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Daniel J Price

Publications and source records attributed to Daniel J Price.

14 recordsLinked to original sources
PubMed2006

Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.

A detailed understanding of the mechanisms by which particular amino acid sequences can give rise to more than one folded structure, such as for proteins that undergo large conformational changes or misfolding, is a long-standing objective of protein chemistry. Here, we describe the crystal structures of a single coiled-coil peptide in distinct parallel and antiparallel tetrameric configurations and further describe the parallel or antiparallel crystal structures of several related peptide sequences; the antiparallel tetrameric assemblies represent the first crystal structures of GCN4-derived peptides exhibiting such a configuration. Intriguingly, substitution of a single solvent-exposed residue enabled the parallel coiled-coil tetramer GCN4-pLI to populate the antiparallel configuration, suggesting that the two configurations are close enough in energy for subtle sequence changes to have important structural consequences. We present a structural analysis of the small changes to the helix register and side-chain conformations that accommodate the two configurations and have supplemented these results using solution studies and a molecular dynamics energetic analysis using a replica exchange methodology. Considering the previous examples of structural nonspecificity in coiled-coil peptides, the findings reported here not only emphasize the predisposition of the coiled-coil motif to adopt multiple configurations but also call attention to the associated risk that observed crytstal structures may not represent the only (or even the major) species present in solution.

Amino Acid Sequence↗
PubMed2005

Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA.

Modern classical force fields have been traditionally parameterized by attempting to maximize agreement to any number of experimental and/or quantum mechanical target properties. As these force fields are pushed towards obtaining quantitative estimates of often subtle energetic differences, stringent and consistent parameterization criteria, particularly in regard to charge distributions, are required to ensure that systematic errors cancel, that parameters are transferable between molecules, and that performance does not significantly deteriorate when using more approximate methods, such as with continuum solvent models. Relative free energies of hydration are presented here for 40 mono- and disubstituted benzenes modeled with the OPLS-AA force field; heats of vaporization and pure liquid densities at standard conditions are presented when experimental data is available. Overall agreement between OPLS-AA and experiment is remarkable (average error = 0.5 kcal/mol for DeltaDeltaG(hydration), 1.0 kcal/mol for DeltaH(vap) (0), 0.02 g/mL for densities), yet several functional groups are identified as having consistent and correctable errors (alkyl-, nitro-, and thiobenzenes). Relative free energies of hydration obtained with rigorous free energy perturbations using explicit solvent are also compared with energies from minimizations using a generalized Born model (GB). There is high correlation between these estimates (R = 0.99), and as demonstrated here, reparameterization of the aforementioned groups can be guided with rapid GB calculations.

Algorithms↗
PubMed2005

Receptor rigidity and ligand mobility in trypsin-ligand complexes.

The trypsin-like serine proteases comprise a structurally similar family of proteins with a wide diversity of biological functions. Members of this family play roles in digestion, hemostasis, immune responses, and cancer metastasis. Bovine trypsin is an archetypical member of this family that has been extensively characterized both functionally and structurally, and that preferentially hydrolyzes Arg/Lys-Xaa peptide bonds. We have used molecular dynamics (MD) simulations to study bovine trypsin complexed with the two noncovalent small-molecule ligands, benzamidine and tranylcypromine, that have the same hydrogen-bond donating moieties as Arg and Lys side-chains, respectively. Multiple (10) simulations ranging from 1 ns to 2.2 ns, with explicit water molecules and periodic boundary conditions, were performed. The simulations reveal that the trypsin binding pocket residues are relatively rigid regardless of whether there is no ligand, a high-affinity ligand (benzamidine), or a low-affinity ligand (tranylcypromine). The thermal average of the conformations sampled by benzamidine bound to trypsin is planar and consistent with the planar internal geometry of the benzamidine crystallographic model coordinates. However, the most probable bound benzamidine conformations are +/-25 degrees out of plane, implying that the observed X-ray electron density represents an average of densities from two mirror symmetric, nonplanar conformations. Solvated benzamidine has free energy minima at +/-45 degrees , and the induction of a more planar geometry upon binding is associated with approximately 1 kcal/mol of intramolecular strain. Tranylcypromine's hydrogen-bonding pattern in the MD differs substantially from that inferred from the X-ray electron density. Early in simulations of this system, tranylcypromine adopts an alternative binding conformation, changing from the crystallographic conformation, with a direct hydrogen bond between its amino moiety and the backbone oxygen of Gly219, to one having a bridging water molecule. This result is consistently seen with the CHARMM22, Amber, or OPLS-AA force fields. The trypsin-tranylcypromine hydrogen-bonding pattern observed in the simulations also occurs as the crystallographic binding mode of the Lys15 side-chain of bovine pancreatic trypsin inhibitor bound to trypsin. In this latter cocrystal, a bridging crystallographic water does reside between the side-chain's amino group and the trypsin Gly219 backbone oxygen. Furthermore, the trypsin-tranylcypromine simulations sample two different stable noncrystallographic binding poses. These data suggest that some of the electron density ascribed to tranylcypromine in the X-ray model is rather due to a bound water molecule, and that multiple tranylcypromine binding conformations (crystallographic disorder) may be the cause of ambiguous electron density. The combined trypsin-benzamidine and trypsin- tranylcypromine results highlight the ability of simulations to augment protein-ligand complex structural data by deconvoluting the effects of thermal and structural averaging, and by finding energetically optimal ligand and bound water positions for weakly bound ligands.

Animals↗
PubMed2004

A modified TIP3P water potential for simulation with Ewald summation.

The charges and Lennard-Jones parameters of the TIP3P water potential have been modified to improve its performance under the common condition for molecular dynamics simulations of using Ewald summation in lieu of relatively short nonbonded truncation schemes. These parameters were optimized under the condition that the hydrogen atoms do not have Lennard-Jones parameters, thus making the model independent of the combining rules used for the calculation of nonbonded, heteroatomic interaction energies, and limiting the number of Lennard-Jones calculations required. Under these conditions, this model provides accurate density (rho = 0.997 g/ml) and heat of vaporization (DeltaH(vap) = 10.53 kcal/mol) at 25 degrees C and 1 atm, but also provides improved structure in the second peak of the O-O radial distribution function and improved values for the dielectric constant (epsilon(0) = 89) and the diffusion coefficient (D = 4.0 x 10(-5) cm(2)/s) relative to the original parametrization. Like the original parameterization, however, this model does not show a temperature density maximum. Several similar models are considered with the additional constraint of trying to match the performance of the optimized potentials for liquid simulation atom force field to that obtained when using the simulation conditions under which it was originally designed, but no model was entirely satisfactory in reproducing the relative difference in free energies of hydration between the model compounds, phenol and benzene. Finally, a model that incorporates a long-range correction for truncated Lennard-Jones interactions is presented, which provides a very accurate dielectric constant (epsilon(0) = 76), however, the improvement in this estimate is on the same order as the uncertainty in the calculation.

Computer Simulation↗
PubMed2004

Synthesis, structure and magnetism of a novel carboxylate bridged manganese(II) sheet structure containing the first unsupported aqua bridge.

The structural characterisation of a 2D sheet complex [[Mn2(Hetheidi)2(mu-H2O)(H2O)].3H2O]n 1 [Hetheidi =DL-N-(1-hydroxymethylpropyl)iminodiacetic acid] assembled from the tetradentate ligand Hetheidi and MnCl2 reveals the presence of rare unsupported mu-aqua bridges and novel hydrogen-bonded water channels, which bind the sheets together.

Journal Article↗
PubMed2004

Role of the aging vasculature and Erb B-2 signaling in epidermal growth factor-dependent intravasion of breast carcinoma cells.

BACKGROUND: The risks for developing breast carcinoma and dying from the disease increase with age. Mortality from breast carcinoma usually is due to metastatic disease. Metastatic cells are able to invade into the vascular tissue in a growth factor-dependent manner. Because breast carcinoma mortality increases with age, examination of breast carcinoma interactions with young and aged endothelial cells is essential. METHODS: We studied a series of breast epithelial cells (HMT-3522 cells) that exhibited either noninvasive characteristics (S-1 cells) or epidermal growth factor (EGF)-dependent invasive characteristics (T4-2 cells). RESULTS: Increased invasion of HMT-3522 cells was observed across an aged rat brain microvascular endothelial cell (BMEC) monolayer that was isolated from aged rats (24 months) compared with young rats (age 1 month). This increased invasion was inhibited by the specific EGF receptor inhibitor, AG1478, and by the Erb B-2-specific inhibitor, AG825. To analyze further the contribution of Erb B-2 to the EGF-dependent invasion of HMT-3522 cells, T4-2 cells were treated with the Erb B-2-specific therapeutic antibody trastuzumab and with the specific inhibitor AG825 and were then assayed for invasion. Both inhibitors led to a significant decrease in EGF-dependent invasion. Erb B-2 expression was found to be elevated in T4-2 cells ( approximately 5-fold higher) compared with S-1 cells. However, treatment of T4-2 cells with the specific Erb B-2 inhibitor, AG825, failed to inhibit EGF-mediated signaling to phosphatidylinositol 3-kinase or extracellular-regulated kinases 1 and 2. CONCLUSIONS: The current study findings indicate that aging of endothelium may contribute to the invasive phenotype of breast carcinoma cells and that "cross-talk" between Erb B-2 and EGF receptor is required for the intravasion of these cells into the surrounding vasculature.

Age Factors↗
PubMed2004

Assessing scoring functions for protein-ligand interactions.

An assessment of nine scoring functions commonly applied in docking using a set of 189 protein-ligand complexes is presented. The scoring functions include the CHARMm potential, the scoring function DrugScore, the scoring function used in AutoDock, the three scoring functions implemented in DOCK, as well as three scoring functions implemented in the CScore module in SYBYL (PMF, Gold, ChemScore). We evaluated the abilities of these scoring functions to recognize near-native configurations among a set of decoys and to rank binding affinities. Binding site decoys were generated by molecular dynamics with restraints. To investigate whether the scoring functions can also be applied for binding site detection, decoys on the protein surface were generated. The influence of the assignment of protonation states was probed by either assigning "standard" protonation states to binding site residues or adjusting protonation states according to experimental evidence. The role of solvation models in conjunction with CHARMm was explored in detail. These include a distance-dependent dielectric function, a generalized Born model, and the Poisson equation. We evaluated the effect of using a rigid receptor on the outcome of docking by generating all-pairs decoys ("cross-decoys") for six trypsin and seven HIV-1 protease complexes. The scoring functions perform well to discriminate near-native from misdocked conformations, with CHARMm, DOCK-energy, DrugScore, ChemScore, and AutoDock yielding recognition rates of around 80%. Significant degradation in performance is observed in going from decoy to cross-decoy recognition for CHARMm in the case of HIV-1 protease, whereas DrugScore and ChemScore, as well as CHARMm in the case of trypsin, show only small deterioration. In contrast, the prediction of binding affinities remains problematic for all of the scoring functions. ChemScore gives the highest correlation value with R(2) = 0.51 for the set of 189 complexes and R(2) = 0.43 for the set of 116 complexes that does not contain any of the complexes used to calibrate this scoring function. Neither a more accurate treatment of solvation nor a more sophisticated charge model for zinc improves the quality of the results. Improved modeling of the protonation states, however, leads to a better prediction of binding affinities in the case of the generalized Born and the Poisson continuum models used in conjunction with the CHARMm force field.

Binding Sites↗
PubMed2003

A hybrid metalloarsenate 3D framework-1D interrupted metal oxide.

Complex metal arsenates of the stoichiometry M(1)(-)(x)()M'(6)(OH)(3)(AsO(4)H(2)(x)()(/3))(3)(HAsO(4)), M = M' = Co, Ni, have been synthesized under hydrothermal conditions. The two compounds display a very similar structural topology to that of the mineral dumortierite, an uncommon complex oxyborosilicate of aluminum. The hybrid structures consist of well separated, vacancy interrupted chains of face sharing MO(6) octahedra, with short M.M distances near 2.5 A, embedded in a metalloarsenate 3D framework having the topology of the aluminosilicate cancrinite. The framework also contains a quadruply bridging hydroxide ion. Magnetic susceptibility measurements reveal a strong antiferromagnetic interaction and magnetic transition to low temperature spin canted phases below 51 K (Co) and 42 K (Ni). The material may be considered as a zeotype framework structure templated by an interrupted one-dimensional metal oxide.

Journal Article↗
PubMed2002

Modern protein force fields behave comparably in molecular dynamics simulations.

Several molecular dynamics simulations were performed on three proteins--bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and domain IIA of bacillus subtilis glucose permease--with each of the AMBER94, CHARMM22, and OPLS-AA force fields as implemented in CHARMM. Structural and dynamic properties such as solvent-accessible surface area, radius of gyration, deviation from their respective experimental structures, secondary structure, and backbone order parameters are obtained from each of the 2-ns simulations for the purpose of comparing the protein portions of these force fields. For one of the proteins, the interleukin-4 mutant, two independent simulations were performed using the CHARMM22 force field to gauge the sensitivity of some of these properties to the specific trajectory. In general, the force fields tested performed remarkably similarly with differences on the order of those found for the two independent trajectories of interleukin-4 with CHARMM22. When all three proteins are considered together, no force field showed any consistent trend in variations for most of the properties monitored in the study.

Animals↗
PubMedDate not supplied

The invasive phenotype in HMT-3522 cells requires increased EGF receptor signaling through both PI 3-kinase and ERK 1,2 pathways.

We studied the invasion of HMT-3522 breast epithelial cells in response to epidermal growth factor (EGF), and the associated signaling pathways. HMT-3522 T4-2 cells were shown to invade Matrigel-coated Transwell membranes in response to EGF while HMT-3522 S-1 cells failed to invade when treated with EGF. Studies utilizing specific molecular inhibitors showed the importance of beta1 integrin, phosphatidylinositol 3 kinase (PI 3-kinase), p38, extracellular regulated kinase 1, 2 (Erk 1,2) MAP kinases, and metalloproteinases in invasion and motility. T4-2 cell invasion was shown to be time-dependent and also gene transcription-dependent as shown by inhibition with Actinomycin D. T4-2 cells exhibited an increased activation of MAP kinases Erk 1,2 (2-fold), EGF receptor (3-fold), and PI 3-kinase (3- to 4-fold) when compared to the S-1 cells. In response to EGF, T4-2 cells showed a 5-fold greater secretion of matrix metalloproteinase-9 (MMP-9) as compared to S-1 cells, and this increase was largely dependent on the activity of PI 3-kinase. These findings indicate that expression of the invasive phenotype in these breast epithelial cells requires increased EGF receptor signaling, involving both PI 3-kinase and Erk 1,2 activities, which leads to multiple downstream effects, including enhanced secretion of MMP-9 and transcription of invasion-related genes.

Breast↗