bluuebunny/crossref_metadata_2025_split huggingface dataset:
Motions and structural variability within toxins: Implication for their use as scaffolds for protein engineering
Authors: Gilquin Bernard , Bourgoin Marjorie , Ménez Renée , Le Du Marie‐Hélène , Servent Denis , Zinn‐Justin Sophie , Ménez André 
Published: January 2003

AbstractAnimal toxins are small proteins built on the basis of a few disulfide bonded frameworks. Because of their high variability in sequence and biologic function, these proteins are now used as templates for protein engineering. Here we report the extensive characterization of the structure and dynamics of two toxin folds, the “three‐finger” fold and the short α/β scorpion fold found in snake and scorpion venoms, respectively. These two folds have a very different architecture; the short α/β scorpion fold is highly compact, whereas the “three‐finger” fold is a β structure presenting large flexible loops. First, the crystal structure of the snake toxin α was solved at 1.8‐Å resolution. Then, long molecular dynamics simulations (10 ns) in water boxes of the snake toxin α and the scorpion charybdotoxin were performed, starting either from the crystal or the solution structure. For both proteins, the crystal structure is stabilized by more hydrogen bonds than the solution structure, and the trajectory starting from the X‐ray structure is more stable than the trajectory started from the NMR structure. The trajectories started from the X‐ray structure are in agreement with the experimental NMR and X‐ray data about the protein dynamics. Both proteins exhibit fast motions with an amplitude correlated to their secondary structure. In contrast, slower motions are essentially only observed in toxin α. The regions submitted to rare motions during the simulations are those that exhibit millisecond time‐scale motions. Lastly, the structural variations within each fold family are described. The localization and the amplitude of these variations suggest that the regions presenting large‐scale motions should be those tolerant to large insertions or deletions.
Turn stability in β‐hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns
Authors: Blandl Tamas , Cochran Andrea G. , Skelton Nicholas J. 
Published: January 2003

AbstractThe turn‐forming ability of a series of three‐residue sequences was investigated by substituting them into a well‐characterized β‐hairpin peptide. The starting scaffold, bhpW, is a disulfide‐cyclized 10‐residue peptide that folds into a stable β‐hairpin with two antiparallel strands connected by a two‐residue reverse turn. Substitution of the central two residues with the three‐residue test sequences leads to less stable hairpins, as judged by thiol‐disulfide equilibrium measurements. However, analysis of NMR parameters indicated that each molecule retains a significant folded population, and that the type of turn adopted by the three‐residue sequence is the same in all cases. The solution structure of a selected peptide with a PDG turn contained an antiparallel β‐hairpin with a 3:5 type I + G1 bulge turn. Analysis of the energetic contributions of individual turn residues in the series of peptides indicates that substitution effects have significant context dependence, limiting the predictive power of individual amino acid propensities for turn formation. The most stable and least stable sequences were also substituted into a more stable disulfide‐cyclized scaffold and a linear β‐hairpin scaffold. The relative stabilities remained the same, suggesting that experimental measurements in the bhpW context are a useful way to evaluate turn stability for use in protein design projects. Moreover, these scaffolds are capable of displaying a diverse set of turns, which can be exploited for the mimicry of protein loops or for generating libraries of reverse turns.
On the evaluation and optimization of protein X‐ray structures for pKa calculations
Authors: Nielsen Jens Erik , McCammon J. Andrew 
Published: January 2003

AbstractThe calculation of the physical properties of a protein from its X‐ray structure is of importance in virtually every aspect of modern biology. Although computational algorithms have been developed for calculating everything from the dynamics of a protein to its binding specificity, only limited information is available on the ability of these methods to give accurate results when used with a particular X‐ray structure. We examine the ability of a pKa calculation algorithm to predict the proton‐donating residue in the catalytic mechanism of hen egg white lysozyme. We examine the correlation between the ability of the pKa calculation method to obtain the correct result and the overall characteristics of 41 X‐ray structures such as crystallization conditions, resolution, and the output of structure validation software. We furthermore examine the ability of energy minimizations (EM), molecular dynamics (MD) simulations, and structure‐perturbation methods to optimize the X‐ray structures such that these give correct results with the pKa calculation algorithm. We propose a set of criteria for identifying the proton donor in a catalytic mechanism, and demonstrate that the application of these criteria give highly accurate prediction results when using unmodified X‐ray structures. More specifically, we are able to successfully identify the proton donor in 85% of the X‐ray structures when excluding structures with crystal contacts near the active site. Neither the use of the overall characteristics of the X‐ray structures nor the optimization of the structure by EM, MD, or other methods improves the results of the pKa calculation algorithm. We discuss these results and their implications for the design of structure‐based energy calculation algorithms in general.
Amino acid sequence and homology modeling of obtustatin, a novel non‐RGD‐containing short disintegrin isolated from the venom ofVipera lebetina obtusa
Authors: Moreno‐Murciano M. Paz , Monleón Daniel , Calvete Juan J. , Celda Bernardo , Marcinkiewicz Cezary 
Published: January 2003

AbstractDisintegrins represent a group of cysteine‐rich peptides occurring inCrotalidaeandViperidaesnake venoms, and are potent antagonists of several integrin receptors. A novel disintegrin, obtustatin, was isolated from the venom of theVipera lebetina obtusaviper, and represents the first potent and selective inhibitor of the binding of integrin α1β1to collagen IV. The primary structure of obtustatin contains 41 amino acids and is the shortest disintegrin described to date. Obtustatin shares the pattern of cysteines of other short disintegrins. However, in contrast to known short disintegrins, the integrin‐binding loop of obtustatin is two residues shorter and does not express the classical RGD sequence. Using synthetic peptides, a KTS motif was identified as the integrin‐binding sequence. A three‐dimensional model of obtustatin, built by homology‐modeling structure calculations using different templates and alignments, strongly indicates that the novel KTS motif may reside at the tip of a flexible loop.
Low free energy cost of very long loop insertions in proteins
Authors: Scalley‐Kim Michelle , Minard Philippe , Baker David 
Published: January 2003

AbstractLong insertions into a loop of a folded host protein are expected to have destabilizing effects because of the entropic cost associated with loop closure unless the inserted sequence adopts a folded structure with amino‐ and carboxy‐termini in close proximity. A loop entropy reduction screen based on this concept was used in an attempt to retrieve folded sequences from random sequence libraries. A library of long random sequences was inserted into a loop of the SH2 domain, displayed on the surface of M13 phage, and the inserted sequences that did not disrupt SH2 function were retrieved by panning using beads coated with a phosphotyrosine containing SH2 peptide ligand. Two sequences of a library of 2 × 108 sequences were isolated after multiple rounds of panning, and were found to have recovery levels similar to the wild‐type SH2 domain and to be relatively intolerant to further mutation in PCR mutagenesis experiments. Surprisingly, although these inserted sequences exhibited little nonrandom structure, they do not significantly destabilize the host SH2 domain. Additional insertion variants recovered at lower levels in the panning experiments were also found to have a minimal effect on the stability and peptide‐binding function of the SH2 domain. The additional level of selection present in the panning experiments is likely to involve in vivo folding and assembly, as there was a rough correlation between recovery levels in the phage‐panning experiments and protein solubility. The finding that loop insertions of 60–80 amino acids have minimal effects on SH2 domain stability suggests that the free energy cost of inserting long loops may be considerably less than polymer theory estimates based on the entropic cost of loop closure, and, hence, that loop insertion may have provided an evolutionary route to multidomain protein structures.
High‐pressure 1H NMR study of pressure‐induced structural changes in the heme environments of metcyanomyoglobins
Authors: Kitahara Ryo , Kato Minoru , Taniguchi Yoshihiro 
Published: January 2003

AbstractThe effect of pressure on the heme environment structure of sperm whale and horse heart metcyanomyoglobins was investigated up to 300 MPa by high‐pressure 1H NMR spectroscopy. Pressure‐induced changes in the distances between the observed protons and the heme iron atom were estimated from changes in the dipolar shift due to the paramagnetic effect on the protons. The changes showed that the heme peripheral structure as a whole was compressed by pressure; the movements of the protons in the heme peripheral residues were in the range of +0.16 to −0.54 Å/300 MPa. One‐dimensional compressibilities for the protons, excluding the protons of the distal His residue, were in the range of 1.0 × 10−4 to 6.1 × 10−4/MPa. The movements of the protons induced by pressure correlated well with the distance between the protons and cavities in the protein. The distal His residue (His 64) moved toward the outside of the heme pocket, but remained in the pocket even at 300 MPa. This movement was driven dominantly by a change in the dihedral angle around the Cα–Cβ rotational bond of the residue. Comparative work on horse heart metcyanomyoglobin implied that the conformational change of the His 64 imidazole ring was larger in the horse heart metcyanomyoglobin than in the sperm whale metcyanomyoglobin.
Dronerarone Acts as a Selective Inhibitor of 3,5,3′-Triiodothyronine Binding to Thyroid Hormone Receptor-α1: In Vitro and in Vivo Evidence
Authors: van Beeren H. C. , Jong W. M. C. , Kaptein E. , Visser T. J. , Bakker O. , Wiersinga W. M. 
Published: January 2003

Dronedarone (Dron), without iodine, was developed as an alternative to the iodine-containing antiarrhythmic drug amiodarone (AM). AM acts, via its major metabolite desethylamiodarone, in vitro and in vivo as a thyroid hormone receptor α1 (TRα1) and TRβ1 antagonist. Here we investigate whether Dron and/or its metabolite debutyldronedarone inhibit T3 binding to TRα1 and TRβ1in vitro and whether dronedarone behaves similarly to amiodarone in vivo.
In vitro , Dron had a inhibitory effect of 14% on the binding of T3 to TRα1, but not on TRβ1. Desethylamiodarone inhibited T3 binding to TRα1 and TRβ1 equally. Debutyldronedarone inhibited T3 binding to TRα1 by 77%, but to TRβ1 by only 25%.
In vivo , AM increased plasma TSH and rT3, and decreased T3. Dron decreased T4 and T3, rT3 did not change, and TSH fell slightly. Plasma total cholesterol was increased by AM, but remained unchanged in Dron-treated animals. TRβ1-dependent liver low density lipoprotein receptor protein and type 1 deiodinase activities decreased in AM-treated, but not in Dron-treated, animals. TRα1-mediated lengthening of the QTc interval was present in both AM- and Dron-treated animals.
The in vitro and in vivo findings suggest that dronedarone via its metabolite debutyldronedarone acts as a TRα1-selective inhibitor.
ABA- and cADPR-mediated effects on respiration and filtration downstream of the temperature-signaling cascade in sponges
Authors: Zocchi Elena , Basile Giovanna , Cerrano Carlo , Bavestrello Giorgio , Giovine Marco , Bruzzone Santina , Guida Lucrezia , Carpaneto Armando , Magrassi Raffaella , Usai Cesare 
Published: January 2003

Recently, the thermosensing pathway in sponges (Porifera) was elucidated. The thermosensor triggering this cascade is a heat-activated cation channel,with the phytohormone abscisic acid (ABA), cyclic ADP-ribose (cADPR) and calcium acting as intracellular messengers, similarly to the drought-stress signaling cascade in higher plants. Here, we investigated the functional effects downstream of the temperature-signaling pathway in Axinella polypoides (Porifera, Demonspongiae).Short-term stimulation followed by long-term depression of amino acid incorporation, oxygen consumption and water filtration were observed after exposure of the sponge to a brief heat stress or to micromolar ABA. These effects could be prevented by the targeted interruption of the signaling pathway either at the level of the cation channel thermosensor or at the level of the cADPR-induced intracellular calcium increase. Moreover, release of cyclase activity into the sea water and generation of extracellular cADPR were observed following brief heat stress. Intact sponge cells were sensitive to extracellular cADPR and addition of purified cyclase increased sponge respiration similarly to heat stress.This is the first observation of functional effects exerted on Metazoa by the phytohormone ABA: conservation of the ABA/cADPR stress-signaling cascade points to its early evolution in a common precursor of modern Metazoa and Metaphyta. The functional effects induced by extracellular cyclase/cADPR suggest an evolutionary origin of cADPR as an ancient stress hormone in Porifera.
Promoting Environmental Innovation in the Energy Sector: An Analytcial Framework for Dynamic Efficiency Assessments
Authors: Christiansen Atle Christer 
Published: January 2003

It is increasingly being recognised that the development, adoption and diffusion of cleaner energy technologies are key determinants to success or failure in environmental policy, at least in the long term. However, it is still unclear what specific role there is for public policies and regulatory intervention in this field, and how to select an appropriate portfolio of policy action and instruments that does justice to all stages in the development cycle of technological change. The key objective of this paper is to provide an analytical framework for analysing and assessing the way in which public policy can promote environmentally benign technological change. The framework comprises a template that blends a mechanistic representation of causal variable-impact relationships with knowledge and insights from empirical research. “It is widely agreed that technical innovation is the ultimate key to successful (meaning affordable as well as quantitatively adequate) global measures to stabilise the concentration of GHGs in the atmosphere” (Toman, 1998: 610)
Superbeads: Immobilization in “Sweet” Chemistry
Authors: Nahalka Jozef , Liu Ziye , Chen Xi , Wang Peng George 
Published: January 2003

AbstractEnzymatic oligosaccharide synthesis using recombinant glycosyltransferases is able to overcome the difficulties associated with chemical methods. Nonetheless, sugar nucleotide regeneration cycles are necessary for the glycosylation. The multistep enzyme reaction can be efficiently carried out on superbeads that are prepared by immobilizing multienzyme mixtures on bead support through fused binding domains.
Diastereoselective Hydroformylation of 2‐Substituted Allylic o‐DPPB‐Esters—On the Origin of 1,2‐Asymmetric Induction
Authors: Breit Bernhard , Heckmann Golo , Zahn Stephan K. 
Published: January 2003

Abstract2‐Substituted secondary alcohol o‐DPPB esters (o‐DPPB=ortho‐diphenylphosphanylbenzoyl) have been prepared and their o‐DPPB‐directed diastereoselective hydroformylation examined. It was found that the diastereoselectivity increased as a function of the steric demand of the substituents both at the stereogenic center and in the alkene 2‐position. Hydrolytic cleavage of the o‐DPPB group afforded—via the lactols 29—the corresponding lactones 30, the relative configurations of the vicinal stereogenic centers of which were ascertainable by 2D‐NOESY spectroscopy. In addition, a crystal structure analysis of the hydroformylation product 2 d provided further confirmation of the relative configuration. Replacement of the ester carbonyl group of the o‐DPPB by a methylene unit resulted in significantly worse diastereoselectivity in the course of the hydroformylation (34→35), which indicates a decisive role for the ester carbonyl function. All the experimental observations were combined in a model of the origin of the 1,2‐asymmetric induction during the title reaction. The key feature is the consideration of diastereomeric trigonal‐bipyramidal rhodium‐hydrido‐olefin complexes I and II, capable on the basis of the Hammond postulate of acting as good models for the transition states of the selectivity‐determining hydrometalation step. Investigation of these complexes by force‐field methods indicated good correlation between theoretically predicted and experimentally determined diastereoselectivities.
Side‐On Bridging Coordination of N2: Spectroscopic Characterization of the Planar Zr2N2 Core and Theoretical Investigation of Its Butterfly Distortion
Authors: Studt Felix , Morello Lara , Lehnert Nicolai , Fryzuk Michael D. , Tuczek Felix 
Published: January 2003

AbstractThe vibrational and electronic structure of the side‐on N2‐bridged Zr complex [{(P2N2)Zr}2(μ‐η2:η2‐N2)] (P2N2=PhP(CH2SiMe2NSiMe2CH2)2PPh) were analyzed. The vibrational characterization of the planar Zr2N2 core was based on resonance Raman and infrared spectroscopy. In the Raman spectrum, the NN stretching band is found at 775 cm−1 with an isotope shift of 22 cm−1. Due to its appearance in many overtones and combination modes, the metal–metal stretch is assigned to the peak at 295 cm−1. The two ungerade modes of the Zr2N2 core were identified in the infrared spectrum. Based on these four vibrations of the Zr2N2 unit, a quantum chemical assisted normal coordinate analysis (QCA‐NCA) was performed. The force constants for the NN and ZrN bonds were calculated to be 1.53 and 2.58 mdyn Å−1, respectively. The butterfly distortion of the Zr2N2 unit obtained in DFT geometry optimizations of planar side‐on N2‐bridged Zr complexes was analyzed in more detail. It was found that on bending of the Zr2N2 core, the lone pairs of the axial amide ligands are rotated by 90°. The bent Zr2N2 unit is 11 kcal mol−1 lower in energy than the planar core due to a more uniform distribution of electron density between the metal atoms and N2 and delocalization of electron density from the amide ligands to the Zr2N2 unit. The spectroscopic implications of this distortion are analyzed.
Central projections of thoracic splanchnic and somatic nerves and the location of sympathetic preganglionic neurons in Xenopus laevis
Authors: Nakano Masato , Kishida Reiji , Funakoshi Kengo , Tsukagoshi Midori , Goris Richard C. , Kadota Tetsuo , Atobe Yoshitoshi , Hisajima Tatsuya 
Published: January 2003

AbstractThe central and peripheral organization of thoracic visceral and somatic nervous elements was studied by applying dextran amines to the proximal cut ends of the thoracic splanchnic and somatic nerves in Xenopus laevis. Many labeled dorsal root ganglion cells of visceral afferents, and all somatic afferents, were located in a single ganglion of one spinal segment, and the two types of cells were distributed topographically within the ganglion. The labeled sympathetic preganglionic neurons were located predominantly in the same area of the thoracic spinal gray as in other frogs and in mammals. The labeled visceral afferents projected to Lissauer's tract and the dorsal funiculus. The visceral fibers of the tract ascended to the level of the subcerebellar area, supplying collateral branches to the lateral one‐third of the dorsal horn and to the area of brainstem nuclei, including lateral cervical and descending trigeminal nucleus, and descended to the filum terminale. The visceral fibers of the dorsal funiculus were distributed to the dorsal column nucleus and the solitary tract. A similar longitudinal projection was also seen in the somatic afferents. The dual central pathway of thoracic primary afferents in the anuran spinal cord is a property held in common with mammals, but the widespread rostrocaudal projection through Lissauer's tract may be a characteristic of the anuran central nervous system. In frogs, the direct transmission of primary afferent information to an extremely wide area of the central nervous system may be important for prompt assessment of environmental factors and control of body functions. J. Comp. Neurol. 456:321–337, 2003. © 2003 Wiley‐Liss, Inc.
Comparison of antiangiogenic activities using paclitaxel (taxol) and docetaxel (taxotere)
Authors: Grant Derrick S. , Williams Torian L. , Zahaczewsky Michael , Dicker Adam P. 
Published: January 2003

AbstractTumor growth requires a competent vascular supply and angiogenesis has been considered as a potential target for the treatment of several cancers. The two clinically approved taxanes, paclitaxel and docetaxel, are novel antimitotic agents that are under extensive investigation in clinical trials. Both taxanes have demonstrated significant activity against many solid tumors, but little is known about the effect of paclitaxel and docetaxel on endothelial cell function and angiogenic processes. The purpose of our study was to examine and compare the effects of these drugs on angiogenic processes in vitro and in vivo. These processes include: proliferation, migration and differentiation of cultured human umbilical vein endothelial cells (HUVEC) (in vitro), capillary sprouting of rat aortic ring explants (ex vivo) and HT1080 tumor growth in vivo. Our results demonstrate that endothelial cells are 10–100‐fold more sensitive to these drugs than tumor cells. Additionally, comparison of the taxanes demonstrated that angiogenesis is blocked by both drugs primarily via inhibition of proliferation and differentiation (tube assay) and induction of cell death. Docetaxel, however, appears to be more potent at inhibiting angiogenesis, with an IC50 concentration 10× less than that of paclitaxel. We conclude that these important findings should be taken in account in clinical trials where tumor angiogenesis is being targeted. © 2002 Wiley‐Liss, Inc.