bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational constraint in protein ligand design and the inconsistency of binding entropy
Authors: Udugamasooriya D. Gomika , Spaller Mark R. 
Published: March 2008

AbstractIt is an accepted practice in ligand design to introduce conformational constraint with the expectation of improving affinity, justified by the theoretical possibility that an unfavorable change in binding entropy will be reduced. This rationale of minimizing the entropic penalty through imposing structural constraints upon a ligand, however, has been voiced more often than verified. Here we examine three modified cyclic peptides, along with multiple versions of their linear control analogs, and determine their thermodynamic parameters when binding the same host, the third PDZ domain (PDZ3) of the mammalian postsynaptic density‐95 (PSD‐95) protein. To begin a two‐stage investigation, the initial evaluation involved solution binding studies with isothermal titration calorimetry (ITC), which provided the changes in Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (TΔS) upon formation of the protein‐ligand complex. In the second stage, a selected macrocycle along with two matched linear controls were subjected to more rigorous analysis by ITC, which included (1) change in heat of buffer ionization (ΔHion) titrations, to examine the role of proton transfer events; (2) change in heat capacity (ΔCp) determinations, to indirectly probe the nature of the binding surface; and (3) osmotic stress experiments, to evaluate desolvation effects and quantitate water release. Together, these demonstrate that the entropic relationship between a macrocyclic ligand and a linear counterpart can be a complex one that is difficult to rationalize. Further, the addition of constraint can, counterintuitively, lead to a less favorable change in binding entropy. This underscores the need to use matched linear control ligands to assure that comparisons are made in a meaningful manner. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 653–667, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
B12‐retro‐Riboswitches: Guanosyl‐Induced Constitutional Switching of B12 Coenzymes
Authors: Gschösser Sigrid , Kräutler Bernhard 
Published: March 2008

AbstractComplete B12 derivatives are natural “molecular switches” as a result of the coordinative switch (“base on” or “base off”) of the natural nucleotide base. Certain predesigned B12–nucleotide conjugates were shown recently to behave as “retro riboswitches”, in which the nucleotide environment modified the equilibrium between these two isomeric B12 structures. In contrast, the “reverse” situation has been discovered in natural B12 riboswitches, in which the binding of coenzyme B12 induces a conformational switch in the RNA species. The first (predesigned) B12‐retro‐riboswitches were DNA conjugates of methylcobalamin. We describe herein two representative B12‐retro‐riboswitches, in which an appended (RNA) nucleotide is used to destabilize the base‐on form and induce the base‐on to base‐off switch. Through use of heterogeneous solid‐phase synthetic methods, Coβ–cyanocobalamin‐(3′′→2′)‐2′′‐methoxyguaninyl‐3′′‐ate was prepared first as the crucial covalent RNA conjugate of vitamin B12. This cyanocorrinoid opened the door to two organometallic B12–nucleotide conjugates, which were made by electrosynthetic means: the cyanocorrinoid was cleanly methylated or adenosylated at the cobalt center to furnish covalent RNA conjugates of the organometallic B12 cofactors methylcobalamin and coenzyme B12, respectively. At room temperature, aqueous solutions of both of these organometallic RNA–B12 conjugates exhibited properties indicative of significant weakening of the axial (CoN) bond (of their base‐on forms) and of an enhanced formation of the base‐off species. The base‐on to base‐off switch was studied by UV/Vis and NMR spectroscopic studies, which showed that the switch was very temperature‐dependent and was accentuated with increasing temperatures. Thermodynamic data of the two organometallic RNA–B12 conjugates revealed an important contribution of entropic effects to the observed base‐on to base‐off switch. The two organometallic RNA–B12 conjugates thus acted as B12‐retro‐riboswitches and allowed the observation of a temperature‐dependent reverse switch in the B12 cofactor moiety, induced by the appended nucleotide moiety. This behavior may be of interest in the “RNA‐world” hypothesis, in which (simple) B12 derivatives are thought to act as possible catalytic enhancers (“cofactors”) in RNA‐based “B12 ribozymes”.
Tin–Oxo Clusters Based on Aryl Arsonate Anions
Authors: Xie Yun‐Peng , Yang Jin , Ma Jian‐Fang , Zhang Lai‐Ping , Song Shu‐Yan , Su Zhong‐Min 
Published: March 2008

AbstractReactions of Ph3SnOH or Ph3SnCl with aryl arsonic acids RAsO3H2, where R=C6H5 (1), 2‐NH2C6H4 (2), 4‐NH2C6H4 (3), 2‐NO2C6H4 (4), 3‐NO2C6H4 (5), 4‐NO2C6H4 (6), 3‐NO2‐4‐OHC6H3 (7), 2‐ClC6H4 (8) and 2,4‐Cl2C6H3 (9), gave 18 Sn–O cluster compounds. These compounds can be classified into four types: type A: [{(PhSn)3(RAsO3)3(μ3‐O)(OH)(R′O)2}2Sn] (R=C6H5, 2‐NH2C6H4, 4‐NH2C6H4, 2‐NO2C6H4, 3‐NO2C6H4, 2‐ClC6H4, 2,4‐Cl2C6H3, and 3‐NO2‐4‐OHC6H3; R′=Me or Et); type B: [{(PhSn)3(RAsO3)2(RAsO3H)(μ3‐O)(R′O)2}2] (R=4‐NO2C6H4, R′=Me); type C: [{(PhSn)3(RAsO3)3(μ3‐O)(R′O)3}2Sn] (R=2,4‐Cl2C6H3, R′=Me); type D: [{Sn3Cl3(μ3‐O)(R′O)3}2(RAsO3)4] (R=2‐NO2C6H4 and 4‐NO2‐C6H4; R′=Me or Et). Structures of types A and B contain [Sn3(μ3‐O)(μ2‐OR′)2] building blocks, while in types C and D the stannoxane cores are built from two [Sn3(μ3‐O)(μ2‐OR′)3] building blocks. The reactions proceeded with partial or complete dearylation of the triphenyltin precursor. These various structural forms are realized by subtle changes in the nature of the organotin precursors and aryl arsonic acids. The syntheses, structures, and structural interrelationship of these organostannoxanes are discussed.
Nonpolar Dihydrogen Bonds—On a Gliding Scale from Weak Dihydrogen Interaction to Covalent HH in Symmetric Radical Cations [HnE‐H‐H‐EHn]+
Authors: Krapp Andreas , Frenking Gernot , Uggerud Einar 
Published: March 2008

AbstractThe electronic structures and bonding patterns for a new class of radical cations, [HnE‐H‐H‐EHn]+(EHn=element hydride, E=element of Groups 15–18), have been investigated by applying quantum‐chemical methods. All structures investigated give rise to symmetric potential energy minimum structures. We envisage clear periodic trends. The HH bond length is shorter for elements toward the bottom of the periodic table of elements, and a short HH bond corresponds to accumulation of electron density in the central HH region. All [HnE‐H‐H‐EHn]+of Groups 15–17 are thermodynamically unstable towards loss of either H2or H. The barriers for these dissociations are rather low. The Group 18 congeners, except E=Xe, appear to be global minima of the respective potential energy surfaces. The findings are discussed in terms of H2bond activation, and a general mechanistic scheme for the standard reduction process 2H++ 2e−→ H2is given. Finally, it is proposed that some of the symmetric radical cations are likely to be observed in mass spectrometric or matrix isolation experiments.
Controllable Synthesis of VSB‐5 Microspheres and Microrods: Growth Mechanism and Selective Hydrogenation Catalysis
Authors: Liu Shu‐Juan , Cheng Hai‐Yang , Zhao Feng‐Yu , Gong Jun‐Yan , Yu Shu‐Hong 
Published: March 2008

AbstractNanoporous VSB‐5 nickel phosphate molecular sieves with relatively well controllable sizes and morphology of microspheres assembled from nanorods were synthesized at 140 °C over a short time in the presence of hexamethylenetetramine (HMT) by a facile hydrothermal method. The pH value, reaction time, and ratio of HMT to NaHPO2⋅H2O crucially influence the morphology and quality of the final products. By adjusting the pH value of the initial reaction solution, the morphology changes from disperse rods to microspheres assembled from rods and finally to a large quantity of fibers, and the diameters of the VSB‐5 rods can be varied. The catalytic activity of VSB‐5 in selective hydrogenation of several unsaturated organic compounds was tested. Nickel(II) in VSB‐5 can selectively catalyze hydrogenation of CC in trans‐cinnamaldehyde and 3‐methylcrotonaldehyde. In addition, since nitrobenzene (NB) and 2‐chloronitrobenzene could be reduced to aniline (AN) and 2‐chloroaniline with high selectivity, VSB‐5 could have potential applications in synthesizing dyes, agrochemicals, and pharmaceuticals.
Photo Gel–Sol/Sol–Gel Transition and Its Patterning of a Supramolecular Hydrogel as Stimuli‐Responsive Biomaterials
Authors: Matsumoto Shinji , Yamaguchi Satoshi , Ueno Shiori , Komatsu Harunobu , Ikeda Masato , Ishizuka Koji , Iko Yuko , Tabata Kazuhito V. , Aoki Hiroyuki , Ito Shinzaburo , Noji Hiroyuki , Hamachi Itaru 
Published: March 2008

AbstractIn a focused library of glycolipid‐based hydrogelators bearing fumaric amide as a trans–cis photoswitching module, several new photoresponsive supramolecular hydrogelators were discovered, the gel–sol/sol–gel transition of which was pseudo‐reversibly induced by light. Studying the optimal hydrogel by NMR spectroscopy and various microscopy techniques showed that the trans–cis photoisomerization of the double bond of the fumaric amide unit effectively caused assembly or disassembly of the self‐assembled supramolecular fibers to yield the macroscopic hydrogel or the corresponding sol, respectively. The entanglement of the supramolecular fibers produced nanomeshes, the void space of which was roughly evaluated to be 250 nm based on confocal laser scanning microscopy observations of the size‐dependent Brownian motion of nanobeads embedded in the supramolecular hydrogel. It was clearly shown that such nanomeshes become a physical obstacle that captures submicro‐ to micrometer‐sized substrates such as beads or bacteria. By exploiting the photoresponsive property of the supramolecular nanomeshes, we succeeded in off/on switching of bacterial movement and rotary motion of bead‐tethered F1‐ATPase, a biomolecular motor protein, in the supramolecular hydrogel. Furthermore, by using the photolithographic technique, gel–sol photopatterning was successfully conducted to produce sol spots within the gel matrix. The fabricated gel–sol pattern not only allowed regulation of bacterial motility in a limited area, but also off/on switching of F1‐ATPase rotary motion at the single‐molecule level. These results demonstrated that the photoresponsive supramolecular hydrogel and the resulting nanomeshes may provide unique biomaterials for the spatiotemporal manipulation of various biomolecules and live bacteria.
Complexation of L‐Lactate with Boronic Acids: A Solution and Holographic Analysis
Authors: Sartain Felicity K. , Yang Xiaoping , Lowe Christopher R. 
Published: March 2008

AbstractBoronic acids have been used as receptors for the detection of diols and α‐hydroxy acids. The incorporation of 3‐acrylamide phenyl boronic acid (3‐APB) into a hydrogel generates a suitably responsive and fully reversible holographic sensor for L‐lactate. However, it was also found that the use of 3‐APB resulted in the sensor being responsive towards a number of other compounds containing two hydroxy groups. This report details the further investigation into the reaction between L‐lactate and three boronic acid‐based receptors, both in the holograms and in solution, in order to establish the mechanism of binding. A novel boronate receptor is proposed based on this understanding.
Three‐Dimensional Mesoporous Gallosilicate with Pm3n Symmetry and its Unusual Catalytic Performances
Authors: Srinivasu Pavuluri , Vinu Ajayan 
Published: March 2008

AbstractThree‐dimensional, mesoporous‐cage‐type, GaSBA‐1 materials with different nSi/nGa ratios have been successfully prepared for the first time by using a low hydrochloric acid to silicon (nHCl/nSi) molar ratio in the synthesis gel by templating with cetyltriethylammonium bromide as the structure‐directing agent in a highly acidic medium. The obtained materials have been unambiguously characterized in detail by several sophisticated techniques including X‐ray diffraction (XRD), N2 adsorption, high‐resolution transmission electron microscopy, high‐resolution scanning electron microscopy, energy dispersive spectroscopy, elemental mapping, and 29Si magic‐angle‐spinning NMR spectroscopy. XRD and nitrogen adsorption results reveal that the structures of the GaSBA‐1 materials resemble that of SBA‐1, which possesses a cubic, three‐dimensional, cage‐type structure with open windows. In addition, the specific surface area and the specific pore volume of the GaSBA‐1 materials are much higher than those of the SBA‐1 silica, which are very important for the catalytic applications. The amount of Ga cation in the SBA‐1 silica framework has been found to play a critical role in controlling the morphology and the pore diameter of the materials. Finally, the catalytic activity in the tert‐butylation of phenol with tert‐butanol as the alkylating agent has been investigated and the results are compared with those of other mesoporous catalysts such as AlMCM‐41, FeMCM‐41, FeAl‐MCM‐41, and FeSBA‐1. Moreover, the effect of various reaction parameters such as the reaction temperature, reactant feed ratio, and time‐on‐stream on the phenol conversion in the tert‐butylation of phenol over GaSBA‐1 catalysts has been demonstrated. Among the catalysts examined, GaSBA‐1(17), in which the number in the parenthesis denotes the nSi/nGa ratio, showed remarkable activity with a high conversion of phenol and selectivity to 4‐tert‐butylphenol; it was found to be superior over other mesoporous catalysts used in the study.
Fast generation of nonresonant and resonant optical rotatory dispersion curves with the help of circular dichroism calculations and Kramers‐Kronig transformations
Authors: Rudolph Mark , Autschbach Jochen 
Published: March 2008

AbstractIt can be computationally expensive to compute smooth, well resolved, optical rotation (OR) dispersion (ORD) curves from first principles theory. Instead of computing the OR at a large number of frequency points, similar results can be obtained by combined use of a computed circular dichroism (CD) spectrum along with a few OR calculations by using subtractive Kramers‐Kronig transformations. We have tested various subtractive schemes for simulated (analytical) CD/ORD and for time‐dependent density functional computations for dimethyloxirane, fenchone, and [4]triangulane. Nonresonant ORD can be obtained with as few as two OR and one CD calculation. For resonant ORD we found that between 7 and 15 OR computations plus the CD spectrum were typically sufficient, depending on the number of excitations within the frequency window of interest. Chirality, 2008. © 2008 Wiley‐Liss, Inc.
First ex‐vivo MRI co‐localization of two LIPOCEST agents
Authors: Terreno Enzo , Castelli Daniela Delli , Milone Luciano , Rollet Simona , Stancanello Joseph , Violante Elisabetta , Aime Silvio 
Published: March 2008

AbstractOne of the major advantages of the CEST methodology deals with the possibility of visualizing more probes in the same MR image voxels. This is a unique property within the contrast media that act on the 1H‐NMR signal of water protons, and it might considerably improve the potential of the technique. In addition to displaying sufficiently different resonance frequencies of their mobile protons, it is also important that the CEST agents designed for this application are highly sensitive. LIPOCEST agents represent the most sensitive class of CEST systems developed so far. On this basis, two LIPOCEST samples, a spherical one and an osmotically shrunken nonspherical one, endowed with markedly different resonance frequencies of their intraliposomal water protons, 3 ppm and 15 ppm, respectively, were prepared and tested both in vitro and in ex‐vivo on a bovine muscle used as tissue‐surrogate. The response of the two agents did not interfere each other, thus allowing the multiple visualization of the two agents present at nanomolar concentrations in the same image voxels. Copyright © 2008 John Wiley & Sons, Ltd.
Developmental expression of NMDA and AMPA receptor subunits in vestibular nuclear neurons that encode gravity‐related horizontal orientations
Authors: Tse Yiu‐Chung , Lai Chun‐Hong , Lai Suk‐King , Liu Jian‐Xiang , Yung Ken K.L. , Shum Daisy K.Y. , Chan Ying‐Shing 
Published: March 2008

AbstractWe examined the expression profile of subunits of ionotropic glutamate receptors [N‐methyl‐D‐aspartate (NMDA) and α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazole‐proprionate (AMPA)] during postnatal development of connectivity in the rat vestibular nucleus. Vestibular nuclear neurons were functionally activated by constant velocity off‐vertical axis rotation, a strategy to stimulate otolith organs in the inner ear. These neurons indicated Fos expression as a result. By immunodetection for Fos, otolith‐related neurons that expressed NMDA/AMPA receptor subunits were identified as early as P7, and these neurons were found to increase progressively up to adulthood. Although there was developmental invariance in the percentage of Fos‐immunoreactive neurons expressing the NR1, NR2A, GluR1, or GluR2/3 subunits, those expressing the NR2B subunit decreased from P14 onward, and those expressing the GluR4 subunit decreased in adults. These double‐immunohistochemical data were corroborated by combined immuno‐/hybridization histochemical data obtained from Fos‐immunoreactive neurons expressing NR2B mRNA or GluR4 mRNA. The staining of both NR2B and GluR4 in the cytoplasm of these neurons decreased upon maturation. The percentage of Fos‐immunoreactive neurons expressing the other ionotropic glutamate receptor subunits (viz. NR1, NR2A, GluR1, and GluR2/3) remained relatively constant throughout postnatal maturation. Triple immunofluorescence further demonstrated coexpression of NR1 and NR2 subunits in Fos‐immunoreactive neurons. Coexpression of NR1 subunit with each of the GluR subunits was also observed among the Fos‐immunoreactive neurons. Taken together, the different expression profiles of ionotropic glutamate receptor subunits constitute the histological basis for glutamatergic neurotransmission in the maturation of central vestibular connectivity for the coding of gravity‐related horizontal head movements. J. Comp. Neurol. 508:343–364, 2008. © 2008 Wiley‐Liss, Inc.
Identity of myelinated cutaneous sensory neurons projecting to nocireceptive laminae following nerve injury in adult mice
Authors: Woodbury C. Jeffery , Kullmann Florenta A. , McIlwrath Sabrina L. , Koerber H. Richard 
Published: March 2008

AbstractIt is widely thought that, after peripheral injury, some low‐threshold mechanoreceptive (LTMR) afferents “sprout” into pain‐specific laminae (I–II) of the dorsal horn and are responsible for chronic pain states such as mechanical allodynia. Although recent studies have questioned this hypothesis, they fail to account for a series of compelling results from single‐fiber analyses showing extensive projections from large‐diameter myelinated afferents into nocireceptive layers after nerve injury. Here we show that, in the thoracic spinal cord of naïve adult mouse, all myelinated nociceptors gave rise to terminal projections throughout the superficial dorsal horn laminae (I–II). Most (70%) of these fibers had large‐diameter axons with recurving flame‐shaped central arbors that projected throughout the dorsal horn laminae I–V. This morphology was reminiscent of that attributed to sprouted LTMRs described in previous studies. After peripheral nerve axotomy, we found that LTMR afferents with narrow, uninflected somal action potentials did not sprout into superficial laminae of the dorsal horn. Only myelinated noiceptive afferents with broad, inflected somal action potentials were found to give rise to recurving collaterals and project into superficial “pain‐specific” laminae after axotomy. We conclude that the previously undocumented central morphology of large, myelinated cutaneous nociceptors may very well account for the morphological findings previously thought to require sprouting of LTMRs. J. Comp. Neurol. 508:500–509, 2008. © 2008 Wiley‐Liss, Inc.
Modified equilibrium on line method for imposition of Neumann boundary conditions in meshless collocation methods
Authors: Sadeghirad A. , Kani I. Mahmoudzadeh 
Published: March 2008

AbstractA modified version of the equilibrium on line method (ELM) for imposition of Neumann boundary conditions in collocation methods is presented. In the ELM, equilibrium on lines in the local coordinate systems on the Neumann boundary is satisfied as Neumann boundary condition equations. In other words, integration domains are straight lines for nodes located on the Neumann boundary. Furthermore, the Heaviside function is used as a weight in these integrals. In this paper, a modified procedure for choosing the integration domains is proposed. Also, application of different test functions is examined. The performance of the modified version of the ELM is studied for collocation methods based on two different methods to construct meshless shape functions: moving least‐squares approximation and radial basis point interpolation. Also, the effects of these two meshless interpolation parameters are investigated. Numerical examples of two‐dimensional linear and generalized nonlinear Poisson's equation, linear elasticity and elasto‐plastic analysis are presented to demonstrate the stability, accuracy and convergence of the proposed method. Copyright © 2008 John Wiley & Sons, Ltd.