Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007.
Real-world observable physical and chemical characteristics are increasingly being calculated from the 3D structures of biomolecules. Methods for calculating pKa values, binding constants of ligands, changes in protein stability are readily available, but often the limiting step in computational biology is the conversion of PDB structures into formats ready for use with biomolecular simulation software. The continued sophistication and integration of biomolecular simulation methods for systems- and genome-wide studies requires a fast, robust, physically realistic and standardized protocol for preparing macromolecular structures for biophysical algorithms. As described previously, the PDB2PQR web server addresses this need for electrostatic field calculations (Dolinsky et al, NAR, 2004). Here we report the significantly-expanded PDB2PQR that includes the following features: robust standalone command line support, improved pKa estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily-incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code. These features are available through a new web interface (http://pdb2pqr.sourceforge.net/) which offers users a wide range of options for PDB file conversion, modification, and parameterization.
Swanson JMJ, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson dielectric boundary with explicit solvent forces and energies: lessons learned with atom-centered dielectric functions. J Chem Theory Comput, 3, 170-83, 2007.
Accurate implicit solvent models require parameters that have been optimized in a system- and/or atom-specific manner based on experimental data or more rigorous explicit solvent simulations. Models based on the Poisson or Poisson-Boltzmann equation are particularly sensitive to the nature and location of the boundary which separates the low dielectric solute from the high dielectric solvent. Here we present a novel method for optimizing the solute radii, which define the dielectric boundary, based on forces and energies from explicit solvent simulations. We use this method to optimize radii for protein systems defined by AMBER ff99 partial charges and a spline-smoothed solute surface. The spline-smoothed surface is an atom-centered dielectric function that enables stable and efficient force calculations. We explore the relative performance of radii optimized with forces alone and those optimized with forces and energies. We show that our radii reproduce the explicit solvent forces and energies more accurately than four other parameter sets commonly used in conjunction with the AMBER force field, each of which has been appropriately scaled for spline-smoothed surfaces. Finally, we demonstrate that spline-smoothed surfaces show surprising accuracy for small, compact systems, but may have limitations for highly-solvated protein systems. The optimization method presented here is efficient and applicable to any system with explicit solvent parameters. It can be used to determine the optimal continuum parameters when experimental solvation energies are unavailable and the computational costs of explicit solvent charging free energies are prohibitive.
Wong CJ, Rice RL, Baker NA, Ju T, Lohman TM. Probing 3′-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: a model for “Chi” recognition complexes. J Mol Biol, 362, 26-43, 2006.
The equilibrium binding of E. coli RecBC and RecBCD helicases to duplex DNA ends containing varying lengths of polyethylene glycol (PEG) spacers within pre-formed 3′-single-stranded (ss) DNA ((dT)_n) tails were studied. These studies were designed to test a previous proposal that the 3′-(dT)_n tail can be looped out upon binding RecBC and RecBCD for 3′-ssDNA tails with n \geq 6 nucleotides. Equilibrium binding of protein to unlabeled DNA substrates with ends containing PEG-substituted 3′-ssDNA tails was examined by competition with a Cy3-labeled reference DNA which undergoes a Cy3 fluorescence enhancement upon protein binding. We find that the binding affinities of both RecBC and RecBCD for a DNA end are unaffected upon substituting PEG for the ssDNA between the sixth and the final two nucleotides of the 3′-(dT)_n tail. However, placing PEG at the end of the 3′-(dT)_n tail increases the binding affinities to their maximum values (i.e. the same as binding constants for RecBC or RecBCD to a DNA end with only a 3′-(dT)_6 tail). Equilibrium binding studies of a RecBC mutant containing a nuclease domain deletion, RecB^{\Delta nuc}C^1 suggest that looping of the 3′-tail (when n \geq 6 nucleotides) occurs even in the absence of the RecB nuclease domain, the nuclease domain stabilizes such loop formation. Computer modeling of the RecBCD-DNA complexes suggests that the loop in the 3′-ssDNA tail may form at the RecB/RecC interface. Based on these results we suggest a model for how a loop in the 3′-ssDNA tail might form upon encounter of a “Chi” recognition sequence during unwinding of DNA by the RecBCD helicase.
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-7, 2004.
Continuum solvation models, such as Poisson-Boltzmann and Generalized Born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. However, the use of such methods requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment of parameters to biomolecular structures. To address this problem, we have developed the PDB2PQR web service (http://agave.wustl.edu/pdb2pqr/). This server automates many of the common tasks of preparing structures for continuum electrostatics calculations, including adding a limited number of missing heavy atoms to biomolecular structures, estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields, and finally generating PQR output compatible with several popular computational biology packages. This service is intended to facilitate the setup and execution of electrostatics calculations for both experts and non-experts and thereby broaden the accessibility to the biological community of continuum electrostatics analyses of biomolecular systems.
Real-world observable physical and chemical characteristics are increasingly being calculated from the 3D structures of biomolecules. Methods for calculating pKa values, binding constants of ligands, changes in protein stability are readily available, but often the limiting step in computational biology is the conversion of PDB structures into formats ready for use with biomolecular simulation software. The continued sophistication and integration of biomolecular simulation methods for systems- and genome-wide studies requires a fast, robust, physically realistic and standardized protocol for preparing macromolecular structures for biophysical algorithms. As described previously, the PDB2PQR web server addresses this need for electrostatic field calculations (Dolinsky et al, NAR, 2004). Here we report the significantly-expanded PDB2PQR that includes the following features: robust standalone command line support, improved pKa estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily-incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code. These features are available through a new web interface (http://pdb2pqr.sourceforge.net/) which offers users a wide range of options for PDB file conversion, modification, and parameterization.
