bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological functions of the disulfides in bovine pancreatic deoxyribonuclease
Authors: Chen Wei‐Jung , Lee I‐Shuan , Chen Ching‐Ying , Liao Ta‐Hsiu 
Published: March 2004

AbstractWe characterized the biochemical functions of the small nonessential (C101–C104) and the large essential (C173–C209) disulfides in bovine pancreatic (bp) DNase using alanine mutants [brDNase(C101A)] and [brDNase(C173A) and brDNase(C209A)], respectively. We also characterized the effects of an additional third disulfide [brDNase(F192C/A217C)]. Without the Ca2+ protection, bpDNase and brDNase(C101A) were readily inactivated by trypsin, whereas brDNase(F192C/A217C) remained active. With Ca2+, all forms of DNase, except for brDNase(C101A), were protected against trypsin. All forms of DNase, after being dissolved in 6 M guanidine‐HCl, were fully reactivated by diluting into a Ca2+‐containing buffer. However, when diluted into a Ca2+‐free buffer, bpDNase and brDNase(C101A) remained inactive, but 60% of the bpDNase activity was restored with brDNase(F192C/A217C). When heated, bpDNase was inactivated at a transition temperature of 65°C, brDNase(C101A) at 60°C, and brDNase(F192C/A217C) at 73°C, indicating that the small disulfide, albeit not essential for activity, is important for the structural integrity, and that the introduction of a third disulfide can further stabilize the enzyme. When pellets of brDNase(C173A) and brDNase(C209A) in inclusion bodies were dissolved in 6 M guanidine‐HCl and then diluted into a Ca2+‐containing buffer, 10%–18% of the bpDNase activity was restored, suggesting that the “essential” disulfide is not absolutely crucial for enzymatic catalysis. Owing to the structure‐based sequence alignment revealing homology between the “nonessential” disulfide of bpDNase and the active‐site motif of thioredoxin, we measured 39% of the thioredoxin‐like activity for bpDNase based on the rate of insulin precipitation (ΔA650nm/min). Thus, the disulfides in bpDNase not only play the role of stabilizing the protein molecule but also may engage in biological functions such as the disulfide/dithiol exchange reaction.
Solution structure of a novel calcium binding protein, MTH1880, from Methanobacterium thermoautotrophicum
Authors: Lee Chang‐Hun , Jung Jin‐Won , Yee Adelinda , Arrowsmith Cheryl H. , Lee Weontae 
Published: March 2004

AbstractMTH1880 is a hypothetical protein from Methanobacterium thermoautotrophicum, a target organism of structural genomics. The solution structure determined by NMR spectroscopy demonstrates a typical α + β‐fold found in many proteins with different functions. The molecular surface of the protein reveals a small, highly acidic pocket comprising loop B (Asp36, Asp37, Asp38), the end of β2 (Glu39), and loop D (Ser57, Ser58, Ser61), indicating that the protein would have a possible cation binding site. The NMR resonances of several amino acids within the acidic binding pocket in MTH1880, shifted upon addition of calcium ion. This calcium binding motif and overall topology of MTH1880 differ from those of other calcium binding proteins. MTH1880 did not show a calcium‐induced conformational change typical of calcium sensor proteins. Therefore, we propose that the MTH1880 protein contains a novel motif for calcium‐specific binding, and may function as a calcium buffering protein.
A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications
Authors: Keskin Ozlem , Tsai Chung‐Jung , Wolfson Haim , Nussinov Ruth 
Published: March 2004

AbstractHere, we present a diverse, structurally nonredundant data set of two‐chain protein–protein interfaces derived from the PDB. Using a sequence order‐independent structural comparison algorithm and hierarchical clustering, 3799 interface clusters are obtained. These yield 103 clusters with at least five nonhomologous members. We divide the clusters into three types. In Type I clusters, the global structures of the chains from which the interfaces are derived are also similar. This cluster type is expected because, in general, related proteins associate in similar ways. In Type II, the interfaces are similar; however, remarkably, the overall structures and functions of the chains are different. The functional spectrum is broad, from enzymes/inhibitors to immunoglobulins and toxins. The fact that structurally different monomers associate in similar ways, suggests “good” binding architectures. This observation extends a paradigm in protein science: It has been well known that proteins with similar structures may have different functions. Here, we show that it extends to interfaces. In Type III clusters, only one side of the interface is similar across the cluster. This structurally nonredundant data set provides rich data for studies of protein–protein interactions and recognition, cellular networks and drug design. In particular, it may be useful in addressing the difficult question of what are the favorable ways for proteins to interact. (The data set is available at http://protein3d.ncifcrf.gov/∼keskino/ and http://home.ku.edu.tr/∼okeskin/INTERFACE/INTERFACES.html.)
Orientational potentials extracted from protein structures improve native fold recognition
Authors: Buchete Nicolae‐Viorel , Straub John E. , Thirumalai Devarajan 
Published: March 2004

AbstractWe develop coarse‐grained, distance‐ and orientation‐dependent statistical potentials from the growing protein structural databases. For protein structural classes (α, β, and α/β), a substantial number of backbone–backbone and backbone–side‐chain contacts stabilize the native folds. By taking into account the importance of backbone interactions with a virtual backbone interaction center as the 21st anisotropic site, we construct a 21 × 21 interaction scheme. The new potentials are studied using spherical harmonics analysis (SHA) and a smooth, continuous version is constructed using spherical harmonic synthesis (SHS). Our approach has the following advantages: (1) The smooth, continuous form of the resulting potentials is more realistic and presents significant advantages for computational simulations, and (2) with SHS, the potential values can be computed efficiently for arbitrary coordinates, requiring only the knowledge of a few spherical harmonic coefficients. The performance of the new orientation‐dependent potentials was tested using a standard database of decoy structures. The results show that the ability of the new orientation‐dependent potentials to recognize native protein folds from a set of decoy structures is strongly enhanced by the inclusion of anisotropic backbone interaction centers. The anisotropic potentials can be used to develop realistic coarse‐grained simulations of proteins, with direct applications to protein design, folding, and aggregation.
Tyrosine phenol‐lyase and tryptophan indole‐lyase encapsulated in wet nanoporous silica gels: Selective stabilization of tertiary conformations
Authors: Pioselli Barbara , Bettati Stefano , Demidkina Tatyana V. , Zakomirdina Lyudmila N. , Phillips Robert S. , Mozzarelli Andrea 
Published: March 2004

AbstractThe pyridoxal 5′‐phosphate‐dependent enzymes tyrosine phenol‐lyase and tryptophan indole‐lyase were encapsulated in wet nanoporous silica gels, a powerful method to selectively stabilize tertiary and quaternary protein conformations and to develop bioreactors and biosensors. A comparison of the enzyme reactivity in silica gels and in solution was carried out by determining equilibrium and kinetic parameters, exploiting the distinct spectral properties of catalytic intermediates and reaction products. The encapsulated enzymes exhibit altered distributions of ketoenamine and enolimine tautomers, increased values of inhibitors dissociation constants, slow attaining of steady‐state in the presence of substrate and substrate analogs, modified steady‐state distribution of catalytic intermediates, and a sixfold–eightfold decrease of specific activities. This behavior can be rationalized by a reduced conformational flexibility for the encapsulated enzymes and a selective stabilization of either the open (inactive) or the closed (active) form of the enzymes. Despite very similar structures and catalytic mechanisms, the influence of encapsulation is more pronounced for tyrosine phenol‐lyase than tryptophan indole‐lyase. This finding indicates that subtle structural and dynamic differences can lead to distinct interactions of the protein with the gel matrix.
Trypsin specificity as elucidated by LIE calculations, X‐ray structures, and association constant measurements
Authors: Leiros Hanna‐Kirsti Schrøder , Brandsdal Bjørn Olav , Andersen Ole Andreas , Os Vibeke , Leiros Ingar , Helland Ronny , Otlewski Jacek , Willassen Nils Peder , Smalås Arne O. 
Published: March 2004

AbstractThe variation in inhibitor specificity for five different amine inhibitors bound to CST, BT, and the cold‐adapted AST has been studied by use of association constant measurements, structural analysis of high‐resolution crystal structures, and the LIE method. Experimental data show that AST binds the 1BZA and 2BEA inhibitors 0.8 and 0.5 kcal/mole more strongly than BT. However, structural interactions and orientations of the inhibitors within the S1 site have been found to be virtually identical in the three enzymes studied. For example, the four water molecules in the inhibitor‐free structures of AST and BT are channeled into similar positions in the S1 site, and the nitrogen atom(s) of the inhibitors are found in two cationic binding sites denoted Position1 and Position2. The hydrophobic binding contributions for all five inhibitors, estimated by the LIE calculations, are also in the same order (−2.1 ± 0.2 kcal/mole) for all three enzymes. Our hypothesis is therefore that the observed variation in inhibitor binding arises from different electrostatic interactions originating from residues outside the S1 site. This is well illustrated by AST, in which Asp 150 and Glu 221B, despite some distance from the S1 binding site, lower the electrostatic potential of the S1 site and thus enhance substrate binding. Because the trends in the experimentally determined binding energies were reproduced by the LIE calculations after adding the contribution from long‐range interactions, we find this method very suitable for rational studies of protein–substrate interactions.
Inhibitor binding in a class 2 dihydroorotate dehydrogenase causes variations in the membrane‐associated N‐terminal domain
Authors: Hansen Majbritt , Le Nours Jérôme , Johansson Eva , Antal Torben , Ullrich Alexandra , Löffler Monika , Larsen Sine 
Published: March 2004

AbstractThe flavin enzyme dihydroorotate dehydrogenase (DHOD; EC 1.3.99.11) catalyzes the oxidation of dihydroorotate to orotate, the fourth step in the de novo pyrimidine biosynthesis of UMP. The enzyme is a promising target for drug design in different biological and clinical applications for cancer and arthritis. The first crystal structure of the class 2 dihydroorotate dehydrogenase from rat has been determined in complex with its two inhibitors brequinar and atovaquone. These inhibitors have shown promising results as anti‐proliferative, immunosuppressive, and antiparasitic agents. A unique feature of the class 2 DHODs is their N‐terminal extension, which folds into a separate domain comprising two α‐helices. This domain serves as the binding site for the two inhibitors and the respiratory quinones acting as the second substrate for the class 2 DHODs. The orientation of the first N‐terminal helix is very different in the two complexes of rat DHOD (DHODR). Binding of atovaquone causes a 12 Å movement of the first residue in the first α‐helix. Based on the information from the two structures of DHODR, a model for binding of the quinone and the residues important for the interactions could be defined. His 56 and Arg 136, which are fully conserved in all class 2 DHODs, seem to play a key role in the interaction with the electron acceptor. The differences between the membrane‐bound rat DHOD and membrane‐associated class 2 DHODs exemplified by the Escherichia coli DHOD has been investigated by GRID computations of the hydrophobic probes predicted to interact with the membrane.
Fast and faster: A designed variant of the B‐domain of protein A folds in 3 μsec
Authors: Arora Pooja , Oas Terrence G. , Myers Jeffrey K. 
Published: March 2004

AbstractWe have introduced the mutation glycine 29 to alanine, designed to increase the rate of protein folding, into the B‐domain of protein A (BdpA). From NMR lineshape analysis, we find the G29A mutation increases the folding rate constant by threefold; the folding time is 3 μsec. Although wild‐type BdpA folds extremely fast, simple‐point mutations can still speed up the folding; thus, the folding rate is not evolutionarily maximized. The short folding time of G29A BdpA (the shortest time yet reported) makes it an attractive candidate for an all‐atom molecular dynamics simulation that could potentially show a complete folding reaction starting from an extended chain. We also constructed a fluorescent variant of BdpA by mutating phenylalanine 13 to tryptophan, allowing fluorescence‐based time‐resolved temperature‐jump measurements. Temperature jumps and NMR complement each other, and give a very complete picture of the folding kinetics.
Observation of a hybrid random ping‐pong mechanism of catalysis for NodST: A mass spectrometry approach
Authors: Pi Na , Yu Yonghao , Mougous Joseph D. , Leary Julie A. 
Published: March 2004

AbstractAn efficient enzyme kinetics assay using electrospray ionization mass spectrometry (ESI‐MS) was initially applied to the catalytic mechanism investigation of a carbohydrate sulfotransferase, NodST. Herein, the recombinant NodST was overexpressed with a His6‐tag and purified via Ni‐NTA metal‐affinity chromatography. In this bisubstrate enzymatic system, an internal standard similar in structure and ionization efficiency to the product was chosen in the ESI‐MS assay, and a single point normalization factor was determined and used to quantify the product concentration. The catalytic mechanism of NodST was rapidly determined by fitting the MS kinetic data into a nonlinear regression analysis program. The initial rate kinetics analysis and product inhibition study described support a hybrid double‐displacement, two‐site ping‐pong mechanism of NodST with formation of a sulfated NodST intermediate. This covalent intermediate was further isolated and detected via trypsin digestion and Fourier transform ion cyclotron resonance mass spectrometry. To our knowledge, these are the first mechanistic data reported for the bacterial sulfotransferase, NodST, which demonstrated the power of mass spectrometry in elucidating the reaction pathway and catalytic mechanism of promising enzymatic systems.
Structure and rheology of semisolid o/w creams containing cetyl alcohol/non‐ionic surfactant mixed emulsifier and different polymers
Authors: Ribeiro H. M. , Morais J. A. , Eccleston G. M. 
Published: March 2004

SynopsisOil‐in‐water (o/w) emulsions for cosmetic use, such as lotions and creams, are complex multiple‐phase systems, which may contain a number of interacting surfactants, fatty amphiphiles, polymers and other excipients. This study investigates the influence of two synthetic cationic polymers, Polyquaternium‐7 and Polyquaternium‐11, and the natural anionic polymer, gum of acacia, on the rheology and microstructure of creams prepared with a non‐ionic mixed emulsifier (cetyl stearyl alcohol‐12EO/cetyl alcohol) using rheology (continuous shear, and viscoelastic creep and oscillation), microscopy and differential scanning calorimetry (DSC). A control cream containing no polymer was also investigated. The semisolid control cream was structured by a swollen lamellar gel network phase formed from the interaction of cetyl alcohol and the POE surfactant, in excess of that required to stabilize oil droplets, with continuous phase water. Endothermic transitions between 25 and 100 °C were identified as components of this phase. Incorporation of cationic polymer into the formulation caused significant loss of structure to produce a mobile semisolid containing larger oil droplets. The microscopical and thermal data implied that the cationic polymer caused the swollen lamellar gel network phase to transform into non‐swollen crystals of cetyl alcohol. In contrast, incorporation of gum of acacia produced a thicker cream than the control, with smaller droplet sizes and little evidence of the gel network. Microscopical and thermal data implied that although there were also interactions between gum of acacia and both the surfactant and the swollen gel network phase, the semisolid properties were probably because of the ability of the gum of acacia to stabilize and thicken the emulsion in the absence of the swollen lamellar network.
Diffusion and distribution of element‐labelled surfactants in human hair
Authors: Wortmann F.‐J. , Gotsche M. , Schmidt‐Lewerkühne H. 
Published: March 2004

SynopsisTo directly follow the diffusion process of cosmetically relevant agents into human hair, a specific methodological approach is presented and elucidated for selected surfactants. For this, practically relevant anionic and cationic surfactants were synthesized with a chlorine atom at the end of their alkyl chain. The property changes of the surfactants through the modification are corresponding to an extension of the alkyl chain by about two methylene groups, thus representing a moderate increase of hydrophobicity. After the application of a modified surfactant to hair, it can be localized and quantified through its chlorine atom in cross‐sections by scanning electron microscopy combined with micro X‐ray fluorescence analysis. The determination of the diffusion coefficient D is realized through the application of the Matano‐equation to element intensity profiles. Values for D vary within the chosen range of pH and temperature between 10−14 and 10−16 m2 s−1. The diffusion coefficients for the anionic surfactants increase with decreasing pH and increasing temperature, The temperature dependence follows in all cases the Arrhenius relationship with activation energies EA of 50–100 kJ mol−1, which decrease with pH. The pH‐related effects, with comparable values for D and EA, are opposite for the cationic surfactant. These observations are consistently interpreted on the basis of ionic and hydrophobic interactions in hair.
Contribution of encapsulation on the biodisponibility of retinol
Authors: Failloux N. , Baron M.‐H. , Abdul‐Malak N. , Perrier E. 
Published: March 2004

SynopsisTo show the benefits of retinol encapsulation in cosmetic industry, we compared the diffusion of two different retinol preparations through skin:oil‐in‐water (o/w) emulsions of retinol, also called ‘free retinol’, and suspension of Cylasphere® including retinol, also called ‘encapsulated retinol’. Two methods were used: Franz cell elucidated retinol release and storage in a hairless mouse skin according to time for the two types of preparations. The dosage of retinol by high performance liquid chromatography (HPLC) showed that encapsulated retinol was maintained into the skin for a longer time than free retinol. Raman microspectrometry measurements established a spectral image of the skin and determined the localization of retinol. Maps were collected according to time. They detailed the shifts of free and encapsulated retinol in the epidermis of a human biopsy. Spheres were smaller than droplets and they moved two times faster at this level of the skin.
Tazobactam‐induced haemolytic anaemia, possibly caused by non‐immunological adsorption of IgG onto patient's red cells
Authors: Broadberry R. E. , Farren T. W. , Bevin S. V. , Kohler J. A. , Yates S. , Skidmore I. , Poole J. , Garratty G. 
Published: March 2004

Summary.  A patient with pneumonia was treated with Tazocin (piperacillin/tazobactam). However, the expected haemoglobin (Hb) increment after transfusion was not achieved. Plasma bilirubin and lactate dehydrogenase were raised. The direct antiglobulin test (DAT) was positive (4+) for immunoglobulin G (IgG) only, but no RBC antibodies were demonstrable in the plasma or an eluate from the patient's RBCs. Drug‐induced haemolysis was suspected. After discontinuing Tazocin administration, Hb and bilirubin levels returned to expected values.The patient's plasma gave a positive (3+) indirect antiglobulin reaction only with RBCs pretreated with tazobactam. However, random patient plasmas also gave weak (± to 1+) reactions, indicating non‐immunological adsorption of IgG onto RBCs rather than specific anti‐tazobactam antibodies.Subsequently, plasma samples with varying IgG levels (0·8–89·7 g L−1) were tested against RBCs pretreated with tazobactam. The amount of plasma IgG non‐immunologically adsorbed onto the drug‐coated RBCs was found to correlate directly with the plasma IgG level. The patient had a high plasma IgG level (41·6 g L−1) which explains why the antiglobulin test was stronger with the patient's plasma than with random plasma samples.Previous reports (Garratty & Arndt, (1998) British Journal of Haematology, 100, 777–783; Arndt & Garratty (2000) Transfusion, 40, 29S) suggested that non‐immunological coating of RBCs with IgG may affect RBC survival; our results would support that suggestion. This is the first reported case of haemolytic anaemia associated with tazobactam.
Studies of the reliability and validity of the Addiction Severity Index
Authors: Mäkelä Klaus 
Published: March 2004

ABSTRACTAims  To examine the reliability and validity of the widely used Addiction Severity Index (ASI).Material  Thirty‐seven studies of the psychometric performance of the ASI.Findings  The inter‐rater and test–retest reliabilities of the severity ratings and composites scores vary from excellent to unsatisfactory. High internal consistencies have been reported regularly for only three of the seven composite scores (medical status, alcohol use, psychiatric status). The remaining four composite scores (employment status, drug use, legal status, family/social relations) have low consistencies in at least four different studies. Coefficients of criterion validity are often low.Conclusions  There is a discrepancy between the psychometric performance of the ASI and its purported clinical, administrative and research uses.
Smoking and the Five‐Factor Model of personality
Authors: Terracciano Antonio , Costa Paul T. 
Published: March 2004

ABSTRACTAims  Investigating the association between personality traits and smoking status using a comprehensive model of personality, the Five‐Factor Model (FFM).Design  Cross‐sectional survey.Setting  Baltimore, MD, USA.Participants  Adult elderly Americans (n = 1638).Measurements  A self‐administered survey on cigarette smoking and the Revised NEO Personality Inventory (NEO‐PI‐R).Findings  Current smokers scored higher than never smokers on neuroticism and lower on agreeableness and conscientiousness; former smokers scored intermediate on these higher‐order dimensions. Neuroticism was related to smoking particularly among individuals with low conscientiousness, as indicated by an interaction effect between the two factors. There were no differences on extraversion and openness to experience. At the lower‐order facet level, smokers were characterized by inability to resist cravings (high impulsiveness), search for stimulation (high excitement‐seeking), lack of perseverance (low self‐discipline) and lack of careful consideration of the consequences of their actions (low deliberation).Conclusions  At the higher‐order factor level, this study replicates and extends previous studies using a comprehensive model of personality (FFM). The greater specificity provided by the facet‐level analysis appears to explain some of the conflicting results in the literature, and the use of an older sample provides insight especially into the former smokers group. Personality research may lead to a deeper understanding of cigarette smoking and can potentially contribute to policies and programs of smoking prevention and cessation.