Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database

Abstract

Recently, we reported a database (Noncoded Amino acids Database; http://recerca.upc.edu/imem/index.htm) that was built to compile information about the intrinsic conformational preferences of nonproteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, the experimentally established conformational propensities, and applications (Revilla-López et al., J Phys Chem B 2010;114:7413-7422). The database initially contained the information available for α-tetrasubstituted α-amino acids. In this work, we extend NCAD to three families of compounds, which can be used to engineer peptides and proteins incorporating modifications at the--NHCO--peptide bond. Such families are: N-substituted α-amino acids, thio-α-amino acids, and diamines and diacids used to build retropeptides. The conformational preferences of these compounds have been analyzed and described based on the information captured in the database. In addition, we provide an example of the utility of the database and of the compounds it compiles in protein and peptide engineering. Specifically, the symmetry of a sequence engineered to stabilize the 3(10)-helix with respect to the α-helix has been broken without perturbing significantly the secondary structure through targeted replacements using the information contained in the database.

Figure 1

Ramachandran maps showing all the minimum energy conformations predicted by quantum mechanical calculations for the N-acetyl-N’-methylamide derivatives of the N-modified α-amino acids included in NCAD (see Table 1): (a) N-methylalanine (gray squares); and (b) N-aminoglycine (black squares) and N-hydroxyalanine (gray squares). The minimum energy conformations of Gly (black triangles) and Ala (grey triangles) have been included for comparison. Minima with relative energies lower and higher than 2.0 kcal/mol are represented by large and small symbols, respectively.

Figure 2

Ramachandran maps showing all the minimum energy conformations predicted by quantum mechanical calculations for the N-acetyl-N’-methylamide derivatives of the thio-α-amino acids included in NCAD (see Table 1): thioglycine (black squares) and thioalanine (gray squares). The minimum energy conformations of Gly (black triangles) and Ala (grey triangles) have been included for comparison. Minima with relative energies lower and higher than 2.0 kcal/mol are represented by large and small symbols, respectively.

Figure 3

Ramachandran maps showing all the minimum energy conformations predicted by quantum mechanical calculations for (a) the N,N’-dimethylamide derivatives of the diacids and (b) the N,N’-diacetyl derivatives of the diamines surrogates of α-amino acids included in NCAD (see Table 2). (a) Diacids: dc-Gly (black squares), dc-Ala (black circles), dc-Aib (gray triangles), dc-Val (gray diamonds) and dc-ΔAla (empty circles); (b) Diamines: dm-Gly (black squares), dm-Ala (black circles), dm-Aib (gray triangles) and dm-Val (gray diamonds). The nomenclature used for the different diacids and diamines is discussed in the text. Minima with relative energies lower and higher than 2.0 kcal/mol are represented by large and small symbols, respectively.

Figure 4

Hydrogen bonding network for the α- and 3₁₀-helices (i←i+4 solid line and i←i+3 dashed line, respectively) of Aib-n and rAib-n.

Figure 5

Side and top views of the 3₁₀-helix adopted by rAib-n.

Figure 6

Search performed with the NCAD database to select nc-aa able to break the symmetry in rAib-n without alter significantly the stability of the 3₁₀-helix (see text).

Figure 7

Detail about the C-H⋯O=C interaction (arrows) in the 3₁₀-helix of rAib-12 and diamine-1. Averaged H⋯O distances are indicated.

Scheme 1

Scheme 2

Scheme 3