Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA

Abstract

Our previously developed peptide-design algorithm was improved by adding an energy minimization strategy which allows the amino acid sidechains to move in a broad configuration space during sequence evolution. In this work, the new algorithm was used to generate a library of 21-mer peptides which could substitute for λ N peptide in binding to boxB RNA. Six potential peptides were obtained from the algorithm, all of which exhibited good binding capability with boxB RNA. Atomistic molecular dynamics simulations were then conducted to examine the ability of the λ N peptide and three best evolved peptides, viz. Pept01, Pept26, and Pept28, to bind to boxB RNA. Simulation results demonstrated that our evolved peptides are better at binding to boxB RNA than the λ N peptide. Sequence searches using the old (without energy minimization strategy) and new (with energy minimization strategy) algorithms confirm that the new algorithm is more effective at finding good RNA-binding peptides than the old algorithm. © 2016 Wiley Periodicals, Inc.

Keywords: RNA tethering; RNA-binding peptide; energy minimization strategy; peptide-design algorithm; λ N peptide-boxB RNA.

Figure 1

Structure of the complex formed by λ N(2-22) peptide and boxB RNA hairpin based on PDB ID: 1QFQ showing the RNA (green ribbon), the peptide (orange ribbon), the positively charged amino acids (blue) and the negatively charged amino acids (red). The other nucleotides and amino acids are not shown for clarity. The secondary structure of the 15-mer nutR boxB RNA hairpin is shown in the box on the left. The primary sequence of λ N peptide from aspartate (D) at site 2 to asparagine (N) at site 22 is shown in the box on the top.

Figure 2

The flow sheet for the search algorithm.

Figure 3

Block diagram showing the energy minimization strategy to determine optimal sidechain configuration for one amino acid repacking.

Figure 4

The profiles of score vs. number of evolution steps during the sequence evolution for the six λ N(2-22) peptide-boxB RNA complexes.

Figure 5

Pept01 binds to boxB RNA with high affinity. (a) The binding structure of Pept01 and boxB RNA obtained from search algorithm showing the peptide backbone (orange ribbon) and the ribose-phosphodiester backbone (green ribbon). Several key residues and nucleotides are specified in blue and red colors, respectively. The table on the right characterizes the contributions of the different binding modes for the Pept01-boxB RNA complex. (b) Individual contributions of each nucleotide to the inter-chain VDW, inter-chain ELE+EGB, and GBSUR. (c) Individual contributions of each amino acid to the inter-chain VDW, inter-chain ELE+EGB, and GBSUR.

Figure 6

Pept26 binds to boxB RNA with high affinity. (a) The binding structure of Pept26 and boxB RNA obtained from search algorithm. The table on the right characterizes the contributions of the different binding modes for the Pept26-boxB RNA complex. (b) Individual contributions of each nucleotide to the inter-chain VDW, inter-chain ELE+EGB, and GBSUR. (c) Individual contributions of each amino acid to the inter-chain VDW, inter-chain ELE+EGB, and GBSUR.

Figure 7

Pept28 binds to boxB RNA with high affinity. (a) The binding structure of Pept28 and boxB RNA obtained from search algorithm. The table on the right characterizes the contributions of the different binding modes for the Pept28-boxB RNA complex. (b) Individual contributions of each nucleotide to the inter-chain VDW, inter-chain ELE+EGB, and GBSUR. (c) Individual contributions of each amino acid to the inter-chain VDW, inter-chain ELE+EGB, and GBSUR.

Figure 8

Atomistic MD simulation studies of the binding of (a) the λ N(2-22) peptide, (b) Pept01, (c) Pept26 and (d) Pept28 with boxB RNA. The profile of RMSD vs. time was shown on the left side of each sub-picture to assure that our simulations reach conformational equilibrium. The binding structure of the peptide and boxB RNA was shown on the right side of each sub-picture, which was extracted as a structural representative by performing cluster analysis for the last 5-ns trajectory. The RNA is represented by the green ribbon. The peptide is represented by the orange ribbon, with the positively charged amino acids in blue and the negatively charged amino acids in red.

Figure 9

Comparison of sequence evolution between the old and the new search algorithms. The profiles of the score vs. the number of evolution steps are plotted.