bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strength of polymer phase boundaries with large interfacial width: Effects of interfacial profile and phase separation morphology
Authors: Chang Chun‐Jie , Lee Yi‐Huan , Chiang Chi‐Ju , Lee Yu‐Ping , Chien Hao‐Ching , Shih Wen‐Pin , Cheng Yao‐Yi , Dai Chi‐An , Chang Chia‐Hwa 
Published: July 2010

AbstractIn this study, we investigate the effect of random copolymer additives on the interfacial profile, the lateral phase separation morphology, and the interfacial fracture toughness (Gc) between two immiscible polymers. The interface between polystyrene (PS)/poly(methyl methacrylate) (PMMA) was reinforced with a random copolymer mixture when two or more PSf ‐r‐PMMA1‐f random copolymers with different volume fraction, f, were blended. For short annealing time (<3 h), the random copolymer mixture exhibits a disordered and large domain structure (>1 lm) from which crazes can be extensively initiated and developed, leading to a large interfacial fracture energy. With increasing annealing time, the random copolymer mixture self‐organizes as multiple layers, with the composition that changes gradually from PS‐rich layers to PMMA‐rich layers across the interface, leading to a large interfacial width. However, within each layer, the random copolymer mixture microphase separates laterally into smaller domains (<200 nm). We found that the microphase‐separated domains with nanometer‐sized structure significantly affect the stability of craze fibrils that can be initiated and widened at the interface, leading to a decrease in the fracture energy. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1834–1846, 2010
Characterization of PBT/POSS nanocomposites prepared by in situ polymerization of cyclic poly(butylene terephthalate) initiated by functionalized POSS
Authors: Wu Fumei , Xie Tingxiu , Yang Guisheng 
Published: July 2010

AbstractNovel poly(butylene terephthalate) (PBT)/polyhedral oligomeric silsesquioxane (POSS) nanocomposites were synthesized by ring‐opening polymerization of cyclic poly(butylene terephthalate) initiated by functionalized POSS with various feed ratios. The impact of POSS incorporation on melting and crystallization behaviors of PBT/POSS nanocomposites was investigated by means of X‐ray diffraction and differential scanning calorimetry. It was found that the novel organic–inorganic association result in the significant alterations in the melting and crystallization behavior of PBT. Thermal studies confirmed that the incorporation of POSS can enhance the thermal stability of the polymers, and the copolymer glass transition temperature increased with the increasing of POSS macromonomer content. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1853–1859, 2010
Comparison of patient and family assessments of quality of life of terminally ill cancer patients in Japan
Authors: Hisamura Kazuho , Matsushima Eisuke , Nagai Hideaki , Mikami Akihiko 
Published: July 2010

AbstractObjective: This study examined the extent and the nature of agreement on health‐related quality of life (QOL) assessments between terminally ill cancer patients and their primary family caregivers in Japan, using a multidimensional QOL instrument including psychosocial and spiritual domains.Methods: The Functional Assessment of Chronic Illness Therapy‐Spiritual well‐being questionnaire was used to assess patients' QOL. Study subjects were inpatients of a palliative care unit (PCU), outpatients who applied for admission to the PCU, and their primary family caregivers.Results: QOL ratings were obtained from 102 of 197 eligible patient–caregiver dyads. A moderate level of patient–family concordance on patients' overall QOL as well as families' underestimation of patients' QOL were observed. Families reported on observable domains of patients' QOL more reliably and assessed subjective aspects, such as psychospiritual concerns less accurately. Families tended to underrate the patients' social aspect of QOL, whereas most patients gave the highest rating on support from their families. The spiritual domain, particularly regarding faith, showed the least agreement. The size of the systematic bias between patient and family assessments on the patients' QOL was moderate (>0.50).Conclusions: Families' limited ability to assess psychosocial and spiritual aspects of patients' QOL may suggest the need for better approaches or measures to assess these aspects of a patient's life. The systematic bias was larger than in earlier studies. Further investigation is needed to identify factors affecting patient–family discord on QOL assessments to guide effective interventions to enhance patient–caregiver agreement. Copyright © 2010 John Wiley & Sons, Ltd.
Familial neuroendocrine cell hyperplasia of infancy
Authors: Popler J. , Gower W.A. , Mogayzel P.J. , Nogee L.M. , Langston C. , Wilson A.C. , Hay T.C. , Deterding R.R. 
Published: July 2010

AbstractBackgroundNeuroendocrine cell hyperplasia of infancy (NEHI) is a recently described children's interstitial lung disease (chILD) disorder of unknown etiology. It manifests clinically with tachypnea, retractions, hypoxemia, and crackles. The characteristic radiographic appearance consists of pulmonary hyperexpansion and ground‐glass densities on high‐resolution computed tomography (HRCT). Lung histology shows hyperplasia of bombesin‐immunopositive neuroendocrine cells within distal bronchioles and alveolar ducts without other identifiable lung pathology or developmental anomaly.MethodsWe describe four families with multiple siblings diagnosed with NEHI. Cases were identified at three pediatric centers. Inclusion criteria included clinical findings consistent with NEHI, lung biopsy confirmation in the index case, and a diagnostic HRCT or biopsy in other siblings.ResultsEach family had a proband diagnosed with NEHI based upon pathologic review, and at least one additional sibling diagnosed either by pathologic review or HRCT. All patients presented between 2 and 15 months of age. Both male and female children were affected. The majority of the patients underwent both HRCT and lung biopsy. There were no deaths among affected children. No environmental exposures or other potential etiologies were identified as a cause of presenting symptoms.ConclusionsThe familial occurrence of NEHI suggests the possibility of a genetic etiology for this disorder and highlights the importance of taking a complete family medical history for infants presenting with a suggestive clinical picture. Identification of familial NEHI patients allows for the opportunity to further our understanding of this disorder, its natural history, the phenotypic spectrum, and potential genetic causes. Pediatr. Pulmonol. 2010; 45:749–755. © 2010 Wiley‐Liss, Inc.
Reduction of thioredoxin significantly decreases its partial specific volume and adiabatic compressibility
Authors: Kaminsky S.M. , Richards F.M. 
Published: July 2010

AbstractThe partial specific volume and adiabatic compressibility were determined at several temperatures for oxidized and reduced Escherichia coli thioredoxin. Oxidized thioredoxin had a partial specific volume of 0.785–0.809 mL/g at the observed upper limit for all proteins whereas the partial specific volume of reduced thioredoxin was 0.745–0.755 mL/g, a value in the range found for a majority of proteins. The adiabatic compressibility of oxidized thioredoxin was also much larger (9.8–18 × 10−12 cm2 dyne−1) than that of the reduced protein (3.8–7.3 × 10−12). Apart from the region immediately around the small disulfide loop, the structures of the oxidized (X‐ray, crystal) and reduced protein (nuclear magnetic resonance, solution) are reported to be very similar. It would appear that alterations in the solvent layer in contact with the protein surface must play a major role in producing these large changes in the apparent specific volumes and compressibilities in this system. Some activities of thioredoxin require the reduced structure but are not electron transfer reactions. The large changes in physical parameters reported here suggest the possibility of a reversible metabolic control function for the SS bond.
Comparison of solution structures of mutant bovine pancreatic trypsin inhibitor proteins using two‐dimensional nuclear magnetic resonance
Authors: Hurle Mark R. , Eads Charles D. , Pearlman David A. , Seibel George L. , Thomason John , Kosen Phyllis Anne , Kollman Peter , Kuntz Irwin D. , Anderson Stephen 
Published: July 2010

AbstractStructural perturbations due to a series of mutations at the 30–51 disulfide bond of bovine pancreatic trypsin inhibitor have been explored using NMR. The mutants replaced cysteines at positions 30 and 51 by alanine at position 51 and alanine, threonine, or valine at position 30. Chemical shift changes occur in residues proximate to the site of mutation. NOE assignments were made using an automated procedure, NASIGN, which used information from the wild‐type crystal structure. Intensity information was utilized by a distance geometry algorithm, VEMBED, to generate a series of structures for each protein. Statistical analyses of these structures indicated larger averaged structural perturbations than would be expected from crystallographic and other information. Constrained molecular dynamics refinement using AMBER at 900 K was useful in eliminating structural movements that were not a necessary consequence of the NMR data. In most cases, statistically significant movements are shown to be those greater than approximately 1 Å. Such movements do not appear to occur between wild type and A30A51, a result confirmed by crystallography (Eigenbrot, C., Randal, M., & Kossiakoff, A.A., 1990, Protein Eng. 3, 591–598). Structural alterations in the T30A51 or V30A51 mutant proteins near the limits of detection occur in the β‐loop (residues 25–28) or C‐terminal α‐helix, respectively.
Broønsted analysis of aspartate aminotransferase via exogenous catalysis of reactions of an inactive mutant
Authors: Toney Michael D. , Kirsch Jack F. 
Published: July 2010

AbstractPrimary amines functionally replace lysine 258 by catalyzing both the 1,3‐prototropic shift and external aldimine hydrolysis reactions with the inactive aspartate aminotransferase mutant K258A. This finding allows classical Brønsted analyses of proton transfer reactions to be applied to enzyme‐catalyzed reactions. An earlier study of the reaction of K258A with cysteine sulfinate (Toney, M.D. & Kirsch, J.F., 1989, Science 243, 1485) provided a β value of 0.4 for the 1,3‐prototropic shift. The β value reported here for the transamination of oxalacetate to aspartate is 0.6. The catalytic efficacy of primary amines is largely determined by basicity and molecular volume. The dependence of the rate constants for the reactions of K258A and K258M on amine molecular volume is nearly identical. This observation argues that the alkyl groups of the added amines do not occupy the position of the lysine 258 side chain in the wild type enzyme. Large primary Cα and insignificant solvent deuterium kinetic isotope effects with amino acid substrates demonstrate that the amine nitrogen of the exogenous catalysts directly abstracts the labile proton in the rate‐determining step.
Stability, quaternary structure, and folding of internal, external, and core‐glycosylated invertase from yeast
Authors: Kern Gunther , Schülke Norbert , Jaenicke Rainer , Schmid Franz X. 
Published: July 2010

AbstractThe role of carbohydrate chains for the structure, function, stability, and folding of glycoproteins has been investigated using invertase as a model. The protein is encoded by several different genes, and its carbohydrate moiety is heterogeneous. Both properties complicate physicochemical comparisons. Here we used the temperature‐sensitive sec18 secretion mutant of yeast with a single invertase gene (SUC2). This mutant produces the carbohydrate‐free internal invertase, the core‐glycosylated form, and, at the permissive temperature, the fully glycosylated external enzyme, all with identical protein moieties. The core‐glycosylated enzyme resembles the nascent glycoprotein chain that folds in the endoplasmic reticulum. Therefore, it may be considered a model for the in vivo folding of glycoproteins. In addition, because of its uniform glycosylation, it can be used to investigate the state of association of native invertase.Glycosylation is found to stabilize the protein with respect to thermal denaturation and chaotropic solvent components; the stabilizing effect does not differ for the external and the core‐glycosylated forms. Unlike the internal enzyme, the glycosylated forms are protected from aggregation.Native internal invertase is a dimer (115 kDa) whereas the core‐glycosylated enzyme is a mixture of dimers, tetramers, and octamers. This implies that core‐glycosylation is necessary for oligomerization to tetramers and octamers. Dimerization is required and sufficient to generate enzymatic activity; further association does not alter the specific activity of core‐glycosylated invertase, suggesting that the active sites of invertase are not affected by the association of the dimeric units.Reconstitution of the glycosylated and nonglycosylated forms of the enzyme after preceding guanidine denaturation depends on protein concentration. The maximum yield (=80%) is obtained at pH 6–8 and protein concentrations ≤4 μg/mL for the nonglycosylated and ≤40 μg/mL for the glycosylated forms of the enzyme. The lower stability of the internal enzyme is reflected by a narrower pH range of reactivation and enhanced aggregation. As indicated by the sigmoidal reactivation kinetics at low protein concentration both folding and association are rate‐determining.
Steric and hydrophobic determinants of the solubilities of recombinant sickle cell hemoglobins
Authors: Bihoreau M.T. , Baudin V. , Marden M. , Lacaze N. , Bohn B. , Kister J. , Poyart C. , Pagnier J. , Schaad O. , Edelstein S.J. , Dumoulin A. 
Published: July 2010

AbstractModels for the structure of the fibers of deoxy sickle cell hemoglobin (Hb S, β6 Glu → Val) have been obtained from X‐ray and electron microscopic studies. Recent molecular dynamics calculations of polymer formation give new insights on the various specific interactions between monomers. Site‐directed mutagenesis with expression of the Hb S β subunits in Escherichia coli provides the experimental tools to test these models. For Hb S, the β6 Val residue is intimately involved in a specific lateral contact, at the donor site, that interacts with the acceptor site of an adjacent molecule composed predominantly of the hydrophobic residues Phe 85 and Leu 88. Comparing natural and artificial mutants indicates that the solubility of deoxyHb decreases in relation to the surface hydropho‐bicity of the residue at the β6 position with Ile > Val > Ala. We also tested the role of the stereospecific adjustment between the donor and acceptor sites by substituting Trp for Glu at the β36 location. Among these hydrophobic substitutions and under our experimental conditions, only Val and Ile were observed to induce polymer formation. The interactions for the Ala mutant are too weak whereas a Trp residue inhibits aggregation through steric hindrance at the acceptor site of the lateral contact. Increasing the hydrophobicity at the axial contact between tetramers of the same strand also contributes to the stability of the double strand. This is demonstrated by associating the β23 Val → Ile mutation at the axial contact with either the β6 Glu → Val or β6 Glu → Ile substitution in the same β subunit. In comparison to native Hb S the solubility of these deoxyHb double mutants is decreased two‐ and fourfold, respectively.
Calculation of the free energy of association for protein complexes
Authors: Horton Nancy , Lewis Mitchell 
Published: July 2010

AbstractWe have developed a method for calculating the association energy of quaternary complexes starting from their atomic coordinates. The association energy is described as the sum of two solvation terms and an energy term to account for the loss of translational and rotational entropy. The calculated solvation energy, using atomic solvation parameters and the solvent accessible surface areas, has a correlation of 96% with experimentally determined values. We have applied this methodology to examine intermediates in viral assembly and to assess the contribution isomerization makes to the association energy of molecular complexes. In addition, we have shown that the calculated association can be used as a predictive tool for analyzing modeled molecular complexes.
Reconstructing history with amino acid sequences1
Authors: Doolittle Russell F. 
Published: July 2010

AbstractThe main goal of the protein evolutionist is the reconstruction of past events leading to the structures of contemporary proteins. The common strategy is to align amino acid sequences and make inferences about matters of common ancestry. The rate of change of amino acid sequence varies greatly from protein to protein, and this naturally affects how far back a given protein's ancestry can be traced. Happily, the rate of change of many proteins is slow enough that very ancient events can be inferred. Many mainstream metabolic enzymes, for example, are 40–50% identical in prokaryotes and eukaryotes, groups that diverged from a common ancestor more than 1.5 billion years ago. Moreover, some eukaryotic proteins like actin and tubulin change so slowly that they are seldom less than 60% identical, no matter from what source they are drawn. As it happens, prokaryotic counterparts for many eukaryotic cytoskeletal proteins are unknown. A recent exception involves the finding that a heat shock protein cognate is a relative of actin. The gene duplication that gave rise to these two proteins must have been an ancient event. The more recent invention of other proteins whose distribution is restricted to one or the other of the major kingdoms may be easier to trace. Among the factors that can confound the reconstruction of events, however, are occasional horizontal gene transfers and exon shuffling. The latter has led to a number of mosaic proteins, many of which contain various combinations of a relatively small set of modules like the epidermal growth factor domain.
Atomic solvation parameters applied to molecular dynamics of proteins in solution
Authors: Wesson Laura , Eisenberg David 
Published: July 2010

AbstractA solvation energy function for use in the molecular simulation of proteins is proposed. It is based on the accessible surface areas of atoms in the protein and on atomic solvation parameters derived from empirical vapor‐to‐water free energies of transfer of amino acid side‐chain analogs. The energy function and its derivatives were added to the CHARMM molecular simulation program (Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S.,&Karplus, M., 1983, J. Comput. Chem. 4(2), 187–217). The effect of the added energy term was evaluated by 110 ps of molecular dynamics on the 26‐residue protein melittin. The melittin monomer and tetramer were studied both with and without the added term. With the added energy term the monomer partially unfolded, while the secondary structure of the tetramer was preserved, in agreement with reported experiments (Brown, L.R., Lauterwein, J.,&Wuethrich, K., 1980, Biochim. Biophys. Acta 622(2), 231–244; Lauterwein, J., Brown, L.R.,&Wuethrich, K., 1980, Biochim. Biophys. Acta 622(2), 219–230).
Characterization, primary structure, and evolution of lamprey plasma albumin
Authors: Gray Jeffrey E. , Doolittle Russell F. 
Published: July 2010

AbstractThe most abundant protein found in blood plasma from the sea lamprey (Petromyzon marinus) has the hallmarks of a plasma albumin: namely, high abundance, solubility in distilled water, a small number of tryptophans, and a high content of cysteines and charged residues. As in other vertebrate albumins, not all the cysteines are disulfide bonded. An unusual feature of this protein is its molecular weight of 175,000, roughly 2.5 times the size of other vertebrate albumins. Its amino acid sequence, deduced from a series of overlapping cDNA clones, can be aligned with other members of the gene family including plasma albumin, alpha‐fetoprotein, and vitamin‐D binding protein, confirming that it is indeed an oversized albumin. An unusual feature of the sequence is a 28‐amino acid stretch consisting of a serine‐threonine repeat with the general motif (STTT). Lamprey albumin contains a 23‐amino acid putative signal peptide and a 6‐residue putative propeptide, which, when cleaved, yield a mature protein of 1,394 amino acids with a calculated molecular weight of 157,000. The sequence also includes nine potential N‐linked glycosylation sites (Asn‐X‐Ser/Thr), consistent with observation that lamprey albumin is a glycoprotein. If all the potential glycosylation sites were occupied by clusters of 2,000 molecular weight each, the total molecular weight would be 175,000. Like other members of the gene family, lamprey albumin is composed of a series of 190‐amino acid repeats, there being seven such domains all together. Quantitative amino acid sequence comparisons of lamprey albumin with the other members of the gene family indicate that it diverged from an ancestral albumin prior to the gene duplications leading to this diverse group. This notion is confirmed by the pattern of amino acid insertions and deletions observed in a consideration of all domains that compose this family. Furthermore, it suggests that the invention of albumin antedates the vertebrate radiation.
Lysine‐21 of Leuconostoc mesenteroides glucose 6‐phosphate dehydrogenase participates in substrate binding through charge–charge interaction
Authors: Lee W. Theodore , Levy H. Richard 
Published: July 2010

AbstractLeuconostoc mesenteroides glucose 6‐phosphate dehydrogenase (G6PD) was isolated in high yield and purified to homogeneity from a newly constructed strain of Escherichia coli which lacks its own glucose 6‐phosphate dehydrogenase gene. Lys‐21 is one of two lysyl residues in the enzyme previously modified by the affinity labels pyridoxal 5′‐phosphate and pyridoxal 5′‐diphosphate‐5′‐adenosine, which are competitive inhibitors of the enzyme with respect to glucose 6‐phosphate (LaDine, J.R., Carlow, D., Lee, W.T., Cross, R.L., Flynn, T.G., & Levy, H.R., 1991, J. Biol. Chem. 266, 5558–5562). K21R and K21Q mutants of the enzyme were purified to homogeneity and characterized kinetically to determine the function of Lys‐21. Both mutant enzymes showed increased Km‐values for glucose 6‐phosphate compared to wild‐type enzyme: 1.4‐fold (NAD‐linked reaction) and 2.1‐fold (NADP‐linked reaction) for the K21R enzyme, and 36‐fold (NAD‐linked reaction) and 53‐fold (NADP‐linked reaction) for the K21Q enzyme. The Km for NADP+ was unchanged in both mutant enzymes. The Km for NAD+ was increased 1.5‐ and 3.2‐fold, compared to the wild‐type enzyme, in the K21R and K21Q enzymes, respectively. For the K21R enzyme the kcat
for the NAD‐ and NADP‐linked reactions was unchanged. The kcat for the K21Q enzyme was increased in the NAD‐linked reaction by 26% and decreased by 30% in the NADP‐linked reaction from the values for the wild‐type enzyme. The data are consistent with Lys‐21 participating in the binding of the phosphate group of the substrate to the enzyme via charge–charge interaction.