Protein helix-coil transformations

Some of the vacuum theories treated earlier in the book are repeated in Chapter 8. Examples are chemical equilibrium, allosteric phenomena, and helix-coil transition. The general procedure to transform a vacuum theory into a solution theory is developed. Then we emphasize possible large solvent effects that can significantly alter the vacuum theory, especially when the solvent is water. A detailed account of the thermodynamics of protein folding and protein association is also presented. 

The helix-coil transition has occupied polypeptide chemists as models for such structural transformations in proteins (Poland and Scheraga, 1970). Both theoretical and experimental approaches have been taken in such studies (Scheraga, 1978) in order to obtain quantitative measures of the tendency of each of the 20 naturally occurring amino acids to adopt the helix vs. the coil (i.e. all other, non-helical) conformations. These tendencies are expressed in terms of the Zimm-Bragg (1959) nucleation and growth parameters, O and s, respectively. The values of a and s may be used directly to predict the locations of a-helices in proteins. The values of a and s have been obtained from experimental studies of thermally-induced helix-coil transitions in host-guest random copolymers... 

The availability of the purified transporter in large quantity has enabled investigation of its secondary structure by biophysical techniques. Comparison of the circular dichroism (CD) spectrum of the transporter in lipid vesicles with the CD spectra of water-soluble proteins of known structure indicated the presence of approximately 82% a-helix, 10% ) -turns and 8% other random coil structure [97]. No / -sheet structure was detected either in this study or in a study of the protein by the same group using polarized Fourier transform infrared (FTIR) spectroscopy [98]. In our laboratory FTIR spectroscopy of the transporter has similarly revealed that... 

The wavelengths of IR absorption bands are characteristic of specific types of chemical bonds. In the past infrared had little application in protein analysis due to instrumentation and interpretation limitations. The development of Fourier transform infrared spectroscopy (FUR) makes it possible to characterize proteins using IR techniques (Surewicz et al. 1993). Several IR absorption regions are important for protein analysis. The amide I groups in proteins have a vibration absorption frequency of 1630-1670 cm. Secondary structures of proteins such as alpha(a)-helix and beta(P)-sheet have amide absorptions of 1645-1660 cm-1 and 1665-1680 cm, respectively. Random coil has absorptions in the range of 1660-1670 cm These characterization criteria come from studies of model polypeptides with known secondary structures. Thus, FTIR is useful in conformational analysis of peptides and proteins (Arrondo et al. 1993). 

One property of many such transformations is their all or none character. For example, if proteins in solution are slowly heated they often remain in their native states until a certain temperature is reached, when they become denatured rather suddenly. Similarly, if we heat a solution of DNA, and follow the structural changes by spectrophotometry, we find that nothing happens until a temperature of about 80 C is reached then, within a few degrees, the helix melts to a form in which the various long-chain molecules are coiled at random. If we write an equilibrium constant as... 

One stereochemically and energetically admissible mechanism [29] involves the linking of a compressor protein (in its a-helical state) at its two ends to two appropriate sites at the double helix this binding enables enforcement of the DNA double-helix state irrespective of the experimentally determined Tm value of the protein-free DNA. The compressor protein can be forcibly extended when random coil extender protein(s) associate with it to transform it into a -conformation (pleated sheet). [S. Lewin manuscript in preparation] see Figure 5. 

Most work on amphiphilic conjugates to date is based either on simple a-helix-fotming polypeptides or on complex pro-teins/enzymes. Work on biomolecular building blocks that fall between the two aforementioned groups, such as the coiled-coil protein tertiary stmctural motif, has been lim-ited. " Recendy, a heterodimer coiled-coil was used to noncovalendy link PEG and PS blocks and the resultant amphiphilic PEG-peptide-PS triblock copolymer assembled into thermoresponsive micellar assemblies in aqueous solution that transformed from rodlike micelles to spherical micelles upon heating, as depiaed in Figure 10(b). ... 

The activity of an adsorbed protein depends upon the orientation and conformation of the protein molecule on material surface. Sometimes, the protein shows structural rearrangements with time (such as transformation of an a-helix structure to a random coil one), which may either cause strengthening of protein attachment or lead to reversible adsorption and protein elution. Thus, the stability of a protein conformation governs the kinetics of its adsorption. Depending upon the type of application, either of the protein rearrangements may be favorable. The adsorption profile and functionality of the protein determines the protein mediated cell responses. From literature, it is unclear on the optimum surface chemistry necessary for a desired cellular... 

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