Generalized Born Implicit Solvent Model Research Articles

Molecular dynamics study of chemically engineered green fluorescent protein mutants: Comparison of intramolecular fluorescence resonance energy transfer rate

Because of its unusual spectroscopic properties, green fluorescent protein (GFP) has become a useful tool in molecular genetics, biochemistry and cell biology. Here, we computationally characterize the behavior of two GFP constructs, designed as bioprobes for enzymatic triggering using intramolecular fluorescence resonance energy transfer (FRET). These constructs differ in the location of an intramolecular FRET partner, an attached chemical chromophore (either near an N-terminal or C-terminal site). We apply the temperature replica exchange molecular dynamics method to the two flexible constructs in conjunction with a generalized Born implicit solvent model. The calculated rate of FRET was derived from the interchromophore distance, R, and orientational factor, kappa(2). In agreement with experiment, the construct with the C-terminally attached dye was predicted to have higher energy transfer rate than observed for the N-terminal construct. The molecular basis for this observation is discussed. In addition, we find that the orientational factor, kappa(2), deviates from the commonly assumed value, the implications of which are also considered.

Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility

We present a Monte Carlo sidechain sampling procedure and apply it to assessing the flexibility of protein binding pockets. We implemented a multiple "time step" Monte Carlo algorithm to optimize sidechain sampling with a surface generalized Born implicit solvent model. In this approach, certain forces (those due to long-range electrostatics and the implicit solvent model) are updated infrequently, in "outer steps", while short-range forces (covalent, local nonbonded interactions) are updated at every "inner step". Two multistep protocols were studied. The first protocol rigorously obeys detailed balance, and the second protocol introduces an approximation to the solvation term that increases the acceptance ratio. The first protocol gives a 10-fold improvement over a protocol that does not use multiple time steps, while the second protocol generates comparable ensembles and gives a 15-fold improvement. A range of 50-200 inner steps per outer step was found to give optimal performance for both protocols. The resultant method is a practical means to assess sidechain flexibility in ligand binding pockets, as we illustrate with proof-of-principle calculations on six proteins: DB3 antibody, thermolysin, estrogen receptor, PPAR-γ, PI3 kinase, and CDK2. The resulting sidechain ensembles of the apo binding sites correlate well with known induced fit conformational changes and provide insights into binding pocket flexibility.

Stochastic Pairwise Alignments and Scoring Methods for Comparative Protein Structure Modeling

Despite recent advances in fold recognition algorithms that identify template structures with distant homology to the target sequence, the quality of the target-template alignment can be a major problem for distantly related proteins in comparative modeling. Here we report for the first time on the use of ensembles of pairwise alignments obtained by stochastic backtracking as a means to improve three-dimensional comparative protein models. In every one of the 35 cases, the ensemble produced by the program probA resulted in alignments that were closer to the structural alignment than those obtained from the optimal alignment. In addition, we examined the lowest energy structure among these ensembles from four different structural assessment methods and compared these with the optimal and structural alignment model. The structural assessment methods consisted of the DFIRE, DOPE, and ProsaII statistical potential energies and the potential energy from the CHARMM protein force field coupled to a Generalized Born implicit solvent model. The results demonstrate that the generation of alignment ensembles through stochastic backtracking using probA combined with one of the statistical potentials for assessing three-dimensional structures can be used to improve comparative models.

Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes.

We optimize a truncated Newton (TN) minimization algorithm and computer package, TNPACK, developed for macromolecular minimizations by applying multiscale methods, analogous to those used in molecular dynamics (e.g., r-RESPA). The molecular mechanics forces are divided into short- and long-range components, with the long-range forces updated only intermittently in the iterative evaluations. This algorithm, which we refer to as MSTN, is implemented as a modification to the TNPACK package and is tested on energy minimizations of protein loops, entire proteins, and protein-ligand complexes and compared with the unmodified truncated Newton algorithm, a quasi-Newton algorithm (LBFGS), and a conjugate gradient algorithm (CG+). In vacuum minimizations, the speedup of MSTN relative to the unmodified TN algorithm (TNPACK) depends on system size and the distance cutoffs used for defining the short- and long-range interactions and the long-range force updating frequency, but it is 4 to 5 times greater in the work reported here. This algorithm works best for the minimization of small portions of a protein and shows some degradation (speedup factor of 2-3) for the minimization of entire proteins. The MSTN algorithm is faster than the quasi-Newton and conjugate gradient algorithms by approximately 1 order of magnitude. We also present a modification of the algorithm which permits minimizations with a generalized Born implicit solvent model, using a self-consistent procedure that increases the computational expense, relative to a vacuum, by only a small factor (∼3-4).

Toward the Accurate First-Principles Prediction of Ionization Equilibria in Proteins

The calculation of pK(a) values for ionizable sites in proteins has been traditionally based on numerical solutions of the Poisson-Boltzmann equation carried out using a high-resolution protein structure. In this paper, we present a method based on continuous constant pH molecular dynamics (CPHMD) simulations, which allows the first-principles description of protein ionization equilibria. Our method utilizes an improved generalized Born implicit solvent model with an approximate Debye-Hückel screening function to account for salt effects and the replica-exchange (REX) protocol for enhanced conformational and protonation state sampling. The accuracy and robustness of the present method are demonstrated by 1 ns REX-CPHMD titration simulations of 10 proteins, which exhibit anomalously large pK(a) shifts for the carboxylate and histidine side chains. The experimental pK(a) values of these proteins are reliably reproduced with a root-mean-square error ranging from 0.6 unit for proteins containing few buried ionizable side chains to 1.0 unit or slightly higher for proteins containing ionizable side chains deeply buried in the core and experiencing strong charge-charge interactions. This unprecedented level of agreement with experimental benchmarks for the de novo calculation of pK(a) values suggests that the CPHMD method is maturing into a practical tool for the quantitative prediction of protein ionization equilibria, and this, in turn, opens a door to atomistic simulations of a wide variety of pH-coupled conformational phenomena in biological macromolecules such as protein folding or misfolding, aggregation, ligand binding, membrane interaction, and catalysis.

Limitations of Atom-Centered Dielectric Functions in Implicit Solvent Models

Many recent advances in Poisson-Boltzmann and generalized Born implicit solvent models have used atom-centered polynomial or Gaussian functions to define the boundary separating low and high dielectric regions. In contrast to the Lee and Richards molecular surface, atom-centered surfaces result in interatomic crevices and buried pockets of high dielectric which are too small for a solvent molecule to occupy. We show that these interstitial high dielectric regions are of significant magnitude in globular proteins, that they artificially increase solvation energies, and that they distort the free energy surface of nonbonded interactions. These results suggest that implicit solvent dielectric functions must exclude interstitial high dielectric regions in order to yield physically meaningful results.

Competition between Intramolecular Hydrogen Bonds and Solvation in Phosphorylated Peptides: Simulations with Explicit and Implicit Solvent

The atomic-level mechanisms of protein regulation by post-translational phosphorylation remain poorly understood, except in a few well-studied systems. Molecular mechanics simulations can in principle be used to help understand and predict the effects of protein phosphorylation, but the accuracy of the results will of course depend on the quality of the force field parameters for the phosphorylated residues as well as the quality of the solvent model. The phosphorylated residues typically carry a -2 charge at physiological pH; however, the effects of phosphorylation can sometimes be mimicked by substituting Asp or Glu for the phosphorylated residue. Here we examine the suitability of explicit and implicit solvent models for simulating phospho-serine in both the -1 and -2 charge states. Specifically, we simulate a capped phosphorylated peptide, Ace-Gly-Ser-pSer-Ser-Nme, and compare the results to each other and to experimental observables from an NMR experiment. The first major conclusion is that explicit water models (TIP3P, TIP4P and SPC/E) and a Generalized Born implicit solvent model provide reasonable agreement with the experimental observables, given appropriate partial charges for the phosphate group. The Generalized Born results, however, show greater hydrogen bonding propensity than the explicit solvent results. Distance dependent dielectric treatments perform poorly. The second major conclusion is that many ensemble-averaged properties obtained for the phosphopeptide in the -1 and -2 charge states are strikingly similar; the -1 species has a slightly higher propensity to form internal hydrogen bonds. All of the results can be rationalized by quantifying the strength of the P-O/H-N hydrogen bond, which depends on a sensitive balance between strongly favorable charge/dipole and dipole/dipole interactions and strongly unfavorable desolvation.

Virtual Screening against Highly Charged Active Sites: Identifying Substrates of Alpha−Beta Barrel Enzymes

We have developed a virtual ligand screening method designed to help assign enzymatic function for alpha-beta barrel proteins. We dock a library of approximately 19,000 known metabolites against the active site and attempt to identify the relevant substrate based on predicted relative binding free energies. These energies are computed using a physics-based energy function based on an all-atom force field (OPLS-AA) and a generalized Born implicit solvent model. We evaluate the ability of this method to identify the known substrates of several members of the enolase superfamily of enzymes, including both holo and apo structures (11 total). The active sites of these enzymes contain numerous charged groups (lysines, carboxylates, histidines, and one or more metal ions) and thus provide a challenge for most docking scoring functions, which treat electrostatics and solvation in a highly approximate manner. Using the physics-based scoring procedure, the known substrate is ranked within the top 6% of the database in all cases, and in 8 of 11 cases, it is ranked within the top 1%. Moreover, the top-ranked ligands are strongly enriched in compounds with high chemical similarity to the substrate (e.g., different substitution patterns on a similar scaffold). These results suggest that our method can be used, in conjunction with other information including genomic context and known metabolic pathways, to suggest possible substrates or classes of substrates for experimental testing. More broadly, the physics-based scoring method performs well on highly charged binding sites and is likely to be useful in inhibitor docking against polar binding sites as well. The method is fast (<1 min per ligand), due largely to an efficient minimization algorithm based on the truncated Newton method, and thus, it can be applied to thousands of ligands within a few hours on a small Linux cluster.

Solvent models for protein–ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations

AbstractSolvent effects play a crucial role in mediating the interactions between proteins and their ligands. Implicit solvent models offer some advantages for modeling these interactions, but they have not been parameterized on such complex problems, and therefore, it is not clear how reliable they are. We have studied the binding of an octapeptide ligand to the murine MHC class I protein using both explicit solvent and implicit solvent models. The solvation free energy calculations are more than 103 faster using the Surface Generalized Born implicit solvent model compared to FEP simulations with explicit solvent. For some of the electrostatic calculations needed to estimate the binding free energy, there is near quantitative agreement between the explicit and implicit solvent model results; overall, the qualitative trends in the binding predicted by the explicit solvent FEP simulations are reproduced by the implicit solvent model. With an appropriate choice of reference system based on the binding of the discharged ligand, electrostatic interactions are found to enhance the binding affinity because the favorable Coulomb interaction energy between the ligand and protein more than compensates for the unfavorable free energy cost of partially desolvating the ligand upon binding. Some of the effects of protein flexibility and thermal motions on charging the peptide in the solvated complex are also considered. © 2001 John Wiley &amp; Sons, Inc. J Comput Chem 22: 591–607, 2001