Polyproline

Figure 13.30 Ribbon diagram of the structure of Src tyrosine kinase. The structure is divided in three units starting from the N-terminus an SH3 domain (green), an SH2 domain (blue), and a tyrosine kinase (orange) that is divided into two domains and has the same fold as the cyclin dependent kinase described in Chapter 6 (see Figure 6.16a). The linker region (red) between SH2 and the kinase is bound to SH3 in a polyproline helical conformation. A tyrosine residue in the carboxy tail of the kinase is phosphorylated and bound to SH2 in its phosphotyrosine-binding site. A disordered part of the activation segment in the kinase is dashed. (Adapted from W. Xu et al.. Nature 385 595-602, 1997.)...

Src tyrosine kinase contains both an SH2 and an SH3 domain linked to a tyrosine kinase unit with a structure similar to other protein kinases. The phosphorylated form of the kinase is inactivated by binding of a phosphoty-rosine in the C-terminal tail to its own SH2 domain. In addition the linker region between the SH2 domain and the kinase is bound in a polyproline II conformation to the SH3 domain. These interactions lock regions of the active site into a nonproductive conformation. Dephosphorylation or mutation of the C-terminal tyrosine abolishes this autoinactivation. 

Figure 14.1 Each polypeptide chain in the collagen molecule folds into an extended polyproline type II helix with a rise per turn along the helix of 9.6 A comprising 3.3 residues. In the collagen molecule three such chains are supercoiled about a common axis to form a 3000-A-long rod-like molecule. The amino acid sequence contains repeats of -Gly-X-Y- where X is often proline and Y is often hydroxyproline. (a) Ball and stick model of two turns of one polypeptide chain.

Figure 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

Jardetzky, T.5., Wiley, D.C. Crystallographic analysis of endogenous peptides associated with HLA-DRl suggests a common, polyproline Il-like conformation for hound peptides. Proc. Natl. Acad. Sci. USA 93 734-728, 1996. 

WW domains (named after the one letter abbreviation for the amino acid tryptophan) are small regions of around 30 residues, which, like SH3 domains, bind to polyproline sequences. These sequences often contain the consensus sequence PPXY or PPLP. Examples of proteins that contain WW domains include Nedd4 E3 ubiquitin ligase (Fig. 1) and IQGAP1. 

Neuropeptide Y (NPY) is a 36 amino acid polypqrtide with tyrosine residues at both ends of the molecule. It is characterised structurally by a PP-fold consisting of an extended polyproline helix and an a-helix connected by a (3-tum [1]. Based on structural and evolutionary criteria, NPY is closely related to peptide YY (PYY) and pancreatic polypeptide (PP). 

PRs also interact with other signaling pathways, which can, e.g., be regulated by phosphorylation. Independent of transcriptional activation of PR, progestins can activate cytoplasmic signaling molecules including SRC and downstream MAP kinase in mammalian cells via interaction by a specific polyproline motif in the N-terminal domain of PR. 

Protein-protein interaction domain that binds to polyproline motifs with the sequence PXXP. Particularly important in assembling protein complexes at activated receptors which contain intrinsic tyrosine kinases. 

Protein-protein interaction domain which, like SH3 domains, bind to polyproline sequences. 

Each polytripeptide chain is twisted around a threefold screw axis and exists in a secondary structure, analogous to the left-handed polyproline II-helix, i.e. with transposition of the peptide bond (pitch 8.4 A, 3 amino acids) (Figs. 2,3). 

Neutral salt-soluble collagen as well as add-soluble collagen show a CD spectrum (Fig. 8) having bands at 198 nm, 0 = -53 (MX) (deg cm2 dmol-1), and at 223 nm, 0 = 7500 (deg cm2 dmol-1), the ratio between both being 7 1. Pysh has calculated the CD spectra of a-helix, -structure, polyproline I and II127 ... 

Bochicchio, B. and Tamburro, A.M., Polyproline II structure in proteins Identification by chiroptical spectroscopies, stability, and functions. Chirality, 14(10), 782-792, 2002. 

Upon binding, the artificial transcription factor recruits the necessary transcriptional machinery for gene activation. (Bottom, left) Ball-and-stick model for a polyamide conjugated to the VP2 activation domain. Symbols are as in Fig. 3.4. (Bottom, right) Structure of the polyamide-VP2 conjugate with the polyproline linker domain in brackets... 

In the absence of an AGAC the ribosomes will prodnce the artificial polypeptides, polyphenylalanine (as specified by the codon UUU) or polyproline (as specified by the codon CCC). However, when streptomycin is added, the ribosomes prodnce a mixture of polythreonine (codon ACU) and poly serine (codon UCU). The misreading of the codons does not appear to be random U is read as A or C and C is read as A or U. If such misreading occurs in whole cells the accumulation of non-functional or toxic proteins would eventually prove fatal to the cells. There is some evidence that the bacterial cell membrane is damaged when the cells attempt to excrete the faulty proteins. 

Molecular insight into the protein conformation states of Src kinase has been revealed in a series of x-ray crystal structures of the Src SH3-SH2-kinase domain that depict Src in its inactive conformation [7]. This form maintains a closed structure, in which the tyrosine-phosphorylated (Tyr527) C-terminal tail is bound to the SH2 domain (Fig. 2). The x-ray data also reveal binding of the SH3 domain to the SH2-kinase linker [adopts a polyproline type II (PP II) helical conformation], providing additional intramolecular interactions to stabilize the inactive conformation. Collectively, these interactions cause structural changes within the catalytic domain of the protein to compromise access of substrates to the catalytic site and its associated activity. Significantly, these x-ray structures provided the first direct evidence that the SH2 domain plays a key role in the self-regulation of Src. 

Three theory papers are also included. Determinants of the Polyproline II Helix from Modeling Studies by Creamer and Campbell reexamines and extends an earlier hypothesis about Pn and its determinants. Hydration Theory for Molecular Biophysics by Paulaitis and Pratt discusses the crucial role of water in both folded and unfolded proteins. Unfolded State of Peptides by Daura et al. focuses on the unfolded state of peptides studied primarily by molecular dynamics. 

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