Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model.
The solution conformation of alpha-conotoxin GI and its two single disulfide analogues are simulated using a polarizable force field in combination with the molecular fragmentation quantum chemical calculation. The polarizability is explicitly described by allowing the partial charges and fragment dipole moments to be variables, with values coming from the linear-scaling energy-based molecular fragmentation calculations at the B3LYP/6-31G(d) level. In comparison with the full quantum chemical calculations, the fragmentation approaches can yield precise ground-state energies, dipole moments, and static polarizabilities for peptides. The B3LYP/6-31G(d) charges and fragment-centered dipole moments are introduced in calculations of electrostatic terms in both AmberFF03 and OPLS force fields. Our test calculations on the gas-phase glucagon (PDB code: 1gcn) and solvated alpha-conotoxin GI (PDB code: 1not) demonstrate that the present polarization model is capable of describing the structural properties (such as the relative conformational energies, intramolecular hydrogen bonds, and disulfide bonds) with accuracy comparable to some other polarizable force fields (ABEEM/MM and OPLS-PFF) and the quantum mechanics/molecular mechanics (QM/MM) hybrid model. The employment of fragment-centered dipole moments in calculations of dipole-dipole interactions can save computational time in comparison with those polarization models using atom-centered dipole moments without much loss of accuracy. The molecular dynamics simulations using the polarizable force field demonstrate that two single disulfide GI analogues are more flexible and less structured than the native alpha-conotoxin GI, in agreement with NMR experiments. The polarization effect is important in simulations of the folding/unfolding process of solvated proteins.
Jiang
Nan
N
School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing 210093, People's Republic of China.
Ma
Jing
J
D000595:Amino Acid Sequence; D003198:Computer Simulation; D020916:Conotoxins / Q000737:chemistry*; D004220:Disulfides / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D020916:Conotoxins; D004220:Disulfides; D012997:Solvents; D014867:Water; C029960:conotoxin GI