Consistent Surgeon Evaluations of Three-Dimensional Rendering of PET/CT Scans of the Abdomen of a Patient with a Ductal Pancreatic Mass.

Two-dimensional (2D) positron emission tomography (PET) and computed tomography (CT) are used for diagnosis and evaluation of cancer patients, requiring surgeons to look through multiple planar images to comprehend the tumor and surrounding tissues. We hypothesized that experienced surgeons would consistently evaluate three-dimensional (3D) presentation of CT images overlaid with PET images when preparing for a procedure. We recruited six Jefferson surgeons to evaluate the accuracy, usefulness, and applicability of 3D renderings of the organs surrounding a malignant pancreas prior to surgery. PET/CT and contrast-enhanced CT abdominal scans of a patient with a ductal pancreatic mass were segmented into 3D surface renderings, followed by co-registration. Version A used only the PET/CT image, while version B used the contrast-enhanced CT scans co-registered with the PET images. The six surgeons answered 15 questions covering a) the ease of use and accuracy of models, b) how these models, with/without PET, changed their understanding of the tumor, and c) what are the best applications of the 3D visualization, on a scale of 1 to 5. The six evaluations revealed a statistically significant improvement from version A (score 3.6±0.5) to version B (score 4.4±0.4). A paired-samples t-test yielded t(14) = -8.964,

Potential Energy Surfaces for Intermolecular Proton Transfers in Crystalline Aspirin: A Computational Study

Ab initio molecular orbital methods and density functional theory were used to model the potential energy surface of intermolecular proton transfers in crystalline aspirin. Using these surfaces the importance of intermolecular interactions and excited states to the proton transfer were also explored. In addition, the ability of ab initio molecular orbital methods and density functional theory to model such a system was examined. First an aspirin homodimer was modeled with various basis sets and levels of theory to develop an efficient theoretical model to use in modeling the proton transfer in a larger crystal model. Both ab initio molecular orbital models and density functional theory using small basis sets were found to be suitable for modeling the homodimer. Second, a C++ program was created to build a model crystal fragment of aspirin from the experimental crystallographic data. Next, this fragment model was used with the chosen theoretical model to compute a potential energy surface of the proton transfer. Using this potential energy surface, reaction coordinates for the proton transfer were examined. The ab initio and density functional theory calculations both displayed a double well potential, but followed two different pathways: ab initio following a pair of symmetrical pathways while density functional theory followed a single linear pathway between the reactant and product well. The curvature of the two wells were then used to compute the vibrational excited states and their relative populations at different temperatures, as well as to valuate the possibility of tunneling. The likelihood of tunneling in the ground state was found to be insignificant, but in excited vibration levels could contribute to the hydrogen transfer observed in neutron diffraction experiments. Changes in the structure of the crystal at high temperatures could affect the process, however, further work in modeling the transition state are required

Potential Energy Surfaces for Intermolecular Proton Transfers in Crystalline Aspirin: A Computational Study

Ab initio molecular orbital methods and density functional theory were used to model the potential energy surface of intermolecular proton transfers in crystalline aspirin. Using these surfaces the importance of intermolecular interactions and excited states to the proton transfer were also explored. In addition, the ability of ab initio molecular orbital methods and density functional theory to model such a system was examined. First an aspirin homodimer was modeled with various basis sets and levels of theory to develop an efficient theoretical model to use in modeling the proton transfer in a larger crystal model. Both ab initio molecular orbital models and density functional theory using small basis sets were found to be suitable for modeling the homodimer. Second, a C++ program was created to build a model crystal fragment of aspirin from the experimental crystallographic data. Next, this fragment model was used with the chosen theoretical model to compute a potential energy surface of the proton transfer. Using this potential energy surface, reaction coordinates for the proton transfer were examined. The ab initio and density functional theory calculations both displayed a double well potential, but followed two different pathways: ab initio following a pair of symmetrical pathways while density functional theory followed a single linear pathway between the reactant and product well. The curvature of the two wells were then used to compute the vibrational excited states and their relative populations at different temperatures, as well as to valuate the possibility of tunneling. The likelihood of tunneling in the ground state was found to be insignificant, but in excited vibration levels could contribute to the hydrogen transfer observed in neutron diffraction experiments. Changes in the structure of the crystal at high temperatures could affect the process, however, further work in modeling the transition state are required

Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of therapeutics targeting EGF ligands or the receptor itself

Sequence alignment of the EGFR ligands.

<p>a) Shown are the seven ligands used in the computational studies. Sequences of only the EGF like domains of each ligand were used in the alignment. “*” represent 100% conservation while “.” and “:” represent partial sequence conservation.</p

Free energy results from MM-PBSA.

<p>All units are given in kcal/mol. The standard state is taken to be 1 M.</p>*<p>: ΔE^ele: coulombic energy.,</p>**<p>:ΔE^vdw : van der Waals energy.</p>***<p>:ΔG^PB: Poisson-Boltzmann polar solvation energy.</p>****<p>:ΔG^SA :non-polar solvation energy. Standard Errors of corresponding values are given in parentheses.</p

Summary of structures used in MD simulations.

*<p>: Root mean square deviation relative to EGF in 1IVO structure,</p>**<p>: SWISS-MODEL repository code for homology model database <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054136#pone.0054136-Arnold1" target="_blank">[41]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054136#pone.0054136-Kopp1" target="_blank">[42]</a>,</p>***<p>: Murine Epiregulin.</p

Docking poses of EGFR ligands.

<p>Using the EGFR dimer bound to EGF as a starting structure, the remaining six ligands were docked to the binding pocket by alignment to the backbone of EGF (Blue). AR is colored purple, BTC cyan, EPG brown, EPR green, HB-EGF yellow and TGF-α orange.</p

A Conserved arginine in loop 3 is important for EGFR ligand binding a) Arg41 forms a salt bridge in the EGF-EGFR x-ray structures (PDB IDs 1IVO and 3NJP) with Asp355.

<p>The energy decomposition values for Arg41 vary for each ligand. GBSA values are depicted as solid black bars and PBSA values as shaded gray bars.</p