Introduction
The stability of proteins determines the correlation between structure and function. Protein stability also plays a role in various properties such as aggregation, solubility, and protein-protein interactions. The stability of proteins is a necessary attribute in cells, as seen in various mechanisms such as unfolded-protein response machines, whose role is to protect cells against the damaging consequences of unfolded proteins. Modern genomics has led to the use of new amino acid sequences of proteins, such as the bioinformatics methods, to deduce the native functions of those proteins (Ghosh and Dill 10654). The process of inferring protein folding stabilities is thought to begin with the identification of the protein’s native structure, secondary structures, and hydrogen bonding patterns, van der Waals packing, and its hydrophobic core residues. However, there is minimal information regarding the stability of a protein’s native structure.
The article by Dyson, Wright, and Scheraga examines various factors used in the determination of protein stability with the view of showing that a simpler model can be adopted. The study uses a single quantitative model that combines all aspects of folding stability and the identification of parameters using modern databases of experimental protein stabilities to provide the universal properties of protein folding stability. This model provides a variety of measures including the heat capacity, the linear dependence of the enthalpy, and entropy of folding on chain length, among other vital measures (Dyson, Wright and Scheraga 13054).
Models for Initiation and propagation
The first model used in the study was based on hydrophobic interactions. This model sought to determine the free energy used to produce a hydrophobic pocket from the amino acid sequence. The evaluation of windows was based on the identification of the most suitably stable pocket, as well as, the existence of multiple initiation sites of successively low free energy for stabilization (Dyson, Wright and Scheraga 13057). The conformation was observed to be of a dynamic nature due to the competing initiation sites of lower stability, which may result in inter-conversion conformations that are in the unfolded state of the protein. The stability of the conformation was enhanced by modifying the environment to provide conducive conditions that allowed the chains to form the native structure with minimal interference. This was also achieved by promoting the effect of electrostatic interactions (Dyson, Wright, and Scheraga 13057).
The second model employs a three-stage folding approach that forms a series of steps leading to a coalesce of the native protein. The first stage involves short-range interactions that cause contact among residues that are close to each other in the amino acid sequence. The second stage involved a decrease in temperature to alter the solvent conditions (Dyson, Wright and Scheraga 13058). This alteration causes an increase in the range of interactions that is capable of disrupting the previously formed structures and re-arranging them. The third stage involves longer-range interactions with rearrangements in structures formed in the two previous stages (Dyson, Wright, and Scheraga 13058).
Experimental verification of models
The analysis of the experiments was based on the evaluation of the formation patterns of apomyoglobin and bovine pancreatic R-Nase. Both the first and second approaches led to similar results in terms of the identification of primary initiation sites in proteins. The second approach led to the identification of six sites in the initiation of R-Nase that were consistent with the first model (Dyson, Wright, and Scheraga 13058). The predicted primary folding initiation site of R-Nase was confirmed with the turn of residues in the native molecule with a high degree of conservation of no polar residues, as well as, with experimental information on intermediates detected in the thermal unfolding of R-Nase (Dyson, Wright and Scheraga 13058).
Analysis was also conducted on the performance of apomyoglobin using the two models. The application of conformational energy calculations on the second approach revealed that interactions among the A, G, and H helices of apomyoglobin could be necessary for folding initiation (Dyson, Wright, and Scheraga 13059). This was consistent with experimental results that implicated the regions in equilibrium intermediates of apomyoglobin (Dyson, Wright and Scheraga 13059).
Analysis
The appropriateness of using mutants of myoglobin, such as apomyoglobin, as a measure for the propagation of folding is supported by the study of Ghosh and Dill (10650), which conducts experiments to show the independence of protein stability from the interference of secondary structures in the native structure. The calorimetric transfer experiment conducted by Gosh and dill (10651) shows minimal variation based on the type of amino acid used in the interpretation of thermal properties when the amino acids are buried in a hydrophobic core. The study also reveals that protein stability can be achieved by burying the backbone hydrogen bonds, which implies that the key attributes of protein stability can be captured within a simple model.
The study by Ghosh and Dill attempts to arrive at the idea of the existence of an ideal thermal protein that has the stability features of a protein with a length of N amino acids. This ideal thermal protein (ITP) can be inferred in the study by Dyson, Wright, and Scheraga, which notes the rate of folding of apomyoglobin, as well as, the importance of side-chain packing. According to Ghosh and Dill (10652), the dominant elements of protein folding stability are dependent on various factors including the “approximate independence of the energy of folding on chain length, the dependence of the energy on the square of the net charge on the side chains, and the inverse square dependence of the energy of confinement on the size of the box in which a protein is confined”.
Conclusion
The study identified that the amino acid sequence, by itself, could fold consistently into the required 3D formation. The study by Dyson, Wright, and Scheraga, claims that the most suitable spot for the process of protein folding can be identified by examining the pattern of amino acids that are located deep within the protein. The efficiency of apomyoglobin, as an ideal thermal protein (ITP) is compromised by the fact that it is a heme protein. This property implies that apomyoglobin lacks a prosthetic group, which influences the structure of the end product of the folded form of the apoprotein. The other complication is because apomyoglobin is an all-helix protein. This aspect causes a lower density of contacts in the contact map of the folded protein (Dyson, Wright, and Scheraga 13060). The stability of the globular proteins can be easily computed using amino acids chain length and the number of acidic and basic groups in the protein using the Dill and Ghosh model (Ghosh and Dill 10654).
References
Dyson, Jane, Peter E. Wright and Harold A. Scheraga. “The Role of Hydrophobic Interactions in Initiation and Propagation of Protein Folding.” Proceedings of the National Academy of Sciences of the United States of America 103(35), (2006): 13057-13061. Print.
Ghosh, Kingshuk and Ken A. Dill. “Computing Protein Stabilities from Their Chain Lengths.” Proceedings of the National Academy of Sciences of the United States of America 106(26), (2009): 10649-10654. Print.