 310 |
| | 3. Direct Analysis of Large Protein Complexes | 311 |
| | 4. Tandem Affinity Purification Tag Procedure | 312 |
| | B. A Nucleic Acid Is Used as a “Hook” or as a “Tracking Label” | 314 |
| | 1. Purification of a Nucleic Acid–Protein Complex in Solution | 316 |
| | 2. Preparative Electrophoretic Mobility Shift Assay | 317 |
| | 3. Surface‐Enhanced Laser Desorption/Ionization | 317 |
| | 4. Surface Plasmon Resonance | 319 |
| | 5. Probing Nucleic Acid–Protein Interactions on Membranes | 320 |
| III. | Supramolecular Analysis in the Gas Phase | 321 |
| IV. | Molecular Structure Characterization | 324 |
| | A. Determination of the Assembly Topology | 324 |
| | 1. Non Site‐Directed Cross‐Links | 326 |
| | 2. Native‐State Chemistry | 330 |
| | 3. Site‐Directed Cross‐Links | 332 |
| | B. Regulation of the Complex's Structure and Function | 334 |
| | 1. Protein Phosphorylation | 334 |
| | 2. Modification of the Basic Residues | 336 |
| | 3. Oxidoreduction Balance‐Related Modifications | 337 |
| V. | Concluding Remarks | 339 |
| | A. Factual Contributions | 339 |
| | B. Perspectives | 340 |
| Acknowledgments | 341 |
| Abbreviations | 341 |
| References | 341 |
Nucleic acid–protein (NA–P) interactions play essential roles in a variety of biological processes—gene expression regulation, DNA repair, chromatin structure regulation, transcription regulation, RNA processing, and translation—to cite only a few. Such biological processes involve a broad spectrum of NA–P interactions as well as protein–protein (P–P) interactions. These interactions are dynamic, in terms of the chemical composition of the complexes involved and in terms of their mere existence, which may be restricted to a given cell‐cycle phase. In this review, the contributions of mass spectrometry (MS) to the deciphering of these intricate networked interactions are described along with the numerous applications in which it has proven useful. Such applications include, for example, the identification of the partners involved in NA–P or P–P complexes, the identification of post‐translational modifications that (may) regulate such complexes' activities, or even the precise molecular mapping of the interaction sites in the NA–P complex. From a biological standpoint, we felt that it was worth the reader's time to be as informative as possible about the functional significance of the analytical methods reviewed herein. From a technical standpoint, because mass spectrometry without proper sample preparation would serve no purpose, each application described in this review is detailed by duly emphasizing the sample preparation—whenever this step is considered innovative—that led to significant analytical achievements. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 21:305–348, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10036