Cluster, hydrophobic

Model peptides that could build up quarternary fibrillar structures are not yet known. Though complete explanation of the interdependence between the primary structure and the stability of the quarternary structure has not yet been possible, i.e. the role of the different amino acids in collagen could be understood completely only in correlation with the fibril formation (formation of polar and hydrophobic clusters ). 

Esler WP, Stimson ER, Ghilardi JR, Lu YA, Felix AM, Vinters HV, Mantyh PW, Lee JP, Maggio JE. Point substitution in the central hydrophobic cluster of a human beta-amyloid congener disrupts peptide folding and abolishes plaque competence. Biochemistry 1996 35 13914-13921. 

Figure 10-5. Representative conformations of the (5 amyloid peptide (10-42) under different pH conditions. The conformations were obtained as centroids of the most populated clusters from the replica-exchange CPHMD folding simulations [43, 44]. The N-terminal residues 10-28 are shown in blue the C-terminal residues 29-42 are shown in red. In the most aggregation-prone state (pH 6), the side chains of the central hydrophobic cluster Leu-17, Val-18, Phe-19, Phe-20 and Ala-21 are shown as van der Waals spheres in pink, grey, cyan, purple and green, respectively...

CBH I 497 core-BA aa sequence in part from protein and in full from gene (cbhl), number and location of SS bridges, region of O-glycosylation, types of carbohydrate, papain cleavage site, hydrophobic cluster analysis, computer model of active site, 2D-NMR on a synthetic tail fragment, SAXS on whole CBH I, head domain and xylan/CBH I complex... 

EG I 437 core-BA aa sequence in part from protein and in full from gene (egll), hydrophobic cluster analysis, SAXS not successful... 

Dong H, Hartgerink JD. Role of hydrophobic clusters in the stability of a-helical coiled coils and their conversion to amyloid-like beta sheets. Biomacromolecules 2007 8 617-623. 

Koepf, E.K., Petrassi, H.M., Sudol, M., and Kelly, J.W. 1999. WW An isolated three-stranded antiparallel P-sheet domain that unfolds and refolds reversibly evidence for a structured hydrophobic cluster in urea and GdnHCl and a disordered thermal unfolded state. Protein Sci. 8 841-853. 

Lu, S. M., and Hodges, R. S. (2004). Defining the minimum size of a hydrophobic cluster in two-stranded alpha-helical coiled-coils Effects on protein stability. Prot. Sci. 13, 714-726. 

The requirement for a certain level of rigidity of the C-2 and C-3 substituents led us to investigate the solution conformation of taxoid 48 (nonataxel) in aqueous media by 2-D NMR and molecular modeling techniques. We found that the two 2-methylprop-l-enyl moieties of this molecule orient themselves with respect to each other quite specifically to form a strong hydrophobic clustering (see Section IV.C).73... 

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