Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2

Abstract

We have investigated covalent conjugation of VPPPVPPRRRX′ peptide (where X′ denotes Nε-chloroacetyl lysine) to N-terminal SH3 domain from adapter protein Grb2. Our experimental results confirmed that the peptide first binds to the SH3 domain noncovalently before establishing a covalent linkage through reaction of X′ with the target cysteine residue C32. We have also confirmed that this reaction involves a thiolate-anion form of C32 and follows the SN2 mechanism. For this system, we have developed a new MD-based protocol to model the formation of covalent conjugate. The simulation starts with the known coordinates of the noncovalent complex. When two reactive groups come into contact during the course of the simulation, the reaction is initiated. The reaction is modeled via gradual interpolation between the two sets of force field parameters that are representative of the noncovalent and covalent complexes. The simulation proceeds smoothly, with no appreciable perturbations to temperature, pressure or volume, and results in a high-quality MD model of the covalent complex. The validity of this model is confirmed using the experimental chemical shift data. The new MD-based approach offers a valuable tool to explore the mechanics of protein-peptide conjugation and build accurate models of covalent complexes.

Beyond structure: Deciphering site‐specific dynamics in proteins from double histidine‐based EPR measurements

“…MD simulations with appropriate Cu(II)NTA force fields were obtained following previous work 38,48 . Autocorrelation times were processed using python scripts provided by Prof. Nikolai Skrynnikov and Sergei Izmailov, similar to pyxmolpp2 77,82 . The autocorrelation functions were fit to a biexponential decay.…”

“…38,48 Autocorrelation times were processed using python scripts provided by Prof. Nikolai Skrynnikov and Sergei Izmailov, similar to pyxmolpp2. 77,82 The autocorrelation functions were fit to a biexponential decay. Errors were obtained by calculating the range of τ R values which resulted in a minimum RMSD.…”

In silico investigation of falcipain-2 inhibition by hybrid benzimidazole-thiosemicarbazone antiplasmodial agents: A molecular docking, molecular dynamics simulation, and kinetics study

“…The close proximity of the pre-reactive species in the 1B‒PF2, 1C‒PF2, and 1E‒PF2 complexes can facilitate any covalent interaction between them. Indeed, the proximity of the ligand binding site to the catalytic residues is an important factor that influences the ease and rate of covalent bond formation between the ligand and the catalytic residues [ 30 , 65 ]. Moreover, the ligands bind mainly in the S1 and S2 (as well as S1′ in some cases) subsites of FP2 (see Table 4 ) to form a noncovalent encounter complex necessary for covalent reaction with Cys42.…”

“…The hybrids were represented by 1B because it possesses a favorable docking score and is the most biologically active molecule among the drug-like and safer hybrids. It must be pointed out that the covalent binding study was preceded by noncovalent docking and MD simulation because the initial contacts or collisions between FP2 and each ligand must initially form an encounter complex before a covalent bond is formed [ 64 , 65 ]. The most representative configuration of the 1B‒FP2 complex was first generated by clustering its 150 ns MD simulation trajectory with the TTClust-4.10.0 [ 66 ] program using the RMSD approach.…”

A Global Review on Short Peptides: Frontiers and Perspectives

“…When the number of rotatable bonds exceeds 5, the entire conformational space of a molecule can become extremely large. In recent years, the methods of molecular dynamics were increasingly used to gain insight into the structure/function relationships in short peptides and proteins [ 183 , 184 , 185 , 186 , 187 ]. One of the key questions to be answered when checking the applicability of molecular dynamic simulations for peptides and/or proteins is the extent to which the simulations appropriately sample the conformational space of these molecules.…”