Factors governing helical preference of peptides containing multiple alpha,alpha-dialkyl amino acids.

Abstract

The presence of multiple a,a-dialkyl amino acids such as a-methylalanine (a-aminoisobutyric acid, Aib) leads to predominantly helical structures, either with a-helical or 310-helical hydrogen bonding patterns. The crystal structure of emerimicin-(1-9) benzyl ester (Ac-Phe-Aib-Aib-AibVal-Gly-Leu-Aib-Aib-OBzl) reported here shows essentially pure a-helical character, whereas other similar compounds show predominantly 310-helical structures. The factors that govern helical preference include the inherent relative stability of the a-helix compared with the 310-helix, the extra hydrogen bond seen with 310-helices, and the enhanced electrostatic dipolar interaction of the 310-helix when packed in a crystalline lattice. The balance of these forces, when combined with the steric requirements of the amino acid side chains, determines the relative stability of the two helical conformations under a given set of experimental conditions. The presence of a,a-dialkyl amino acids in microbial natural products, such as the peptaibol antibiotics, requires novel biosynthetic pathways to produce and incorporate these unusual amino acids in the face of the usual ribosomal mechanisms available for normal amino acids. This argues strongly for a special role related to function, one aspect of which may be their increased resistance to proteolytic degradation. Another aspect is the conformational restrictions imposed by these amino acids as first pointed out by Marshall and Bosshard (1, 2) and verified by others (3-7). While most work has focused on a-methylalanine (a-aminoisobutyric acid, Aib), a-ethylalanine (isovaline) has also been found to be a natural component of several peptaibol antibiotics (8,9). In addition, chiral a,a-dialkyl amino acids, such as amethylphenylalanine, have been incorporated into naturally occurring peptides in an effort to restrict their conformational freedom (10, 11).From the Ramachandran plots published by Marshall and Bosshard in 1972 (1), the presence of an additional alkyl substituent on the a-carbon severely restricted the values of the torsional variables 4 and qk as compared with those available to normal amino acids. While the two major allowed conformational areas were associated with either right-or left-handed helical conformations (both a and 310), the calculation also revealed other sets of energetically feasible values for 4 and q, adjacent to the a,a-dialkyl residue associated with extended structures as well as turns. The effect on conformation of alkyl groups larger than methyl as substituents in a,a-dialkyl amino acids has also been investigated (11,12). Despite the variety of conformations theoretically available to a,a-dialkyl amino acids, the impact of multiple substitutions ofthis type of amino acid on the overall conformation of a peptide is dramatic. The crystal structure of alamethicin (13), which contains 8 Aib residues out of 20, is predominantly a-helical, with NMR data (14) supporting a similar solution conformation in methanol. A review (15) of crystal structures of tr...

Back to the future: Ribonuclease A

“…These plots indicate why proline, or any other N-methyl amino acid, has difficulties being accommodated within the helical segments of proteins. The most dramatic change was seen, however, when the a-hydrogen of the alanine was replaced by a methyl group, acetyl-L-aminoisobutyric N-methylamide ( Figure 7D), simultaneously restricting both u and w. This prediction that a-methyl amino acids would restrict the flexibility of the peptide backbone to only those regions of u,w space common to both acetyl-L-alanine N-methylamide ( Figure 7A) and acetyl-D-alanine N-methylamide ( Figure 7E) has been confirmed subsequently by numerous experimental/theoretical studies by the Marshall, [65][66][67][68][69] Karle, 70,71 Toniolo,72,73 Balaram, 70 and Millhauser 74 groups. By focusing the minimal energy states of the peptide backbone to u,w space associated with right-or left-handed helices, substitutions with a-methyl amino acids preorganize the peptide…”

“…75 The only negative aspect of their use is the ambiguity regarding which type (a-helix, 3 10 helix, or a mixture of the two) of helix is being recognized upon binding. 65 The ability to form rigidified complementary helical surfaces by subtle changes in backbone torsional angles may, in fact, turn out to be a compelling argument for the use of oligomers of a-methyl amino acids as generalized helical mimetics.…”

“…As the simplest example of preorganization, incorporation of aminoisobutyric acid (Aib, a-methylalanine) into peptides/proteins restricts the u and w backbone angles adjacent to Aib to those associated with helix formation (Figure 7). 63,65 The Marshall lab utilized this observation to investigate the receptor-bound conformation of several peptides binding to GPCRs. [80][81][82][83] By restriction of the adjacent dihedral torsions, insertion of an Aib should also lower the entropic penalty of turn/helix formation upon protein folding, due to preorganization.…”

Crystal structure of the channel-forming polypeptide antiamoebin in a membrane-mimetic environment

“…The preponderance of C ␣ -disubstituted amino acid residues in compound 1 suggested a 3 10 -helix formation (15)(16)(17) for the first half of the peptide rather than an ␣-helix as found in compound 2 (5-7). Actually, despite the high Aib content in compound 1, the backbone conformations of compounds 1 and 2 are almost identical.…”

Stereochemical Control of Peptide Folding

“…59 There has been considerable discussion in the literature on the nature of the helical conformations adopted by Aib rich sequences. 51,53,60,61 Both 3 10 and a-helical conformations have been characterized depending upon peptide length, sequence and Aib content. Several structures of heteromeric sequences containing Aib have revealed mixed 3 10 /a-helical structures, 51,62,63 with the 3 10 segment often occuring at the N-terminus.…”