What vibrations tell about proteins

1. Introduction 370 2. Infrared (IR) spectroscopy – general principles 372 2.1 Vibrations 372 2.2 Information that can be derived from the vibrational spectrum 372 2.3 Absorption of IR light 375 3. Protein IR absorption 376 3.1 Amino-acid side-chain absorption 376 3.2 Normal modes of the amide group 381 4. Interactions that shape the amide I band 382 4.1 Overview 382 4.2 Through-bond coupling 383 4.3 Hydrogen bonding 383 4.4 Transition dipole coupling (TDC) 383 5. The polarization and IR activity of amide I modes 387 5.1 The coupled oscillator system 387 5.2 Optically allowed transitions 388 5.3 The infinite parallel β-sheet 388 5.4 The infinite antiparallel β-sheet 389 5.5 The infinite α-helix 390 6. Calculation of the amide I band 391 6.1 Overview 391 6.2 Perturbation treatment by Miyazawa 393 6.3 The parallel β-sheet 394 6.4 The antiparallel β-sheet 395 6.5 The α-helix 396 6.6 Other secondary structures 398 7. Experimental analysis of protein secondary structure 398 7.1 Band fitting 398 7.2 Methods using calibration sets 401 7.3 Prediction quality 403 8. Protein stability 404 8.1 Thermal stability 404 8.2 1H/2H exchange 406 9. Molecular reaction mechanisms of proteins 408 9.1 Reaction-induced IR difference spectroscopy 408 9.2 The origin of difference bands 409 9.3 The difference spectrum seen as a fingerprint of conformational change 410 9.4 Molecular interpretation: strategies of band assignment 416 10. Outlook 419 11. Acknowledgements 420 12. References 420 This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, 1H/2H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.

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