Polyproline conformational structure

The study of the conformational behavior of polypeptides has intrinsic interest in a complex and challenging theoretical and experimental problem. There are also strong biological implications inasmuch as there are many known naturally occurring polypeptides, both linear and cyclic, with potent effects as hormones, toxins, antibiotics, and ionophores. It is very probable that these functions are closely related to the polymer chain conformations. Investigations of model polypepetides have been extremely useful for the interpretation of conformational behavior and for the elucidation of the interaction between proteins and other macromolecules. The conformational structures of polyproline and related compounds have been of particular interest due to the important role L-proline plays in effecting protein structure. 

A). This conformation is very similar to that of collagen (Dickerson and Geis, 1969 Schellmann and Schellmann, 1964). Of these regular structures, only segments of polyproline conformation can exist in globular proteins. 

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. 

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. 

Experimental and theoretical approaches are now converging on the polyproline II backbone conformation as the most stable structure for short alanine peptides in water. It becomes of urgent importance to determine the energy differences between polyproline II and other possible backbone conformations, as well as to determine how amino acid composition and sequence affect backbone conformation. 

A few other helical conformations occur occasionally in globular protein structures. The polyproline helix, of the same sort as one strand out of a collagen structure, has been found in pancreatic trypsin inhibitor (Huber et al., 1971) and in cytochrome c551 (Almassy and Dickerson, 1978). An extended e helix has been described as occurring in chymotrypsin (Srinivasan et al., 1976). In view of the usual variability and irregularity seen in local protein conformation it is unclear that either of these last two helix types is reliably distinguishable from simply an isolated extended strand however, the presence of prolines can justify the designation of polyproline helix. 

The next three sections (Sections 7.7.1, 7.7.2, and 7.7.3) cover fluorescence spectroscopy, I15-18 infrared, and circular dichroism, three powerful approaches to characterize the structure and conformational considerations of synthetic peptides. Section 7.7.1 deals with the use of fluorophores and broad aspects of fluorescence spectroscopy to characterize conformational aspects of peptide structure. In a similar manner, Section 7.7.2 covers a broad aspect of the uses of infrared (IR) techniques to study peptide conformations 19-22 Many IR techniques are discussed, as are approaches for the study of specific peptidic structures including amyloid, p-turn, and membrane peptides. Finally, there is a section on circular dichroism (Section 7.7.3) that covers the major issues of concern for peptide synthetic chemists such as the assignments of a-helix, 310-helix, -sheets and P-turns, and polyproline helices 23-25 There is also a brief description of cyclic peptides. 

Ma, K., and Wang, K. (2003). Malleable conformation of the elastic PEVK segment of titin Non-cooperative interconversion of polyproline II helix, beta-turn and unordered structures. Biochem.J. 374, 687-695. 

One such small molecule, alanine dipeptide (Ace-Ala-NMe, AD, Figure 18-1) has often been used as a model system in studies of backbone conformational equilibrium in proteins. It is composed of an alanine unit blocked by an acetyl group at the N-terminus (Ace) and a A-methylamide group (NMe) at the C-terminus. A number of experimental [1,3,4,5,6,7] and theoretical [8,9,10,11,12,13,14,15,16,17,18, 19,20,21,22,23,24,25], studies indicate that the potential energy surface for AD in vacuum and in solution are considerably different while in the gas phase the global minimum is believed to be a C7eq structure ( -83°, t/r 73°) [16], it has only recently been shown that interaction with water favors the polyproline-H (PPn, y> -75°, t/r 150°) conformation [3,7],... 

The protein collagen, from skin and tendons, is composed of approximately 30 percent proline and hydroxyproline and 30 percent glycine. This protein has an unusual structure in which three chains, each with a conformation very similar to that of polyproline, are twisted about each other to make a triple helix. The three strands are hydrogen bonded to each other, through hydrogen bonds between the —NH of glycine residues and the — C=0 groups of the other amino acids. 

In addition to the order-disorder transition, observed for a helices, helical structures can also be induced to undergo transitions from one ordered form to another. For example, a crystalline form of poly[p-(p-chlorobenzyl)-L-aspartate] can be made to undergo a phase transition from an a-helical to an co-helical form by heating rotational entropy is computed to play a role in this process.68 Another order-order transition is the solvent-induced interconversion between polyproline 1 (with cis peptide bonds) and polyproline 11 (with trans peptide bonds), a process that has also been subjected to conformational energy calculations.85 The transition has been accounted for in terms of differences in the binding of solvent components to the peptide 0=0 groups. 

Additionally, a recent study on the gas-phase conformations of varying lengths of polyproline ions demonstrated that while PPI conformation is maintained in the gas phase, PPII conformation is not. The authors sustain that as the aqueous phase was removed from the PPII-structured polyproline during an electrospray process, the loss of water destabilized the PPII helix. Although it was not clear what conformations were formed from PPII polyproline in the gas phase, a mixture of cis- and frfliis-proline was evident (Coimterman and Clemmer, 2004). This study also clearly demonstrated the critical importance of water in stabilizing the PPII helix. 

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