Folded proteins, molecular

The way in which molecular chaperones interact with polypeptides during the folding process is not completely understood. What is clear is that chaperones bind effectively to the exposed hydrophobic regions of partially folded structures. These folding intermediates are less compact than the native folded proteins. They contain large amounts of secondary and even some tertiary... 

Molecular chaperones are able to temporarily stabihze unfolded or partially folded proteins and prevent inappropriate inter- and intramolecular interactions. They reduce the free concentration of aggregation-sensitive folding in-... 

Fluorescent probes are divided in two categories, i.e., intrinsic and extrinsic probes. Tryptophan is the most widely used intrinsic probe. The absorption spectrum, centered at 280 nm, displays two overlapping absorbance transitions. In contrast, the fluorescence emission spectrum is broad and is characterized by a large Stokes shift, which varies with the polarity of the environment. The fluorescence emission peak is at about 350 nm in water but the peak shifts to about 315 nm in nonpolar media, such as within the hydrophobic core of folded proteins. Vitamin A, located in milk fat globules, may be used as an intrinsic probe to follow, for example, the changes of triglyceride physical state as a function of temperature [20]. Extrinsic probes are used to characterize molecular events when intrinsic fluorophores are absent or are so numerous that the interpretation of the data becomes ambiguous. Extrinsic probes may also be used to obtain additional or complementary information from a specific macromolecular domain or from an oil water interface. 

Although the underlying physics and mathematics used to convert relaxation rates into molecular motions are rather complex (Lipari and Szabo, 1982), the most important parameter obtained from such analyses, the order parameter. S 2, has a simple interpretation. In approximate terms, it corresponds to the fraction of motion experienced by a bond vector that arises from slow rotation as a rigid body of roughly the size of the macromolecule. Thus, in the interior of folded proteins, S2 for Hn bonds is always close to 1.0. In very flexible loops, on the other hand, it may drop as low as 0.6 because subnanosecond motions partially randomize the bond vector before it rotates as a rigid body. 

For folded proteins, relaxation data are commonly interpreted within the framework of the model-free formalism, in which the dynamics are described by an overall rotational correlation time rm, an internal correlation time xe, and an order parameter. S 2 describing the amplitude of the internal motions (Lipari and Szabo, 1982a,b). Model-free analysis is popular because it describes molecular motions in terms of a set of intuitive physical parameters. However, the underlying assumptions of model-free analysis—that the molecule tumbles with a single isotropic correlation time and that internal motions are very much faster than overall tumbling—are of questionable validity for unfolded or partly folded proteins. Nevertheless, qualitative insights into the dynamics of unfolded states can be obtained by model-free analysis (Alexandrescu and Shortle, 1994 Buck etal., 1996 Farrow etal., 1995a). An extension of the model-free analysis to incorporate a spectral density function that assumes a distribution of correlation times on the nanosecond time scale has recently been reported (Buevich et al., 2001 Buevich and Baum, 1999) and better fits the experimental 15N relaxation data for an unfolded protein than does the conventional model-free approach. 

Perczel, A., W. Viviani, and I. G. Csizmadia. 1992. Peptide Conformational Potential Energy Surfaces and Their Relevance to Protein Folding in Molecular Aspects of Biotechnology Computational Models and Theories, Bertran, J., ed., Kluwer Academic Publishers, 39-82. 

Proteins translated on the RER generally fold and assemble into subimits in the ER before being transferred to the Golgi apparatus. Other proteins fold in the cytoplasm. Molecular chaperones (proteins such as calnexin and BiP) assist in this process of protein folding. Proteins that are misfolded are targeted for destruction by ubiquitin and digested in cytoplasmic protein-digesting complexes called proteasomes. 

Kim, E. I., Paliwal, S., Wilcox, C. S., Measurements of molecular electrostatic field effects in edge- to-face aromatic interactions and CH-p interactions with implications for protein folding and molecular recognition. J. Am. Chem. Soc. 

Computational biochemistry and computer-assisted molecular modeling have rapidly become a vital component of biochemical research. Mechanisms of ligand-receptor and enzyme-substrate interactions, protein folding, protein-protein and protein-nucleic acid recognition, and de novo protein engineering are but a few examples of problems that may be addressed and facilitated by this technology. 

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