Protein folding behavior

To conclude, although the models used in lattice simulations are very simplified, the results provide general information on possible protein folding scenarios, albeit not on the detailed behavior of specific proteins, which would require more complex models and more accurate potentials. The contribution made by these simulations is that they enable an analysis of the structures, energetics, and dynamics of folding reactions at a level of detail not accessible to experiment. 

SUMOylation. Figure 1 SUMOylation is a reversible and regulated process. Target protein modification by SUMO can be initiated and terminated by different cues. Sumoylation leads to changes in the behavior of the modified protein, for example, different cellular localization, enhanced/reduced activity, or increased stability. These changes are due to alterations either in protein interactions or protein folding. 

Favrin G, Irback A, Wallin S. Sequence-based study of two related proteins with different folding behaviors. Proteins 2004 54 8-12. 

Schafer, H., Daura, X., Mark, A. E., and van Gunsteren, W. F. (2001). Entropy calculations on a reversibly folding peptide Changes in solute free energy cannot explain folding behavior. Proteins Strud. Fund. Genet. 43, 45-56. 

To illustrate these methods, we consider the main biological problems that have motivated their development. The problems that have received the most attention are the receptor-ligand binding problem [12-16] and the calculation of proton binding affinities (pKa shifts) [17-20], The methods described can also be applied to many related problems, such as redox protein behavior, protein-protein association, protein folding, or membrane insertion. 

Proper protein folding is a concern in the production of a bioactive protein therapeutic, and it is of interest to verify that the conformation of a recombinant protein is the same as the wild-type molecule. Because retention in RPLC depends on the surface hydrophobic contact area, comparable chromatographic behavior of a recombinant protein with that of the wild-type molecule provides evidence of similar 3-D structure.17 38... 

RQA were thermal stability, protein-peptide interactions, and folding behavior. 

A large number of macromolecules possess a pronounced amphiphilicity in every repeat unit. Typical examples are synthetic polymers like poly(l-vinylimidazole), poly(JV-isopropylacrylamide), poly(2-ethyl acrylic acid), poly(styrene sulfonate), poly(4-vinylpyridine), methylcellulose, etc. Some of them are shown in Fig. 23. In each repeat unit of such polymers there are hydrophilic (polar) and hydrophobic (nonpolar) atomic groups, which have different affinity to water or other polar solvents. Also, many of the important biopolymers (proteins, polysaccharides, phospholipids) are typical amphiphiles. Moreover, among the synthetic polymers, polyamphiphiles are very close to biological macromolecules in nature and behavior. In principle, they may provide useful analogs of proteins and are important for modeling some fundamental properties and sophisticated functions of biopolymers such as protein folding and enzymatic activity. 

THERMODYNAMICS OF STRUCTURAL STABILITY AND COOPERATIVE FOLDING BEHAVIOR IN PROTEINS... 

It has been shown that the hierarchical approach illustrated above for the case of a two-domain protein can be performed at a more fundamental level in order to account for the cooperative folding behavior of single-domain proteins (Freire and Murphy, 1991). This approach involves the use of the crystallographic structure of a pro-... 

Thermodynamics of Structural Stability and Cooperative Folding Behavior in Proteins... 

The hemoglobin family of macromolecules exhibits virtually all the important features of protein structure, function, and evolution, principles of protein folding, subunit movement and allosteric control in regulating activity, effects of point mutations on molecular behavior, and gene structure and genetic control. 

In chemical reactions, orbits on stable and unstable manifolds of NHIMs describe movements of reaction coordinates. In some cases, these reaction coordinates are those degrees of freedom describing the behavior of individual nuclei such as a bond length between a pair of atoms. In other cases such as protein folding, reaction coordinates describe collective behavior where multiple nuclei participate. In either case, the processes of leaving a NHIM and approaching another one involve reformulation of reaction coordinates. In particular, when reaction coordinates are collective variables, reformulation processes themselves are of interest. We think that the study of intersections is crucial to understand how a certain collective movement is replaced by another one. 

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