bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contribution of dipole–dipole interactions to the stability of the collagen triple helix
Authors: Improta Roberto , Berisio Rita , Vitagliano Luigi 
Published: March 2008

AbstractUnveiling sequence–stability and structure–stability relationships is a major goal of protein chemistry and structural biology. Despite the enormous efforts devoted, answers to these issues remain elusive. In principle, collagen represents an ideal system for such investigations due to its simplified sequence and regular structure. However, the definition of the molecular basis of collagen triple helix stability has hitherto proved to be a difficult task. Particularly puzzling is the decoding of the mechanism of triple helix stabilization/destabilization induced by imino acids. Although the propensity‐based model, which correlates the propensities of the individual imino acids with the structural requirements of the triple helix, is able to explicate most of the experimental data, it is unable to predict the rather high stability of peptides embedding Gly–Hyp–Hyp triplets. Starting from the available X‐ray structures of this polypeptide, we carried out an extensive quantum chemistry analysis of the mutual interactions established by hydroxyproline residues located at the X and Y positions of the Gly–X–Y motif. Our data clearly indicate that the opposing rings of these residues establish significant van der Waals and dipole–dipole interactions that play an important role in triple helix stabilization. These findings suggest that triple helix stabilization can be achieved by distinct structural mechanisms. The interplay of these subtle but recurrent effects dictates the overall stability of this widespread structural motif.
N15 Cro and λ Cro: Orthologous DNA‐binding domains with completely different but equally effective homodimer interfaces
Authors: Dubrava Matthew S. , Ingram Wendy M. , Roberts Sue A. , Weichsel Andrzej , Montfort William R. , Cordes Matthew H.J. 
Published: March 2008

AbstractBacteriophage Cro proteins bind to target DNA as dimers but do not all dimerize with equal strength, and differ in fold in the region of the dimer interface. We report the structure of the Cro protein from Enterobacteria phage N15 at 1.05 Å resolution. The subunit fold contains five α‐helices and is closely similar to the structure of P22 Cro (1.3 Å backbone room mean square difference over 52 residues), but quite different from that of λ Cro, a structurally diverged member of this family with a mixed α‐helix/β‐sheet fold. N15 Cro crystallizes as a biological dimer with an extensive interface (1303 Å2 change in accessible surface area per dimer) and also dimerizes in solution with a Kd of 5.1 ± 1.5 μM. Its dimerization is much stronger than that of its structural homolog P22 Cro, which does not self‐associate detectably in solution. Instead, the level of self‐association and interfacial area for N15 Cro is similar to that of λ Cro, even though these two orthologs do not share the same fold and have dimer interfaces that are qualitatively different in structure. The common Cro ancestor is thought to be an all‐helical monomer similar to P22 Cro. We propose that two Cro descendants independently developed stronger dimerization by entirely different mechanisms.
Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain
Authors: Gan Siok Wan , Ng Lifang , Lin Xin , Gong Xiandi , Torres Jaume 
Published: March 2008

AbstractThe small hydrophobic (SH) protein from the human respiratory syncytial virus (hRSV) is a glycoprotein of ∼64 amino acids with one putative α‐helical transmembrane domain. Although SH protein is important for viral infectivity, its exact role during viral infection is not clear. Herein, we have studied the secondary structure, orientation, and oligomerization of the transmembrane domain of SH (SH‐TM) in the presence of lipid bilayers. Only one oligomer, a pentamer, was observed in PFO‐PAGE. Using polarized attenuated total reflection‐Fourier transform infrared (PATR‐FTIR) spectroscopy, we show that the SH‐TM is α‐helical. The rotational orientation of SH‐TM was determined by site‐specific infrared dichroism (SSID) at two consecutive isotopically labeled residues. This orientation is consistent with that of an evolutionary conserved pentameric model obtained from a global search protocol using 13 homologous sequences of RSV. Conductance studies of SH‐TM indicate ion channel activity, which is cation selective, and inactive below the predicted pKa of histidine. Thus, our results provide experimental evidence that the transmembrane domain of SH protein forms pentameric α‐helical bundles that form cation‐selective ion channels in planar lipid bilayers. We provide a model for this pore, which should be useful in mutagenesis studies to elucidate its role during the virus cycle.
Correspondences between low‐energy modes in enzymes: Dynamics‐based alignment of enzymatic functional families
Authors: Zen Andrea , Carnevale Vincenzo , Lesk Arthur M. , Micheletti Cristian 
Published: March 2008

AbstractProteins that show similarity in their equilibrium dynamics can be aligned by identifying regions that undergo similar concerted movements. These movements are computed from protein native structures using coarse‐grained elastic network models. We show the existence of common large‐scale movements in enzymes selected from the main functional and structural classes. Alignment via dynamics does not require prior detection of sequence or structural correspondence. Indeed, a third of the statistically significant dynamics‐based alignments involve enzymes that lack substantial global or local structural similarities. The analysis of specific residue–residue correspondences of these structurally dissimilar enzymes in some cases suggests a functional relationship of the detected common dynamic features. Including dynamics‐based criteria in protein alignment thus provides a promising avenue for relating and grouping enzymes in terms of dynamic aspects that often, though not always, assist or accompany biological function.
A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein–water interface as a determinant of pKavalues
Authors: Harms Michael J. , Schlessman Jamie L. , Chimenti Michael S. , Sue Gloria R. , Damjanović Ana , García‐Moreno E. Bertrand 
Published: March 2008

AbstractPreviously we reported that Lys, Asp, and Glu residues at positions 66 and 92 in staphylococcal nuclease (SNase) titrate with pKa values shifted by up to 5 pKa units in the direction that promotes the neutral state. In contrast, the internal Lys‐38 in SNase titrates with a normal pKa. The crystal structure of the L38K variant shows that the side chain of Lys‐38 is buried. The ionizable moiety is ∼7 Å from solvent and ion paired with Glu‐122. This suggests that the pKa value of Lys‐38 is normal because the energetic penalty for dehydration is offset by a favorable Coulomb interaction. However, the pKa of Lys‐38 was also normal when Glu‐122 was replaced with Gln or with Ala. Continuum electrostatics calculations were unable to reproduce the pKa of Lys‐38 unless the protein was treated with an artificially high dielectric constant, consistent with structural reorganization being responsible for the normal pKa value of Lys‐38. This reorganization must be local because circular dichroism and NMR spectroscopy indicate that the L38K protein is native‐like under all conditions studied. In molecular dynamics simulations, the ion pair between Lys‐38 and Glu‐122 is unstable. The simulations show that a minor rearrangement of a loop is sufficient to allow penetration of water to the amino moiety of Lys‐38. This illustrates both the important roles of local flexibility and water penetration as determinants of pKa values of ionizable groups buried near the protein–water interface, and the challenges faced by structure‐based pKa calculations in reproducing these effects.
Structural basis for the NAD‐hydrolysis mechanism and the ARTT‐loop plasticity of C3 exoenzymes
Authors: Ménétrey Julie , Flatau Gilles , Boquet Patrice , Ménez André , Stura Enrico A. 
Published: March 2008

AbstractC3‐like exoenzymes are ADP‐ribosyltransferases that specifically modify some Rho GTPase proteins, leading to their sequestration in the cytoplasm, and thus inhibiting their regulatory activity on the actin cytoskeleton. This modification process goes through three sequential steps involving NAD‐hydrolysis, Rho recognition, and binding, leading to Rho ADP‐ribosylation. Independently, three distinct residues within the ARTT loop of the C3 exoenzymes are critical for each of these steps. Supporting the critical role of the ARTT loop, we have shown previously that it adopts a distinct conformation upon NAD binding. Here, we present seven wild‐type and ARTT loop‐mutant structures of C3 exoenzyme of Clostridium botulinum free and bound to its true substrate, NAD, and to its NAD‐hydrolysis product, nicotinamide. Altogether, these structures expand our understanding of the conformational diversity of the C3 exoenzyme, mainly within the ARTT loop.
Crystallographic and biochemical studies revealing the structural basis for antizyme inhibitor function
Authors: Albeck Shira , Dym Orly , Unger Tamar , Snapir Zohar , Bercovich Zippy , Kahana Chaim 
Published: March 2008

AbstractAntizyme inhibitor (AzI) regulates cellular polyamine homeostasis by binding to the polyamine‐induced protein, Antizyme (Az), with greater affinity than ornithine decarboxylase (ODC). AzI is highly homologous to ODC but is not enzymatically active. In order to understand these specific characteristics of AzI and its differences from ODC, we determined the 3D structure of mouse AzI to 2.05 Å resolution. Both AzI and ODC crystallize as a dimer. However, fewer interactions at the dimer interface, a smaller buried surface area, and lack of symmetry of the interactions between residues from the two monomers in the AzI structure suggest that this dimeric structure is nonphysiological. In addition, the absence of residues and interactions required for pyridoxal 5′‐phosphate (PLP) binding suggests that AzI does not bind PLP. Biochemical studies confirmed the lack of PLP binding and revealed that AzI exists as a monomer in solution while ODC is dimeric. Our findings that AzI exists as a monomer and is unable to bind PLP provide two independent explanations for its lack of enzymatic activity and suggest the basis for its enhanced affinity toward Az.
Miranda cargo‐binding domain forms an elongated coiled‐coil homodimer in solution: Implications for asymmetric cell division in Drosophila
Authors: Yousef Mohammad S. , Kamikubo Hironari , Kataoka Mikio , Kato Ryuichi , Wakatsuki Soichi 
Published: March 2008

AbstractMiranda is a multidomain adaptor protein involved in neuroblast asymmetric division in Drosophila melanogaster. The central domain of Miranda is necessary for cargo binding of the neural transcription factor Prospero, the Prospero‐mRNA carrier Staufen, and the tumor suppressor Brat. Here, we report the first solution structure of Miranda central “cargo‐binding” domain (residues 460–660) using small‐angle X‐ray scattering. Ab initio modeling of the scattering data yields an elongated “rod‐like” molecule with a maximum linear dimension (Dmax) of ∼22 nm. Moreover, circular dichroism and cross‐linking experiments indicate that the cargo‐binding domain is predominantly helical and forms a parallel coiled‐coil homodimer in solution. Based on the results, we modeled the full‐length Miranda protein as a double‐headed, double‐tailed homodimer with a long central coiled‐coil region. We discuss the cargo‐binding capacity of the central domain and propose a structure‐based mechanism for cargo release and timely degradation of Miranda in developing neuroblasts.
The C3 domain ofPasteurella multocidatoxin is the minimal domain responsible for activation of Gq‐dependent calcium and mitogenic signaling
Authors: Aminova Leila R. , Luo Shuhong , Bannai Yuka , Ho Mengfei , Wilson Brenda A. 
Published: March 2008

AbstractThe large 1285‐amino‐acid protein toxin fromPasteurella multocida(PMT) is a multifunctional single‐chain polypeptide that binds to and enters eukaryotic cells and acts intracellularly to promote Gqand G12/13protein‐dependent calcium and mitogenic signal transduction. Previous studies indicated that the intracellular activity domain responsible for PMT action was located within the C‐terminal 600–700 amino acids. In this study, we have exogenously expressed a series of N‐ and C‐terminal PMT fragments directly in mammalian cells and have used the dual luciferase reporter system to assay for toxin‐mediated activation of calcium‐calcineurin‐NFAT signaling (NFAT‐luciferase) and mitogenic serum response signaling (SRE‐luciferase). Using this approach, we have defined the last 180 amino acids, which encompass the C3 domain in the crystal structure, as the minimum domain sufficient to activate both NFAT and SRE signaling pathways.
The influence of sunlight or dietary vitamin D on plasma 25‐hydroxyvitamin D in institutionalized elderly patients in a sub‐tropical climate
Authors: Lovell Geoffrey A. , Byth Jenny L. , Craswell Peter W. , Phillips Peter A. , Thomas Mansel J. 
Published: March 2008

Plasma 25‐hydroxyvitamin D (25(OH)D) concentrations in a group of thirty‐eight nursing‐home residents (age range 55–95 years) living in a sub‐tropical climate (Brisbane, Australia) were less than 25 nmol/1 in 50% of cases. The effects of endogenously and exogenously derived vitamin D have been studied over three months (April‐June) using the following treatment groups: A, placebo; B, daily sun exposure; C, 18.8 nmol vitamin D/day and D, 56.3 nmol vitamin D/day. Exposure to ultra‐violet radiation of group B patients was monitored by meter and polysulphone film.Group D exhibited a significant increase in Plasma 25(OH)D (P‐CO.001) after one month of treatment and groups B and C, respectively, after two months (P < 0.01). No significant changes were observed in plasma concentrations of creatinine, calcium, phosphate and alkaline phosphatase during the study period.A daily oral supplement of vitamin D in the range 18.8–56.3 nmol is proposed as the treatment of choice. It provides a safe and effective means of protection for elderly, institutionalized people against the effects of vitamin D deficiency.
Evaluation of the effectiveness of a nutritional health education leaflet in changing public knowledge and attitudes about eating and health
Authors: Nichols Sally , Waters W. E. , Woolaway M. , Hamilton‐Smith Margaret B. 
Published: March 2008

A nutritional health education leaflet EAT WELL, BE WELL was written and produced by a Wessex working party on diet and health. The leaflet's effectiveness in changing people's knowledge about, and attitudes towards, healthy eating was evaluated by means of a postal survey. Half of a random sample of electors were sent the nutritional leaflet. A few weeks later, the whole sample were sent a short ‘Eating and Health’ questionnaire. There was a 62 per cent response rate, with no significant difference between the group who had previously received the leaflet and the group who had not.The mean scores on the factual questions did not differ significantly between the two groups, providing little evidence that the nutritional leaflet increased public knowledge. The evaluation suggests that the mass distribution of this leaflet is not an effective method of health education.The survey did indicate that previous nutrition education has successfully put across the message to eat less sugar, fat and salt, and more fibre. It also showed, however, that there is still confusion about some aspects of healthy eating, including the place of starchy foods in the diet.
The B vitamin content of hospital meals and potential low intake by elderly inpatients
Authors: Thomas Anita J. , Finglas Paul , Bunker Valda W. 
Published: March 2008

The content of thiamin, riboflavin, vitamin B6 (pyridoxamine, pyridoxal, pyridoxine), niacin and total folate were determined in the meal choices comprising a typical day's menu in a teaching hospital. Thiamine, riboflavine, and B6 were measured by HPLC analysis, folate by microbiological assay, and niacin content was calculated from food tables.The results were compared with UK Recommended Daily Amounts (RDA) whenever possible (thiamine, riboflavine and niacin). Vitamin B6 and folate results were compared with the US Recommended Daily Dietary Amount (RDDA) as no British recommendation was available.Elderly inpatients selected meals which, even if completely consumed, provided half the current recommendation for vitamin B6 and one‐third of the recommendation for folate. More than half the meal selections provided less than recommended amounts of riboflavine, and in a quarter of cases less than the recommended amount of thiamine.
Studies on the consumption of ‘fibre‐filler’ for twelve weeks in humans: effects on iron status and plasma zinc
Authors: Fairweather‐Tait Susan J. , Piper Zoe , Hurren Caroline A. , Fox Thomas E. 
Published: March 2008

Forty adult subjects (14 male, 14 female omnivores; five male, seven female vegetarians) were given a daily fibre supplement of cereals, fruits and nuts (‘fibre‐filler’, F‐plan diet, Eyton, 1982) incorporated into their normal diet for twelve weeks. Various haematological parameters were monitored from fasting blood samples taken at regular intervals throughout the study.Two‐way analysis of variance of the data from the initial blood samples showed that habitual diet had no effect on any of the measured variables, but that there was a significant difference between men and women for all but % transferrin saturation. Mean Hb levels gradually increased during the course of the study, and there were fluctuations in plasma zinc. No other parameters changed with time.It was concluded that the fibre supplement under investigation, which contributed an additional 12 mg iron and 2.6 mg zinc to the daily intake, had no adverse effect on iron or zinc status when consumed by subjects as part of their normal diet.
‘Can I afford the diet? 1988’
Authors: Hanes F. A. , MacDonald A. 
Published: March 2008

In 1986 the British Dietetic Association issued the Discussion Paper ‘Can I Afford the Diet’ which outlined the concern that Dietitians felt regarding the ability of people on low incomes to eat either a healthy or a therapeutic diet. Further to the provisions of the Social Security Act 1986, which came into effect in April 1988, evidence from costings indicates that a healthy diet for a normal person can cost half the weekly income of an individual on Income Support and that therapeutic diets, e.g. those for patients with diabetes mellitus and cystic fibrosis can cost substantially more than this.The outcome is that individuals cannot be expected to adhere to dietary recommendations, thus endangering their health. Additional reductions in entitlements to free school meals, free milk and vitamins are also of concern and the effects of these reductions should be assessed.
Dynamics of food habits of newly married couples: food‐related activities and attitudes towards food
Authors: Craig Pippa L. , Truswell A. Stewart 
Published: March 2008

Sixty young couples were interviewed on three occasions—before marriage, after 5 months of marriage and after 21/2 years of marriage. The roles taken by each spouse in food provision and preparation are reported. Expressed attitudes towards food‐ and health‐related factors were also discussed.Wives took the major responsibility for food purchasing and preparation, although husbands played a significant role. The impact of children on these roles remains to be seen.After 2 1/2 years of marriage, there was a reduction in the number of shared meals, with the exception of the evening meal which remained the focal meal at which to influence a spouse's eating habits. The opportunity for more individualized meals during the day may lessen potential conflict over who gets their preferred foods in the evening.There were small but noticeable differences between wives and husbands stated likes and dislikes, and stated concerns about food. These may affect how much and in which way people are prepared to change their eating habits, and should be taken into account when planning nutrition education programmes.
Nutrition knowledge assessed by a structured questionnaire in a group of medical in‐patients
Authors: Anderson Annie S. , Umapathy Dolores , Palumbo Luigina , Pearson D. W. M. 
Published: March 2008

A short questionnaire to test understanding of the principles of nutrition was designed and administered to 128 patients in a general medical ward.The questionnaire was based on three components: familiarity with nutrition terms, knowledge of the principles of current recommendations, and understanding of the practical application of these recommendations. Although scores for each of the three components of nutrition knowledge correlated strongly with the overall understanding of individuals, there was rather poor correlation between the components, the lowest correlation being between knowledge of theoretical principles and understanding of the practical measures needed to implement current recommendations.Compared with the remainder of the sample, significantly better total scores were recorded by subjects in the age group 20–39 and significantly worse in the age group 60–79. Significantly better scores were also found in subjects who had received dietary advice from a dietitian.
Infant Nutrition
Authors: Lucas A. 
Published: March 2008

Initial findings from a multicentre study to examine the long term effects of different feeding regimes assigned randomly to premature babies during the early weeks postpartum are reported. Some early clinical and metabolic differences between randomized feed groups do not persist at 18 months. In other instances, however, the diet assigned in the postpartum period may have important effects over 18 months later. These findings emphasize the importance of long‐term follow up in such studies and provide preliminary evidence supporting the view that the early weeks may be a critical period for nutrition in preterm infants in terms of their later performance.Studies using the doubly‐labelled water method are presented which show its potential for approaching key issues in energy metabolism. One study shows that infants of obese mothers who themselves become overweight did not consume more energy than control infants of normal weight, but they exhibited a reduction in energy expenditure sufficient to account for their excessive weight gain. A second study suggests that the energy content of breast milk consumed by the infant is substantially less than that frequently reported in ‘unphysiologically’ expressed milk. These findings have important implications for infant nutrition.