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The limitations of Slater's element-dependent exchange functional from analytic density-functional theory.

Our recent formulation of the analytic and variational Slater-Roothaan (SR) method, which uses Gaussian basis sets to variationally express the molecular orbitals, electron density, and the one-body effective potential of density-functional theory, is reviewed. Variational fitting can be extended to the resolution of identity method, where variationality then refers to the error in each two-electron integral and not to the total energy. However, a Taylor-series analysis shows that all analytic ab initio energies calculated with variational fits to two-electron integrals are stationary. It is proposed that the appropriate fitting functions be charge neutral and that all ab initio energies be evaluated using two-center fits of the two-electron integrals. The SR method has its root in Slater's Xalpha method and permits an arbitrary scaling of the Slater-Gàspàr-Kohn-Sham exchange-correlation potential around each atom in the system. The scaling factors are Slater's exchange parameters alpha. Of several ways of choosing these parameters, two most obvious are the Hartree-Fock (HF) alpha(HF) values and the exact atomic alpha(EA) values. The former are obtained by equating the self-consistent Xalpha energy and the HF energies, while the latter set reproduces exact atomic energies. In this work, we examine the performance of the SR method for predicting atomization energies, bond distances, and ionization potentials using the two sets of alpha parameters. The atomization energies are calculated for the extended G2 set of 148 molecules for different basis-set combinations. The mean error (ME) and mean absolute error (MAE) in atomization energies are about 25 and 33 kcal/mol, respectively, for the exact atomic alpha(EA) values. The HF values of exchange parameters alpha(HF) give somewhat better performance for the atomization energies with ME and MAE being about 15 and 26 kcal/mol, respectively. While both sets give performance better than the local-density approximation or the HF theory, the errors in atomization energy are larger than the target chemical accuracy. To further improve the performance of the SR method for atomization energies, a new set of alpha values is determined by minimizing the MAE in atomization energies of 148 molecules. This new set gives atomization energies half as large (MAE approximately 14.5 kcal/mol) and that are slightly better than those obtained by one of the most widely used generalized-gradient approximations. Further improvements in atomization energies require going beyond Slater's functional form for exchange employed in this work to allow exchange-correlation interactions between electrons of different spins. The MAE in ionization potentials of 49 atoms and molecules is about 0.5 eV and that in bond distances of 27 molecules is about 0.02 A. The overall good performance of the computationally efficient SR method using any reasonable set of alpha values makes it a promising method for study of large systems.

Journal Article↗

The role of fluid wall association on adsorption of chain molecules at functionalized surfaces: a density functional approach.

We present a density functional theory to describe adsorption in systems where selected segments of chain molecules of fluids can bond (or associate) with functional groups attached to the surfaces. Association of active segments with the surface is modeled within the framework of the first-order thermodynamic perturbation theory. We discuss the influence of several parameters such as the density of surface active sites, the energy of association, the chain length, and the number of the active segment in the chain molecule on the structure of the fluid adjacent to the wall. The proposed model can be considered as a first step towards developing a density functional theory of molecular brushes chemically bonded to solid surfaces.

Journal Article↗

Legendre-transform functionals for spin-density-functional theory.

We provide a rigorous proof that the Hohenberg-Kohn theorem holds for spin densities by extending Lieb's Legendre-transform formulation to spin densities. The resulting spin-density-functional theory resolves several troublesome issues. Most importantly, the present paper provides an explicit construction for the spin potentials at any point along the adiabatic connection curve, thus providing a formal basis for the use of exchange-correlation functionals of the spin density in the Kohn-Sham density-functional theory (DFT). The practical implications of this result for unrestricted Kohn-Sham DFT calculations is considered, and the existence of holes below the Fermi level is discussed. We argue that an orbital's energy tends to increase as its occupation number increases, which provides the basis for a computational algorithm for determining the occupation numbers in Kohn-Sham DFT and helps explain the origin of Hund's rules and holes below the Fermi level.

Journal Article↗

Benchmarking the performance of density functional theory based Green's function formalism utilizing different self-energy models in calculating electronic transmission through molecular systems.

Electronic transmission through a metal-molecule-metal system is calculated by employing a Green's function formalism in the scattering based scheme. Self-energy models representing the bulk and the potential bias are used to describe electron transport through the molecular system. Different self-energies can be defined by varying the partition between device and bulk regions of the metal-molecule-metal model system. In addition, the self-energies are calculated with different representations of the bulk through its Green's function. In this work, the dependence of the calculated transmission on varying the self-energy subspaces is benchmarked. The calculated transmission is monitored with respect to the different choices defining the self-energy model. In this report, we focus on one-dimensional model systems with electronic structures calculated at the density functional level of theory.

Journal Article↗

Age-dependent changes in regional diastolic function evaluated by color Doppler myocardial imaging: a comparison with pulsed Doppler indexes of global function.

The goals of this study were to evaluate possible normal age-related changes in regional myocardial relaxation as detected by color Doppler myocardial imaging (CDMI) velocities and to compare the extent of any such changes with age-induced changes in global diastolic function. In 80 healthy subjects (aged 21 to 72 years, equally subdivided by decades) the mitral flow velocities in early diastole (E) and atrial contraction (A) were recorded as were the velocities of left ventricular (LV) motion of early (EDV) and late diastole (LDV) in the 16 standard LV segments, and their ratios were calculated. In healthy persons younger than 40 years, all segments showed an EDV/LDV ratio > 1, whereas in healthy persons aged 40 years or older the mean EDV of all segments decreased, and the mean LDV increased, resulting in a significant decrease of the mean EDV/LDV ratio with age. Values of EDV/LDV ratios were higher than E/A ratios (P <.0001), but their changes with age correlated well with each other (r = 0.805). With increasing age, an EDV/LDV ratio <1 was observed more often in basal segments (P <.001, compared with mid and apical segments) and less often in segments of anteroseptal and posterior walls viewed from the parasternal window. The presence of >50% segments with an EDV/LDV ratio <1 was associated with an E/A ratio <1. Regional diastolic function indexes as evaluated by CDMI changed with increasing age in a heterogeneous way and influenced global diastolic function parameters.

Adult↗

Genomewide gain-of-function genetic screen identifies functionally active genes in mouse embryonic stem cells.

Embryonic stem (ES) cells hold great promise for the future of medicine. To elucidate the molecular mechanisms that control ES cell self-renewal and differentiation, a comprehensive knowledge of the molecules involved in these processes is required. Here we describe an effective approach for genomewide identification of functionally active genes in ES cells. This approach combines genetic screens based on cDNA libraries with microarray detection methods to permit high-throughput functional analyses. We implement this strategy to identify genes whose overexpression can maintain phenotypic properties of undifferentiated mouse ES cells under differentiation-inducing conditions, specifically in the absence of leukemia inhibitory factor. The identified genes encode a variety of regulatory proteins whose function in ES cells was previously unknown. Moreover, our approach is capable of detecting genes whose overexpression promote differentiation or cell death. Overall, our studies establish a methodology for highly sensitive identification of genes that confer particular phenotypes on ES cells.

Animals↗

Two functional equations preserving functional forms.

Two functional equations are considered that are motivated by three considerations: work in utility theory and psychophysics, questions concerning when pairs of degree 1 homogeneous functions can be homomorphic and calculating their homomorphisms, and the link of the latter questions to quasilinear mean values. The first equation is h(σ(y)x + [1 - σ(y)]y) = τ(y)h(x) + [1 - τ(y)]h(y) (x ≥ y ≥ 0), where h maps [0, ∞[into a subset of [0, ∞[and is strictly increasing and continuously differentiable; the functions σ and τ map [0, ∞[continuously into [0,1], σ(y) > 0 for y > 0 but σ is not 1 on]0, ∞[. The solutions are fully determined. (Recently Zsolt Páles has eliminated the differentiability assumption.) The second equation is h[y + f(x - y)] = h(y) + g[h(x) - h(y)] (x ≥ y ≥ 0), where h maps [0, ∞[onto a subinterval of positive length of [0, ∞[and is strictly increasing and twice continuously differentiable, f and g map [0, ∞[onto[0, ∞[and are twice differentiable, and either f"(0) ≠ 0 or g"(0) ≠ 0. The solutions are fully determined under these conditions. When f"(0) = g"(0) = 0 and h" is not identically zero, we determine the solutions under the added assumption of analyticity. It remains an open problem to find the solutions in the latter case under the assumption of only second order differentiability. A more general open problem is to eliminate all differentiability conditions for the second equation.

Journal Article↗

Mono- and multisite phosphorylation enhances Bcl2's antiapoptotic function and inhibition of cell cycle entry functions.

Bcl2 functions to suppress apoptosis and retard cell cycle entry. Single-site phosphorylation at serine 70 (S70) is required for Bcl2's antiapoptotic function, and multisite phosphorylation at threonine 69 (T69), S70, and S87 has been reported to inactivate Bcl2. To address this apparent conflict and identify the regulatory role for Bcl2 phosphorylation in cell death and cell cycle control, a series of serine/threonine (S/T) --> glutamate/alanine (E/A) mutants including T69E/A, S70E/A, S87E/A, T69E/S70A/S87A (EAA), T69A/S70E/S87A (AEA), T69A/S70A/S87E (AAE), T69E/S70E/S87E (EEE), and T69A/S70A/S87A (AAA) was created to mimic or abrogate, respectively, either single-site or multisite phosphorylation. The survival and cell cycle status of cells expressing the phosphomimetic or nonphosphorylatable Bcl2 mutants were compared. Surprisingly, all of the E but not the A Bcl2 mutants potently enhance cell survival after stress and retard G(1)/S cell cycle transition. The EEE Bcl2 mutant is the most potent, indicating a possible cumulative advantage for multisite phosphorylation of Bcl2 in survival and retardation of G(1)/S transition functions. Because the E-containing Bcl2 mutants, but not the A-containing mutants, can more potently block cytochrome c release from mitochondria during apoptotic stress, even at times when steady-state expression levels are similar for all mutants, we conclude that phosphorylation at one or multiple sites within the flexible loop domain of Bcl2 not only stimulates antiapoptotic activity but also can regulate cell cycle entry.

Amino Acid Substitution↗

Note on the convergence of sequences of rational functions of best approximation to a meromorphic function.

If the function f(z) is meromorphic at every finite point of the plane, analytic on C: [unk]z[unk] </= 1, there are results that can be established concerning the convergence of the sequence R(n)(z) of rational functions of each degree n of best approximation to f(z) on C. However, we need to assume certain additional conditions on the convergence of the sequence R(n)(z) itself. The results generalize to more general sets C and to more general functions.

Journal Article↗

Bounds for a joint distribution function with fixed sub-distribution functions: Application to competing risks.

This paper gives sharp bounds for the joint survival function G(t(1), t(2),...,t(r)) identical with P(X(1) > t(1), X(2) > t(2),...,X(r) > t(r)), and for the marginal survival functions S(j)(t) identical with P(X(j) > t), j = 1,2,...,r, when the sub-survival functions S(j) (*)(t) identical with P(X(j) > t, X(j) = min(k=1,2),...,(r)X(k)) are fixed. Theorem 1 gives the bounds for r = 2, and Theorem 2 gives the bounds for general r. Theorem 3 applies the result to the competing risks problem, and presents empirical bounds based on the observations. Finally, an example illustrates the bounds.

Journal Article↗

Structure from function: screening structural models with functional data.

Structural constraints derived from different antibody epitopes on human growth hormone (hGH) were used to screen three-dimensional models of hGH that were generated by computer algorithms. Previously, alanine-scanning mutagenesis defined the residues that modulate binding to 21 different monoclonal antibodies to hGH. These functional epitopes were composed of 4-14 side chains whose alpha-carbons clustered within 4-23 A. Distance and topographic constraints for these functional epitopes were virtually the same as constraints derived from known x-ray structures of protein-antigen complexes. The constraints were used to evaluate about 1400 models of hGH that were computer-generated by a secondary-structure prediction and packing algorithm. On average each functional epitope reduced the number of models in the pool by a factor of 2, so that 8 monoclonal antibodies could reduce the number of possible models to < 10. The average root-mean-square deviation of alpha-carbon coordinates between the x-ray structure and either the pool of starting models or final models ranged from 13 to 16 A or 4 to 7 A, respectively, depending on the pool of starting models and the level of constraints imposed. All of the final models had the correct folding topography, and the best model was within 3.8 A root-mean-square deviation of the x-ray coordinates. This model was as close as it could have been because the models were built by using ideal helices and those in the x-ray structure are not. Our studies suggest that epitope mapping data can effectively screen structural models and, when coupled to predictive algorithms, can help to generate low-resolution models of a protein.

Amino Acid Sequence↗

Gain of function mutations for paralogous Hox genes: implications for the evolution of Hox gene function.

To investigate the functions of paralogous Hox genes, we compared the phenotypic consequences of altering the embryonic patterns of expression of Hoxb-8 and Hoxc-8 in transgenic mice. A comparison of the phenotypic consequences of altered expression of the two paralogs in the axial skeletons of newborns revealed an array of common transformations as well as morphological changes unique to each gene. Divergence of function of the two paralogs was clearly evident in costal derivatives, where increased expression of the two genes affected opposite ends of the ribs. Many of the morphological consequences of expanding the mesodermal domain and magnitude of expression of either gene were atavistic, inducing the transformation of axial skeletal structures from a modern to an earlier evolutionary form. We propose that regional specialization of the vertebral column has been driven by regionalization of Hox gene function and that a major aspect of this evolutionary progression may have been restriction of Hox gene expression.

Animals↗

Graft-versus-host-disease-associated lymphoid hypoplasia and B cell dysfunction is dependent upon donor T cell-mediated Fas-ligand function, but not perforin function.

Allogeneic bone marrow transplant recipients often exhibit a graft-versus-host-disease (GVHD)-associated immune deficiency that can be prolonged and lead to life-threatening infections. We have examined the role of donor T cell-mediated cytotoxic function in the development of GVHD-associated immune deficiency. A major histocompatibility complex-matched model of allogeneic bone marrow transplantation was employed in which lethally irradiated C3H.SW mice received a nonlethal dose of T cells from either perforin-deficient (B6-perforin 0/0), Fas-ligand (FasL)-defective (B6-gld), or normal (B6) allogeneic donor mice. T cell-depleted marrow from B6-Ly-5.1 congenic donor mice was transplanted along with the donor T cell populations to determine the effects of donor T cell-mediated cytotoxicity on engraftment. Our results demonstrate that recipients of perforin-deficient or normal allogeneic T cells exhibit profound lymphoid hypoplasia and severely reduced splenic proliferative responses to lipopolysaccharide in vitro. In contrast, GVHD-associated lymphoid hypoplasia is dramatically reduced and in vitro B cell function is intact in recipients of FasL-defective allogeneic T cells. Engraftment of myeloid and erythroid lineage cells occurs irrespective of donor T cell cytotoxic function. Although recipients of perforin-deficient or normal allogeneic T cells exhibited hematopoietic engraftment exclusively of donor origin, recipients of FasL-defective donor T cells exhibited significant mixed chimerism (Ly-5.1/Ly-5.2). Because only marrow of donor origin was transplanted, this finding suggests that Fas-mediated antirecipient cytotoxicity is required for clearance of residual hematopoietic stem cells of host origin that persist following lethal irradiation.

Animals↗

Biophysical and functional characterization of full-length, recombinant human tissue inhibitor of metalloproteinases-2 (TIMP-2) produced in Escherichia coli. Comparison of wild type and amino-terminal alanine appended variant with implications for the mechanism of TIMP functions.

Matrix metalloproteinases (MMPs) function in the remodeling of the extracellular matrix that is integral for many normal and pathological processes. The tissue inhibitor of metalloproteinases family, including tissue inhibitor of metalloproteinases-2 (TIMP-2), regulates the activity of these multifunctional metalloproteinases. TIMP family members are proteinase inhibitors that contain six conserved disulfide bonds, one involving an amino-terminal cysteine residue that is critical for MMP inhibitor activity. TIMP-2 has been expressed in Escherichia coli, folded from insoluble protein, and functionally characterized. The wild type protein inhibited gelatinase A (MMP-2), whereas a variant with an alanine appended to the amino terminus (Ala+TIMP-2) was inactive. Removal of amino-terminal alanine by exopeptidase digestion restored protease inhibitor activity. This confirms the mechanistic importance of the amino-terminal amino group in the metalloproteinase inhibitory activity, as originally suggested from the x-ray structure of a complex of MMP-3 with TIMP-1 and a complex of TIMP-2 with MT-1-MMP. The Ala+TIMP-2 variant exhibited conformational, pro-MMP-2 complex formation and fibroblast growth modulating properties of the wild type protein. These findings demonstrate that Ala+TIMP-2 is an excellent biochemical tool for examining the specific role of MMP inhibition in the multiple functions ascribed to TIMPs.

Escherichia coli↗

Renin-dependent cardiovascular functions and renin-independent blood-brain barrier functions revealed by renin-deficient mice.

Renin plays a key role in controlling blood pressure through its specific cleavage of angiotensinogen to generate angiotensin I (AI). Although possible existence of the other angiotensin forming enzymes has been discussed to date, its in vivo function remains to be elucidated. To address the contribution of renin, we generated renin knockout mice. Homozygous mutant mice show neither detectable levels of plasma renin activity nor plasma AI, lowered blood pressure 20-30 mm Hg less than normal, increased urine and drinking volume, and altered renal morphology as those observed in angiotensinogen-deficient mice. We recently found the decreased density in granular layer cells of hippocampus and the impaired blood-brain barrier function in angiotensinogen-deficient mice. Surprisingly, however, such brain phenotypes were not observed in renin-deficient mice. Our results demonstrate an indispensable role for renin in the circulating angiotensin generation and in the maintenance of blood pressure, but suggest a dispensable role for renin in the blood-brain barrier function.

Angiotensin I↗

Gram-positive DsbE proteins function differently from Gram-negative DsbE homologs. A structure to function analysis of DsbE from Mycobacterium tuberculosis.

Mycobacterium tuberculosis, a Gram-positive bacterium, encodes a secreted Dsb-like protein annotated as Mtb DsbE (Rv2878c, also known as MPT53). Because Dsb proteins in Escherichia coli and other bacteria seem to catalyze proper folding during protein secretion and because folding of secreted proteins is thought to be coupled to disulfide oxidoreduction, the function of Mtb DsbE may be to ensure that secreted proteins are in their correctly folded states. We have determined the crystal structure of Mtb DsbE to 1.1 A resolution, which reveals a thioredoxin-like domain with a typical CXXC active site. These cysteines are in their reduced state. Biochemical characterization of Mtb DsbE reveals that this disulfide oxidoreductase is an oxidant, unlike Gram-negative bacteria DsbE proteins, which have been shown to be weak reductants. In addition, the pK(a) value of the active site, solvent-exposed cysteine is approximately 2 pH units lower than that of Gram-negative DsbE homologs. Finally, the reduced form of Mtb DsbE is more stable than the oxidized form, and Mtb DsbE is able to oxidatively fold hirudin. Structural and biochemical analysis implies that Mtb DsbE functions differently from Gram-negative DsbE homologs, and we discuss its possible functional role in the bacterium.

Amino Acid Sequence↗

Chondroitin sulfate chains on syndecan-1 and syndecan-4 from normal murine mammary gland epithelial cells are structurally and functionally distinct and cooperate with heparan sulfate chains to bind growth factors. A novel function to control binding of midkine, pleiotrophin, and basic fibroblast growth factor.

A comparative analysis was carried out of heparan sulfate (HS) and chondroitin sulfate (CS) chains of the ectodomains of hybrid type transmembrane proteoglycans, syndecan-1 and -4, synthesized simultaneously by normal murine mammary gland epithelial cells. Although the HS chains were structurally indistinguishable, intriguingly the CS chains were structurally and functionally distinct, probably reflecting the differential regulation of sulfotransferases involved in the synthesis of HS and CS. The CS chains of the two syndecans comprised nonsulfated, 4-O-, 6-O-, and 4,6-O-disulfated N-acetylgalactosamine-containing disaccharide units and were significantly different, with a higher degree of sulfation for syndecan-4. Functional analysis using a BIAcore system showed that basic fibroblast growth factor (bFGF) specifically bound only to the HS chains of both syndecans, whereas midkine (MK) and pleiotrophin (PTN) bound not only to the HS but also to the CS chains. Stronger binding of MK and PTN to the CS chains of syndecan-4 than those of syndecan-1 was revealed, supporting the structural and functional differences. Intriguingly, removal of the CS chains decreased the association and dissociation rate constants of MK, PTN, and bFGF for both syndecans, suggesting the simultaneous binding of these growth factors to both types of chains, producing a ternary complex that transfers the growth factors to the corresponding cell surface receptors more efficiently compared with the HS chains alone. The involvement of the core protein was also shown in the binding of MK and PTN to syndecan-1, suggesting the possibility of cooperation with the HS and/or CS chains in the binding of these growth factors and their delivery to the cell surface receptors.

Animals↗

Protein-tyrosine phosphatase (PTP) wedge domain peptides: a novel approach for inhibition of PTP function and augmentation of protein-tyrosine kinase function.

Inhibition of protein-tyrosine phosphatases (PTPs) counterbalancing protein-tyrosine kinases (PTKs) offers a strategy for augmenting PTK actions. Conservation of PTP catalytic sites limits development of specific PTP inhibitors. A number of receptor PTPs, including the leukocyte common antigen-related (LAR) receptor and PTPmu, contain a wedge-shaped helix-loop-helix located near the first catalytic domain. Helix-loop-helix domains in other proteins demonstrate homophilic binding and inhibit function; therefore, we tested the hypothesis that LAR wedge domain peptides would exhibit homophilic binding, bind to LAR, and inhibit LAR function. Fluorescent beads coated with LAR or PTPmu wedge peptides demonstrated PTP-specific homophilic binding, and LAR wedge peptide-coated beads precipitated LAR protein. Administration of LAR wedge Tat peptide to PC12 cells resulted in increased proliferation, decreased cell death, increased neurite outgrowth, and augmented Trk PTK-mediated responses to nerve growth factor (NGF), a phenotype matching that found in PC12 cells with reduced LAR levels. PTPmu wedge Tat peptide had no effect on PC12 cells but blocked the PTPmu-dependent phenotype of neurite outgrowth of retinal ganglion neurons on a PTPmu substrate, whereas LAR wedge peptide had no effect. The survival- and neurite-promoting effect of the LAR wedge peptide was blocked by the Trk inhibitor K252a, and reciprocal co-immunoprecipitation demonstrated LAR/TrkA association. The addition of LAR wedge peptide inhibited LAR co-immunoprecipitation with TrkA, augmented NGF-induced activation of TrkA, ERK, and AKT, and in the absence of exogenous NGF, induced activation of TrkA, ERK, and AKT. PTP wedge domain peptides provide a unique PTP inhibition strategy and offer a novel approach for augmenting PTK function.

Amino Acid Sequence↗