bluuebunny/crossref_metadata_2025 huggingface dataset:
MR diffusion kurtosis imaging for neural tissue characterization
Authors: Wu Ed X. , Cheung Matthew M.
Published: July 2010

In conventional diffusion tensor imaging (DTI), water diffusion distribution is described as a 2nd‐order three‐dimensional (3D) diffusivity tensor. It assumes that diffusion occurs in a free and unrestricted environment with a Gaussian distribution of diffusion displacement, and consequently that diffusion weighted (DW) signal decays with diffusion factor (b‐value) monoexponentially. In biological tissue, complex cellular microstructures make water diffusion a highly hindered or restricted process. Non‐monoexponential decays are experimentally observed in both white matter and gray matter. As a result, DTI quantitation is b‐value dependent and DTI fails to fully utilize the diffusion measurements that are inherent to tissue microstructure. Diffusion kurtosis imaging (DKI) characterizes restricted diffusion and can be readily implemented on most clinical scanners. It provides a higher‐order description of water diffusion process by a 2nd‐order 3D diffusivity tensor as in conventional DTI together with a 4th‐order 3D kurtosis tensor. Because kurtosis is a measure of the deviation of the diffusion displacement profile from a Gaussian distribution, DKI analyses quantify the degree of diffusion restriction or tissue complexity without any biophysical assumption. In this work, the theory of diffusion kurtosis and DKI including the directional kurtosis analysis is revisited. Several recent rodent DKI studies from our group are summarized, and DKI and DTI compared for their efficacy in detecting neural tissue alterations. They demonstrate that DKI offers a more comprehensive approach than DTI in describing the complex water diffusion process in vivo. By estimating both diffusivity and kurtosis, it may provide improved sensitivity and specificity in MR diffusion characterization of neural tissues. Copyright © 2010 John Wiley & Sons, Ltd.
Metabolic profile of intact tissue from uterine leiomyomas using high‐resolution magic‐angle‐spinning 1H NMR spectroscopy
Authors: Mazzei Pierluigi , Piccolo Alessandro , Nugnes Loredana , Mascolo Massimo , De Rosa Gaetano , Staibano Stefania
Published: July 2010

High‐resolution magic‐angle‐spinning (HRMAS) one‐ and two‐dimensional 1H and 13C NMR spectroscopy was used to study intact healthy (myometrium) and benign (leiomyoma) uterine tissues of 10 patients. Twenty‐eight metabolites were detected and assigned in both types of tissue. Principal component analysis (PCA) was applied to a conventional water‐suppressed 1H HRMAS NMR spectrum, and two NMR spectral editing methods, namely Carr–Purcell– Meiboom–Gill (CPMG) spin‐echo and diffusion‐edited techniques, were used. Only the PCA of CPMG spectra resulted in a good differentiation between the two tissue types. The CPMG spin‐echo spectra were also useful in indicating depleted levels of taurine in uterine leiomyomas, which were well correlated with the histopathological determination. In addition, statistical analysis revealed that most leiomyomas contained elevated concentrations of glutamate and glutamine. Our results suggest that HRMAS represents a valuable adjunct to histopathology to improve the diagnostic accuracy of uterine leiomyomas, whilst concomitantly reducing the diagnosis time. Copyright © 2010 John Wiley & Sons, Ltd.
A novel energy‐based approach for merging finite elements
Authors: Yogev Or , Shapiro Andrew A. , Antonsson Erik K.
Published: July 2010

A novel approach for merging two intersecting finite elements is presented and demonstrated. The solution mimics concepts from biology and uses principles rooted in continuum mechanics.

The problem of attaching (or merging) two coincident finite elements is common when using the plastering technique as part of the advancing front method. This problem is particularly challenging for 3‐D meshes of non‐convex shapes. Some automatic meshing methods require portions of the partially formed mesh to coincide and merge. This problem is generally solved with heuristic rules, which lack generality, and may have difficulties with unforeseen situations.

The problem of merging two overlapping polyhedra may also appear in other applications such as computer graphics and CAD software.

A new approach to address the problem of merging is presented here. This solution does not utilize heuristic rules, but rather uses an approach based on minimization of strain energy. A fully automatic merging routine has been created that can address, in an optimum way, any situation of two nearby or overlapping elements that are to be merged. This approach, with minor adjustments, is suitable for most types of 3‐D elements. Copyright © 2010 John Wiley & Sons, Ltd.
A variationally consistent αFEM (VCαFEM) for solution bounds and nearly exact solution to solid mechanics problems using quadrilateral elements
Authors: Liu G. R. , Nguyen‐Xuan H. , Nguyen‐Thoi T.
Published: July 2010

A variationally consistent alpha finite element method (VC αFEM) for quadrilateral isoparametric elements is presented by constructing an assumed strain field in which the gradient of the compatible strain field is scaled with a free parameter α. The assumed strain field satisfies the orthogonal condition and the Hellinger–Reissner variational principle is used to establish the discretized system of equations. It is shown that the strain energy is a second‐order continuous function of α, and the VC αFEM can produce both lower and upper bounds to the exact solution in the strain energy for all elasticity problems by choosing a proper α∈[0, αupper]. Based on this bound property, an exact‐α approach has been devised to give an ultra‐accurate solution that is very close to the exact one in the strain energy. Furthermore, the exact‐α approach also works well for volumetric locking problems, by simply replacing the strain gradient matrix by a stabilization matrix. In addition, a regularization‐α approach has also been suggested to overcome possible hourglass instability. Intensive numerical studies have been conducted to confirm the properties of the present VC αFEM, and a very good performance has been found in comparing to a large number of existing FEM models. Copyright © 2010 John Wiley & Sons, Ltd.
Optimization of a variable mouth acoustic horn
Authors: Udawalpola Rajitha , Wadbro Eddie , Berggren Martin
Published: July 2010

By using boundary shape optimization on the end part of a semi‐infinite waveguide for acoustic waves, we design transmission‐efficient interfacial devices without imposing an upper bound on the mouth diameter. The boundary element method solves the Helmholtz equation modeling the exterior wave propagation problem. A gradient‐based optimization algorithm solves the resulting least‐squares problem and the adjoint method provides the necessary gradients. The results demonstrate that there appears to be a natural limit on the optimal mouth diameter. Copyright © 2010 John Wiley & Sons, Ltd.
Superabsorbent composite XXII: Effects of modified sepiolite on water absorbency and swelling behavior of chitosan‐g‐poly(acrylic acid)/sepiolite superabsorbent composite
Authors: Xie Yuntao , Wang Aiqin , Liu Gang
Published: July 2010

In this work, a series of chitosan‐g‐poly(acrylic acid)/sepiolite (CTS‐g‐PAA/ST) superabsorbent composites containing raw sepiolite, acid‐activated sepiolite, and cation‐exchanged sepiolite were synthesized by free‐radical graft polymerization in aqueous solution, using N,N′‐methylenebisacrylamide as a crosslinker and ammonium persulfate as an initiator. The effects of raw sepiolite, acid‐activated sepiolite, and cation‐exchanged sepoilite on equilibrium water absorbency, swelling rate, and swelling behavior in different pH value solution of superabsorbent composites were systematically investigated. The results from FTIR spectra showed that chitosan and sepiolite participated in graft polymerization reaction with acrylic acid. The introduction of acid‐activated and cation‐exchanged sepiolite into chitosan‐g‐poly(acrylic acid) polymeric network could improve water absorbency and swelling rate compared with that of the raw sepiolite. All prepared samples have similar swelling behavior in different pH solutions and the equilibrium water absorbencies of samples keep roughly constant in the pH range from 4 to 12. POLYM. COMPOS., 2010. © 2009 Society of Plastics Engineers
Influence of composition and phase morphology on rheological properties of polypropylene/poly(ethylene‐co‐octene) blends
Authors: Zhu Lin , Xu Xinhua , Ye Ning , Song Na , Sheng Jing
Published: July 2010

In this article, the phase morphology and rheological properties of polypropylene (PP)/poly(ethylene‐co‐octene) (POE) blends with a droplet‐matrix microstructure were studied by scanning electron microscopy and rheological experiments. The data were analyzed to yield the variations of rheological behavior with blend composition and insight into the microstructure of PP/POE blends. The Palierne's emulsion type model was used to extract information on rheological properties, and the interfacial tensions between the PP and POE were determined by fitting the experimental data with this model. The results indicated that the interfacial tensions were shown to depend on blend composition and temperature. Rheological properties of PP/POE blends were investigated in a systemic way with varying shear histories. The results showed that shear history had an important effect on the rheological properties of the blends due to the dispersed phase (POE) domains refined with increasing preshear rate and preshear time. POLYM. COMPOS., 2010. © 2009 Society of Plastics Engineers
Water absorption behavior of different types of organophilic montmorillonite‐filled polyamide 6/polypropylene nanocomposites
Authors: Kusmono  , Mohd Ishak Z.A. , Chow W.S. , Takeichi T. , Rochmadi
Published: July 2010

The water absorption behavior of different types of organophilic montmorillonite (OMMT)‐filled polyamide 6/polypropylene nanocomposites with and without compatibilizers (maleated PP or PP‐g‐MA and maleated styrene‐ethylene/butylene‐styrene or SEBS‐g‐MA) was evaluated. Four different types of OMMT, i.e., dodecylamine‐modified MMT (D‐MMT), 12 aminolauric acid‐modified MMT (A‐MMT), stearylamine‐modified MMT (S‐MMT), and commercial organo‐MMT (C‐MMT) were used as reinforcement. The water absorption response of the nanocomposites was studied and analyzed by tensile test and morphology assessment by scanning electron microscopy (SEM). The kinetics of water absorption of the nanocomposites conforms to Fick's law. The Mm and D are dependent on the types of OMMT and compatibilizers. The equilibrium water content and diffusivity of PA6/PP blend were increased by the addition of OMMT but decreased in the presence of compatibilizers. On water absorption, both strength and stiffness of the nanocomposites were drastically decreased, but the ductility was remarkably increased. Both PP‐g‐MA and SEBS‐g‐MA played an effective role as compatibilizers for the nanocomposites. This was manifested by their higher retention ability in strength and stiffness (in the wet and re‐dried states), reduced the equilibrium water content, and diffusivity of the nanocomposites. POLYM. COMPOS., 2010. © 2009 Society of Plastics Engineers
The impact of silane chemistry conditions on the properties of wood plastic composites with low density polyethylene and high wood content
Authors: Geng Yu , Laborie Marie‐Pierre G.
Published: July 2010

Silane chemistry was implemented on various formulations of wood/thermoplastic polymer composites (WPCs) with low density polyethylene (LDPE) and high wood content (60 wt%). Taguchi analysis was used to evaluate the impact of vinyltrimethoxysilane content (VTMS), dicumyl peroxide content (DCP), and processing temperature on the rheological, morphological, and dynamic mechanic properties of WPCs. The torque power was measured by a Haake torque rheometer and indicated that the VTMS content and temperature most significantly impacted the rheological properties related to silane reactions. Differential scanning calorimetry also showed a larger depression in LDPE melting point and crystallinity index when a high VTMS content (35 phr), high DCP content (0.5 phr), and a high compounding temperature (200°C) were used. With dynamic mechanical analysis (DMA), it was shown that the compounded formulations had a higher storage modulus over a wide range of temperature whereas the β transition temperature increased with higher content in silane reactants. Interestingly, the high humidity/temperature conditioning step aimed at crosslinking resulted in a drop of dynamic moduli compared to the freshly compounded formulations. This was explained by the fact that during compounding of LDPE with high wood content and silane reactants, significant amounts of matrix and interfacial silane crosslinking already occurred. Subsequent conditioning in a high humidity and temperature environment was proposed to hydrolyze the interfacial siloxane bonds resulting in a degradation of mechanical properties. POLYM. COMPOS., 2010. © 2009 Society of Plastics Engineers
Liquid Crystal Polymers. IV. Liquid Crystalline Aromatic Polyesters
Authors: Jackson W. Jerome
Published: July 2010

Melt‐spun and injection‐moulded liquid crystalline polyesters have very high strength and stiffness and a very low coefficient of linear thermal expansion. The exceptional properties that characterise these polyesters are due to the presence of stiff, rod‐like polymeric chains, which become highly oriented during melt‐spinning or injection‐moulding, and long relaxation times, which permit the chains to retain their orientation while the polymer is cooling. The introduction of either flexible aliphatic groups or kinks in the rod‐like polymer chains reduces the polyester melting points and thereby permits easier melt processing but also adversely affects the strength and stiffness properties which are obtained. The effects of composition on the melting point and properties of plastics and fibres of liquid crystalline aromatic polyesters is discussed.
Observations on the Melt Rheology of Thermotropic Aromatic Polyesters
Authors: Wissbrun Kurt F.
Published: July 2010

Rheological measurements were made on a variety of substantially aromatic copolyesters. All of them differ from flexible chain polymers in having unusually long relaxation times, estimated from shear rate dependence of viscosity and from melt elasticity. This behaviour is not accounted for by an unusual molecular weight distribution (MWD); limited measurements indicate that the MWD is somewhat narrower than that of conventional condensation polymers.

Numerous anomalous flow phenomena have been observed, though not necessarily with all samples. These include the occurrence of a yield stress, large secondary shear stress maximum after start‐up of steady shear, transient negative normal stress, and shear‐thickening of melt viscosity. Although the melts are highly elastic, they do not exhibit swelling after extrusion from a capillary.

The melt rheology is often very sensitive to temperature and dependent upon thermal history. In one material this dependence has been linked to the destruction and/or growth of crystallites formed from blocks of one comonomer.
MassSieve: Panning MS/MS peptide data for proteins
Authors: Slotta Douglas J. , McFarland Melinda A. , Markey Sanford P.
Published: July 2010

We present MassSieve, a Java‐based platform for visualization and parsimony analysis of single and comparative LC‐MS/MS database search engine results. The success of mass spectrometric peptide sequence assignment algorithms has led to the need for a tool to merge and evaluate the increasing data set sizes that result from LC‐MS/MS‐based shotgun proteomic experiments. MassSieve supports reports from multiple search engines with differing search characteristics, which can increase peptide sequence coverage and/or identify conflicting or ambiguous spectral assignments.
Synthesis and properties of novel benzimidazole‐containing sulfonated polyethersulfones for fuel cell applications
Authors: Qi Yinghua , Gao Yan , Tian Shuanghong , Hlil Antisar R. , Gaudet Julie , Guay Daniel , Hay Allan S.
Published: July 2010

A novel series of benzimidazole‐containing sulfonated poly(arylene sulfones)s with controllable amount of basic 2,6‐bis(benzimidazol‐2‐yl)pyridine (BIP) and sulfonic acid groups have been prepared by the copolycondensation of a new BIP‐containing arylene difluoride monomer (DFSBIP) with a sulfonated arylene difluoride (DSDFS) and 4,4′‐biphenol (BP). All the resulting polymers have high molecular weights, good thermal stability, and can form uniform and tough membranes by simple solution casting. Because of the strong acid–base interaction between BIP and sulfonic acid groups, ionic crosslinking networks forms that resulted in polymer membranes with good dimensional stability in water even at high temperature (e.g., 100 °C). The ion exchange capacity (IEC) of the polymer membranes was investigated through a new simple pH‐determination method. A comparison between the experimental IEC values with the calculated ones based on the polymer structures indicated that each BIP unit interacted with one sulfonic acid group. Thus, by controlling the relative content of BIP units and sulfonate groups in the polymers, the intra‐ and intermolecular acid–base interactions could be readily optimized so as to achieve polymers with high IEC values, high proton conductivities as well as low swelling ratios, demonstrating good potential for proton exchange membrane applications. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1920–1929, 2009
Single‐step process to produce functionalized multiresponsive polymeric particles
Authors: Bousquet Antoine , Ibarboure Emmanuel , HÉRoguez ValÉRie , Papon Eric , Labrugere Christine , Rodríguez‐Hernández Juan
Published: July 2010

Monodisperse functional multiresponsive particles were prepared by encapsulation of an amphiphilic diblock copolymer during the precipitation polymerization of polystyrene and divinylbenzene in one single step. The amphiphilic diblock copolymer employed throughout this study, polystyrene‐b‐poly (dimethylaminoethyl methacrylate) (PS‐b‐PDMAEMA) has been synthesized by ATRP in two consecutive polymerization steps. After encapsulation of the block copolymer within the microsphere, the surface modification of the particle occurs spontaneously upon exposure to water by surface segregation of the hydrophilic PDMAEMA block, thus without any additional post‐polymerization and/or chemical modification steps. The response of the functionalized particles both to pH and temperature was analyzed by potential zeta and DSC measurements. Upon dispersion of the particles in acidic media, the PDMAEMA block in its charged state is soluble and does not exhibit any change by heating. At higher pH values and temperatures above 35 °C (Low Critical Solubility Temperature of the PDMAEMA block) the hydrophilic segment collapses as detected by differential scanning calorimetry. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3523–3533, 2010
Complex, degradable polyester materials via ketoxime ether‐based functionalization: Amphiphilic, multifunctional graft copolymers and their resulting solution‐state aggregates
Authors: Iha Rhiannon K. , van Horn Brooke A. , Wooley Karen L.
Published: July 2010

Degradable, amphiphilic graft copolymers of poly(ε‐caprolactone)‐graft‐poly(ethylene oxide), PCL‐g‐PEO, were synthesized via a grafting onto strategy taking advantage of the ketones presented along the backbone of the statistical copolymer poly(ε‐caprolactone)‐co‐(2‐oxepane‐1,5‐dione), (PCL‐co‐OPD). Through the formation of stable ketoxime ether linkages, 3 kDa PEO grafts and p‐methoxybenzyl side chains were incorporated onto the polyester backbone with a high degree of fidelity and efficiency, as verified by NMR spectroscopies and GPC analysis (90% grafting efficiency in some cases). The resulting block graft copolymers displayed significant thermal differences, specifically a depression in the observed melting transition temperature, Tm, in comparison with the parent PCL and PEO polymers. These amphiphilic block graft copolymers undergo self‐assembly in aqueous solution with the P(CL‐co‐OPD‐co‐(OPD‐g‐PEO)) polymer forming spherical micelles and a P(CL‐co‐OPD‐co‐(OPD‐g‐PEO)‐co‐(OPD‐g‐pMeOBn)) forming cylindrical or rod‐like micelles, as observed by transmission electron microscopy and atomic force microscopy. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3553–3563, 2010
Preparation of thermoresponsive polymers bearing amino acid diamide derivatives via RAFT polymerization
Authors: Liu Zhilei , Hu Jiwen , Sun Jianping , He Guping , Li Yinghui , Zhang Ganwei
Published: July 2010

We report here the synthesis of well‐defined homopolymer bearing amino acid diamide, poly(N‐acryloyl‐L‐valine N′‐methylamide), via reversible addition fragmentation chain transfer (RAFT) polymerization using alkynyl‐functionalized 2‐dodecylsulfanylthiocarbonylsulfanyl‐2‐methyl‐propionic acid propargyl alcohol ester as chain transfer agent (CTA) and 2,2′‐azobis(isobutyronitrile) as initiator. The effects of a variety of parameters, such as temperature and solvent, on RAFT polymerization were examined to determine the optimal control of the polymerization. The controlled nature of RAFT polymerization was evidenced by the controllable molecular weight and low‐molecular‐weight polydispersity index (Mw/Mn) of resulting homopolymers and further demonstrated to have retained end‐group functionality by the fact of the successful formation of block copolymers from further RAFT polymerization by using the resultant polymer as macro‐CTA, as well as from “click” chemistry. Thermoresponsive property of the prepared polymer was evaluated in terms of the lower critical solution temperature in aqueous solution by measuring the transmittance variation at 500 nm from UV/vis spectroscopy. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3573–3586, 2010
Synthesis of highly luminescent organoboron polymers connected by bifunctional 8‐aminoquinolate linkers
Authors: Tokoro Yuichiro , Nagai Atsushi , Chujo Yoshiki
Published: July 2010

New organoboron aminoquinolate‐based polymers linked by π‐conjugated bridge were prepared by Sonogashira–Hagihara coupling of organoboron aminoquinolate‐based bisiodo monomers bearing biphenyl or bithiophene moiety with 1,4‐diethynylbenzene derivatives. Tetracoordination states of boron atoms in the obtained polymers were confirmed by 11B NMR spectroscopy, and they were also characterized by 1H NMR and IR spectroscopies and size‐exclusion chromatography. Their optical properties were studied by UV–vis absorption and photoluminescence spectroscopies. In the region above 400 nm, the polymers prepared from 1,4‐diethynyl‐2,5‐dioctyloxybenzene showed bathochromic shifts when compared with those prepared from 1.4‐diethynyl‐2‐perfluorooctyl‐5‐trifluoromethylbenzene. The polymers with biphenyl moiety showed higher absolute fluorescence quantum yields (ϕF = 0.28 and 0.65), whereas those with bithiophene moiety led to decreasing of the low quantum yields (ϕF = 0.19 and 0.00). The density‐functional theory (DFT) and time‐dependent–DFT calculations of model compounds corresponding to the polymers were in good agreement with the results from UV–vis properties. The calculations revealed that the electronic structure of the polymer with bithiophene moiety is different from that with biphenyl moiety, and predicted the electron transfer from the bithiophene moiety to the π‐extended quinoline moiety in transition state. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3693–3701, 2010
Theoretical implications of the elastic modulus discontinuity in rubber networks
Authors: Hanson David E. , Roland C. M.
Published: July 2010

The existence of a discontinuity in the modulus of rubber as the strain transitions from compression to extension is strongly suggested by multiple experiments. Classical rubber elasticity theories, however, do not admit such behavior. Here, we investigate a modification of the assumptions of classical elasticity theory to reconcile this discrepancy. We present an analysis of the consequences of assuming that chain forces are nonzero only for chain extension relative to the unstrained state, in contrast to the classical elasticity theory, which assumes that the chain force is directly proportional to the chain end‐to‐end distance (an entropic spring). Assuming an affine transformation of the network node coordinates, we derive two modulus discontinuity factors between compression and extension:D1, based on the differing number of network chains being extended andD2, based on the average differential chain extension. The discontinuities arise due to geometric effects, inherent in the affine transformation between compressive and extensive strains. We find thatD1, the ratio of the numbers of participating chains (compressive/extensive = 1.37), suffices to account for the experimentally observed modulus discontinuity in natural rubber of 1.34. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1795–1798, 2010
Cancer as the cause of changes in work situation (a NOCWO study)
Authors: Lindbohm M.‐L. , Kuosma E. , Taskila T. , Hietanen P. , Carlsen K. , Gudbergsson S. , Gunnarsdottir H.
Published: July 2010

Objective: To investigate the frequency of changes in work situation due to cancer and to analyze the association of physically demanding work, social support from supervisors, colleagues or occupational health services, and disease‐related factors, with changing employers due to cancer.

Methods: Working‐aged patients with breast, testicular or prostate cancer, or lymphoma with a good prognosis between 1997 and 2002 were identified from a hospital or cancer registry in four Nordic countries. The registers provided data on the disease‐related factors. Information on changes in work situation, received support, and other work‐related factors was collected using a questionnaire (response rate 72%). The frequency of changes in work situation was evaluated among a total of 2030 survivors. Further analyses were carried out among 688 survivors using a multivariable logistic regression model, to investigate factors affecting the risk of changing employers due to cancer.

Results: Altogether, 5–10% of cancer survivors had changed employers, occupations or work tasks, 5% had been unemployed, and 9% had retired due to cancer. The physical demands of previous work were the most important reason behind changing employers after cancer. Among women, weak support from supervisors and occupational health personnel increased the risk of changing employers because of cancer.

Conclusions: A minority of cancer survivors changed employers, occupations, or work tasks because of cancer. Supervisors' support in the form of lightening physically demanding jobs and taking illness into consideration when planning work tasks, and health‐care workers' advice on coping at work may help survivors to maintain their jobs. Copyright © 2010 John Wiley & Sons, Ltd.
Biochemical characterization, localization, and tissue distribution of the longer form of mouse SIRT3
Authors: Jin Lei , Galonek Heidi , Israelian Kristine , Choy Wendy , Morrison Michael , Xia Yu , Wang Xiaohong , Xu Yihua , Yang Yuecheng , Smith Jesse J. , Hoffmann Ethan , Carney David P. , Perni Robert B. , Jirousek Michael R. , Bemis Jean E. , Milne Jill C. , Sinclair David A. , Westphal Christoph H.
Published: July 2010

SIRT3 is a key mitochondrial protein deacetylase proposed to play key roles in regulating mitochondrial metabolism but there has been considerable debate about its actual size, the sequences required for activity, and its subcellular localization. A previously cloned mouse SIRT3 has high sequence similarity with the C‐terminus of human SIRT3 but lacks an N‐terminal mitochondrial targeting sequence and has no detectable deacetylation activity in vitro. Using 5′ rapid amplification of cDNA ends, we cloned the entire sequence of mouse SIRT3, as well as rat and rabbit SIRT3. Importantly, we find that full‐length SIRT3 protein localizes exclusively to the mitochondria, in contrast to reports of SIRT3 localization to the nucleus. We demonstrate that SIRT3 has no deacetylation activity in vitro unless the protein is truncated, consistent with human SIRT3. In addition, we determined the inhibition constants and mechanism of action for nicotinamide and a small molecule SIRT3 inhibitor against active mouse SIRT3 and show that the mechanisms are different for the two compounds with respect to peptide substrate and NAD+. Thus, identification and characterization of the actual SIRT3 sequence should help resolve the debate about the nature of mouse SIRT3 and identify new mechanisms to modulate enzymatic activity.
Gln‐41 is intermolecularly cross‐linked to Lys‐113 in F‐actin by N‐(4‐azidobenzoyl)‐putrescine
Authors: Hegyi G. , Chatterjie N. , Healy‐Louie G. , Elzinga M. , Michel H. , Shabanowitz J. , Hunt D.F.
Published: July 2010

The bifunctional reagent N‐(4‐azidobenzoyl)‐putrescine was synthesized and covalently bound to rabbit skeletal muscle actin. The incorporation was mediated by guinea pig liver transglutaminase under conditions similar to those described by Takashi (1988, Biochemistry 27, 938–943); up to 0.5 M/M were incorporated into G‐actin, whereas F‐actin was refractory to incorporation. Peptide fractionation showed that at least 90% of the label was bound to Gln‐41. The labeled G‐actin was polymerized, and irradiation of the F‐actin led to covalent intermo‐lecular cross‐linking. A cross‐linked peptide complex was isolated from a tryptic digest of the cross‐linked actin in which digestion was limited to arginine; sequence analysis as well as mass spectrometry indicated that the linked peptides contained residues 40–62 and residues 96–116, and that the actual cross‐link was between Gln‐41 and Lys‐113. Thus the γ‐carboxyl group of Gln‐41 must be within 10.7 Å of the side chain (probably the amino group) of Lys‐113 in an adjacent actin monomer. In the atomic model for F‐actin proposed by Holmes et al. (1990, Nature 347, 44–49), the α‐carbons of these residues in adjacent monomers along the two‐start helices are sufficiently close to permit cross‐linking of their side chains, and, pending atomic resolution of the side chains, the results presented here seem to support the proposed model.
Modeling the effects of mutations on the denatured states of proteins
Authors: Shortle David , Chan Hue Sun , Dill Ken A.
Published: July 2010

We develop a model for the reversible denaturation of proteins and for the effects of single‐site mutations on the denatured states. The model is based on short chains of sequences of H (hydrophobic) and P (other) monomers configured as self‐avoiding walks on the two‐dimensional square lattice. The N (native) state is defined as the unique conformation of lowest contact energy, whereas the D (denatured) state is defined as the collection of all other conformations. With this model we are able to determine the exact partition function, and thus the exact native‐denatured equilibrium for various solvent conditions, using the computer to exhaustively enumerate every possible configuration. Previous studies confirm that this model shows many aspects of protein‐like behavior. The present study attempts to model how the denatured state (1) depends on the amino acid sequence, and (2) is changed by single‐site mutations. The model accounts for two puzzling experimental results: (1) the replacement of a polar residue by a hydrophobic amino acid on the surface of a protein can destabilize a native protein, and (2) the “denaturant slope,” m = ∂δG/∂c (where c is the concentration of denaturant – urea, guanidine hydrochloride), can sometimes change by as much as 30% due to a single mutation. The principal conclusion of the present study is that, under strong folding conditions, the denatured conformations that are in equilibrium with the native state are not open random configurations. Instead, they are an ensemble of highly compact conformations with a distribution that depends on the residue sequence and that can be substantially altered by single mutations. Most importantly, we conclude that mutations can exert their dominant effects on protein stability by changing the entropy of folding.
NMR structure of oxidized Escherichia coli glutaredoxin: Comparison with reduced E. coli glutaredoxin and functionally related proteins
Authors: Xia Tai‐He , Bushweller John H. , Sodano Patrick , Billeter Martin , Björnberg Olof , Holmgren Arne , Wüthrich Kurt
Published: July 2010

The determination of the NMR structure of oxidized Escherichia coli glutaredoxin in aqueous solution is described, and comparisons of this structure with that of reduced E. coli glutaredoxin and the related proteins E. coli thioredoxin and T4 glutaredoxin are presented. Based on nearly complete sequence‐specific 1H‐NMR assignments, 804 nuclear Overhauser enhancement distance constraints and 74 dihedral angle constraints were obtained as the input for the structure calculations, for which the distance geometry program DIANA was used followed by simulated annealing with the program X‐PLOR. The molecular architecture of oxidized glutaredoxin is made up of three helices and a four‐stranded β‐sheet. The three‐dimensional structures of oxidized and the recently described reduced glutaredoxin are very similar. Quantitative analysis of the exchange rates of 34 slowly exchanging amide protons from corresponding series of two‐dimensional [15N, 1H]‐correlated spectra of oxidized and reduced glutaredoxin showed close agreement, indicating almost identical hydrogen‐bonding patterns. Nonetheless, differences in local dynamics involving residues near the active site and the C‐terminal α‐helix were clearly manifested. Comparison of the structure of E. coli glutaredoxin with those of T4 glutaredoxin and E. coli thioredoxin showed that all three proteins have a similar overall polypeptide fold. An area of the protein surface at the active site containing Arg 8, Cys 11, Pro 12, Tyr 13, 11e 38, Thr 58, Val 59, Pro 60, Gly 71, Tyr 72, and Thr 73 is proposed as a possible site for interaction with other proteins, in particular ribonucleotide reductase. It was found that this area corresponds to previously proposed interaction sites in T4 glutaredoxin and E. coli thioredoxin. The solvent‐accessible surface area at the active site of E. coli glutaredoxin showed a general trend to increase upon reduction. Only the sulfhydryl group of Cys 11 is exposed to the solvent, whereas that of Cys 14 is buried and solvent inaccessible.
Direct observation by X‐ray analysis of the tetrahedral “intermediate” of aspartic proteinases
Authors: Veerapandian B. , Cooper Jon B. , Šali Andrej , Blundell Tom L. , Rosati Robert L. , Dominy Beryl W. , Damon David B. , Hoover Dennis J.
Published: July 2010

We report the X‐ray analysis at 2.0 Å resolution for crystals of the aspartic proteinase endothiapepsin (EC 3.4.23.6) complexed with a potent difluorostatone‐containing tripeptide renin inhibitor (CP‐81,282). The scissile bond surrogate, an electrophilic ketone, is hydrated in the complex. The pro‐(R) (statine‐like) hydroxyl of the tetrahedral carbonyl hydrate is hydrogen‐bonded to both active‐site aspartates 32 and 215 in the position occupied by a water in the native enzyme. The second hydroxyl oxygen of the hydrate is hydrogen‐bonded only to the outer oxygen of Asp 32. These experimental data provide a basis for a model of the tetrahedral intermediate in aspartic proteinase‐mediated cleavage of the amide bond. This indicates a mechanism in which Asp 32 is the proton donor and Asp 215 carboxylate polarizes a bound water for nucleophilic attack. The mechanism involves a carboxylate (Asp 32) that is stabilized by extensive hydrogen bonding, rather than an oxyanion derivative of the peptide as in serine proteinase catalysis.
A functional protein hybrid between the glucose transporter and the N‐acetylglucosamine transporter of Escherichia coli
Authors: Hummel Urs , Nuoffer Claude , Zanolari Bettina , Erni Bernhard
Published: July 2010

The glucose and N‐acetylglucosamine‐specific transporters (IIGlc/IIIGlc and IIGlcNAc) of the bacterial phosphotransferase system mediate carbohydrate uptake across the cytoplasmic membrane concomitant with substrate phosphorylation. The two transporters have 40% amino acid sequence identity. Eight chimeric proteins between the two transporters were made by gene reconstruction. All hybrid proteins could be expressed, some inhibited cell growth, and one was active. The active hybrid transporter consists of the transmembrane domain (residues 1–386) of the IIGlc subunit and the two hydrophilic domains (residues 370–648) of IIGlcNAc. The N‐terminal hydrophilic domain of IIGlcNAc contains the transiently phosphorylated cysteine‐412. The hybrid protein is specific for glucose, which indicates that the sugar specificity determinant is in the transmembrane domain and that the cysteine from which the phosphoryl group is transferred to the substrate is not part of the binding site. The protein sequence (LKTPGRED) at which the successful fusion occurred has the characteristic properties of an interdomain oligopeptide linker (Argos, P., 1990, J. Mol. Biol. 211, 943–958).
Quantitative analysis of cyclic β‐turn models
Authors: Perczel Andraás , Fasman Gerald D.
Published: July 2010

The β‐turn is a frequently found structural unit in the conformation of globular proteins. Although the circular dichroism (CD) spectra of the α‐helix and β‐pleated sheet are well defined, there remains some ambiguity concerning the pure component CD spectra of the different types of β‐turns. Recently, it has been reported (Hollósi, M., Koövér, K.E., Holly, S., Radics, L., & Fasman, G.D., 1987, Biopolymers 26, 1527–1572; Perczel, A., Hollósi, M., Foxman, B.M., & Fasman, G.D., 1991a, J. Am. Chem. Soc. 113, 9772–9784) that some pseudohexapeptides (e.g., the cyclo[(δ)Ava–Gly–Pro–Aaa–Gly] where Aaa = Ser, Ser(OtBu), or Gly) in many solvents adopt a conformational mixture of type I and the type II β‐turns, although the X‐ray‐determined conformation was an ideal type I β‐turn. In addition to these pseudohexapeptides, conformational analysis was also carried out on three pseudotetrapeptides and three pseudooctapeptides. The target of the conformation analysis reported herein was to determine whether the ring stress of the above β‐turn models has an influence on their conformational properties.

Quantitative nuclear Overhauser effect (NOE) measurements yielded interproton distances. The conformational average distances so obtained were interpreted utilizing molecular dynamics (MD) simulations to yield the conformational percentages. These conformational ratios were correlated with the conformational weights obtained by quantitative CD analysis of the same compounds. The pure component CD curves of type I and type II β‐turns were also obtained, using a recently developed algorithm (Perczel, A., Tusnády, G., Hollósi, M., & Fasman, G.D., 1991b, Protein Eng. 4(6), 669–679). For the first time the results of a CD deconvolution, based on the CD spectra of 14 β‐turn models, were assigned by quantitative NOE results. The NOE experiments confirmed the ratios of the component curves found for the two major β‐turns by CD analysis. These results can now be used to enhance the conformational determination of globular proteins on the basis of their CD spectra.
Selection of representative protein data sets
Authors: Hobohm Uwe , Scharf Michael , Schneider Reinhard , Sander Chris
Published: July 2010

The Protein Data Bank currently contains about 600 data sets of three‐dimensional protein coordinates determined by X‐ray crystallography or NMR. There is considerable redundancy in the data base, as many protein pairs are identical or very similar in sequence. However, statistical analyses of protein sequence‐structure relations require nonredundant data. We have developed two algorithms to extract from the data base representative sets of protein chains with maximum coverage and minimum redundancy. The first algorithm focuses on optimizing a particular property of the selected proteins and works by successive selection of proteins from an ordered list and exclusion of all neighbors of each selected protein. The other algorithm aims at maximizing the size of the selected set and works by successive thinning out of clusters of similar proteins. Both algorithms are generally applicable to other data bases in which criteria of similarity can be defined and relate to problems in graph theory. The largest nonredundant set extracted from the current release of the Protein Data Bank has 155 protein chains. In this set, no two proteins have sequence similarity higher than a certain cutoff (30% identical residues for aligned subsequences longer than 80 residues), yet all structurally unique protein families are represented. Periodically updated lists of representative data sets are available by electronic mail from the file server “netserv@embl‐heidelberg.de.” The selection may be useful in statistical approaches to protein folding as well as in the analysis and documentation of the known spectrum of three‐dimensional protein structures.
Dissociation of peripheral protein‐membrane complexes by high pressure
Authors: Plager Douglas A. , Nelsestuen Gary L.
Published: July 2010

The ability of high pressure to dissociate several peripheral protein‐membrane complexes was investigated. Three vitamin K‐dependent proteins (factor X, protein Z, and prothrombin) dissociated from small unilamellar vesicles (SUVs, 30 nm diameter) composed of 25% phosphatidylserine (PS) and 75% phosphatidylcholine (PC) at comparable pressures (midpoints of 0.3–0.6 kbar). The pressure‐induced dissociation curves for the factor X‐SUV interaction followed the expected behavior for an interaction with an apparent dissociation equilibrium constant at atmospheric pressure, KD(atm), of 9 × 10−7 M and a change in volume of association, ΔVa, of 88 mL/mol. Factor X also dissociated from large unilamellar vesicles (LUVs, 100 nm diameter, 25% PS:75% PC) with a midpoint of 0.5 kbar. A second group of calcium‐dependent membrane‐binding proteins included protein kinase C (PKC), a 64‐kDa protein, and a 32‐kDa protein. The 32‐kDa protein dissociated from SUVs (midpoint of 0.8 kbar), whereas PKC and the 64‐kDa protein did not dissociate to a significant degree. The differences in dissociability of these proteins appeared to be a result of the differences in their KD(atm)'s (decreased dissociability with decreased KD(atm)). This pattern was further demonstrated by the relatively high midpoint of dissociation (1.1–1.4 kbar) of serum amyloid P component (SAP; KD(atm) ca. 10−11) and the limited dissociation of factor Va light chain (KD(atm) ca. 10−11). Changing the vesicle composition to phosphatidylethanolamine in place of PC gave higher affinity and decreased dissociation of the 32‐kDa protein and SAP. Thus, the susceptibility of various peripheral membrane‐binding proteins to high pressure dissociation was governed by both the KD(atm) and the ΔVa of the particular protein‐membrane interaction, with the ΔVa's of the dissociable proteins being relatively small (< 150 mL/mol).
Zinc‐ and sequence‐dependent binding to nucleic acids by the N‐terminal zinc finger of the HIV‐1 nucleocapsid protein: NMR structure of the complex with the Psi‐site analog, dACGCC
Authors: South Terri L. , Summers Michael F.
Published: July 2010

The nucleic acid interactive properties of a synthetic peptide with sequence of the N‐terminal CCHC zinc finger (CCHC = Cys‐X2‐Cys‐X4‐His‐X4‐Cys; × = variable amino acid) of the human immunodeficiency virus (HIV) nucleocapsid protein, Zn(HIV1‐F1), have been studied by 1H NMR spectroscopy. Titration of Zn(HIV1‐F1) with oligodeoxyribonucleic acids containing different nucleotide sequences reveals, for the first time, sequence‐dependent binding that requires the presence of at least one guanosine residue for tight complex formation. The dynamics of complex formation are sensitive to the nature of the residues adjacent to guanosine, with residues on the 3′ side of guanosine having the largest influence. An oligodeoxyribonucleotide with sequence corresponding to a portion of the HIV‐1 psi‐packaging signal, d(ACGCC), forms a relatively tight complex with Zn(HIV1‐F1) (Kd = 5 × 10−6 M). Two‐dimensional nuclear Overhauser effect (NOESY) data indicate that the bound nucleic acid exists predominantly in a single‐stranded, A‐helical conformation, and the presence of more than a dozen intermolecular NOE cross peaks enabled three‐dimensional modeling of the complex. The nucleic acid binds within a hydrophobic cleft on the peptide surface. This hydrophobic cleft is defined by the side chains of residues Val1, Phe4, Ile12, and Ala13. Backbone amide protons of Phe4 and Ala13 and the backbone carbonyl oxygen of Lys2 that lie within this cleft appear to form hydrogen bonds with the guanosine O6 and N1H atoms, respectively. In addition, the positively charged side chain of Arg14 is ideally positioned for electrostatic interactions with the phosphodiester backbone of the nucleic acid. The structural findings provide a rationalization for the general conservation of these hydrophobic and basic residues in CCHC zinc fingers, and are consistent with site‐directed mutagenesis results that implicate these residues as direct participants in viral genome recognition.
Modeling α‐helical transmembrane domains: The calculation and use of substitution tables for lipid‐facing residues
Authors: Blundell Tom L. , Donnelly Dan , Overington John P. , Ruffle Stuart V. , Nugent Jonathan H.A.
Published: July 2010

Amino acid substitution tables are calculated for residues in membrane proteins where the side chain is accessible to the lipid. The analysis is based upon the knowledge of the three‐dimensional structures of two homologous bacterial photosynthetic reaction centers and alignments of their sequences with the sequences of related proteins. The patterns of residue substitutions show that the lipid‐accessible residues are less conserved and have distinctly different substitution patterns from the inaccessible residues in water‐soluble proteins. The observed substitutions obtained from sequence alignments of transmembrane regions (identified from, e.g., hydrophobicity analysis) can be compared with the patterns derived from the substitution tables to predict the accessibility of residues to the lipid. A Fourier transform method, similar to that used for the calculation of a hydrophobic moment, is used to detect periodicity in the predicted accessibility that is compatible with the presence of an α‐helix. If the putative transmembrane region is identified as helical, then the buried and exposed faces can be discriminated. The presence of charged residues on the lipid‐exposed face can help to identify the regions that are in contact with the polar environment on the borders of the bilayer, and the construction of a meaningful three‐dimensional model is then possible. This method is tested on an alignment of bacteriorhodopsin and two related sequences for which there are structural data at near atomic resolution.