Peptidomimetics and the template approach to nucleation of beta-sheets and alpha-helices in peptides.

Introducing structural constraints into engineered analogs of natural proteins is important for defining essential characteristics, such as specificity or stability, of the protein. This may be achieved by the use of peptidomimetics--elements which mimic the structure of natural peptide components, or conformational templates which induce specific structure formation in contiguous peptide sequence.

Novel class of silicon-based protective groups for the side chain of tyrosine.

A novel class of silyl-based protective groups compatible with the Bpoc/t-Bu strategy has been developed for the side chain of tyrosine. Carbobenzyloxy (CBZ) and biphenylisopropyloxy (Bpoc)-O-beta-trimethylsilylethyl-tyrosine (10 and 12) and CBZ-O-beta-dimethylphenylsilylethyl-tyrosine 14 were prepared in reasonable yields and in very high purity. The trimethylsilylethyl (TMSE) group proved to be 3-4 times more stable than the tert-butyl ether group towards 0.5% TFA. The latter is removed up to 4% during the acidolysis of the Bpoc group. As expected, the dimethylphenylsilylethyl (DMPSE) group was even more resistant towards 0.5% TFA (five time greater than the TMSE analog). Both silyl protective groups were found to be resistant towards a variety of reagents used in peptide synthesis, such as trialkylamines, hydroxybenzotriazole, trialkylphosphine and nucleophiles. They are readily removed in neat TFA in 5-20 min in the absence of cation scavengers, without any detectable alkylation of the phenolic ring. The application of the new silyl-based protective group was demonstrated by the synthesis of the C-terminal 29 amino acid peptide of the basic pancreatic trypsin inhibitor by the prior thiol capture methodology. The protected octapeptide BocC(Acm)QT)(tBu)FVY(TMSE)GG-PO-dibenzofuranthiol++ + was synthesized by solid-phase peptide synthesis using Bpoc-(O-TMSE)-Tyr-OH in greater than 90% yield and coupled to an unprotected 21-mer. The partially blocked, purified peptide was deprotected quantitatively in neat TFA in 1 h.

Resolution of proline acylation problem for thiol capture strategy by use of a chloro-dibenzofuran template.

The acyl transfer rate for proline, in the prior thiol capture strategy, was enhanced by changing the electronic character of the dibenzofuran template. The rate of amide bond formation between proline and cysteine by the 1-chloro-4-hydroxy-6-mercaptodibenzofuran was measured to be 0.012 min-1, which translates to a half-life of 53 min. Further enhancement of the reaction rate was accomplished by the use of a 1,3-dichloro-dibenzofuran template. The k1 for the reaction was measured to be 0.093 min-1, and the half-life was calculated to be 7 min. To test the applicability of the activated template, 1-chloro-4-hydroxy-6-mercaptodibenzofuran, in peptide synthesis, the 34 amino acid long peptide, H-RPDFCLEPPYTGPCRKARNNFKSADECMRTCGGA-OH, was synthesized. This peptide represents the condensation of the N-terminal 13-mer and the C-terminal 21-mer of the basic pancreatic trypsin inhibitor.

Short, solubilized polyalanines are conformational chameleons: exceptionally helical if N- and C-capped with helix stabilizers, weakly to moderately helical if capped with rigid spacers.

Isolating spacers introduced between solubilizing lysine regions and a polyalanine core permit rigorous characterization of context-free alanine helices. The preferred building blocks for isolating spacers are amino acids with rigid, extended conformations such as proline, isonipecotic acid, and tert-leucine. Replacing isolating spacers by conventional N- and C-caps dramatically increases the helicity of dodecaalanine. Solubilized, isolated polyalanines provide optimal tools for testing polypeptide helicity algorithms, central to resolution of the protein folding problem.

The helical s constant for alanine in water derived from template-nucleated helices.

Formation of alpha helices from disordered polypeptides depends on the degree to which amino acids favour the helical state. The folding of helical oligopeptides can be modelled by two parameters: sigma which reflects helix initiation and s which reflects propagation of a pre-existing helix and measures helical bias. Scheraga has reported s values for oligopeptides of about 1.1, implying a weak helical bias for amino-acid residues. By contrast, certain helical peptides studied by Baldwin seem to require much larger s values for alanine. Resolution of this inconsistency requires experiments that disentangle the ease of propagation from that of initiation. In this study varying lengths of polyalanine are linked to a 'template' that initiates helical structure and permits study solely of propagation. We report here that the s value for alanine in water is close to 1, supporting the earlier results of Scheraga but not the more recent results of Baldwin.

Optimal N-caps for N-terminal helical templates: effects of changes in H-bonding efficiency and charge.

A family of efficient helix-initiating N-terminal caps X-Hel is introduced that expand the scope and versatility of the previously reported reporting conformational template Ac-Hel, (Kemp, D. S.; Allen, T. J.; Oslick, S. J. Am. Chem. Soc. 1995, 117, 6641-6657) and a working principle for predicting cap performance is described, based on structurally specific intramolecular hydrogen bond formation. Replacement of the N-acetyl by urethane, urea, or sulfonamide generated less efficient polypeptide helix inducers. The N-formyl cap is found to be equivalent to the N-acetyl and may provide more convenient quantitative helix reporting properties. Anionic N-caps derived from the series X = (-)O(2)C-(CH(2))(n)-CO, 0 < or = n < or = 3, are superior to N-acetyl, as are N-acylglycyl and N-acyl-beta-aspartyl. The latter pair of caps permit introduction of the X-Hel functionality within a polypeptide chain, allowing control of helicity of a peptide sub-sequence. Applications of these capping functions are discussed. This work has been focused primarily on immediate practical goals directed toward enhancing the maximum helicity of isolated short to medium-sized peptides in aqueous solution, but its developing concepts and working hypotheses are likely to significantly enhance our understanding at a chemical level of the protein folding problem.

Practical preparation and deblocking conditions for N-alpha-(2-(p-biphenylyl)-2-propyloxycarbonyl)-amino acid (N-a-Bpoc-Xxx-OH) derivatives.

Reproducible preparations are given for salts of the following L-amino acid derivatives: Bpoc-Ala-OH, Bpoc-Arg(Mtr)-OH, Bpoc-Asn-OH, Bpoc-Asp(OtBu)-OH, Bpoc-Cys(Acm)-OH, Bpoc-Cys(S-tBu)-OH, Bpoc-Gln-OH, Bpoc-Glu(OtBu)-OH, Bpoc-Gly-OH, Bpoc-Ile-OH, Bpoc-Leu-OH, N-alpha-Bpoc-Lys(epsilon-Boc)-OH, Bpoc-Met-OH, Bpoc-Phe-OH, Bpoc-Pro-OH, Bpoc-Ser(OtBu)-OH, Bpoc-Thr(OtBu)-OH, Bpoc-Tyr-OH, Bpoc-Val-OH. A study of the deblocking of N-alpha-Bpoc peptides in dichloromethane containing 0.5% trifluoroacetic acid revealed that a rapid equilbrium is established between the first-formed monomeric alkene 2-p-biphenylylpropene and the hindered dimer 2,4-bis(p-biphenylyl)-4-methyl-1-pentene. Thioethers were found to be inefficient carbocation scavengers for the deblocking reaction. The most efficient scavengers were found to be thiophenol and benzyl mercaptan, and the following approximate reactivity order was established: benzyl mercaptan approximately thiophenol greater than indole much greater than 1,3-dimethoxybenzene approximately resorcinol greater than 1,3,5-trimethoxybenzene approximately dimethyl sulfide approximately thioanisole.

Template-nucleated alanine-lysine helices are stabilized by position-dependent interactions between the lysine side chain and the helix barrel.

The helicity in water has been determined for several series of alanine-rich peptides that contain single lysine residues and that are N-terminally linked to a helix-inducing and reporting template termed Ac-Hel1. The helix-propagating constant for alanine (sAla value) that best fits the properties of these peptides lies in the range of 1.01-1.02, close to the value reported by Scheraga and coworkers [Wojcik, J., Altmann, K.-H. & Scheraga, H.A. (1990) Biopolymers 30, 121-134], but significantly lower than the value assigned by Baldwin and coworkers [Chakrabartty, A., Kortemme, T. & Baldwin, R.L. (1994) Protein Sci. 3,843-852]. From a study of conjugates Ac-Hel1-Ala(n)-Lys-Ala(m)-NH2 and analogs in which the methylene portion of the lysine side chain is truncated, we find that the unusual helical stability of Ala(n)Lys peptides is controlled primarily by interactions of the lysine side chain with the helix barrel, and only passively by the alanine matrix. Using 1H NMR spectroscopy, we observe nuclear Overhauser effect crosspeaks consistent with proton-proton contacts expected for these interactions.