AMBER99SB Force Field Research Articles

Protonation/deprotonation Effects on the Stability of Trp-cage Miniprotein

The effect on the folding/unfolding equilibrium of protonating the aspartic acid on the Trp-cage miniprotein is studied by explicit solvent moleclular dynamics simulations. Replica exchange molecular dynamics (REMD) simulations spanning the temperature range from 280K to 538K were carried out to the micro second scale using the AMBER99SB forcefield in explicit TIP3P water. The root mean square distance from the backbone of the NMR structure shows two highly populated basins close to the native state with peaks at 0.6 A and 1.6 A which are consistent with previous simulations using the same forcefield. The fraction of folded replicas shows a drastic decrease because of the breaking of the salt bridge. However, significant populations of conformations with the arginine sidechain completely exposed to the solvent, but within the folded basin. This shows the possibility to reach the folded state without formation of the ion pair contrary to the expected.

Energy Landscape of the Trpzip2 Peptide

Replica exchange simulations are used to study the energy landscape of trpzip2, a model beta-hairpin system, using the AMBER99sb force field and explicit solvent. The total simulation time is 300 ns per replica (approximately 10 mus total). The trp side chains are observed to adopt multiple packing arrangements with a freezing temperature below 273 K in the simulated system. The secondary structure and native hydrogen bonds melt out cooperatively around 273 K. The residual beta-strand structure and antiparallel bonding persist at high temperature. These results provide a model for the three apparent melting transitions observed experimentally in this system. The dominant folding mechanism of trpzip2 in this model appears to be zipping, which is consistent with recent measurements on similar hairpins. Structures for which the turn is native-like and the termini are non-native-like collectively form a metastable intermediate. Most of the stabilizing enthalpy is gained after the formation of the turn. Equilibrium thermodynamic quantities are compared against experiment. Although the AMBER99sb force field reproduces the native structure with good fidelity, the stability of the native state is significantly underpredicted with a melting temperature near 273 K, and the relative heat capacity is only about one tenth of its experimental value.

Quantitative Molecular Ensemble Interpretation of NMR Dipolar Couplings without Restraints

At room temperature, proteins undergo dynamic excursions away from their average three-dimensional structure. Ensembles obeying the laws of statistical thermodynamics that describe these excursions well are essential for understanding their influence on function. Here we report an unrestrained molecular dynamics ensemble of ubiquitin using the recently refined AMBER99SB force field, which reproduces experimental residual dipolar couplings in multiple alignment media, on the ensemble level, comparable to or better than high resolution averaged structures.

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field.

Biological function of biomolecules is accompanied by a wide range of motional behavior. Accurate modeling of dynamics by molecular dynamics (MD) computer simulations is therefore a useful approach toward the understanding of biomolecular function. NMR spin relaxation measurements provide rigorous benchmarks for assessing important aspects of MD simulations, such as the amount and time scales of conformational space sampling, which are intimately related to the underlying molecular mechanics force field. Until recently, most simulations produced trajectories that exhibited too much dynamics particularly in flexible loop regions. Recent modifications made to the backbone φ and ψ torsion angle potentials of the AMBER and CHARMM force fields indicate that these changes produce more realistic molecular dynamics behavior. To assess the consequences of these changes, we performed a series of 5-20 ns molecular dynamics trajectories of human ubiquitin using the AMBER99 and AMBER99SB force fields for different conditions and water models and compare the results with NMR experimental backbone N-H S(2) order parameters. A quantitative analysis of the trajectories shows significantly improved agreement with experimental NMR data for the AMBER99SB force field as compared to AMBER99. Because NMR spin relaxation data (T1, T2, NOE) reflect the combined effects of spatial and temporal fluctuations of bond vectors, it is found that comparison of experimental and back-calculated NMR spin-relaxation data provides a more objective way of assessing the quality of the trajectory than order parameters alone. Analysis of a key mobile β-hairpin in ubiquitin demonstrates that the dynamics of mobile sites are not only reduced by the modified force field, but the extent of motional correlations between amino acids is also markedly diminished.