Dynamics and function of different conformational structures in proteins

Abstract

Proteins are dynamic structures. Under equilibrium conditions, proteins can adopt multiple conformations that are very similar to each other. These conformations are called conformational substrates, and they show different functional properties. In this thesis, hemoglobin is used as a model protein to study thermally driven interconversions of conformational substates using techniques of laser spectroscopy. Hemoglobin and myoglobin are especially useful proteins for these studies because there is an extensive amount of information available on their spectroscopic and functional properties. The dynamic behavior that is observed in hemoglobin is likely to resemble the general dynamic properties of other proteins. Besides helping us reach a better understanding of proteins in general, the hemoglobin experiments also give us valuable information about the dynamics and functional behavior of hemoglobin itself.;Information has been obtained about hemoglobin dynamics under different viscosity and temperature conditions. In addition, differences in the functional properties of conformational substates have been detected. In order to monitor hemoglobin dynamics and function, an absorption band called band III that is located in the near infrared region of the absorption spectrum of hemoglobin has been used. This band exhibits static and time dependent changes in its peak position and shape. These spectroscopic properties of band III have been used to obtain information about the different conformational structures that the hemoglobin proteins are in and also about how these conformational structures differ from each other in their functional properties. In order to detect the subtle changes that take place in the peak position and shape of band III, new algorithms for the analysis of the spectroscopic data obtained have been developed, and computer programs based on these algorithms have been used in the studies.;Band III spectra from photoproducts of the carbonmonoxide derivative of hemoglobin A have been obtained under high viscosity conditions. Two phenomena that give information about the function and dynamics of different hemoglobin conformational substates have been detected and studied. These two phenomena are called kinetic hole burning and dynamic hole filling. Using a hemoglobin solution, containing 75 per cent of glycerol by volume, kinetic hole burning and dynamic hole filling have been detected at temperatures of -50, -70 and -90 degrees Celsius. At higher temperatures the phenomena are not seen.;Experiments using hemoglobin cobalt hybrids are also presented in this thesis. From these experiments, one can conclude that the hemoglobin hybrid protein molecules can adopt more than one structural conformation. These conformations, in addition, show different functional properties. The different conformations are likely to be the quaternary R structure and the quaternary T structure of the hemoglobin hybrids. The two hemoglobin hybrids studied have also shown differences in their functional properties. It is possible that these differences are due to general differences between the alpha and the beta subunits of hemoglobin. If this is the case, we could say that, when a hemoglobin molecule is studied, the beta subunits produce a spectrum of band III whose peak is located at a lower wavenumber than the peak of band III from the spectrum of the alpha subunits in the same molecule. So, the conformations adopted by the alpha and the beta subunits of the same molecule would be different.