bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of maxillofacial brown tumors after parathyroidectomy in primary hyperparathyroidism
Authors: Reséndiz‐Colosia Jaime Alonso , Rodríguez‐Cuevas Sergio Arturo , Flores‐Díaz Rutilio , Juan Martín Hernández‐San , Gallegos‐Hernández José Francisco , Barroso‐Bravo Sinhué , Gómez‐Acosta Fernando
Published: August 2008

Background.

Brown tumor occasionally affects the facial bones. Clinically, these lesions can be mistaken for a neoplasm. Opinions are divided on the course of management of the bony lesions once parathyroidectomy has been carried out.

Methods.

We treated 22 patients with primary hyperparathyroidism and osteitis fibrosa cystica and observed their clinical and biochemical recovery.

Results.

Fifteen patients (68.2%) had brown tumors in mandible, and 7 (31.8%) in maxilla. After parathyroidectomy, 21 patients had normal total serum calcium values. All brown tumors presented a spontaneous progressive regression; in 18cases, regression was total, with a mean time period of 10months. Two patients had partial regression after nearly 2years. Another 2 patients were lost to follow‐up.

Conclusions.

After successful parathyroid surgery, the bony lesions tended to regress spontaneously, either partially or completely. However, if the lesion is disfiguring or symptomatic, surgical excision may be indicated. © 2008 Wiley Periodicals, Inc. Head Neck, 2008
Extrahepatic cholestasis increases liver stiffness (FibroScan) irrespective of fibrosis
Authors: Millonig Gunda , Reimann Frank M. , Friedrich Stephanie , Fonouni Hamidreza , Mehrabi Arianeb , Büchler Markus W. , Seitz Helmut Karl , Mueller Sebastian
Published: August 2008

Transient elastography (FibroScan [FS]) is a novel non-invasive tool to assess liver fibrosis/cirrhosis. However, it remains to be determined if other liver diseases such as extrahepatic cholestasis interfere with fibrosis assessment because liver stiffness is indirectly measured by the propagation velocity of an ultrasound wave within the liver. In this study, we measured liver stiffness immediately before endoscopic retrograde cholangiopancreatography and 3 to 12 days after successful biliary drainage in patients with extrahepatic cholestasis mostly due to neoplastic invasion of the biliary tree. Initially elevated liver stiffness decreased in 13 of 15 patients after intervention, in 10 of them markedly. In three patients, liver stiffness was elevated to a degree that suggested advanced liver cirrhosis (mean, 15.2 kPa). Successful drainage led to a drop of bilirubin by 2.8 to 9.8 mg/dL whereas liver stiffness almost normalized (mean, 7.1 kPa). In all patients with successful biliary drainage, the decrease of liver stiffness highly correlated with decreasing bilirubin (Spearman's ρ = 0.67,

P

< 0.05) with a mean decrease of liver stiffness of 1.2 ± 0.56 kPa per 1 g/dL bilirubin. Two patients, in whom liver stiffness did not decrease despite successful biliary drainage, had advanced liver cirrhosis and multiple liver metastases, respectively. The relationship between extrahepatic cholestasis and liver stiffness was reproduced in an animal model of bile duct ligation in landrace pigs where liver stiffness increased from 4.6 kPa to 8.8 kPa during 120 minutes of bile duct ligation and decreased to 6.1 kPa within 30 minutes after decompression.

Conclusion:

Extrahepatic cholestasis increases liver stiffness irrespective of fibrosis. Once extrahepatic cholestasis is excluded (e.g., by liver imaging and laboratory parameters) transient elastography is a valuable tool to assess liver fibrosis in chronic liver diseases. (Hepatology 2008.)
Advancing process‐based watershed hydrological research using near‐surface geophysics: a vision for, and review of, electrical and magnetic geophysical methods
Authors: Robinson D. A. , Binley A. , Crook N. , Day‐Lewis F. D. , Ferré T. P. A. , Grauch V. J. S. , Knight R. , Knoll M. , Lakshmi V. , Miller R. , Nyquist J. , Pellerin L. , Singha K. , Slater L.
Published: August 2008

We want to develop a dialogue between geophysicists and hydrologists interested in synergistically advancing process based watershed research. We identify recent advances in geophysical instrumentation, and provide a vision for the use of electrical and magnetic geophysical instrumentation in watershed scale hydrology. The focus of the paper is to identify instrumentation that could significantly advance this vision for geophysics and hydrology during the next 3–5 years. We acknowledge that this is one of a number of possible ways forward and seek only to offer a relatively narrow and achievable vision. The vision focuses on the measurement of geological structure and identification of flow paths using electrical and magnetic methods. The paper identifies instruments, provides examples of their use, and describes how synergy between measurement and modelling could be achieved. Of specific interest are the airborne systems that can cover large areas and are appropriate for watershed studies. Although airborne geophysics has been around for some time, only in the last few years have systems designed exclusively for hydrological applications begun to emerge. These systems, such as airborne electromagnetic (EM) and transient electromagnetic (TEM), could revolutionize hydrogeological interpretations. Our vision centers on developing nested and cross scale electrical and magnetic measurements that can be used to construct a three‐dimensional (3D) electrical or magnetic model of the subsurface in watersheds. The methodological framework assumes a ‘top down’ approach using airborne methods to identify the large scale, dominant architecture of the subsurface. We recognize that the integration of geophysical measurement methods, and data, into watershed process characterization and modelling can only be achieved through dialogue. Especially, through the development of partnerships between geophysicists and hydrologists, partnerships that explore how the application of geophysics can answer critical hydrological science questions, and conversely provide an understanding of the limitations of geophysical measurements and interpretation. Copyright © 2008 John Wiley & Sons, Ltd.
Antibiotic use predicts an increased risk of cancer
Authors: Kilkkinen Annamari , Rissanen Harri , Klaukka Timo , Pukkala Eero , Heliövaara Markku , Huovinen Pentti , Männistö Satu , Aromaa Arpo , Knekt Paul
Published: August 2008

Antibiotic use has been hypothesized to be associated with the risk of cancer but the evidence is sparse and inconsistent. The aim of the present study was to determine whether antibiotic use predicts the development of various cancers. This nationwide cohort study included 3,112,624 individuals, aged 30–79 years, with no history of cancer. Information on their antibiotic use between 1995 and 1997 was obtained from the Drug Prescription Registry. During the period 1998–2004, 134,070 cancer cases were ascertained from the Finnish Cancer Registry. Cox proportional hazards regression was used to estimate the relative risks (RRs) with 95% confidence intervals (95% CIs). Antibiotic use was associated with an increased risk of cancer: for categories of increasing antibiotic use (0–1, 2–5 and ≥6 prescriptions), RRs (95% CIs) for cancer were 1.0 (reference), 1.27 (1.26–1.29) and 1.37 (1.34–1.40). RRs (for comparison of lowest and highest exposure group) for the most common primary sites i.e. prostate, breast, lung and colon were 1.39 (1.31–1.48), 1.14 (1.09–1.20), 1.79 (1.67–1.92), and 1.15 (1.04–1.26), respectively. RRs for other primary sites varied between 0.90 (0.76–1.05) for ovary to 2.60 (1.60–4.20) for endocrine gland (excluding thyroid). In conclusion, antibiotic use predicts an increased risk of cancer. Because of the design of our study the possibility of residual confounding cannot be excluded and further studies are required to confirm the results. © 2008 Wiley‐Liss, Inc.
Evidence for a pathophysiological role of cysteinyl leukotrienes in classical Hodgkin lymphoma
Authors: Schain Frida , Tryselius Ylva , Sjöberg Jan , Porwit Anna , Backman Linda , Malec Maria , Xu Dawei , Vockerodt Martina , Baumforth Karl R.N. , Wei Wenbin , Murray Paul G. , Björkholm Magnus , Claesson Hans‐Erik
Published: August 2008

Classical Hodgkin lymphoma (cHL) is characterized histologically by a minority of malignant Hodgkin Reed‐Sternberg cells surrounded by abundant inflammatory cells, generally believed to be of major importance in the pathophysiology of the disease. Here, we present data that link inflammatory cell‐derived arachidonic acid metabolites, the cysteinyl leukotrienes (CysLT), to the pathogenesis of cHL. Two HL cell lines, L1236 and KMH2, were shown to express functional CysLT1 receptors, responding with a robust calcium signal upon leukotriene (LT) D4 challenge. LTD4 stimulated protein release of tumor necrosis factor‐α, interleukin‐6 and ‐8 by L1236 cells and interleukin‐8 by KMH2 cells. Importantly, all these LTD4‐induced effects were blocked by the CysLT1 receptor‐specific antagonist zafirlukast. Immunohistochemical studies of cHL biopsies and microarray analysis of microdissected cells revealed that the CysLT1 receptor is expressed also by primary Hodgkin Reed‐Sternberg cells. As these cells are surrounded by CysLT‐producing eosinophils, macrophages and mast cells, our results suggest the CysLTs as mediators in the pathogenesis of cHL, contributing to the aberrant cytokine network of this lymphoma. © 2008 Wiley‐Liss, Inc.
Activated carbons from peach stones and pine sawdust by phosphoric acid activation used in clarification and decolorization processes
Authors: Muñoz‐González Yuvisa , Arriagada‐Acuña Renán , Soto‐Garrido G , García‐Lovera Rafael
Published: August 2008

BACKGROUND: A comparative study of the influence of preparation variables in the activation of pine sawdust and peach stones with phosphoric acid is presented. Adsorptive properties of these materials were tested for the clarification of apple juice and the decolorization of red wine. The main objective of this study was to identify the influence of the textural and chemical properties of activated carbons on clarification and decolorization processes.

RESULTS: The role of impregnation conditions in porosity development was more important for activated carbons originating from peach stones than in those originating from pine sawdust, mainly due to their morphological differences. The amount of phosphoric acid retained on the precursors was found to be a function of the impregnation variables. Furthermore, porosity development dependence on phosphoric acid content per gram of precursor was confirmed. For both precursors, the best microporosity development was obtained at a heat treatment temperature of 450 °C. Independently of the preparation variables used, activated carbons from pine sawdust and peach stones had the same type of surface functional groups: mainly phenolic, quinonic and phosphoric ester‐like structures.

CONCLUSIONS: From the results of clarifications and decolorization tests, it was confirmed that to obtain good performance in these assays, the development of mesoporosity is crucial. However, when activated carbons had similar mesoporosities, the presence of surface functional groups contributed to improved performance in clarification and decolorization process. Copyright © 2008 Society of Chemical Industry
Too big to bind? Will the purification of large and complex therapeutic targets spell the beginning of the end for column chromatography?
Authors: Willoughby Nik
Published: August 2008

Progress in some areas of medical research is leading to larger and more complex therapeutic products—for example, cellular or gene therapies. For decades, the bioprocessing industry has relied upon column chromatography as the mainstay of purification processes. Whilst highly effective for the purification of proteins and smaller molecules, chromatographic techniques are not necessarily well suited to purification of these newer, larger targets. This article considers the approaches adopted in the purification of large, complex targets and emphasises the need for more focused development of purification techniques more suited to the target's size and complexity. Copyright © 2008 Society of Chemical Industry
Octanol/water partition coefficients of ionic liquids
Authors: Lee Sang Hyun , Lee Sun Bok
Published: August 2008

BACKGROUND: Room temperature ionic liquids (ILs) are attractive alternatives to environmentally unfriendly volatile organic solvents. Partitioning is one of the most important and fundamental properties of a chemical, and the octanol/water partition coefficient is widely used to measure the tendency of a chemical to cross biological membranes. However, there is very limited information on the concentration dependence of the partition coefficients of ILs. This study investigated the octanol/water partitioning of 1‐butyl‐3‐methylimidazolium ([bmim]) ILs containing either hexafluorophosphate ([PF6]) or bis[(trifluoromethyl)sulfonyl]amide ([Tf2N]) over a wide range of IL concentrations of three to five orders of magnitude.

RESULTS: It was found that the apparent partition coefficients of the ILs increased with increasing IL concentration. A model based on the ionic nature of ILs was proposed to explain this behaviour, and the results showed a good fit with the experimental data. The intrinsic partition coefficients and dissociation constants of the ILs were determined using the equations from the proposed model. The differences in the intrinsic partition parameter values between the two ILs showed a good correlation with other physicochemical properties.

CONCLUSIONS: The present study clearly shows that the octanol/water partition coefficients of ILs increase with increasing IL concentration owing to the formation of ion pairs. By using the proposed partition model, it was possible to determine the intrinsic partition coefficients of ILs, and it was found that the apparent partition coefficients of ILs converge to the intrinsic partition coefficients of the ionic species and ion pairs of ILs with decreasing and increasing IL concentration respectively. Copyright © 2008 Society of Chemical Industry
Sand dune fixation: A solar‐powered Sahara seawater pipeline macroproject
Authors: Badescu V. , Cathcart R. B. , Bolonkin A. A.
Published: August 2008

The paper proposes macro‐engineering using tactical technologies that stabilize and vegetate barren near‐coast sand dune fields with seawater. Seawater that would otherwise, as commonly postulated, increase the Earth–ocean volume. Anthropogenic saturation of the ground with pumped seawater should fix widespread active sand dune fields in deserts (such as the westernmost Sahara). Seawater extraction from the ocean, and its deposition on dune sand, is made via solar‐powered pipeline. Stabilisation of one major erg in Mauritania is evaluated as a case study. The financial cost of the macroproject is estimated as a few billion US$—less than about 0·1 per cent of the USA's 2007 gross domestic product. The initial investment may be between 0·6 and 1·1 billions US$. Copyright © 2008 John Wiley & Sons, Ltd.
Non‐Bioengineered Silk Fibroin Protein 3D Scaffolds for Potential Biotechnological and Tissue Engineering Applications
Authors: Mandal Biman B. , Kundu Subhas C.
Published: August 2008

This paper describes a new source for fabricating high‐strength, non‐bioengineered silk gland fibroin 3D scaffolds from Indian tropical tasar silkworm, Antheraea mylitta using SDS for dissolution. The scaffolds were fabricated by freeze drying at different prefreezing temperatures for pore size and porosity optimization. Superior mechanical properties with compressive strength in the range of 972 kPa were observed. The matrices were degraded by proteases within 28 d of incubation. Biocompatibility was assessed by feline fibroblast culture in vitro and confocal microscopy further confirmed adherence, spreading, and proliferation of primary dermal fibroblasts. Results indicate nonmulberry 3D silk gland fibroin protein as an inexpensive, high‐strength, slow biodegradable, biocompatible, and alternative natural biomaterial.

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Room Temperature Processable Silicon‐Containing Molecular Resist
Authors: Park Ji Young , Kim Myung Gi , Kim Jin‐Baek
Published: August 2008

A novel silicon‐containing molecular resist material based on polyhedral oligomeric silsesquioxane, possessing trimethoxysilyl groups, was designed in order to reduce post‐exposure delay problems and to improve resolution. Since the acid‐catalyzed cross‐linking reaction of trimethoxysilyl groups occurs at room temperature, there is no necessity of post‐exposure bake. The molecular resist showed 0.7 µm line‐and‐space patterns using a mercury–xenon lamp in a contact printing mode and 100 nm line‐and‐space patterns using electron beam lithography.

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Ring Opening Polymerization of Lactide under Solvent‐Free Conditions Catalyzed by a Chlorotitanium Calix[4]arene Complex
Authors: Frediani Marco , Sémeril David , Mariotti Alfredo , Rosi Luca , Frediani Piero , Rosi Laura , Matt Dominique , Toupet Loïc
Published: August 2008

A novel chlorotitanium calix[4]arene complex was synthesized and tested, without activator, as catalyst for the polymerization of L‐ and rac‐lactide under solvent‐free conditions. The catalyst displayed high activity, which depended on the monomer‐to‐catalyst molar ratio, and led to highly isotactic PLLA. Despite concomitant transesterification during the polymerization, polylactide formation was well‐controlled, the molar mass distribution indexes remaining in the restricted range of 1.2–1.4.

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Macromol. Theory Simul. 6/2008
Authors: John Andreas , Sommer Jens‐Uwe
Published: August 2008

Cover: The picture on the left shows a plot of the contour surface in the simulation box for the system representing 90 % consumption of the reactive graft monomers, where the density difference of the two monomer species A, B equals zero. The picture on the right shows a plot of a slice through different contour surfaces each of equal monomer density difference for the same system. Further details can be found in the article by A. John* and J.‐U. Sommer page 274.
Synthesis and characterization of PbS/polyaniline core–shell nanocomposites based on octahedral PbS nanocrystals colloid
Authors: Jing Shengyu , Xing Shuangxi , Dong Fengxia , Zhao Chun
Published: August 2008

PbS/polyaniline core–shell nanocomposites were successfully synthesized via in situ chemical oxidation polymerization of aniline based on the octahedral PbS nanocrystals colloid. The morphology and structure of the products were characterized by transmission electron microscopy, X‐ray diffraction, Fourier transform infrared spectra, UV–vis spectra, and conductivity measurement. A possible formation mechanism of the PbS/polyaniline core–shell nanocomposites was also proposed. POLYM. COMPOS., 2008. © 2008 Society of Plastics Engineers
Modelling of the chemo–rheological behavior of thermosetting polymer nanocomposites
Authors: Lelli Govanni , Terenzi Andrea , Kenny Jose M. , Torre Luigi
Published: August 2008

Epoxy/amine/montmorillonite nanocomposite systems are studied in this article. Both a thermo−kinetic analysis (performed using a differential scanning calorimeter) and a chemorheological characterization were carried out. The comparison of DSC thermograms has shown that the addition the nanofiller does not change the mechanism of crosslinking from a qualitative standpoint, but the nanoreinforcement seemed to produce an evident hindrance on the molecular mobility, which in turn influences the cure reactions. As none of the kinetic models available in literature was able to describe the cure behavior of the aforementioned materials, a new phenomenological model is proposed in this work, which considers the activation energy of the networking process a function of the degree of cure (rising exponentially towards infinity when thesystem approaches vitrification). The effects of the presence of the clay on the chemorheology of the composites was resumed as follows: the viscosity of the nanocomposite was higher at any temperature, furthermore the composite viscosity showed an higher heating sensitivity before networking and gelation occurred at lower degrees of cure, thus determining a narrower shape of the chemoviscosity behavior. A modified version of the classical Williams–Landel–Ferry (WLF) equation that took into account the gelation and the effects of crosslinking was uses as chemorheological model. Once the characteristic parameters of both the neat resin and the nanocomposite were found, the chemoviscosity models were integrated using a numerical algorithm, to check their ability to foresee the behavior of the systems during a dynamic cure process. A very good correspondence between the results and the experimental data was obtained. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Preparation of the γ‐Al2O3/PANI nanocomposite via enzymatic polymerization
Authors: Nabid Mohammad Reza , Golbabaee Maryam , Moghaddam Abdolmajid Bayandori , Mahdavian Ali Reza , Amini Mostafa Mohammadpour
Published: August 2008

Peroxidase‐catalyzed template‐guided polymerization of aniline in the presence of γ‐ alumina nanosheet (NS) particles have been carried out in aqueous media and γ‐Al2O3/PANI nanocomposite was obtained. The polymerization of aniline occurred in aqueous solution in the presence of SPS (sulfonated polystyrene) as a template and SDS (sodium dodecyl sulfate) as a surfactant. Both obtained nanocomposites were comparable by SEM images. It was demonstrated that the γ‐Al2O3 NS/PANI‐SPS nanocomposite has higher conductivity and the γ‐Al2O3 NS/PANI‐SDS nanocomposite has higher void areas. The higher conductivity of γ‐Al2O3 NS/PANI‐SPS nanocomposite is attributed to the higher coated areas of γ‐Al2O3 NS during polymerization in comparison with γ‐Al2O3 NS/PANI‐SDS which are not coated efficiently as the former. The FT‐IR studies showed that the γ‐Al2O3 NS/PANI nanocomposite was formed by interaction of the polyaniline (PANI) and γ‐Al2O3 NS. FTIR also showed that the amount of PANI in γ‐Al2O3 NS/PANI‐SPS is more than in γ‐Al2O3 NS/PANI‐SDS. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Tensile creep of a long‐fibre glass mat thermoplastic (GMT) composite. II. Viscoelastic‐viscoplastic constitutive modeling
Authors: Dasappa Prasad , Lee‐Sullivan Pearl , Xiao Xinran , Foss Peter H.
Published: August 2008

In Part I of this article, the short‐term tensile creep of a 3‐mm‐thick continuous long‐fibre glass mat thermoplastic composite was characterized and found to be linear viscoelastic up to 20 MPa. Subsequently, a nonlinear viscoelastic model has been developed for stresses up to 60 MPa for relatively short creep durations. The creep response was also compared with the same composite material having twice the thickness for a lower stress range. Here in Part II, the work has been extended to characterize and model longer term creep and recovery in the 3‐mm composite for stresses up to near failure. Long‐term creep tests consisting of 1‐day loading followed by recovery were carried out in the nonlinear viscoelastic stress range of the material, i.e., 20–80 MPa in increments of 10 MPa. The material exhibited tertiary creep at 80 MPa and hence data up‐to 70 MPa has been used for model development. It was found that viscoplastic strains of about 10% of the instantaneous strains were developed under load. Hence, a non‐linear viscoelastic–viscoplastic constitutive model has been developed to represent the considerable plastic strains for the long‐term tests. Findley's model which is the reduced form of the Schapery non‐linear viscoelastic model was found to be sufficient to model the viscoelastic behavior. The viscoplastic strains were modeled using the Zapas and Crissman viscoplastic model. A parameter estimation method which isolates the viscoelastic component from the viscoplastic part of the nonlinear model has been developed. The model predictions were found to be in good agreement with the average experimental curves. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Protein unlocking procedures of formalin‐fixed paraffin‐embedded tissues: Application to MALDI‐TOF Imaging MS investigations
Authors: Ronci Maurizio , Bonanno Elena , Colantoni Alfredo , Pieroni Luisa , Di Ilio Carmine , Spagnoli Luigi Giusto , Federici Giorgio , Urbani Andrea
Published: August 2008

Archival formalin‐fixed paraffin‐embedded (FFPE) tissues are a powerful tool for examining the clinical course of diseases. These specimens represent an incredible mine of valuable clinical and biological information for proteomic investigation. MALDI‐TOF imaging MS (MALDI‐IMS) is a protein profiling technique which enables the direct sampling of histological section; however, the quality of molecular data are strongly influenced by the tissue preparation condition. In fact, in previous years most of the studies employing such a technological platform have been conducted using cryo‐preserved tissues. We have developed an in vitro approach using “tissue surrogate” samples in order to explore different protein unlocking procedures which might enable a suitable recovery of polypeptides for MS analysis. The developed protocols have been compared both by MALDI‐TOF MS and nLC‐MSE analysis either on surrogate samples or on FFPE specimen from human breast cancer. The collected evidence has been applied for the preparation of FFPE tissue sections following MALDI‐IMS analysis. Our results outline the possibility to obtain valuable peptide mass spectra profiles form FFPE preparations by applying a combined two steps procedure of heat induced antigen retrieval (HIAR) in presence of EDTA and on target trypsin hydrolysis. A multivariate statistical evaluation is presented and discussed according to molecular spatial distributions and tissue morphology.
Analysis of nonadditive protein accumulation in young primary roots of a maize (Zea mays L.) F1‐hybrid compared to its parental inbred lines
Authors: Hoecker Nadine , Lamkemeyer Tobias , Sarholz Barbara , Paschold Anja , Fladerer Claudia , Madlung Johannes , Wurster Karl , Stahl Mark , Piepho Hans‐Peter , Nordheim Alfred , Hochholdinger Frank
Published: August 2008

Heterosis describes the superior performance of heterozygous F1‐hybrids compared to their homozygous parental inbred lines. Heterosis is already manifested during early maize (Zea mays L.) primary root development. In this study, the most abundant soluble proteins have been investigated before the phenotypic manifestation of heterosis in 3.5‐day‐old primary roots in the flint inbred line UH002, the dent inbred line UH301 and the corresponding hybrid UH301×UH002. In CBB‐stained 2‐DE gels, 150 of 304 detected proteins (49%) were accumulated in a nonadditive fashion in the hybrid compared to the average of their parental inbred lines (Student's t‐test: p < 0.05). Remarkably, expression of 51% (76/150) of the nonadditively accumulated proteins exceeded the high parent or was below the low parent. ESI‐MS/MS identified 75 of the 76 proteins that belonged to these expression classes. The most abundant functional classes among the 75 proteins that were encoded by 60 different genes were metabolism (58%) and disease and defense (19%). Nonadditive protein accumulation in primary roots of maize hybrids might be associated with heterosis manifestation. Identification of these proteins could therefore contribute to the better understanding of the molecular basis of heterosis.
X‐ray structure of HIV‐1 protease in situ product complex
Authors: Bihani Subhash , Das Amit , Prashar Vishal , Ferrer J.‐L. , Hosur M. V.
Published: August 2008

HIV‐1 protease is an effective target for design of different types of drugs against AIDS. HIV‐1 protease is also one of the few enzymes that can cleave substrates containing both proline and nonproline residues at the cleavage site. We report here the first structure of HIV‐1 protease complexed with the product peptides SQNY and PIV derived by in situ cleavage of the oligopeptide substrate SQNYPIV, within the crystals. In the structure, refined against 2.0‐Å resolution synchrotron data, a carboxyl oxygen of SQNY is hydrogen‐bonded with the N‐terminal nitrogen atom of PIV. At the same time, this proline nitrogen atom does not form any hydrogen bond with catalytic aspartates. These two observations suggest that the protonation of scissile nitrogen, during peptide bond cleavage, is by a gem‐hydroxyl of the tetrahedral intermediate rather than by a catalytic aspartic acid. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Structural coupling between FKBP12 and buried water
Authors: Szep Szilvia , Park Sheldon , Boder Eric T. , Van Duyne Gregory D. , Saven Jeffery G.
Published: August 2008

Globular proteins often contain structurally well‐resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 binding protein‐12 (FKBP12) (Park and Saven, Proteins 2005; 60:450–463). In particular, simulations suggested that disrupting a hydrogen bond to Wat3 by mutating E60 to either A or Q would cause a structural perturbation involving the distant W59 side chain, which rotates to a new conformation in response to the mutation. This effectively remodels the ligand‐binding pocket, as the side chain in the new conformation is likely to clash with bound FK506. To test whether the protein structure is in effect modulated by the binding of a buried water in the distance, we determined high‐resolution (0.92–1.29 Å) structures of wild‐type FKBP12 and its two mutants (E60A, E60Q) by X‐ray crystallography. The structures of mutant FKBP12 show that the ligand‐binding pocket is indeed remodeled as predicted by the substitution at position 60, even though the water molecule does not directly interact with any of the amino acids of the binding pocket. Thus, these structures support the view that buried water molecules constitute an integral, noncovalent component of the protein structure. Additionally, this study provides an example in which predictions from molecular dynamics simulations are experimentally validated with atomic precision, thus showing that the structural features of protein–water interactions can be reliably modeled at a molecular level. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Structural determinants of species‐selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies
Authors: Kaufmann Kristian W. , Dawson Eric S. , Henry L. Keith , Field Julie R. , Blakely Randy D. , Meiler Jens
Published: August 2008

To identify potential determinants of substrate selectivity in serotonin (5‐HT) transporters (SERT), models of human and Drosophila serotonin transporters (hSERT, dSERT) were built based on the leucine transporter (LeuTAa) structure reported by Yamashita et al. (Nature 2005;437:215–223), PBDID 2A65. Although the overall amino acid identity between SERTs and the LeuTAa is only 17%, it increases to above 50% in the first shell of the putative 5‐HT binding site, allowing de novo computational docking of tryptamine derivatives in atomic detail. Comparison of hSERT and dSERT complexed with substrates pinpoints likely structural determinants for substrate binding. Forgoing the use of experimental transport and binding data of tryptamine derivatives for construction of these models enables us to critically assess and validate their predictive power: A single 5‐HT binding mode was identified that retains the amine placement observed in the LeuTAa structure, matches site‐directed mutagenesis and substituted cysteine accessibility method (SCAM) data, complies with support vector machine derived relations activity relations, and predicts computational binding energies for 5‐HT analogs with a significant correlation coefficient (R = 0.72). This binding mode places 5‐HT deep in the binding pocket of the SERT with the 5‐position near residue hSERT A169/dSERT D164 in transmembrane helix 3, the indole nitrogen next to residue Y176/Y171, and the ethylamine tail under residues F335/F327 and S336/S328 within 4 Å of residue D98. Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Dissection, residue conservation, and structural classification of protein‐DNA interfaces
Authors: Biswas Sumit , Guharoy Mainak , Chakrabarti Pinak
Published: August 2008

The basic DNA‐binding modules of 128 protein‐DNA interfaces have been analyzed. Although these are less planar, like the protein–protein interfaces, the protein‐DNA interfaces can also be dissected into core regions in which all the fully‐buried atoms are located, and rim regions having atoms with residual accessibilities. The sequence entropy of the core residues is smaller than those in the rim, indicating that the former are better conserved and possibly contribute more towards the binding free energy, as has been implicated in protein–protein interactions. On the protein side, 1014 Å2 of the surface is buried of which 63% belong to the core. There are some differences in the propensities of residues to occur in the core and the rim. In the DNA strands, the nucleotide(s) containing fully‐buried atoms in all three components usually occupy central positions of the binding region. A new classification scheme for the interfaces has been introduced based on the composition of secondary structural elements of residues and the results compared with the conventional classification of DNA‐binding proteins, as well as the protein class of the molecule. It appears that a common framework may be developed to understand both protein–protein and protein‐DNA interactions. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Cell cycle kinases predicted from conserved biophysical properties
Authors: Wrzeszczynski Kazimierz O. , Rost Burkhard
Published: August 2008

Machine‐learning techniques can classify functionally related proteins where homology‐transfer as well as sequence and structure motifs fail. Here, we present a method that aimed at complementing homology‐transfer in the identification of cell cycle control kinases from sequence alone. First, we identified functionally significant residues in cell cycle proteins through their high sequence conservation and biophysical properties. We then incorporated these residues and their features into support vector machines (SVM) to identify new kinases and more specifically to differentiate cell cycle kinases from other kinases and other proteins. As expected, the most informative residues tend to be highly conserved and tend to localize in the ATP binding regions of the kinases. Another observation confirmed that ATP binding regions are typically not found on the surface but in partially buried sites, and that this fact is correctly captured by accessibility predictions. Using these highly conserved, semi‐buried residues and their biophysical properties, we could distinguish cell cycle S/T kinases from other kinase families at levels around 70–80% accuracy and 62–81% coverage. An application to the entire human proteome predicted at least 97 human proteins with limited previous annotations to be candidates for cell cycle kinases. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Calcium binding to the purple membrane: A molecular dynamics study
Authors: Wassenaar Tsjerk A. , Daura Xavier , Padrós Esteve , Mark Alan E.
Published: August 2008

The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a highly detailed model of the PM have been used to investigate the stability of calcium ions placed at three proposed cation binding sites within bR, one near the Schiff base, one in the region of the proton release group, and one near Glu9. The simulations suggest that, of the sites investigated, the binding of calcium ions was most likely at the proton release group. Binding in the region of the Schiff base, while possible, was associated with significant changes in local geometry. Calcium ions placed near Glu9 in the interior of bR (simultaneously to a Ca2+ near the Schiff base and another one near the Glu194–Glu204 site) were not stable. The results obtained are discussed in relation to recent experimental observations and theoretical considerations. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Information theory provides a comprehensive framework for the evaluation of protein structure predictions
Authors: Swanson Rosemarie , Vannucci Marina , Tsai Jerry W.
Published: August 2008

Protein structure prediction has a number of important ad hoc similarity measures for evaluating predictions, but would benefit from a measure that is able to provide a common framework for a broad range of comparisons. Here we show that a mutual information‐like measure can provide a comprehensive framework for evaluating protein structure prediction of all types. We discuss the concept of information, its application to secondary structure, and the obstacle to applying it to 3D structure. On the basis of the insights from the secondary structure case, we present an approach to work around the 3D difficulties, and develop a method to measure the mutual information provided by a 3D structure prediction. We integrate the evaluation of all types of protein structure prediction into a single framework, and compare the amount of information provided by various prediction methods, including secondary structure prediction. Within this broadened framework, the idea that structure is better preserved than sequence during evolution is evaluated quantitatively for the globin family. A nearly perfect sequence match in the globin family corresponds to about 300 bits of information, whereas a nearly perfect structural match for the same two proteins corresponds to about 2500 bits of information, where bits of information describes the probability of obtaining a match of similar closeness by chance. Mutual information provides both a theoretical basis for evaluating structure similarity and an explanatory surround for existing similarity measures. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins
Authors: da Silveira Carlos H. , Pires Douglas E. V. , Minardi Raquel C. , Ribeiro Cristina , Veloso Caio J. M. , Lopes Julio C. D. , Meira Wagner , Neshich Goran , Ramos Carlos H. I. , Habesch Raul , Santoro Marcelo M.
Published: August 2008

In this study, we carried out a comparative analysis between two classical methodologies to prospect residue contacts in proteins: the traditional cutoff dependent (CD) approach and cutoff free Delaunay tessellation (DT). In addition, two alternative coarse‐grained forms to represent residues were tested: using alpha carbon (CA) and side chain geometric center (GC). A database was built, comprising three top classes: all alpha, all beta, and alpha/beta. We found that the cutoff value at about 7.0 Å emerges as an important distance parameter. Up to 7.0 Å, CD and DT properties are unified, which implies that at this distance all contacts are complete and legitimate (not occluded). We also have shown that DT has an intrinsic missing edges problem when mapping the first layer of neighbors. In proteins, it may produce systematic errors affecting mainly the contact network in beta chains with CA. The almost‐Delaunay (AD) approach has been proposed to solve this DT problem. We found that even AD may not be an advantageous solution. As a consequence, in the strict range up to 7.0 Å, the CD approach revealed to be a simpler, more complete, and reliable technique than DT or AD. Finally, we have shown that coarse‐grained residue representations may introduce bias in the analysis of neighbors in cutoffs up to 6.8 Å, with CA favoring alpha proteins and GC favoring beta proteins. This provides an additional argument pointing to the value of 7.0 Å as an important lower bound cutoff to be used in contact analysis of proteins. Proteins 2009. © 2008 Wiley‐Liss, Inc.
The utility of molecular dynamics simulations for understanding site‐directed mutagenesis of glycine residues in biotin carboxylase
Authors: Bordelon Tee , Nilsson Lill Sten O. , Waldrop Grover L.
Published: August 2008

Biotin carboxylase from Escherichia coli catalyzes the ATP‐dependent carboxylation of biotin and is one component of the multienzyme complex acetyl‐CoA carboxylase, which catalyzes the committed step in long‐chain fatty acid synthesis. Comparison of the crystal structures of biotin carboxylase in the absence and presence of ATP showed a central B‐domain closure when ATP was bound. Peptidic NH groups from two active site glycine residues (Gly165 and Gly166) that form hydrogen bonds to the phosphate oxygens of ATP were postulated to act as a “trigger” for movement of the B‐domain. The function of these two glycine residues in the catalytic mechanism was studied by disruption of the hydrogen bonds using site‐directed mutagenesis. Both single (G165V) and (G166V) and double mutants (G165V‐G166V) were constructed. The mutations did not affect the maximal velocity of a partial reaction, the bicarbonate‐dependent ATPase activity. This suggests that the peptidic NH groups of Gly165 and Gly166 are not triggers for domain movement. However, the Km values for ATP for each of the mutants was increased over 40‐fold when compared with wild‐type indicating the peptidic NH groups of Gly165 and Gly166 play a role in binding ATP. Consistent with ATP binding, the maximal velocity for the biotin‐dependent ATPase activity (i.e. the complete reaction) was decreased over 100‐fold suggesting the mutations have misaligned the reactants for optimal catalysis. Molecular dynamics studies confirm perturbation of the hydrogen bonds from the mutated residues to ATP, whereas the double mutant exhibits antagonistic effects such that hydrogen bonding from residues 165 and 166 to ATP is similar to that in the wild‐type. Consistent with the site‐directed mutagenesis results the molecular dynamics studies show that ATP is misaligned in the mutants. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Prediction of helix–helix contacts and interacting helices in polytopic membrane proteins using neural networks
Authors: Fuchs Angelika , Kirschner Andreas , Frishman Dmitrij
Published: August 2008

Despite rapidly increasing numbers of available 3D structures, membrane proteins still account for less than 1% of all structures in the Protein Data Bank. Recent high‐resolution structures indicate a clearly broader structural diversity of membrane proteins than initially anticipated, motivating the development of reliable structure prediction methods specifically tailored for this class of molecules. One important prediction target capturing all major aspects of a protein's 3D structure is its contact map. Our analysis shows that computational methods trained to predict residue contacts in globular proteins perform poorly when applied to membrane proteins. We have recently published a method to identify interacting α‐helices in membrane proteins based on the analysis of coevolving residues in predicted transmembrane regions. Here, we present a substantially improved algorithm for the same problem, which uses a newly developed neural network approach to predict helix–helix contacts. In addition to the input features commonly used for contact prediction of soluble proteins, such as windowed residue profiles and residue distance in the sequence, our network also incorporates features that apply to membrane proteins only, such as residue position within the transmembrane segment and its orientation toward the lipophilic environment. The obtained neural network can predict contacts between residues in transmembrane segments with nearly 26% accuracy. It is therefore the first published contact predictor developed specifically for membrane proteins performing with equal accuracy to state‐of‐the‐art contact predictors available for soluble proteins. The predicted helix–helix contacts were employed in a second step to identify interacting helices. For our dataset consisting of 62 membrane proteins of solved structure, we gained an accuracy of 78.1%. Because the reliable prediction of helix interaction patterns is an important step in the classification and prediction of membrane protein folds, our method will be a helpful tool in compiling a structural census of membrane proteins. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV‐1 protease
Authors: Lexa Katrina W. , Damm Kelly L. , Quintero Jerome J. , Gestwicki Jason E. , Carlson Heather A.
Published: August 2008

The 1TW7 crystal structure of HIV‐1 protease shows the flaps placed wider and more open than what is seen in other examples of the semi‐open, apo form. It has been proposed that this might be experimental evidence of allosteric control, because crystal packing creates contacts to the “elbow region” of the protease, which may cause deformation of the flaps. Recent dynamics simulations have shown that the conformation seen in 1TW7 relaxes into the typical semi‐open conformation in the absence of the crystal contacts, definitively showing that the crystal contacts cause the deformation (Layten et al., J Am Chem Soc 2006;128:13360–13361). However, this does not prove or disprove allosteric modulation at the elbow. In this study, we have conducted additional simulations, supplemented with experimental testing, to further probe the possibility of 1TW7 providing an example of allosteric control of the flap region. We show that the contacts are unstable and do not restrict the conformational sampling of the flaps. The deformation seen in the 1TW7 crystal structure is simply opportunistic crystal packing and not allosteric control. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Identification of putative, stable binding regions through flexibility analysis of HIV‐1 gp120
Authors: Tan Hepan , Rader A. J.
Published: August 2008

The acquired‐immunodeficiency syndrome has evolved into a major worldwide epidemic. Significant effort has been made in the development of antiviral therapies. A new strategy for vaccine and drug design that complements the existing cocktail therapy is to target entry of the human immunodeficiency virus (HIV). Such an approach provides the advantage of interfering with multiple intermediates in this multi‐step process. The extraordinary conformational flexibility, glycosylation, and strain variations of viral glycoprotein gp120 cause general viral evasion of humoral immune response and thus complicate the development of an effective vaccine. Especially difficult to define are the conformation of gp120 before CD4 engagement as well as the relative orientations of the V1/V2 and V3 loops with respect to the inner and outer domains. In this study, we used Floppy Inclusion and Rigid Substructure Topography (FIRST), a program based on graph theory, to analyze the flexibility and rigidity of all known HIV‐1 gp120 structures. A flexibility index is used to describe and compare the spatial distribution of protein flexibility and rigidity of these structures in isolation and in complex with CD4, CD4‐mimics, and neutralizing antibodies. Using this flexibility analysis, we identified a universal rigid region (the α2 helix) as well as the consensus largest rigid cluster involving a β‐sheet located on the coreceptor binding face. Both of these regions may serve as stable targets for vaccine design and drug discovery. Detailed comparisons of the changes in flexibility based on strain variations, stabilizing mutations, binding features of CD4 mimics, and impact of b12 binding are reported. Proteins 2009. © 2008 Wiley‐Liss, Inc.