Vibrational frequencies, protein folding

Transition state theory (Chapter 2, section A) was derived for chemical bonds that obey quantum theory. An equation analogous to that for transition state theory may be derived even more simply for protein folding because classical low energy interactions are involved and we can use the Boltzmann equation to calculate the fraction of molecules in the transition state i.e., = exp(— AG -D/RT), where A G D is the mean difference in energy between the conformations at the saddle point of the reaction and the ground state. Then, if v is a characteristic vibration frequency along the reaction coordinate at the saddle point, and k is a transmission coefficient, then... 

Raman peaks in the spectrum are displayed as frequency shifts from the incident laser-line, or Av = vq v. Each peak corresponds to the energy of a vibrational normal, which depends on molecular strucmre as well as the characteristics of chemical bonds comprising each normal mode. Hence, Raman spectrum is called the molecular fingerprint of the molecules and materials. Raman spectra of DNA and proteins, for example, contain rich information on their chemical bonds and stmctures. The Raman spectmm not only provides information about the stmcture, conformation, and identity of the sample but also the dynamics and interactions between biomolecules such as protein folding and DNA-protein interactions. 

Fourier-transformed infrared (FTIR) is another excellent method to study protein folding. Unlike the well-known use of FTIR as a method for the identification of functional groups, in terms of protein structure this method allows the determination of secondary structure. The frequency of vibration of the amide I band of the peptide chain (1500-1600 cm M heavily depends on the structure of the protein. FTIR has the advantage of being more sensitive for the study of proteins that contain (3-sheet elements as compared to CD. Furthermore, since FTIR spectroscopy can be applied to solids also, it allows the structural analysis of aggregated protein deposits. The availability of the rapid step-scan method for FTIR is also very useful for the study of rapid folding reactions (see Vibrational Spectroscopy). 

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