bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amide exchange rates in Escherichia coli acyl carrier protein: Correlation with protein structure and dynamics
Authors: Andrec Michael , Blake Hill R. , Prestegard James H. 
Published: June 2010

AbstractThe acyl carrier protein (ACP) of Escherichia coli is a 77‐amino acid, highly negatively charged three‐helix protein that plays a central role in fatty acid biosynthesis. Previous NMR studies have suggested the presence of multiple conformations and marginally stable secondary structural elements. The stability of these elements is now examined by monitoring amide exchange in apo‐ACP using NMR‐based methods. Because ACP exhibits many rapid exchange rates, application of traditional isotope exchange methods is difficult. In one approach, heteronuclear correlation experiments with pulsed field‐gradient coherence selection have reduced the time needed to collect two‐dimensional 1H‐15N correlation spectra to the point where measurement of exchange of amide protons for deuterium on the timescale of minutes can be made. In another approach, water proton selective inversion‐exchange experiments were performed to estimate the exchange rates of protons exchanging on timescales of less than a second. Backbone amide protons in the region of helix II were found to exchange significantly more rapidly than those in helices I and III, consistent with earlier structural models suggesting a dynamic disruption of the second helix. Highly protected amides occur on faces of the helices that may pack into a hydrophobic core present in a partially disrupted state.
Crystallization of the MS2 translational repressor alone and complexed to bromouridine
Authors: Ni Chao‐Zhou , Hettinga Bradley S. , Wickersham John , Mitchell Richard S. , Williamson Michael M. , Celikel Reha , Ely Kathryn R. , Prangé Thierry , Fourme Roger , Krapcho Karen J. , Thulin Craig , Talbot Phil , Gesteland Raymond F. 
Published: June 2010

AbstractThe coat protein from the MS2 bacteriophage plays a dual role by encapsidating viral RNA and also by binding RNA as a translational repressor. In order to study the isolated dimer in a conformation not influenced by capsid interactions, a mutant molecule was crystallized that is defective in capsid assembly but is an active repressor. The unassembled dimer crystallized in the space group P21212 with a = 76.2, b = 55.7, and c = 28.4 Å. In these crystals, monomers were related by twofold symmetry. When this dimer was co‐crystallized with 5‐bromouridine, crystals formed in space group R3 with a = b = 155.9 Å, c = 29.9 Å, γ = 120°; the dimer was the asymmetric unit.
Quantitative measurements of the cooperativity in an EF‐hand protein with sequential calcium binding
Authors: Linse Sara , Chazin Walter J. 
Published: June 2010

AbstractPositive cooperativity, defined as an enhancement of the ligand affinity at one site as a consequence of binding the same type of ligand at another site, is a free energy coupling between binding sites. It can be present both in systems with sites having identical ligand affinities and in systems where the binding sites have different affinities. When the sites have widely different affinities such that they are filled with ligand in a sequential manner, it is often difficult to quantify or even detect the positive cooperativity, if it occurs. This study presents verification and quantitative measurements of the free energy coupling between the two calcium binding sites in a mutant form of calbindin D9k. Wild‐type calbindin D9k binds two calcium ions with similar affinities and positive cooperativity — the free energy coupling, ΔΔG, is around ‐8 kJ · mol−1 (Linse S, et al., 1991, Biochemistry 30: 154–162). The mutant, with the substitution Asn 56 → Ala, binds calcium in a sequential manner. In the present work we have taken advantage of the variations among different metal ions in terms of their preferences for the two binding sites in calbindin D9k. Combined studies of the binding of Ca2+, Cd2+, and La3+ have allowed us to conclude that in this mutant ΔΔG < ‐6.4 kJ · mol−1, and that Cd2+ and La3+ also bind to this protein with positive cooperativity. The results justify the use of the (Ca2+), state of the Asn 56 → Ala mutant, as well as the (Cd2+)1 state of the wild type, as models for the half‐saturated states along the two pathways of cooperative Ca2+ binding in calbindin D9k.
Identification of functionally important amino acids in the cellulose‐binding domain of Trichoderma reesei cellobiohydrolase I
Authors: Linder Markus , Mattinen Maija‐Liisa , Kontteli Maarit , Lindeberg Gunnar , Ståhlberg Jerry , Drakenberg Torbjörn , Reinikainen Tapani , Pettersson GÖRan , Annila Arto 
Published: June 2010

AbstractCellobiohydrolase I (CBHI) of Trichoderma reesei has two functional domains, a catalytic core domain and a cellulose binding domain (CBD). The structure of the CBD reveals two distinct faces, one of which is flat and the other rough. Several other fungal cellulolytic enzymes have similar two‐domain structures, in which the CBDs show a conserved primary structure. Here we have evaluated the contributions of conserved amino acids in CBHI CBD to its binding to cellulose. Binding isotherms were determined for a set of six synthetic analogues in which conserved amino acids were substituted. Two‐dimensional NMR spectroscopy was used to assess the structural effects of the substitutions by comparing chemical shifts, coupling constants, and NOEs of the backbone protons between the wild‐type CBD and the analogues. In general, the structural effects of the substitutions were minor, although in some cases decreased binding could clearly be ascribed to conformational perturbations. We found that at least two tyrosine residues and a glutamine residue on the flat face were essential for tight binding of the CBD to cellulose. A change on the rough face had only a small effect on the binding and it is unlikely that this face interacts with cellulose directly.
Three‐dimensional structure of the complex of 4‐guanidino‐Neu5Ac2en and influenza virus neuraminidase
Authors: Varghese Joseph N. , Chandana Epa V. , Colman Peter M. 
Published: June 2010

AbstractThe three‐dimensional X‐ray structure of a complex of the potent neuraminidase inhibitor 4‐guanidino‐Neu5Ac2en and influenza virus neuraminidase (Subtype N9) has been obtained utilizing diffraction data to 1.8 Å resolution. The interactions of the inhibitor, solvent water molecules, and the active site residues have been accurately determined. Six water molecules bound in the native structure have been displaced by the inhibitor, and the active site residues show no significant conformational changes on binding. Sialic acid, the natural substrate, binds in a half‐chair conformation that is isosteric to the inhibitor. The conformation of the inhibitor in the active site of the X‐ray structure concurs with that obtained by theoretical calculations and validates the structure‐based design of the inhibitor. Comparison of known high‐resolution structures of neuraminidase subtypes N2, N9, and B shows good structural conservation of the active site protein atoms, but the location of the water molecules in the respective active sites is less conserved. In particular, the environment of the 4‐guanidino group of the inhibitor is strongly conserved and is the basis for the antiviral action of the inhibitor across all presently known influenza strains. Differences in the solvent structure in the active site may be related to variation in the affinities of inhibitors to different subtypes of neuraminidase.
Probing the solution structure of the DNA‐binding protein Max by a combination of proteolysis and mass spectrometry
Authors: Cohen Steven L. , Chait Brian T. , Ferré‐D'Amaré Adrian R. , Burley Stephen K. 
Published: June 2010

AbstractA simple biochemical method that combines enzymatic proteolysis and matrix‐assisted laser desorption ionization mass spectrometry was developed to probe the solution structure of DNA‐binding proteins. The method is based on inferring structural information from determinations of protection against enzymatic proteolysis, as governed by solvent accessibility and protein flexibility. This approach was applied to the study of the transcription factor Max —a member of the basic/helix‐loop‐helix/zipper family of DNA‐binding proteins. In the absence of DNA and at low ionic strengths, Max is rapidly digested by each of six endoproteases selected for the study, results consistent with an open and flexible structure of the protein. At physiological salt levels, the rates of digestion are moderately slowed; this and the patterns of cleavage are consistent with homodimerization of the protein through a predominantly hydrophobic interface. In the presence of Max‐specific DNA, the protein becomes dramatically protected against proteolysis, exhibiting up to a 100‐fold reduction in cleavage rates. Over a 2‐day period, both complete and partial proteolysis of the Max‐DNA complex is observed. The partial proteolytic fragmentation patterns reflect a very high degree of protection in the N‐terminal and helix‐loop‐helix regions of the protein, correlating with those expected of a stable dimer bound to DNA at its basic N‐terminals. Less protection is seen at the C‐terminal where a slow, sequential proteolytic cleavage occurs, correlating to the presence of a leucine zipper. The results also indicate a high affinity of Max for its target DNA that remains high even when the leucine zipper is proteolytically removed. In addition to the study of the helix‐loop‐helix protein Max, the present method appears well suited for a range of other structural biological applications.
Crystallization and preliminary X‐ray investigation of lipoxygenase‐3 from soybeans
Authors: Axelrod Bernard , Steczko Janusz , Minor Wladek , Stojanoff Vivian 
Published: June 2010

AbstractSoybean lipoxygenase‐3 has been crystallized by the vapor diffusion method in 16–20% polyethylene glycol (average Mr, 3,400), 0.2 M sodium acetate buffer, pH 5.7, at 21 °C, at a protein concentration of 8–15 mg/mL. The crystals, which diffract to 3‐Å spacings, belong to the monoclinic space group C2. Cell constants are a = 111.9, b= 136.4, and c = 61.6 Å and β = 95.7°. The calculated value of Matthews's constant, Vm = 2.48 Å3 /kDa, is consistent with the presence of one molecule of lipoxygenase per crystallographic asymmetric unit (Z = 4).
Disulfide bond tethering of extracellular loops does not affect the closure of OmpF porin at acidic pH
Authors: Wager Beau , Baslé Arnaud , Delcour Anne H. 
Published: June 2010

AbstractThe permeability of the outer membrane of gram‐negative bacteria is essentially controlled by pore‐forming proteins of the porin family. The trimeric E. coli porin OmpF is assembled as a triple β‐barrel, where each monomer contains a central pore and extracellular loops. Electrophysiological analysis of the behavior of OmpF at acidic pH reveals that the protein undergoes a conformational change leading to the sequential step‐wise closure of the three monomers. A previous atomic force microscopy study suggested that the conformational change might be due to a bending of extracellular loops over the pore opening, and loop deletion experiments suggested that loops L1, L7, and L8 are involved. In order to test the hypothesis for loop movement, we engineered a series of double cysteine mutants in loops L1, L6, L7 and L8 in order to create disulfide bonds linking two loops to each other, or the two branches of a loop, or a loop to the β‐barrel. Five out of the six mutants showed the formation of the disulfide bond. However, none of these had an altered response to acidic pH relative to the wildtype channel. Although we cannot dismiss the possibility that the mobility restriction introduced by each disulfide bond was too localized to impact a more global conformational change of the three loops, the fact that all of the different types of disulfide bond tethering were similarly ineffective suggests that the extracellular loops L1, L7, and L8 may not undergo a major acidic‐pH induced conformational change leading to channel closure. Proteins 2010. © 2010 Wiley‐Liss, Inc.
A structural dissection of amino acid substitutions in helical transmembrane proteins
Authors: Mokrab Younes , Stevens Tim J. , Mizuguchi Kenji 
Published: June 2010

AbstractThe evolution of protein folds is under strong constraints from their surrounding environment. Although folding in water‐soluble proteins is driven primarily by hydrophobic forces, the nature of the forces that determine the folding and stability of transmembrane proteins are still not fully understood. Furthermore, the chemically heterogeneous lipid bilayer has a non‐uniform effect on protein structure. In this article, we attempt to get an insight into the nature of this effect by examining the impact of various types of local structure environment on amino acid substitution, based on alignments of high‐resolution structures of polytopic helical transmembrane proteins combined with sequences of close homologs. Compared to globular proteins, burying amino acid sidechains, especially hydrophilic ones, led to a lower increase in conservation in both the lipid‐water interface region and the hydrocarbon core region. This observation is due to surface residues in HTM proteins especially in the HC region being relatively highly conserved, suggesting higher evolutionary constraints from their specific interactions with the surrounding lipid molecules. Polar and small residues, particularly Pro and Gly, show a noticeable increase in conservation as they are positioned more towards the centre of the membrane, which is consistent with their recognized key roles in structural stability. In addition, the examination of hydrogen bonds in the membrane environment identified some exposed hydrophilic residues being better conserved when not hydrogen‐bonded to other residues, supporting the importance of lipid‐protein sidechain interactions. The conclusions presented in this study highlight the distinct features of substitution matrices that take into account the membrane environment, and their potential role in improving sequence‐structure alignments of transmembrane proteins. Proteins 2010; © 2010 Wiley‐Liss, Inc.
ReplicOpter: A replicate optimizer for flexible docking
Authors: Demerdash Omar N. A. , Buyan Amanda , Mitchell Julie C 
Published: June 2010

AbstractWe present a computationally efficient method for flexible refinement of docking predictions that reflects observed motions within a protein's structural class. Using structural homologs, we derive deformation models that capture likely motions. The models or “replicates” typically align along a rigid core, with a handful of flexible loops, linkers and tails. A few replicates can generate a much larger number of conformers, by exchanging each flexible region independently of the others. In this way, 10 replicates of a protein having 6 flexible regions can be used to generate a million conformations of a molecule. While this has obvious advantages in terms of sampling, the cost of assessing energies at every conformer is prohibitive, particularly when both molecules are flexible. Our approach addresses this combinatorial explosion, using key assumptions to compress the sampling by many orders of magnitude. ReplicOpter can perform hierarchical clustering from a list of rigid docking predictions and find nearby structures to any promising cluster representatives. These predicted complexes can then be refined and rescored. ReplicOpter's scoring function includes a Lennard‐Jones potential softened using the Anderson‐Chandler‐Weeks decomposition, a desolvation term derived from the Atomic Contact Energy function, Coulombic electrostatics, hydrogen bonding, and terms to model pi‐pi and pi‐cation interactions. ReplicOpter has performed well on several recent CAPRI systems. We are presently benchmarking ReplicOpter on the complete docking benchmark set to fully establish its utility in refining rigid docking predictions and identifying near‐native solutions. © 2010 Wiley‐Liss, Inc.
Docking by structural similarity at protein‐protein interfaces
Authors: Sinha Rohita , Kundrotas Petras J. , Vakser Ilya A. 
Published: June 2010

AbstractRapid accumulation of experimental data on protein‐protein complexes drives the paradigm shift in protein docking from “traditional,” template free approaches to template based techniques. Homology docking algorithms based on sequence similarity between target and template complexes can account for up to 20% of known protein‐protein interactions. When highly homologous templates for the target complex are not available, but the structure of the target monomers is known, docking by local structural alignment may provide an adequate solution. Such an algorithm was developed based on the structural comparison of monomers to cocrystallized interfaces. A library of the interfaces was generated from cocrystallized protein‐protein complexes in PDB. The partial structure alignment algorithm was validated on the DOCKGROUND benchmark sets. The optimal performance of the partial (interface) structure alignment was achieved with the interface residues defined by 12 Å distance across the interface. Overall, the partial structure alignment yielded more accurate models than the full structure alignment. Most templates identified by the partial structure alignment had low sequence identity to the target, which makes them hard to detect by sequence‐based methods. The results indicate that the structure alignment techniques provide a much needed addition to the docking arsenal, with the combined structure alignment and template free docking success rate significantly surpassing that of the free docking alone. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Correlation of anatase particle size with photocatalytic properties
Authors: Lee Sangwook , Cho In‐Sun , Noh Jun‐Hong , Hong Kug Sun , Han Gill Sang , Jung Hyun Suk , Jeong Seonghoon , Lee Chanjong , Shin Hyunho 
Published: June 2010

AbstractThe influence of the anatase TiO2 particle size on the photocatalytic properties was systematically investigated on the nanometer‐size scale. The anatase TiO2 crystallite size estimated using the Scherrer equation was varied from 8.0 to 16.4 nm, and the photocatalytic properties were significantly deteriorated with decreasing crystallites size. The photocurrent measurements showed that the charge generation diminished with decreasing TiO2 particle size. The bandgap energies were measured as a function of the particle size using UV–Vis spectroscopy in order to investigate the origin of the lowered charge‐generation characteristics. The absorption band edge shift was found in the anatase nanocrystallites, which was attributed to the quantum size effect. Therefore, the increased bandgap energy induced the low light absorption capability, which was responsible for the low photoactivity of the very tiny anatase nanoparticles. These findings demonstrated that the particle‐size reduction was not the best way to maximize the photocatalytic properties of TiO2 because of the diminished light absorption.
Properties of zinc‐oxide nanoparticles synthesized by electrical‐discharge technique in liquids
Authors: Tarasenko Nikolai , Nevar Alena , Nedelko Mikhail 
Published: June 2010

AbstractThe capabilities of a plasma‐assisted technique based on electrical discharge in liquids for synthesis of N‐doped and In–N codoped ZnO nanocrystals have been analyzed. The synthesis was carried out in a reactor containing aqueous ammonium nitrate solution of 0.001 M concentration. The pulsed‐spark discharges between Zn–Zn and Zn–In electrodes have been used with further deposition of the synthesized particles on the silicon substrates. The optical properties, morphology, and composition of the nanoparticles formed were investigated by means of UV–Vis absorption spectroscopy, SEM, EDX, and XRD. As it followed from the XRD patterns the synthesized product was composed of hexagonal ZnO nanocrystals. The positions of the reflection peaks were observed to be varied with the composition of dopants. The influence of doping level on the structural and optical properties of synthesized nanoparticles has been discussed.
Compact modeling of optically gated carbon nanotube field effect transistor
Authors: Liao Si‐Yu , Maneux Cristell , Pouget Vincent , Frégonèse Sébastien , Zimmer Thomas 
Published: June 2010

AbstractNanoelectronic circuit design flow is based on device description through the compact models available in the designer device library. We have developed a compact model for the optically gated carbon nanotube field effect transistor (OG‐CNTFET) by investigating the trapping and detrapping of electron effects in the device. This compact model represents an important enhancement of conventional CNTFET models already released. Especially, it includes the optical writing, the electrical reset, and the non‐volatile memory effect of the device operations. We also demonstrate that the simulation results obtained using this compact model, are in close agreement with preliminary experimental measurements.
Modification of response properties of the Be(0001) surface upon adsorption of a potassium monolayer: An ab initio calculation
Authors: Silkin V. M. , Chulkov E. V. , Echeverry J. P. , Echenique P. M. 
Published: June 2010

AbstractCollective electronic excitations associated with a potassium monolayer (1 ML) on a Be(0001) substrate are studied using ab initio evaluations of the surface response function with the use of energies and wave functions obtained from the self‐consistent pseudopotential calculations. The plasmon dispersion relations as well as real and imaginary parts of the dynamical induced charge density oscillations are presented. Comparison of the collective modes of the 1 ML K/Be(0001) system with that of a clean Be(0001) surface is given. It is shown that the K monolayer adsorption leads to appearance, additionally to the conventional surface plasmon of a clean Be surface, of a low‐energy mode with characteristic acoustic‐like dispersion in the 0–2 eV energy range. The existence of this mode owes to the presence of a K‐induced quantum‐well‐state band whose wave function is strongly localized in the K adlayer. Also we observe a K‐derived multipole plasmon with energy around 3 eV. Some other modifications in the Be surface plasmon properties upon K adsorption are discussed as well.
An ab initio study of hydrogen adsorption on the (020) surface of α‐Pu
Authors: Islam M. Fhokrul , Ray Asok K. 
Published: June 2010

AbstractAtomic hydrogen adsorptions on the (020) surface of α‐Pu and the effects of surface relaxation on adsorption properties have been studied using a relativistic extension of the full‐potential augmented plane wave with local orbital basis method. The surface has been modeled by a four‐layer periodic slab consisting of 32 Pu atoms with a layer by layer anti‐ferromagnetic arrangement. The adsorption properties for four different adsorption sites, namely the top, hollow, short bridge and long bridge sites have been investigated in detail. All computations have been carried out at two different theoretical levels, namely the scalar relativistic level without spin–orbit interaction (SR‐NSO) and the fully relativistic level with spin–orbit interaction (FR‐SO). The effect of relaxation has also been studied by calculating adsorption properties both on relaxed and non‐relaxed Pu surfaces. Our studies show that the short bridge is the most favorable site for hydrogen adsorption with chemisorptions energies of 2.78 and 2.75 eV, respectively, at the two levels of theory. Neither spin–orbit coupling nor surface relaxation appears to have significant effects on adsorption.