Study of peptide conformation in terms of the ABEEM/MM method

Abstract

The ABEEM/MM model (atom-bond electronegativity equalization method fused into molecular mechanics) is applied to study of the polypeptide conformations. The Lennard-Jones and torsional parameters were optimized to be consistent with the ABEEM/MM fluctuating charge electrostatic potential. The hydrogen bond was specially treated with an electrostatic fitting function. Molecular dipole moments, dimerization energies, and hydrogen bond lengths of complexes are reasonably achieved by our model, compared to ab initio results. The ABEEM/MM fluctuating charge model reproduces both the peptide conformational energies and structures with satisfactory accuracy with low computer cost. The transferability is tested by applying the parameters of our model to the tetrapeptide of alanine and another four dipeptides. The overall RMS deviations in conformational energies and key dihedral angles for four di- or tetrapeptide, is 0.39 kcal/mol and 7.7 degrees . The current results agree well with those by the accurate ab initio method, and are comparable to those from the best existing force fields. The results make us believe that our fluctuating charge model can obtain more promising results in protein and macromolecular modeling with good accuracy but less computer cost.

New investigation of potential acting on an electron in a molecule to draw molecular faces

“…where r is the position vector of an electron in a molecule; V(r) denotes the potential acting on this internal electron at position r; R A is the position vector of atomic nucleus A in the molecule; λ is a correction factor which equal to 1.44; Q A is the partial charge condensed on atoms in the molecule when the given electron takes a local position r. To obtain the partial charge Q A , the interactions of this electron in the molecule with all the atoms, bonds and lone-pair electrons are introduced in the total electronic energy based on the atom-bond electronegativity equalization method(ABEEMσπ) [14][15][16][17][18][19] . The total energy(E) of a molecule at the ground state can be defined as…”

Reversible folding/unfolding of small a-helix in explicit solvent investigated by ABEEMσπ/MM

“…The molecular dynamics simulations of the Ala 5 were performed by ABEEMσπ fluctuating charge force field [44][45][46][47][48][49][50][51][52][53][54] , which was proposed by Yang et al ABEEMσπ model divides a molecular system into not only atomic regions, but also lone pair regions and bond regions (including σ and π bond regions). The atomic partial charge plus four or five negative partial charges, such as σ, π bond regions or lone pair regions, around a nonhydrogen atom, such as C, N or O atom, may give proper response to the environmental change.…”

Calculating solvation energies by means of a fluctuating charge model combined with continuum solvent model

“…In the ABEEMσ π fluctuating charge force field, based on previous papers, [128][129][130] the total potential energy, E ABEEMσ π/MM , is expressed as follows:…”

“…[118][119][120][121][122] The ABEEM fluctuating charge model has been applied to the water systems 9, 117 and ion-water systems [123][124][125] as well as to the conformations of alkane and peptide. [126][127][128] To better account for the polarization effect, a molecular system in ABEEMσ π model is further decomposed into atomic regions, lone-pair regions, and σ and π bond regions, and each region is assigned by a partial charge. 129 This partition scheme well elucidates the polarization effect due to more freedom and larger flexibility in calculating the fluctuating partial charge associated with each of the regions.…”