Experimental approaches, including circular dichroism, small angle X-ray scattering, steady-state fluorescence, and fluorescence energy transfer, were applied to study the 3D-structure of apomyolgobin in different conformational states. These included the native and molten globules, along with either less ordered conformations induced by the addition of anions or completely unfolded states. The results show that the partially folded forms of apomyoglobin stabilized by KCl and/or Na(2)SO(4) under unfolding conditions (pH 2) exhibit a significant amount of secondary structure (circular dichroism), low packing density of protein molecules (SAXS), and native-like dimensions of the AGH core (fluorescence energy transfer). This finding indicates that a native-like tertiary fold of the polypeptide chain, i.e., the spatial organization of secondary structure elements, most likely emerges prior to the formation of the molten globule state.

Direct nonradiative energy transfer (DET) experiments were carried out on five polyisoprene-poly(methyl methacrylate) diblock copolymers with polyisoprene volume fractions ranging from 0.07 to 0.5 (polyisoprene microdomains dispersed in a poly(methyl methacrylate) matrix). These experiments yield the ratio R/δ of the microdomain size R to the thickness of the domain-boundary interface δ as a function of the block copolymer overall chain length N. A plot of ln(R/δ) vs ln N indicates that the microdomain size varies as N 0.65 , close to the N 2/3 predicted by theory, while the interfacial thickness δ (26 Å) is independent of the degree of polymerization covered in this work. In addition, the Flory-Huggins interaction parameter χ for PI-PMMA was determined from the DET data (0.077). We conclude from these experiments that PI-PMMA belongs to the class of strongly segregated systems.

Though highly desirable, neither a single experimental technique nor a computational approach can be sufficient enough to rationalize a protein structure. The incorporation of biophysical constraints, which can be rationalized based on conventional biophysical measurements, might lead to considerable improvement of the simulation procedures. In this regard, our analysis of 180 proteins in different conformational states allows prediction of the overall protein dimension based on the chain length, i.e., the protein molecular weight, with an accuracy of 10%.