Probes secondary structures

Sicoli G, Wachowius F, Bennati M, Hobartner C (2010) Probing secondary structures of spin-labeled RNA by pulsed EPR spectroscopy. Angew Chem Int Ed Engl 49(36) 6443-6447. doi 10.1002/anie.201000713... 

Plenary 2. S A Asher et al, e-mail address asher ,vms.cis.pitt.edu/asher+ (RRS, TRRRS). UV RRS is used to probe methodically the secondary structure of proteins and to follow unfolding dynamics. Developing a library based approach to generalize the mediod to any protein. 

Seebach, D., Ciceri, P. E., Overhand, M.,Jaun, B., Rigo, D., Oberer, L., Hommel, U., AmsUttz, R., and Widmer, H. (1996). Probing the helical secondary structure of short-chain /3-peptides. Helv. Chim. A da 79, 2043-2066. 

The knowledge of amino acid sequences of proteins may provide their three-dimensional structures if CD predictions are valid. However, the CD prediction for the secondary structure of a given protein, especially having (3-sheet structures, is not valid enough to probe the structure-function relationships in native proteins. We are awaiting the development of a more precise prediction method for secondary structures of proteins. 

In my talk I surveyed recent advances in the methodology and selected 2D-IR spectra of secondary structures. The results promise to provide structurally based kinetic probes for conformational dynamics, sharp tests of anharmonic potential surfaces and novel information regarding the transient and equilibrium vibrational dynamics of peptides. The heterodyned 2D-IR approach has proven useful in determining structures of peptides in solution and the anharmonic nature of the potential surfaces of peptides and secondary structures [1-10], as have polarized photon echo [2,6,10-12] or pump-probe techniques [4,13-16]. 

A two-state transition is usually identified by all spectroscopic probes changing simultaneously as the equilibrium changes. The far ultraviolet circular dichroism signals, which are a measure of secondary structure, should change in parallel with the near ultraviolet, which are a measure of tertiary structure. Fluorescence and near ultraviolet absorbance spectra also probe tertiary structure and should change in parallel with each other and the circular dichroism spectra. Ideally, there should be isosbestic or isodichroic points where spectra converge. 

There is substantial history regarding the application of conventional vibrational spectroscopy methods to study the intact surface of skin, the extracted stratum corneum and the ceramide-cholesterol-fatty acid mixtures that constitute the primary lipid components of the barrier. The complexity of the barrier and the multiple phases formed by the interactions of the barrier components have begun to reveal the role of each of these substances in barrier structure and stability. The use of bulk phase IR to monitor lipid phase behavior and protein secondary structures in the epidermis, as well as in stratum corneum models, is also well established 24-28 In addition, in vivo and ex vivo attenuated total reflectance (ATR) techniques have examined the outer layers of skin to probe hydration levels, drug delivery and percutaneous absorption at a macroscopic level.29-32 Both mid-IR and near-IR spectroscopy have been used to differentiate pathological skin samples.33,34 The above studies, and many others too numerous to mention, lend confidence to the fact that the extension to IR imaging will produce useful results. 

Karbstein, K., Lee, J., and Herschlag, D. (2007). Probing the role of a secondary structure element at the 5 - and splice sites in group I intron self-splicing The Tetrahymena L-16ScaI ribozyme reveals a new role for the G U pair in self-splicing. Biochemistry 46, 4861-4875. 

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