bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the synthesis and optical properties of sulfur‐bridged analogues of triangulenium cations and their precursors
Authors: Nicolas Cyril , Bernardinelli Gérald , Lacour Jérôme 
Published: June 2010

AbstractSeveral sulfur‐bridged heterocyclic carbocations of the acridinium and triangulenium family were prepared using 9‐(2,6‐dimethoxyphenyl)‐1,8‐dimethoxy‐thioxanthenium tetrafluoroborate [7][BF4] as key synthetic intermediate. Thanks to simple yet not so facile aromatic nucleophilic substitution reactions, thiachromenoacridinium, azaoxa‐ and dioxathiotriangulenium salts (e.g., [8][BF4], [9][BF4], and [10][BF4], respectively) were obtained in moderate to good yields. Importantly, from the crystal structural analysis of 9‐(2,6‐dimethoxyphenyl)‐1,8‐dimethoxy‐9H‐thioxanthen‐9‐ol 16, bond lengths between sulfur and carbon atoms were confirmed to be much longer than that of classical CO or CN in analogous frameworks. This clearly triggers a distortion of the sulfur‐containing six‐membered ring which can be invoked to explain the relative lack of stabilization of the resulting carbenium ions. The increased electrophilicity of the central carbon set off a strongly reduced reactivity towards SNAr reactions. A comparison between electronic absorption spectra of the sulfur‐bridged dyes and their aza analogues was also carried out. A ca. 50 nm shift towards the low energy region was found to occur upon the insertion of the sulfur atom. Copyright © 2010 John Wiley & Sons, Ltd.
Hyperconjugation in β,β′‐silyl substituted vinyl cations – indications from IR spectroscopy
Authors: Klaer Andrea , Müller Thomas 
Published: June 2010

AbstractAlkyl substituted vinyl cations 1a–c have been synthesized in the form of their [B(C6F5)4]− salts and have been characterized by NMR and IR spectroscopy. The IR absorption bands detected for the νas(CC+) vibrations in vinyl cations are of great diagnostic value, due to their high intensity and relative isolated position in the IR spectra ($\tilde {\nu }$ = 1930–2020 cm−1). DFT calculations of the harmonic force constants at the B3LYP/cc‐pvtz level of theory allowed for an unequivocal assignment of the band after scaling of the theoretical values to account for the anharmonicity of the experimental vibrational potential. A study on the energy of the νas(CC+) of alkyl (1) and aryl substituted vinyl cations (2) revealed a systematic trend, which indicates a decreasing stabilization of the vinyl cations by β‐SiC hyperconjugation when the electron donating ability of the substituent R2 next to the positively charged carbon atom is increased. Copyright © 2010 John Wiley & Sons, Ltd.
Three‐dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping
Authors: Lee Hsiau‐Wei , Wylie Greg , Bansal Sonal , Wang Xu , Barb Adam W. , Macnaughtan Megan A. , Ertekin Asli , Montelione Gaetano T. , Prestegard James H. 
Published: June 2010

AbstractThe traditional NMR‐based method for determining oligomeric protein structure usually involves distinguishing and assigning intra‐ and intersubunit NOEs. This task becomes challenging when determining symmetric homo‐dimer structures because NOE cross‐peaks from a given pair of protons occur at the same position whether intra‐ or intersubunit in origin. While there are isotope‐filtering strategies for distinguishing intra from intermolecular NOE interactions in these cases, they are laborious and often prove ineffectual in cases of weak dimers, where observation of intermolecular NOEs is rare. Here, we present an efficient procedure for weak dimer structure determination based on residual dipolar couplings (RDCs), chemical shift changes upon dilution, and paramagnetic surface perturbations. This procedure is applied to the Northeast Structural Genomics Consortium protein target, SeR13, a negatively charged Staphylococcus epidermidis dimeric protein (Kd 3.4 ± 1.4 mM) composed of 86 amino acids. A structure determination for the monomeric form using traditional NMR methods is presented, followed by a dimer structure determination using docking under orientation constraints from RDCs data, and scoring under residue pair potentials and shape‐based predictions of RDCs. Validation using paramagnetic surface perturbation and chemical shift perturbation data acquired on sample dilution is also presented. The general utility of the dimer structure determination procedure and the possible relevance of SeR13 dimer formation are discussed.
Structure and dynamics of the water around myoglobin
Authors: Phillips George N. , Montgomery Pettitt B. 
Published: June 2010

AbstractThe interplay between simulations at various levels of hydration and experimental observables has led to a picture of the role of solvent in thermodynamics and dynamics of protein systems. One of the most studied protein‐solvent systems is myoglobin, which serves as a paradigm for the development of structure‐function relationships in many biophysical studies. We review here some aspects of the solvation of myoglobin and the resulting implications. In particular, recent theoretical and simulation studies unify much of the diverse set of experimental results on water near proteins.
Early intermediates in the folding of dihydrofolate reductase from escherichia coli detected by hydrogen exchange and NMR
Authors: Jones Bryan E. , Robert Matthews C. 
Published: June 2010

AbstractThe kinetic folding mechanism for Escherichia coli dihydrofolate reductase postulates two distinct types of transient intermediates. The first forms within 5 ms and has substantial secondary structure but little stability. The second is a set of four species that appear over the course of several hundred milliseconds and have secondary structure, specific tertiary structure, and significant stability (Jennings PA, Finn BE, Jones BE, Matthews CR, 1993, Biochemistry 52:3783–3789). Pulse labeling hydrogen exchange experiments were performed to determine the specific amide hydrogens in α‐helices and β‐strands that become protected from exchange through the formation of stable hydrogen bonds during this time period. A significant degree of protection was observed for two subsets of the amide hydrogens within the dead time of this experiment (6 ms). The side chains of one subset form a continuous nonpolar strip linking six of the eight strands in the β‐sheet. The other subset corresponds to a non‐polar cluster on the opposite face of the sheet and links three of the strands and two α‐helices. Taken together, these data demonstrate that the complex strand topology of this eight‐stranded sheet can be formed correctly within 6 ms. Measurement of the protection factors at three different folding times (13 ms, 141 ms, and 500 ms) indicates that, of the 13 amide hydrogens displaying significant protection within 6 ms, 8 exhibit an increase in their protection factors from ∼5 to ∼50 over this time range; the remaining five exhibit protection factors >100 at 13 ms. Only approximately half of the population of molecules form this set of stable hydrogen bonds. Thirteen additional hydrogens in the β‐sheet become protected from exchange as the set of native conformers appear, suggesting that the stabilization of this network reflects the global cooperativity of the folding reaction.
Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c
Authors: Lo Terence P. , Murphy Michael E.P. , Guy Guillemette J. , Smith Michael , Brayer Gary D. 
Published: June 2010

AbstractA cluster of highly conserved leucine side chains from residues 9, 68, 85, 94, and 98 is located in the hydrophobic heme pocket of cytochrome c. The contributions of two of these, Leu 85 and Leu 94, have been studied using a protein structure‐function‐mutagenesis approach to probe their roles in the maintenance of overall structural integrity and electron transfer activity. Structural studies of the L85C, L85F, L85M, and L94S mutant proteins show that, in each case, the overall fold of cytochrome c is retained, but that localized conformational shifts are required to accommodate the introduced side chains. In particular, the side chains of Cys 85 and Phe 85 form energetically favorable interactions with Phe 82, whereas Met 85 takes on a more remote conformation to prevent an unfavorable interaction with the phenyl ring of Phe 82. In the case of the L94S mutant protein, the new polar group introduced is found to form hydrogen bonds to nearby carbonyl groups. In all proteins with substitutions at Leu 85, the hydrophobic nature of the heme pocket is preserved and no significant decrease in heme reduction potential is observed. Despite earlier predictions that Leu 85 is an important determinant in cytochrome c electron transfer partner complexation, our studies show this is unlikely to be the case because the considerable surface contour perturbations made by substitutions at this residue do not correspondingly translate into significant changes in electron transfer rates. For the L94S mutant protein, the substitution of a polar hydroxyl group directly into the hydrophobic heme pocket has a larger effect on heme reduction potential, but this is mitigated by two factors. First, the side chain of Ser 94 is rotated away from the heme group and, second, the side chain of Leu 98 shifts into a portion of the new space available, partially shielding the heme group. The Leu 94 Ser substitution does not perturb the highly conserved interface formed by the nearly perpendicular packing of the N‐ and C‐terminal helices of cytochrome c, ruling this out as the cause of this mutant protein becoming thermally labile and having a lower functional activity. Our results show these effects are most likely attributable to disruption of the heme pocket region. Much of the ability of cytochrome c to absorb the introduction of mutations at Leu 85 and Leu 94 appears to be a consequence of the conformational flexibility afforded by the leucine cluster in this region as well as the presence of a nearby internal cavity. It is possible that these two structural features play a part in providing structural flexibility between oxidation states in the course of cytochrome c electron transfer.
Neural networks for secondary structure and structural class predictions
Authors: Chandonia John‐Marc , Karplus Martin 
Published: June 2010

AbstractA pair of neural network‐based algorithms is presented for predicting the tertiary structural class and the secondary structure of proteins. Each algorithm realizes improvements in accuracy based on information provided by the other. Structural class prediction of proteins nonhomologous to any in the training set is improved significantly, from 62.3% to 73.9%, and secondary structure prediction accuracy improves slightly, from 62.26% to 62.64%. A number of aspects of neural network optimization and testing are examined. They include network overtraining and an output filter based on a rolling average. Secondary structure prediction results vary greatly depending on the particular proteins chosen for the training and test sets; consequently, an appropriate measure of accuracy reflects the more unbiased approach of “jackknife” cross‐validation (testing each protein in the database individually).
Strategies and rationales for the de novo design of a helical hairpin peptide
Authors: Fezoui Youcef , Weaver David L. , Osterhout John J. 
Published: June 2010

AbstractThe de novo design of αtα, a helical hairpin peptide, is described. αtα (α‐helix/turn/α‐helix) was developed to provide a model system for protein folding at the level of secondary structure association and stabilization. According to the prevailing models of protein folding, the second step in the folding process is the association and stabilization of secondary structural elements or microdomains. A brief description of the design, along with CD and NMR evidence confirming the conformation of the peptide in solution, has been published (Fezoui Y, Weaver DL, Osterhout JJ, 1994, Proc Natl Acad Sci USA 91:3675–3679). The present work includes a full description of the design process, including the trade‐offs that were made during the development of the peptide, a discussion of recent experimental results that were not available at the time of the original design, indications of areas where, in retrospect, the design might have been done differently, and a discussion of how the present work fits into the field of de novo protein design.
Protein structure refinement based on paramagnetic NMR shifts: Applications to wild‐type and mutant forms of cytochromec
Authors: Gochin Miriam , Roder Heinrich 
Published: June 2010

AbstractA new approach to NMR solution structure refinement is introduced that uses paramagnetic effects on nuclear chemical shifts as constraints in energy minimization or molecular dynamics calculations. Chemical shift differences between oxidized and reduced forms of horse cytochromecfor more than 300 protons were used as constraints to refine the structure of the wild‐type protein in solution and to define the structural changes induced by a Leu 94 to Val mutation. A single round of constrained minimization, using the crystal structure as the starting point, converged to a low‐energy structure with an RMS deviation between calculated and observed pseudo‐contact shifts of 0.045 ppm, 7.5‐fold lower than the starting structure. At the same time, the procedure provided stereospecific assignments for more than 45 pairs of methylene protons and methyl groups. Structural changes caused by the mutation were determined to a precision of better than 0.3 A. Structure determination based on dipolar paramagnetic (pseudocontact) shifts is applicable to molecules containing anisotropic paramagnetic centers with short electronic relaxation times, including numerous naturally occurring metalloproteins, as well as proteins or nucleic acids to which a paramagnetic metal ion or ligand may be attached. The long range of paramagnetic shift effects (up to 20 Å from the iron in the case of cytochrome c) provides global structural constraints, which, in conjunction with conventional NMR distance and dihedral angle constraints, will enhance the precision of NMR solution structure determination.
Binding of phosphorus‐containing inhibitors to thermolysin studied by the Poisson‐Boltzmann method
Authors: Shen Jian , Wendoloski John 
Published: June 2010

AbstractZinc endopeptidase thermolysin can be inhibited by a series of phosphorus‐containing peptide analogues, Cbz‐Gly‐ψ(PO2)‐X‐Leu‐Y‐R (ZGP(X)L(Y)R), where X = NH, O, or CH2; Y = NH or O; and R = Leu, Ala, Gly, Phe, H, or CH3. The affinity correlation as well as an X‐ray crystallography study suggest that these inhibitors bind to thermolysin in an identical mode. In this work, we calculate the electrostatic binding free energies for a series of 13 phosphorus‐containing inhibitors with modifications at X, Y, and R moieties using finite difference solution to the Poisson‐Boltzmann equation. A method has been developed to include the solvation entropy changes due to binding different ligands to a macromolecule. We demonstrate that the electrostatic energy and empirically derived solvation entropy can account for most of the binding energy differences in this series. By analyzing the binding contribution from individual residues, we show that the energy of a hydrogen bond is not confined to the donor and acceptor. In particular, the positive charges on Zn and Arg 203, which are not the acceptors, contribute significantly to the hydrogen bonds between two amides of ZGPLL and the thermolysin.
Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and two‐dimensional polyacrylamide gel electrophoresis
Authors: Haebel Sophie , Jensen Charlotte , Roepstorff Peter , Andersen Svend Olav 
Published: June 2010

AbstractSimultaneous sequencing, using a combination of mass spectrometry and Edman degradation, of three approximately 15‐kDa variants of a cuticular protein extracted from the meal beetle Tenebrio molitor larva is demonstrated. The information obtained by matrix‐assisted laser desorption ionization mass spectrometry (MALDI MS) time‐course monitoring of enzymatic digests was found essential to identify the differences among the three variants and for alignment of the peptides in the sequence. To determine whether each individual insect larva contains all three protein variants, proteins extracted from single animals were separated by two‐dimensional gel electrophoresis, electroeluted from the gel spots, and analyzed by MALDI MS. Molecular weights of the proteins present in each sample could be obtained, and mass spectrometric mapping of the peptides after digestion with trypsin gave additional information. The protein isoforms were found to be allelic variants.
Refined solution structure of human profilin I
Authors: Metzler William J. , Farmer Bennett T. , Constantine Keith L. , Friedrichs Mark S. , Mueller Luciano , Lavoie Thomas 
Published: June 2010

AbstractProfilin is a ubiquitous eukaryotic protein that binds to both cytosolic actin and the phospholipid phospha‐tidylinositol‐4,5‐bisphosphate. These dual competitive binding capabilities of profilin suggest that profilin serves as a link between the phosphatidyl inositol cycle and actin polymerization, and thus profilin may be an essential component in the signaling pathway leading to cytoskeletal rearrangement.The refined three‐dimensional solution structure of human profilin I has been determined using multidimensional heteronuclear NMR spectroscopy. Twenty structures were selected to represent the solution conformational ensemble. This ensemble of structures has root‐mean‐square distance deviations from the mean structure of 0.58 Å for the backbone atoms and 0.98 Å for all non‐hydrogen atoms. Comparison of the solution structure of human profilin to the crystal structure of bovine profilin reveals that, although profilin adopts essentially identical conformations in both states, the solution structure is more compact than the crystal structure. Interestingly, the regions that show the most structural diversity are located at or near the actin‐binding site of profilin. We suggest that structural differences are reflective of dynamical properties of profilin that facilitate favorable interactions with actin. The global folding pattern of human profilin also closely resembles that of Acanthamoeba profilin I, reflective of the 22% sequence identity and ∼45% sequence similarity between these two proteins.
An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins
Authors: Sowdhamini R. , Blundell Tom L. 
Published: June 2010

AbstractWith a growing number of structures available in the Brookhaven Protein Data Bank, automatic methods for domain identification are required for the construction of databases. Domains are considered to be clusters of secondary structure elements. Thus, helices and strands are first clustered using intersecondary structural distances between Cα positions, and dendrograms based on this distance measure are used to identify domains. Individual domains are recognized by a disjoint factor, which enables the automatic identification and classification into disjoint, interacting, and conjoint domains. Application to a database of 83 protein families and 18 unique structures shows that the approach provides an effective delineation of boundaries and identifies those proteins that can be considered as a single domain. A quantitative estimate of the interaction between domains has been proposed. The database of protein domains is a useful tool for understanding protein folding, for recognizing protein folds, and for understanding structure‐activity relationships.
Competing interactions contributing to α‐helical stability in aqueous solution
Authors: Bodkin Michael J. , Goodfellow Julia M. 
Published: June 2010

AbstractThe stability of a 15‐residue peptide has been investigated using CD spectroscopy and molecular simulation techniques. The sequence of the peptide was designed to include key features that are known to stabilize α‐helices, including ion pairs, helix dipole capping, peptide bond capping, and aromatic interactions. The degree of helicity has been determined experimentally by CD in three solvents (aqueous buffer, methanol, and trifluoroethanol) and at two temperatures. Simulations of the peptide in the aqueous system have been performed over 500 ps at the same two temperatures using a fully explicit solvent model. Consistent with the CD data, the degree of helicity is decreased at the higher temperature. Our analysis of the simulation results has focused on competition between different side‐chain/side‐chain and side‐chain/main‐chain interactions, which can, in principle, stabilize the helix. The unfolding in aqueous solution occurs at the amino terminus because the side‐chain interactions are insufficient to stabilize both the helix dipole and the peptide hydrogen bonds. Loss of capping of the peptide backbone leads to water insertion within the first peptide hydrogen bond and hence unfolding. In contrast, the carboxy terminus of the α‐helix is stable in both simulations because the C‐terminal lysine residue stabilizes the helix dipole, but at the expense of an ion pair.
An NMR and spin label study of the effects of binding calcium and troponin I inhibitory peptide to cardiac troponin C
Authors: Howarth Jack W. , Krudy George A. , Lin Xin , Putkey John A. , Rosevear Paul R. 
Published: June 2010

AbstractThe paramagnetic relaxation reagent, 4‐hydroxy‐2,2,6,6‐tetramethylpiperidinyl‐1‐oxy (HyTEMPO), was used to probe the surface exposure of methionine residues of recombinant cardiac troponin C (cTnC) in the absence and presence of Ca2+ at the regulatory site (site II), as well as in the presence of the troponin I inhibitory peptide (cTnIp). Methyl resonances of the 10 Met residues of cTnC were chosen as spectral probes because they are thought to play a role in both formation of the N‐terminal hydrophobic pocket and in the binding of cTnIp. Proton longitudinal relaxation rates (R1's) of the [13C‐methyl] groups in [13C‐methyl]Met‐labeled cTnC(C35S) were determined using a T1 two‐dimensional heteronuclear single‐ and multiple‐quantum coherence pulse sequence. Solvent‐exposed Met residues exhibit increased relaxation rates from the paramagnetic effect of HyTEMPO. Relaxation rates in 2Ca2+‐loaded and Ca2+‐saturated cTnC, both in the presence and absence of HyTEMPO, permitted the topological mapping of the conformational changes induced by the binding of Ca2+ to site II, the site responsible for triggering muscle contraction. Calcium binding at site II resulted in an increased exposure of Met residues 45 and 81 to the soluble spin label HyTEMPO. This result is consistent with an opening of the hydrophobic pocket in the N‐terminal domain of cTnC upon binding Ca2+ at site II. The binding of the inhibitory peptide cTnlp, corresponding to Asn 129 through Ile 149 of cTnl, to both 2Ca2+‐loaded and Ca2+‐saturated cTnC was shown to protect Met residues 120 and 157 from HyTEMPO as determined by a decrease in their measured R1 values. These results suggest that in both the 2Ca2+‐loaded and Ca2+‐saturated forms of cTnC, cTnlp binds primarily to the C‐terminal domain of cTnC.