In this study, we apply both palrwise AMBER03 force field and the recently developed polarized force field to study the folding process of EK peptide under various ion strength and pH conditions. The polarized force field is based on our newly proposed adaptive hydrogen bond-specific charge （AHBC） scheme. These two force fields differ only by the atomic charges. Solvent effect is described with generalized Born models （IGB5 in AMBER 10 package）. The result shows that although when applying AMBER03 charge, the helical structure is preferred, its dependence on salt concentration and pH is qualitatively wrong. While using AHBC the peptide finds its native structure within 10 ns, and then fluctuates around this folded state. Under high salt concentration or extreme pH conditions the calculated helical structure probability drops, which is in qualitative agreement with the experiment. Analysis of the atomic charges and the interaction between the donor-acceptor pair in main hydrogen bonds shows that the helical structure is stabilized when polarization effect is counted. It again shows that polarization effect is a very important improvement over traditional force field and is essential for protein folding. We also prove that the salt bridge interaction between 4-residue apart GLU and LYS residues is not critical to the stability of helical structure of EK peptide, but is merely an auxiliary factor, also in agreement with the experiment.
MEI YeZHANG DaWeiDUAN LiZHANG QingGangZHANG John ZengHui
Potential of mean force (PMF) with respect to localized reaction coordinates (RCs) such as distance is often applied to evaluate the free energy profile along the reaction pathway for complex molecular systems.However,calculation of PMF as a function of global RCs is still a challenging and important problem in computational biology.We examine the combined use of the weighted histogram analysis method and the umbrella sampling method for the calculation of PMF as a function of a global RC from the coarse-grained Langevin dynamics simulations for a model protein.The method yields the folding free energy profile projected onto a global RC,which is in accord with benchmark results.With this method rare global events would be sufficiently sampled because the biased potential can be used for restricting the global conformation to specific regions during free energy calculations.The strategy presented can also be utilized in calculating the global intra- and intermolecular PMF at more detailed levels.
The binding of Endonuclease colicin 9 (E9) by Immunity protein 9 (Im9) was found to involve some hotspots from helix III of Im9 on protein-protein interface that contribute the dominant binding energy to the complex.In the current work,MD simulations of the WT and three hotspot mutants (D51A,Y54A and Y55A of Im9) of the E9-Im9 complexes were carried out to investigate specific interaction mechanisms of these three hotspot residues.The changes of binding energy between the WT and mutants of the complex were computed by the MM/PBSA method using a polarized force field and were in excellent agreement with experiment values,verifying that these three residues were indeed hotspots of the binding complex.Energy decomposition analysis revealed that binding by D51 to E9 was dominated by electrostatic interaction due to the presence of the carboxyl group of Asp51 which hydrogen bonds to K89.For binding by hotspots Y54 and Y55,van der Waals interaction from the aromatic side chain of tyrosine provided the dominant interaction.For comparison,calculation by using the standard (nonpolarizable) AMBER99SB force field produced binding energy changes from these mutations in opposite direction to the experimental observation.Dynamic hydrogen bond analysis showed that conformations sampled from MD simulation in the standard AMBER force field were distorted from the native state and they disrupted the inter-protein hydrogen bond network of the protein-protein complex.The current work further demonstrated that electrostatic polarization plays a critical role in modulating protein-protein binding.
