Residues in the longitudinal, hydrophobic strip-of-helix relate to terminations and crossings of alpha-helices

Structural studies by 1H NMR of a prototypic alpha-helical peptide (LYQELQKLTQTLK) and homologs in trifluoroethanol/water and on sodium dodecyl sulfate micelles

The 1H NMR-determined structure and dynamics of a synthetic, amphiphilic alpha-helical peptide, PH-1.0 (LYQELQKLTQTLK), and several homologs were compared in 50% trifluoroethanol-d2 (TFE-d2)/H20 and in sodium dodecyl-d25 sulfate (SDS-d25) micelles. The peptides were designed to test the influence on secondary structure of placement of favored and disfavored residues relative to a "longitudinal, hydrophobic strip-of-helix" defined by the repeating leucines. PH-1.0 was highly ordered as an alpha-helix in 50% TFE-d2/H20 and in SDS-d25 micelles. Homologs PH-1.1, in which L1 was replaced by T, and PH-1,4, in which L12 was replaced by T. were found to be partially helical in both media. Calculated structures in SDS-d25 revealed that the helix of PH-1.1 was slightly disordered at the N-terminus, but that of PH-1.4 was completely disordered at the C-terminus. Examination of distributions of hydrophobic residues in protein structures revealed that, when [symbol: see text] = LIVFM and [symbol: see text] = nonLIVFM, the pattern [symbol: see text] is favored and [symbol: see text] is disfavored in alpha-helices. Several analogs of PH-1.0 incorporating these patterns were studied. Peptide PH-1.12 (LYQELQKLLQTLK) retained alpha-helical structure in both 50% TFE-d2/H20 and in SDS-d25 micelles. However, although PH-1.13 (LYQELQKLTLTLK) was fully helical in 50% TFE, it was helical only through residue 6 in SDS micelles. Two homologs containing an additional loop of the helix and repeats of favored (PH-5.0, NYLQTLLETLKTLLQK) or suppressed LL patterns (PH-5.11, NYLQTLETLKLTQK) gave similar results, i.e. the latter peptide was helical only through residue 6 in SDS micelles. The degree of local order in these SDS micelle-adsorbed peptides correlates to placement of hydrophobic residues in motifs which are favored or disfavored in proteins in general and in alpha-helices specifically.

1H NMR studies of prototypical helical designer peptides. A comparative study of the amide chemical shift dependency on temperature and polypeptide sequence

A series of designer alpha-helical peptides with hydrophobic residues located at different positions along the sequence (PH-1.0 = LYQELQKLTQTLK, PH-1.19 = LYQELQKLTQTFK, PH-1.12 = LYQELQKLLQTLK, PH-1.13 = LYQELQKLTLTLK, PH-1.4 = LYQELQKLTQTTK) were analyzed using one- and two-dimensional NMR methods (TOCSY and NOESY). The central feature of these designer peptides is the incorporation of a maximal hydrophobic strip which may play a role in antigen processing and the nucleation of alpha-helices in proteins (J. Immunol. 145, 899, 1990). Using the 2D-NMR, sequence specific assignments and NOE connectivities were determined in all peptides when dissolved in H2O/TFE mixtures. NOE connectivities indicated that all these peptides are helical in this medium. An unusually large number of NOEs was found for all these designer peptides. This is in accord with ultracentrifugation studies that showed that PH-1.0 forms a trimer in 50% H2O/TFE mixtures. Other peptides in the series behave in similar manner as PH-1.0. The structural differences among these peptides was addressed using the backbone amide chemical shift temperature coefficients, [symbol: see text], and the differences between the observed and random coil values, delta delta HN. The delta delta HN patterns along the peptide sequence are consistent with those expected for amphiphilic alpha-helices, where most delta delta HN values are below zero. However, no significant differences among the peptides in this series can be detected on the delta delta HN patterns, with the exception of PH-1.12. The [symbol: see text] values reveal differences among the peptides of the series. The patterns of [symbol: see text] along the peptide sequences are similar to that found for delta delta HN for PH-1.0, PH-1.19 and PH-1.4. The other peptides in the series, PH-1.12 and PH-1.13, showed different patterns for [symbol: see text]. The latter parameter was used to evaluate the helicity of this series of peptides. According to this parameter the relative helicity of this series is as follows: PH-1.12 > PH-1.0 > PH-1.4 > PH-1.19 > PH-1.13 The NMR data shown here correlated well with the helical propensities predicted for polypeptide sequences using statistical arguments (Proc. Natl. Acad. Sci. USA, 90, 9100, 1993).

Defining topological similarities among ion transport proteins with anti-amiloride antibodies

The structural features of amiloride binding sites on amiloride-sensitive transport proteins have received limited characterization. An antibody that recognizes limited regions of amiloride and can mimic, in binding specificity, certain amiloride-sensitive transport proteins was used as a model to elucidate potential amino acid residue relationships that might define putative amiloride contact sites. Analysis of the structure of this antibody has allowed us to identify sequence relationships among several Na+ selective transport proteins. A structure-based relational database was employed to re-examine sequence homologies among these ion transport proteins. A search of the protein sequence databank identified representative amino acid tracts among amiloride sensitive proteins involving planar residues that might be involved in interacting with amiloride. Computer models of sites within transmembrane domains of NHE1 and NHE2 isoforms of the Na+/H+ exchanger reflective of these planar tracts indicate that amiloride probably spans two helices for interaction with the Na+/H+ exchanger. Structural analysis of this monoclonal anti-amiloride antibody appears to mimic some of the salient features of amiloride binding sites on these proteins.

Assessment of homology with the helical mimicry algorithm

Homologies based on structural motifs characterize conserved structures and mechanisms of maintaining function. An algorithm was developed to quantitate homology among segments of two proteins based upon structural characteristics of an amphipathic alpha-helix. This helical mimicry algorithm scored homology among sequences of two proteins in terms of: (i) presence of Leu, Ile, Val, Phe, or Met in a longitudinal, hydrophobic strip-of-helix at positions n, n + 4, n + 7, n + 11, etc. in the primary sequence, (ii) identity or chemical similarity of amino acids at intervening positions and (iii) exchanges of amino acids from positions n to n - 1, n + 3, n + 4, n + 1, n - 3, n - 4 around n (on the surface of a putative helix). While such exchanges of amino acids on the surfaces of homologous helices may conserve function, they did not maintain specific interactions of those residues with apposing groups.

Adsorption and helical coiling of amphipathic peptides on lipid vesicles leads to negligible protection from cathepsin B or cathepsin D

The processing of antigenic peptides for presentation by MHC molecules to T cells, may depend upon the function of a second, consensus sequence in or near the T cell-presented epitope. One such processing-regulating sequence appears to be composed of amino acids Leu, Ile, Val, Phe, and Met recurring in a fashion to form a longitudinal, hydrophobic strip when the excised peptide is coiled as an alpha-helix. Such a hydrophobic strip-of-helix may: (a) scavenge peptides from lumens onto lipid membranes of digestion vesicles, (b) stabilize peptides there as protease-resistant helices, (c) specify recognition by the antigenic peptide-binding sites of chaperonin proteins, transmembranal transporters, or MHC molecules. By circular dichroism and electron paramagnetic resonance, we demonstrated that peptides with recurrent hydrophobic residues potentially forming longitudinal strips adsorbed to, and partially coiled as helices on, di-O-hexadecyl, D-L-alpha-phosphatidylcholine (DHPC) vesicles. Cathepsin B or cathepsin D cleavages of three such peptides were identified. With either enzyme, it made no significant difference whether a peptide substrate was in solution or bound to vesicles in terms of efficiency and specificity of peptide bond cleavages. We conclude that protease resistance, per se, of membrane-adsorbed, helically coiled peptides is not a major factor in the selection for T cell presentation of epitopes in peptides which have a motif with a longitudinal hydrophobic strip.

Comparison of actual and random-positioning-model distributions of peptide scavenging and T cell-presented sites in antigenic proteins

In a peptide with a T cell-presented epitope (T site), a folded structure with a hydrophobic surface, 'the scavenger (S) site', may regulate transfer to major histocompatibility complex class II molecules. Three procedures which were proposed to identify T sites selected for amphipathic helical patterns but not T sites. In testing whether S sites lay in or near T sites, we found their linkage was not greater than that generated by a model in which segments of equal length and number to the S and T sites for each protein were distributed at random. This study establishes criteria for evaluation of schemes to predict functional motifs in antigenic proteins.

Hypothesis for the control of clotting factor VIII inhibitory antibodies by decreasing potency of helper T-cell-recognized epitopes in factor VIII

The study of the immunobiology of FVIII inhibitors may lead to new therapies for this potentially severe complication of haemophilia A and to new principles for the use of therapeutic proteins. In order to characterize the idiotype-anti-idiotype networks regulating FVIII inhibitors, we developed rabbit anti-idiotypic sera to 7 murine inhibitors and found at least 12 independent FVIII loci to which inhibitors could be raised. Rabbit antisera to the FVIII peptide, Ser1687-Thr1695, characterized one functional site to which about 46% of patients' inhibitor sera reacted. The multiplicity of inhibitor-recognized epitopes in FVIII makes it impractical, at the present time, to develop clinically useful specific anti-idiotypic therapies for FVIII inhibitors. Alternatively, one might induce genomic mutations in recombinant FVIII molecules to decrease immunogenicity of epitopes recognized by T helper cells. Methods to design such altered therapeutic proteins are presented, based on changing the longitudinal hydrophobic strip-of-helix which is in or near many T-cell-presented epitopes.