Proteins hydrophobic core

Munson, M., S. Balasubramanian, K.G. Fleming, A.D. Nagi, R. O Brien, J.M. Sturtevant, and L. Regan. 1996. What makes a protein a protein Hydrophobic core designs that specify stability and structural properties. Protein Sci 5 1584—1593. 

L. Vugmeyster, D. Ostrovsky,. . Ford, S.D. Burton, A.S. Lipton, G.L. Hoatson, R.L. Void, Probing the dynamics of a protein hydrophobic core by deuteron sohd-state nuclear magnetic resonance spectroscopy,. Am. Chem. Soc. 131 (2009) 13651-13658. 

When water is confined in a hydrophobic substrate, it exhibits a lower 7p than water confined in a hydrophilic substrate, and the protein hydration water crossover temperature decreases with pressure. This P effect reflects the increase in the protein-water interaction and the increase in the water s ability to access the protein hydrophobic core [32]. Using UV spectroscopy, similar P effects on the dynamic properties of biomolecules have been studied in p iactoglobulin [33], which is also a sensitive food protein. These results suggest that these pressure effects on proteins have universality. 

Proteins often have the same high-affinity isotherms as do synthetic polymers and are also slow to equilibrate, due to many contacts with the surface. Proteins, however, have the additional complication that they can partially or completely unfold at the solid-liquid interface to expose their hydrophobic core units to a hydrophobic surface... 

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

WA Lim, A Hodel, RT Sauer, FM Richards. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc Natl Acad Sci USA 91 423-427, 1994. PB Harbury, B Tidor, PS Kim. Repacking proteins cores with backbone freedom Structure prediction for coiled coils. Pi oc Natl Acad Sci USA 92 8408-8412, 1995. 

The secondary structure elements, formed in this way and held together by the hydrophobic core, provide a rigid and stable framework. They exhibit relatively little flexibility with respect to each other, and they are the best-defined parts of protein structures determined by both x-ray and NMR techniques. Functional groups of the protein are attached to this framework, either directly by their side chains or, more frequently, in loop regions that connect sequentially adjacent secondary structure elements. We will now have a closer look at these structural elements. 

Figure 3.6 Four-helix bundles frequently occur as domains in a proteins. The arrangement of the a helices is such that adjacent helices in the amino acid sequence are also adjacent in the three-dimensional structure. Some side chains from all four helices are buried in the middle of the bundle, where they form a hydrophobic core, (a) Schematic representation of the path of the polypeptide chain in a four-helrx-bundle domain. Red cylinders are a helices, (b) Schematic view of a projection down the bundle axis. Large circles represent the main chain of the a helices small circles are side chains. Green circles are the buried hydrophobic side chains red circles are side chains that are exposed on the surface of the bundle, which are mainly hydrophilic.

The globin fold has been used to study evolutionary constraints for maintaining structure and function. Evolutionary divergence is primarily constrained by conservation of the hydrophobicity of buried residues. In contrast, neither conserved sequence nor size-compensatory mutations in the hydrophobic core are important. Proteins adapt to mutations in buried residues by small changes of overall structure that in the globins involve movements of entire helices relative to each other. 

Why should the cores of most globular and membrane proteins consist almost entirely of a-helices and /3-sheets The reason is that the highly polar N—H and C=0 moieties of the peptide backbone must be neutralized in the hydrophobic core of the protein. The extensively H-bonded nature of a-helices and /3-sheets is ideal for this purpose, and these structures effectively stabilize the polar groups of the peptide backbone in the protein core. 

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