Biomedical subjects

William A Goddard

Publications and source records attributed to William A Goddard.

At least 19 recordsLinked to original sources

PubMed2025

A hypoxia-responsive tRNA-derived small RNA confers renal protection through RNA autophagy.

Transfer RNA-derived small RNAs (tsRNAs or tDRs) perform a range of cellular functions. Here, we showed that tRNA-Asp-GTC-3'tDR, a hypoxia-induced tDR derived from the 3' end of tRNA-Asp-GTC, activated autophagic flux in kidney cells and its silencing blocked autophagic flux. Functional gain-/loss-of-function studies in murine kidney disease models demonstrated a substantial renoprotective function of tRNA-Asp-GTC-3'tDR. Mechanistically, tRNA-Asp-GTC-3'tDR assembled stable G-quadruplex structures and sequestered pseudouridine synthase 7 (PUS7), preventing catalytic pseudouridylation of histone mRNAs. The resulting pseudouridylation deficiency directed histone mRNAs to the autophagosome-lysosome pathway, triggering RNA autophagy. This tDR-induced RNA autophagy pathway was activated during murine and human kidney diseases, suggesting clinical relevance. Thus, tRNA-Asp-GTC-3'tDR plays a role in regulating RNA autophagy, which helps to maintain homeostasis in kidney cells and protects against kidney injury.

Animals↗

PubMed2006

Solvent quality changes the structure of G8 PAMAM dendrimer, a disagreement with some experimental interpretations.

We have performed approximately 20-40 ns of molecular dynamics (MD) simulations for the generation 8 PAMAM dendrimer in explicit water under varying pH conditions to study the structure of the dendrimer (approximately 156,738 atoms at low pH). This is the first report of such a long MD simulation of a larger generation PAMAM dendrimer including the effect of salt and counterions with explicit water molecules. We find that changing the pH from a high value (approximately 12) to a low value (approximately 3) changes the radius of gyration from Rg = 37.8 to 43.1 A (increasing by 13%). We also find significant back-folding of the primary amines and a large amount of water penetration inside the polymer. The increase in size with decrease in pH is consistent with our earlier studies on G3-G6 and agrees with the Monte Carlo theory by Welch and Muthukumar of G8 (Macromolecules, 1998, 31, 5892) and the experiments on G5 and G8 PAMAM dendrimer by Topp et al. (Macromolecules, 1999, 32, 7232). However, these results disagree dramatically with the interpretations of SANS experiments of G8 PAMAM dendrimers by Nisato et al. (Macromolecules, 2000, 33, 4172) who observe no change in the size of the dendrimer with variations of solution pH and ionic strength. We assume that the disagreement might arise from neglecting nonspherical shape, penetration of water and ions into the core, and aggregation, all of which might depend on pH.

Journal Article↗

PubMed2006

Scanning tunneling microscopy of ethylated Si(111) surfaces prepared by a chlorination/alkylation process.

Scanning tunneling microscopy (STM) and computational modeling have been used to study the structure of ethyl-terminated Si(111) surfaces. The ethyl-terminated surface was prepared by treating the H-terminated Si(111) surface with PCl5 to form a Cl-terminated Si(111) surface with subsequent exposure to C(2)H(5)MgCl in tetrahydrofuran to produce an alkylated Si(111) surface. The STM data at 77 K revealed local, close-packed, and relatively ordered regions with a nearest-neighbor spacing of 0.38 nm as well as disordered regions. The average spot density corresponded to approximately 85% of the density of Si atop sites on an unreconstructed Si(111) surface. Molecular dynamics simulations of a Si(111) surface randomly populated with ethyl groups to a total coverage of approximately 80% confirmed that the ethyl-terminated Si(111) surface, in theory, can assume reasonable packing arrangements to accommodate such a high surface coverage, which could be produced by an exoergic surface functionalization route such as the two-step chlorination/alkylation process. Hence, it is possible to consistently interpret the STM data within a model suggested by recent X-ray photoelectron spectroscopic data and infrared absorption data, which indicate that the two-step halogenation/alkylation method can provide a relatively high coverage of ethyl groups on Si(111) surfaces.

Journal Article↗

PubMed2006

Mechanism of direct molecular oxygen insertion in a palladium(II)-hydride bond.

The mechanism of the direct insertion of molecular oxygen into a palladium hydride bond has been elucidated using quantum mechanics (B3LYP/LACVP** with the PBF continuum solvent model). The key step is found to be the abstraction of the hydrogen atom resulting in the formation of a PdI/HO2 (triplet) radical pair, which then proceeds to form a singlet palladium hydroperoxo species. Potential palladium(0) pathways were explored and were found to be inaccessible. The results are in agreement with recent experimental results and are consistent with our previously predicted mechanism for an analogue system.

Journal Article↗

PubMed2006

Functional selectivity of dopamine D1 receptor agonists in regulating the fate of internalized receptors.

Recently, we demonstrated that D(1) agonists can cause functionally selective effects when the endpoints of receptor internalization and adenylate cyclase activation are compared. The present study was designed to probe the phenomenon of functional selectivity at the D(1) receptor further by testing the hypothesis that structurally dissimilar agonists with efficacies at these endpoints that equal or exceed those of dopamine would differ in ability to influence receptor fate after internalization, a functional endpoint largely unexplored for the D(1) receptor. We selected two novel agonists of therapeutic interest that meet these criteria (the isochroman A-77636, and the isoquinoline dinapsoline), and compared the fates of the D(1) receptor after internalization in response to these two compounds with that of dopamine. We found that dopamine caused the receptor to be rapidly recycled to the cell surface within 1h of removal. Conversely, A-77636 caused the receptor to be retained intracellularly up to 48 h after agonist removal. Most surprisingly, the D(1) receptor recovered to the cell surface 48 h after removal of dinapsoline. Taken together, these data indicate that these agonists target the D(1) receptor to different intracellular trafficking pathways, demonstrating that the phenomenon of functional selectivity at the D(1) receptor is operative for cellular events that are temporally downstream of immediate receptor activation. We hypothesize that these differential effects result from interactions of the synthetic ligands with aspects of the D(1) receptor that are distal from the ligand binding domain.

Adamantane↗

PubMed2006

The ferroelectric and cubic phases in BaTiO3 ferroelectrics are also antiferroelectric.

Using quantum mechanics (QM, Density Functional Theory) we show that all four phases of barium titanate (BaTiO(3)) have local Ti distortions toward 111 (an octahedral face). The stable rhombohedral phase has all distortions in phase (ferroelectric, FE), whereas higher temperature phases have antiferroelectric coupling (AFE) in one, two, or three dimensions (orthorhombic, tetragonal, cubic). This FE-AFE model from QM explains such puzzling aspects of these systems as the allowed Raman excitation observed for the cubic phase, the distortions toward 111 observed in the cubic phase using x-ray fine structure, the small transition entropies, the heavily damped soft phonon modes, and the strong diffuse x-ray scattering in all but the rhombohedral phase. In addition, we expect to see additional weak Bragg peaks at the face centers of the reciprocal lattice for the cubic phase. Similar FE-AFE descriptions are expected to occur for other FE materials. Accounting for this FE-AFE nature of these phases is expected to be important in accurately simulating the domain wall structures, energetics, and dynamics, which in turn may lead to the design of improved materials.

Journal Article↗

PubMed2006

Continuous self-avoiding walk with application to the description of polymer chains.

We develop the continuous self-avoiding walk (CSAW) methodology for investigating temperature dependent thermodynamic properties of finite polymer chains without imposing a lattice. This leads to a new concept: the free energy theta temperature, T(theta)(F), at which the free energy is proportional to chain length. Above T(theta)(F), the polymer chain-solvent mixture leads to a single phase, whereas below T(theta)(F) the polymer solvent system has a positive surface tension with a tendency to phase separation to form a globular phase. For finite chains this coil-globule transition lies above the geometric theta temperature at which the distribution describes a Gaussian coil. CSAW provides the basis for a new approach to predict globular properties of real polymers.

Journal Article↗

PubMed2006

STRUCTFAST: protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring.

STRUCTFAST is a novel profile-profile alignment algorithm capable of detecting weak similarities between protein sequences. The increased sensitivity and accuracy of the STRUCTFAST method are achieved through several unique features. First, the algorithm utilizes a novel dynamic programming engine capable of incorporating important information from a structural family directly into the alignment process. Second, the algorithm employs a rigorous analytical formula for profile-profile scoring to overcome the limitations of ad hoc scoring functions that require adjustable parameter training. Third, the algorithm employs Convergent Island Statistics (CIS) to compute the statistical significance of alignment scores independently for each pair of sequences. STRUCTFAST routinely produces alignments that meet or exceed the quality obtained by an expert human homology modeler, as evidenced by its performance in the latest CAFASP4 and CASP6 blind prediction benchmark experiments.

Algorithms↗

PubMed2006

Exploring the molecular mechanism for color distinction in humans.

We examine here the role of the red, green, and blue human opsin structures in modulating the absorption properties of 11-cis-retinal bonded to the protein via a protonated Schiff base (PSB). We built the three-dimensional structures of the human red, green, and blue opsins using homology modeling techniques with the crystal structure of bovine rhodopsin as the template. We then used quantum mechanics (QM) combined with molecular mechanics (MM) (denoted as QM/MM) techniques in conjunction with molecular dynamics to determine how the room temperature molecular structures of the three human color opsin proteins modulate the absorption frequency of the same bound 11-cis-retinal chromophore to account for the differences in the observed absorption spectra. We find that the conformational twisting of the 11-cis-retinal PSB plays an important role in the green to blue opsin shift, whereas the dipolar side chains in the binding pocket play a surprising role of red-shifting the blue opsin with respect to the green opsin, as a fine adjustment to the opsin shift. The dipolar side chains play a large role in the opsin shift from red to green.

Amino Acid Sequence↗

PubMed2006

Quantum mechanics calculations of the thermodynamically controlled coverage and structure of alkyl monolayers on Si(111) surfaces.

The heat of formation, Delta E, for silicon (111) surfaces terminated with increasing densities of the alkyl groups CH3- (methyl), C2H5- (ethyl), (CH3)2CH- (isopropyl), (CH3)3C- (tert-butyl), CH3(CH2)5- (hexyl), CH3(CH2)7- (octyl), and C6H5- (phenyl) was calculated using quantum mechanics (QM) methods, with unalkylated sites being H-terminated. The free energy, Delta G, for the formation of both Si-C and Si-H bonds from Si-Cl model compounds was also calculated using QM, with four separate Si-H formation mechanisms proposed, to give overall Delta G(S) values for the formation of alkylated Si(111) surfaces through a two step chlorination/alkylation method. The data are in good agreement with measurements of the packing densities for alkylated surfaces formed through this technique, for Si-H free energies of formation, Delta G(H), corresponding to a reaction mechanism including the elimination of two H atoms and the formation of a C=C double bond in either unreacted alkyl Grignard groups or tetrahydrofuran solvent.

Journal Article↗

PubMed2006

Mechanism of the aerobic oxidation of alcohols by palladium complexes of N-heterocyclic carbenes.

Quantum mechanics (B3LYP density functional theory) combined with solvation (Poisson-Boltzmann polarizable continuum solvent model) was used to investigate six mechanisms for the aerobic oxidation of alcohols catalyzed by (NHC)Pd(carboxylate)(2)(H(2)O) complexes (NHC = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene). Of these, we find that "reductive beta-hydride elimination", in which the beta-hydrogen of a palladium-bound alkoxide is transferred directly to the free oxygen of the bound carboxylate, provides the lowest-energy route and explains the published kinetic isotope effect, activation enthalpy, reaction orders, and dependence of rate on carboxylate pK(a). The traditional beta-hydride elimination mechanism cannot be responsible for the experimentally observed kinetic parameters, which we find could result from the subsequent reductive elimination of acetic acid, which yields a slightly higher calculated activation barrier. Reversible beta-hydride elimination may provide a mechanism for the racemization of chiral alcohols, which would undermine attempts at an enantioselective oxidation. Competition among these pathways can be influenced by changing the electronic properties of the carboxylate and substrate.

Journal Article↗

PubMed2006

Sulfation patterns of glycosaminoglycans encode molecular recognition and activity.

Although glycosaminoglycans contribute to diverse physiological processes, an understanding of their molecular mechanisms has been hampered by the inability to access homogeneous glycosaminoglycan structures. Here, we assembled well-defined chondroitin sulfate oligosaccharides using a convergent, synthetic approach that permits installation of sulfate groups at precise positions along the carbohydrate backbone. Using these defined structures, we demonstrate that specific sulfation motifs function as molecular recognition elements for growth factors and modulate neuronal growth. These results provide both fundamental insights into the role of sulfation and direct evidence for a 'sulfation code' whereby glycosaminoglycans encode functional information in a sequence-specific manner analogous to that of DNA, RNA and proteins.

Animals↗

PubMed2006

Facile functionalization of a metal carbon bond by O-atom transfer.

The facile conversion of M-R to M-OR that could be useful for the functionalization of electron-rich metal alkyl intermediates is shown to proceed via a Baeyer-Villiger-type pathway involving a nonredox, electrophilic, O-atom insertion in reactions with non-peroxo O-donors.

Journal Article↗

PubMed2006

Predictions of CCR1 chemokine receptor structure and BX 471 antagonist binding followed by experimental validation.

A major challenge in the application of structure-based drug design methods to proteins belonging to the superfamily of G protein-coupled receptors (GPCRs) is the paucity of structural information (1). The 19 chemokine receptors, belonging to the Class A family of GPCRs, are important drug targets not only for autoimmune diseases like multiple sclerosis but also for the blockade of human immunodeficiency virus type 1 entry (2). Using the MembStruk computational method (3), we predicted the three-dimensional structure of the human CCR1 receptor. In addition, we predicted the binding site of the small molecule CCR1 antagonist BX 471, which is currently in Phase II clinical trials (4). Based on the predicted antagonist binding site we designed 17 point mutants of CCR1 to validate the predictions. Subsequent competitive ligand binding and chemotaxis experiments with these mutants gave an excellent correlation to these predictions. In particular, we find that Tyr-113 and Tyr-114 on transmembrane domain 3 and Ile-259 on transmembrane 6 contribute significantly to the binding of BX 471. Finally, we used the predicted and validated structure of CCR1 in a virtual screening validation of the Maybridge data base, seeded with selective CCR1 antagonists. The screen identified 63% of CCR1 antagonists in the top 5% of the hits. Our results indicate that rational drug design for GPCR targets is a feasible approach.

Animals↗

PubMed2006

Cluster phase chemistry: gas-phase reactions of anionic sodium salts of dicarboxylic acid clusters with water molecules.

A homologous series of anionic gas-phase clusters of dicarboxylic acids (oxalic acid, malonic acid, succinic acid, glutaric acid, and adipic acid) generated via electrospray ionization (ESI) are investigated using collision-induced dissociation (CID). Sodiated clusters with the composition (Na(+))(2)(n+1)(dicarboxylate(2-)(n+1) for singly charged anionic clusters, where n = 1-4, are observed as major gas-phase species. Isolation of the clusters followed by CID results mainly in sequential loss of disodium dicarboxylate moieties for the clusters of succinic acid, glutaric acid, and adipic acid (C4-C6). However, all oxalate (C2) and malonate (C3) clusters and dimers (n = 1) of succinate (C4) and glutarate (C5) exhibit more complex chemistry initiated by collision of the activated cluster with water molecules. For example, with water addition, malonate clusters dissociate to yield sodium acetate, carbon dioxide, and sodium hydroxide. More generally, water molecules serve as proton donors for reacting dicarboxylate anions in the cluster and introduce energetically favorable dissociation pathways not otherwise available. Density functional theory (DFT) calculations of the binding energy of the cluster correlate well with the cluster phase reactions of oxalate and malonate clusters. Clusters of larger dicarboxylate ions (C4-C6) are more weakly bound, facilitating the sequential loss of disodium dicarboxylate moieties. The more strongly bound small dicarboxylate anions (oxalate and malonate) preferentially react with water molecules rather than dissociate to lose disodium dicarboxylate monomers when collisionally activated. Implications of these results for the atmospheric aerosol chemistry of dicarboxylic acids are discussed.

Anions↗

PubMed2006

Carboxylic solvents and O-donor ligand effects on CH activation by Pt(II).

We report on the design of more efficient C-H activation catalysts based on DFT calculations. The first examples of well-defined, N,O-donor ligated platinum complexes that are competent for fast C-H activation are detailed. These complexes exhibit thermal and protic stability and are efficient catalysts for H/D exchange reactions with benzene. The C-H activation is shown to benefit from design elements that (A) reduce the barrier for substrate coordination and (B) retain a low barrier for CH cleavage via a novel six-membered transition state involving the carboxylate group of the solvent.

Journal Article↗

PubMed2006

Water formation on Pt and Pt-based alloys: a theoretical description of a catalytic reaction.

In the past, the modeling of catalytic processes was limited by the size and complexity of the systems involved. However, the enormous progress in both computer power and theoretical methods has made computational modeling a valuable tool in increasing our knowledge of catalytic reactions on the atomic scale. While complex reactions can be studied by dividing the overall reaction into a series of steps calculable by quantum mechanics, the combination with methods appropriate for larger time and length scales enables the gap between these regimes to be bridged. This provides a more realistic modeling of the experimental system and allows important environmental effects such as solvation to be taken into account. In this Minireview we describe some of the main theoretical methodologies that are used to study catalytic properties and reactions on surfaces. Using these methods, we study the seemingly simple reaction of water formation out of hydrogen and oxygen on Pt and Pt/Ni alloy catalysts. To provide a more realistic description we also discuss the interesting effects determined by hydrating the system or using alloy nanoparticles rather than extended surfaces.

Journal Article↗

PubMed2006

Theoretical investigation of the structure and coverage of the Si(111)-OCH3 surface.

The surface structure, strain energy, and charge profile of the methoxylated Si(111) surface, Si(111)-OCH3, has been studied using quantum mechanics, and the results are compared to those obtained previously for Si(111)-CH3 and Si(111)-C2H5. The calculations indicate that 100% coverage is feasible for Si(111)-OCH3 (similar to the methylated surface), as compared to only approximately 80% coverage for the ethylated surface. These differences can be understood in terms of nearest-neighbor steric and electrostatic interactions. Enthalpy and free energy calculations indicate that the formation of the Si(111)-OCH3 surface from Si(111)-H and methanol is favorable at 300 K. The calculations have also indicated the conditions under which stacking faults can emerge on Si(111)-OCH3, and such conditions are contrasted with the behavior of Si(111)-CH3 and Si(111)-CH2CH3 surfaces, for which stacking faults are calculated to be energetically feasible when etch pits with sufficiently long edges are present on the surface.

Journal Article↗