Carlos Simmerling

The Amber biomolecular simulation programs.

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

Comparison of multiple Amber force fields and development of improved protein backbone parameters.

The ff94 force field that is commonly associated with the Amber simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over‐stabilization of α‐helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of “Amber” force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in Amber of two sets of backbone φ/ψ dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the φ/ψ dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems. Proteins 2006.

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.

Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data

Force-field validation is essential for the identification of weaknesses in current models and the development of more accurate models of biomolecules. NMR coupling and relaxation methods have been used to effectively diagnose the strengths and weaknesses of many existing force fields. Studies using the ff99SB force field have shown excellent agreement between experimental and calculated order parameters and residual dipolar calculations. However, recent studies have suggested that ff99SB demonstrates poor agreement with J-coupling constants for short polyalanines. We performed extensive replica-exchange molecular-dynamics simulations on Ala(3) and Ala(5) in TIP3P and TIP4P-Ew solvent models. Our results suggest that the performance of ff99SB is among the best of currently available models. In addition, scalar coupling constants derived from simulations in the TIP4P-Ew model show a slight improvement over those obtained using the TIP3P model. Despite the overall excellent agreement, the data suggest areas for possible improvement.

MOIL: A program for simulations of macromolecules

Abstract A package of computer programs for molecular dynamics simulations-MOIL-is described. A flexible data structure enables the study of macromolecules with potentials consistent with the AMBER/OPLS force field. The supplied parameter set has proteins in mind. In addition to ‘wide spread’ applications such as energy, energy minimization, normal modes, dynamics and free energy calculations code is also provided to pursue less common applications. This includes reaction path calculations (in condensed phases), uses of the mean field approach for enhanced sampling (LES-locally enhanced sampling) and calculations of curve crossing using the Landau-Zener model. A brief review of the overall program is provided. A few modules are discussed in considerable detail.

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

The use of parallel tempering or replica exchange molecular dynamics (REMD) simulations has facilitated the exploration of free energy landscapes for complex molecular systems, but application to large systems is hampered by the scaling of the number of required replicas with increasing system size. Use of continuum solvent models reduces system size and replica requirements, but these have been shown to provide poor results in many cases, including overstabilization of ion pairs and secondary structure bias. Hybrid explicit/continuum solvent models can overcome some of these problems through an explicit representation of water molecules in the first solvation shells, but these methods typically require restraints on the solvent molecules and show artifacts in water properties due to the solvation interface. We propose an REMD variant in which the simulations are performed with a fully explicit solvent, but the calculation of exchange probability is carried out using a hybrid model, with the solvation shells calculated on the fly during the fully solvated simulation. The resulting reduction in the perceived system size in the REMD exchange calculation provides a dramatic decrease in the computational cost of REMD, while maintaining a very good agreement with results obtained from the standard explicit solvent REMD. We applied several standard and hybrid REMD methods with different solvent models to alanine polymers of 1, 3, and 10 residues, obtaining ensembles that were essentially independent of the initial conformation, even with explicit solvation. Use of only a continuum model without a shell of explicit water provided poor results for Ala3 and Ala10, with a significant bias in favor of the α-helix. Likewise, using only the solvation shells and no continuum model resulted in ensembles that differed significantly from the standard explicit solvent data. Ensembles obtained from hybrid REMD are in very close agreement with explicit solvent data, predominantly populating polyproline II conformations. Inclusion of a second shell of explicit solvent was found to be unnecessary for these peptides.

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model

Potentials of mean force (PMFs) of salt bridge formation between oppositely charged amino acid side chains were calculated both in explicit solvent and in a Generalized Born (GB) continuum solvent model to quantify the potential overstabilization of side chain ion pairs in GB relative to explicit solvation. These show that salt bridges are too stable by as much as 3-4 kcal/mol in the GB solvent models that we tested, consistent with previously reported observations of significantly different structural ensembles in GB models and explicit solvent for proteins containing ionizable groups. We thus investigated a simple empirical correction, wherein the intrinsic GB radii of hydrogen atoms bound to charged nitrogen atoms are reduced, effectively increasing the desolvation penalty of the positively charged groups. The thermodynamics of salt bridge formation were considerably improved, as exemplified by the close match of the corrected GB PMF to the reference explicit solvent PMF, and more significantly by our ability to closely reproduce the experimental temperature melting profile of the TC5b Trp-cage miniprotein, which is otherwise highly distorted by prevalent non-native salt bridges when using standard GB parameters.

Structure of Acyl Carrier Protein Bound to FabI, the FASII Enoyl Reductase from Escherichia coli

Acyl carrier proteins play a central role in metabolism by transporting substrates in a wide variety of pathways including the biosynthesis of fatty acids and polyketides. However, despite their importance, there is a paucity of direct structural information concerning the interaction of ACPs with enzymes in these pathways. Here we report the structure of an acyl-ACP substrate bound to the Escherichia coli fatty acid biosynthesis enoyl reductase enzyme (FabI), based on a combination of x-ray crystallography and molecular dynamics simulation. The structural data are in agreement with kinetic studies on wild-type and mutant FabIs, and reveal that the complex is primarily stabilized by interactions between acidic residues in the ACP helix α2 and a patch of basic residues adjacent to the FabI substrate-binding loop. Unexpectedly, the acyl-pantetheine thioester carbonyl is not hydrogen-bonded to Tyr156, a conserved component of the short chain alcohol dehydrogenase/reductase superfamily active site triad. FabI is a proven target for drug discovery and the present structure provides insight into the molecular determinants that regulate the interaction of ACPs with target proteins.

Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent.

The millisecond time scale needed for molecular dynamics simulations to approach the quantitative study of protein folding is not yet routine. One approach to extend the simulation time scale is to perform long simulations on specialized and expensive supercomputers such as Anton. Ideally, however, folding simulations would be more economical while retaining reasonable accuracy, and provide feedback on structure, stability and function rapidly enough if partnered directly with experiment. Approaches to this problem typically involve varied compromises between accuracy, precision, and cost; the goal here is to address whether simple implicit solvent models have become sufficiently accurate for their weaknesses to be offset by their ability to rapidly provide much more precise conformational data as compared to explicit solvent. We demonstrate that our recently developed physics-based model performs well on this challenge, enabling accurate all-atom simulated folding for 16 of 17 proteins with a variety of sizes, secondary structure, and topologies. The simulations were carried out using the Amber software on inexpensive GPUs, providing ∼1 μs/day per GPU, and >2.5 ms data presented here. We also show that native conformations are preferred over misfolded structures for 14 of the 17 proteins. For the other 3, misfolded structures are thermodynamically preferred, suggesting opportunities for further improvement.

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins

The transferability of molecular mechanics parameters derived for small model systems to larger biopolymers such as proteins can be difficult to assess. Even for small peptides, molecular dynamics simulations are typically too short to sample structures significantly different than initial conformations, making comparison to experimental data questionable. We employed a PC cluster to generate large numbers of native and non‐native conformations for peptides with experimentally measured structural data, one predominantly helical and the other forming a β‐hairpin. These atomic‐detail sets do not suffer from slow convergence, and can be used to rapidly evaluate important force field properties. In this case a suspected bias toward α‐helical conformations in the ff94 and ff99 force fields distributed with the AMBER package was verified. The sets provide critical feedback not only on force field transferability, but may also predict modifications for improvement. Such predictions were used to modify the ff99 parameter set, and the resulting force field was used to test stability and folding of model peptides. Structural behavior during molecular dynamics with the modified force field is found to be very similar to expectations, suggesting that these basis sets of conformations may themselves have significant transferability among force fields. We continue to improve and expand this data set and plan to make it publicly accessible. The calculations involved in this process are trivially parallel and can be performed using inexpensive personal computers with commodity components.