Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding

Abstract

Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is challenging to simulate both binding and unbinding of peptides and calculate peptide binding free energies through conventional molecular dynamics, due to long biological timescales and extremely high flexibility of the peptides. Based on the Gaussian accelerated molecular dynamics (GaMD) enhanced sampling technique, we have developed a new computational method "Pep-GaMD," which selectively boosts essential potential energy of the peptide in order to effectively model its high flexibility. In addition, another boost potential is applied to the remaining potential energy of the entire system in a dual-boost algorithm. Pep-GaMD has been demonstrated on binding of three model peptides to the SH3 domains. Independent 1 µs dual-boost Pep-GaMD simulations have captured repetitive peptide dissociation and binding events, which enable us to calculate peptide binding thermodynamics and kinetics. The calculated binding free energies and kinetic rate constants agreed very well with available experimental data. Furthermore, the all-atom Pep-GaMD simulations have provided important insights into the mechanism of peptide binding to proteins that involves long-range electrostatic interactions and mainly conformational selection. In summary, Pep-GaMD provides a highly efficient, easy-to-use approach for unconstrained enhanced sampling and calculations of peptide binding free energies and kinetics.

FIG. 1.

Pep-GaMD simulations have captured repetitive dissociation and binding of three model peptides to the SH3 domains: [(a)–(c)] x-ray structures of the SH3 domains bound by peptides (a) “PAMPAR” (PDB: 1SSH), (b) “PPPALPPKK” (PDB: 1CKA), and (c) “PPPVPPRR” (PDB: 1CKB). The SH3 domains and peptides are shown in green and magenta cartoon, respectively. Key protein residues Asp19 and Trp40 in the 1SSH structure and Asp150 and Trp169 in the 1CKA and 1CKB structures, and peptide residues Arg10 in the 1SSH structure, Lys8 in the 1CKA structure, and Arg7 in the 1CKB structure are highlighted in sticks. The “N” and “C” labels denote the N-terminus and C-terminus of the peptides. [(d)–(f)] Time courses of peptide backbone RMSDs relative to x-ray structures with the protein aligned calculated from three independent 1 µs Pep-GaMD simulations of the (d) 1SSH, (e) 1CKA, and (f) 1CKB structures. [(g)–(i)] The corresponding PMF profiles of the peptide backbone RMSDs averaged over three Pep-GaMD simulations of the (g) 1SSH, (h) 1CKA, and (i) 1CKB structures. Error bars are standard deviations of the free energy values calculated from three Pep-GaMD simulations.

FIG. 2.

Free energy profiles and low-energy conformational states of peptide binding to the SH3 domains: (a) 2D PMF profiles regarding the peptide backbone RMSD and the distance between protein Asp19 and peptide Arg10 in the 1SSH structure. (b) 2D PMF profiles regarding the peptide backbone RMSD and the distance between protein Asp150 and peptide Lys8 in the 1CKA structure. (c) 2D PMF profiles regarding the peptide backbone RMSD and the distance between protein Asp150 and peptide Arg7 in the 1CKB structure. [(d)–(f)] Low-energy intermediate conformations (red) as identified from the 2D PMF profiles of the (d) 1SSH, (e) 1CKA, and (f) 1CKB structures, respectively. X-ray structures of the peptide-bound complexes are shown in green and magenta for protein and peptide, respectively. Protein residues Asp19 and Trp40 in the 1SSH structure and Asp150 and Trp169 in the 1CKA and 1CKB structures, and peptide residues Arg10 in the 1SSH structure, Lys8 in the 1CKA structure, and Arg7 in the 1CKB structure are highlighted in sticks. The “N” and “C” labels denote the N-terminus and C-terminus of the peptides.

FIG. 3.

(a) 2D PMF profiles of peptide backbone RMSD and the distance between protein Asp19 and Trp40 calculated from Pep-GaMD simulations of the 1SSH structure. [(b) and (c)] 2D PMF profiles of the peptide backbone RMSD and the distance between protein Asp150 and Trp169 calculated from Pep-GaMD simulations of the (b) 1CKA and (c) 1CKB structures. [(d)–(f)] 2D PMF profiles regarding the peptide backbone RMSD and peptide R_g in the (d) 1SSH, (e) 1CKA, and (f) 1CKB structures.