Helical protein interfaces

Rational Design Strategies for Developing Synthetic Inhibitors of Helical Protein Interfaces... 

Jochim AL, Arora PS (2010) Systematic analysis of helical protein interfaces reveals targets for synthetic inhibitors. ACS Chem Biol 5 919-923... 

Bullock BN, Jochim AL, Arora PS (2011) Assessing helical protein interfaces for inhibitor design. J Am Chem Soc 133 14220-14223... 

The most common element of secondary structure in proteins is the helix. Helices are enriched at protein/protein interfaces, where a helixxleft motif is often employed to recognize hot spot residues at the protein/protein interface. Helices are also enriched in protein/nucleic acid interactions, where the helical motif facilitates molecular recognition by projecting residues into the grooves of nucleic acid helices. 

Complexes that feature a-helices at interfaces were studied because a-helices constitute the largest class of protein secondary structure and mediate many protein interactions [30, 51]. Helices located within the protein core are vital for the overall stability of protein tertiary structure, whereas exposed a-helices on protein surfaces constitute central bioactive regions for the recognition of numerous proteins, DNAs, and RNAs. Importantly, helix mimetics have emerged as a highly effective class of PPI inhibitors [32, 36, 44, 52-55]. 

Fig. 9 (a) Percent occurrence of hot spot amino acids in helix-mediated protein interfaces, (b) percent occurrence of hot spot residues classified into similar groups, (c) representation of hot spot amino acids normalized to natural abundance of amino acids in proteins, and (d) average predicted decrease in binding energy of helical interfaces upon mutation of hot spot residues to alanine (Reprinted with permission from Bullock et al. [67], Copyright (2011) American Chemical Society)... 

As in miniature proteins, much of the focus of pro-teomimetic research has been on a-helices, owing to their predominance within protein interface regions. As was... 

Biophysical and computational analysis of macrocyclic ot-helical peptides e.g. stapled peptides) have provided significant insights to their moleeular recognition at a-helical protein-protein interfaces and their inherent eon-formational dynamics properties. " ° " "° High-... 

The proteins thus adapt to mutations of buried residues by changing their overall structure, which in the globins involves movements of entire a helices relative to each other. The structure of loop regions changes so that the movement of one a helix is not transmitted to the rest of the structure. Only movements that preserve the geometry of the heme pocket are accepted. Mutations that cause such structural shifts are tolerated because many different combinations of side chains can produce well-packed helix-helix interfaces of similar but not identical geometry and because the shifts are coupled so that the geometry of the active site is retained. 

Residues 50-64 of the GAL4 fragment fold into an amphipathic a helix and the dimer interface is formed by the packing of these helices into a coiled coil, like those found in fibrous proteins (Chapters 3 and 14) and also in the leucine zipper families of transcription factors to be described later. The fragment of GAL4 comprising only residues 1-65 does not dimerize in the absence of DNA, but the intact GAL4 molecule does, because in the complete molecule residues between 65 and iOO also contribute to dimer interactions. 

Figure 17.10 Construction of a two helix truncated Z domain, (a) Diagram of the three-helix bundle Z domain of protein A (blue) bound to the Fc fragment of IgG (green). The third helix stabilizes the two Fc-binding helices, (b) Three phage-display libraries of the truncated Z-domaln peptide were selected for binding to the Fc. First, four residues at the former helix 3 interface ("exoface") were sorted the consensus sequence from this library was used as the template for an "intrafece" library, in which residues between helices 1 and 2 were randomized. The most active sequence from this library was used as a template for five libraries in which residues on the Fc-binding face ("interface") were randomized. Colored residues were randomized blue residues were conserved as the wild-type amino acid while yellow residues reached a nonwild-type consensus, [(b) Adapted from A.C. Braisted and J.A. Wells,...

Less commonly, an a-helix can be completely buried in the protein interior or completely exposed to solvent. Citrate synthase is a dimeric protein in which a-helical segments form part of the subunit-subunit interface. As shown in Figure 6.24, one of these helices (residues 260 to 270) is highly hydrophobic and contains only two polar residues, as would befit a helix in the protein core. On the other hand. Figure 6.24 also shows the solvent-exposed helix (residues 74 to 87) of cahnodulln, which consists of 10 charged residues, 2 polar residues, and only 2 nonpolar residues. 

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