Proteins with similar architecture exhibit similar large-scale dynamic behavior

We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold family with a coarse-grained Gaussian network model. Specifically, we consider the cofactor binding fragment of CysB; the lysine/arginine/ornithine-binding protein (LAO); the enzyme porphobilinogen deaminase (PBGD); the ribose-binding protein (RBP); the N-terminal lobe of ovotransferrin in apo-form (apo-OVOT); and the leucine/isoleucine/valine-binding protein (LIVBP). All have domains that resemble a Rossmann fold, but there are also some significant differences. Results indicate that similar global dynamic behavior is preserved for the members of a fold family, and that differences usually occur in regions only where specific function is localized. The present work is a computational demonstration that the scaffold of a protein fold may be utilized for diverse purposes. LAO requires a bound ligand before it conforms to the large-scale fluctuation behavior of the three other members of the family, CysB, PBGD, and RBP, all of which contain a substrate (cofactor) at the active site cleft. The dynamics of the ligand-free enzymes LIVBP and apo-OVOT, on the other hand, concur with that of unliganded LAO. The present results suggest that it is possible to construct structure alignments based on dynamic fluctuation behavior.     

Effect of hCG vs. GnRH at the beginning of the Ovsynch on first ovulation and conception rates in cyclic lactating dairy cows

Ovulatory response to the first GnRH of Ovsynch is a very important factor for determining the outcome of a successful synchronization. The aim of the present study was to develop a protocol to increase the percentage of cows that ovulated in response to the first administration of Ovsynch. This study was designed to compare ovulation rates in response to GnRH or hCG at the beginning of Ovsynch and to evaluate the effects of this manipulation on pregnancy. Cows (n = 371) with corpus luteum (CL) and at least one follicle greater than 10 mm diameter size on either ovary were included in the study. Cows were divided into two groups. The Ovsynch protocol began with GnRH (10 μg) in the GPG group (n = 161; GnRH-7d-PGF2α-56h-GnRH-18h-AI), whereas in the HPG group, the first GnRH of the Ovsynch was replaced with 1500 IU hCG (n = 210; hCG-7d-PGF2α-56h-GnRH-18h-AI). Ovarian ultrasonography was performed at the times of GnRH or hCG and of PGF2α administration, at the time of artificial insemination (AI) and seven days after AI, to determine ovulation. Maximal follicle size at the beginning of the Ovsynch did not affect on response to the first GnRH/hCG treatment. Conception rate (31 d) was 0.6 times more likely to be higher (P < 0.001) in cows that responded to the first hormonal administration of Ovsynch than in those that did not respond (95% CI = 0.29-0.71). Conception rate was found to be different between the HPG (37.6%, 79/210) and the GPG groups (48.4%, 78/161). Thus, beginning of the Ovsynch protocol with hCG did not increase ovulation and conception rate in lactating dairy cows, suggesting that hCG is not a suitable replacement of the first GnRH of Ovsynch. However, our results do show that increasing the ovulation rate in response to the first hormonal administration of Ovsynch can have a significant effect on conception rate.     

Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes

Apoptosis is a matter of life and death for cells and both inhibited and enhanced apoptosis may be involved in the pathogenesis of human diseases. The structures of protein-protein complexes in the apoptosis signaling pathway are important as the structural pathway helps in understanding the mechanism of the regulation and information transfer, and in identifying targets for drug design. Here, we aim to predict the structures toward a more informative pathway than currently available. Based on the 3D structures of complexes in the target pathway and a protein-protein interaction modeling tool which allows accurate and proteome-scale applications, we modeled the structures of 29 interactions, 21 of which were previously unknown. Next, 27 interactions which were not listed in the KEGG apoptosis pathway were predicted and subsequently validated by the experimental data in the literature. Additional interactions are also predicted. The multi-partner hub proteins are analyzed and interactions that can and cannot co-exist are identified. Overall, our results enrich the understanding of the pathway with interactions and provide structural details for the human apoptosis pathway. They also illustrate that computational modeling of protein-protein interactions on a large scale can help validate experimental data and provide accurate, structural atom-level detail of signaling pathways in the human cell.     

Lack of complete regression of the Day 5 corpus luteum after one or two doses of PGF2α in nonlactating Holstein cows

The early corpus luteum (CL) (before Day 6) does not regress after a single PGF_2α treatment. We hypothesized that increasing PGF_2α dose or number of treatments would allow regression of the early CL (Day 5). Nonlactating Holstein cows (N = 22) were synchronized using the Ovsynch protocol. On Day 5 (Day 0 = second GnRH treatment), cows were assigned to: (1) control (N = 5): no further treatment; (2) 1PGF (N = 6): one dose of 25 mg PGF_2α; (3) 2PGF (N = 5): two doses of 25 mg PGF_2α (50 mg) given 8 hours apart (second PGF_2α on Day 5 at the same time as the other PGF_2α treatments); (4) DPGF (N = 6): double dose of 25 mg PGF_2α (50 mg) given on Day 5. Blood samples were collected to monitor progesterone (P4) profiles in two periods. In the first period (0 to 24 hours), there were effects of treatment (P = 0.01), time (P < 0.01), and an interaction of treatment and time (P = 0.02). Group 1PGF versus control was different only at 12 hours (P = 0.02). Cows treated with DPGF were different than control at 4 hours (P = 0.04), 12 hours (P < 0.01), and 24 hours (P < 0.01). Only cows treated with 2PGF had lower P4 than control during the entire period and low P4 (0.37 ± 0.17 ng/mL) at 24 hours, usually indicative of luteolysis. In the second period (Day 5 to 15 of the cycle), there were effects of treatment (P < 0.01), time (P < 0.01), and interaction of treatment and time (P = 0.002). Group 1PGF was not different than control from Day 5 to 13 and P4 was greater than control on Day 14 (P = 0.01) and 15 (P < 0.01). Circulating P4 in DPGF cows was lower than control from Day 7 (P = 0.05) through 12 (P < 0.01). Likewise, there were differences between control and 2PGF from Day 7 to 13, but not on Day 14 and 15. On Day 15, all PGF_2α-treated groups had circulating P4 consistent with an active CL. Ultrasound evaluation confirmed that no CL from any group completely regressed during the experiment and no new ovulations occurred to account for functional CL later in cycle. In summary, a double dose of PGF_2α (twice on Day 5 or 8 hours apart) can dramatically decrease P4, consistent with classical definitions of luteolysis; however, these CL recover and become fully functional. Thus, the Day 5 CL of mature Holstein cows do not regress even to two doses of PGF_2α.     

Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

PDZ domains (PDZs), the most common interaction domain proteins, play critical roles in many cellular processes. PDZs perform their job by binding specific protein partners. However, they are very promiscuous, binding to more than one protein, yet selective at the same time. We examined the binding related dynamics of various PDZs to have insight about their specificity and promiscuity. We used full atomic normal mode analysis and a modified coarse‐grained elastic network model to compute the binding related dynamics. In the latter model, we introduced specificity for each single parameter constant and included the solvation effect implicitly. The modified model, referred to as specific‐Gaussian Network Model (s‐GNM), highlights some interesting differences in the conformational changes of PDZs upon binding to Class I or Class II type peptides. By clustering the residue fluctuation profiles of PDZs, we have shown: (i) binding selectivities can be discriminated from their dynamics, and (ii) the dynamics of different structural regions play critical roles for Class I and Class II specificity. s‐GNM is further tested on a dual‐specific PDZ which showed only Class I specificity when a point mutation exists on the βA‐βB loop. We observe that the binding dynamics change consistently in the mutated and wild type structures. In addition, we found that the binding induced fluctuation profiles can be used to discriminate the binding selectivity of homolog structures. These results indicate that s‐GNM can be a powerful method to study the changes in binding selectivities for mutant or homolog PDZs. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Cytotoxicity and DNA interactions of some platinum(II) complexes with substituted benzimidazole ligands

In the present study, four Pt(II) complexes with 2-ethyl (1)/or benzyl (2)/or p-chlorobenzyl (3)/or 2-phenoxymethyl (4) benzimidazole carrier ligands were evaluated for their in vitro cytotoxic activities against the human HeLa cervix, oestrogen receptor-positive MCF-7 breast, and oestrogen receptor-negative MDA-MB 231 breast cancer cell lines. The plasmid DNA interactions and inhibition of the BamHI restriction enzyme activities of the complexes were also studied. Complex 3 was found to be more active than carboplatin for all examined cell lines and comparable with cisplatin, except for the HeLa cell line.     

Influence of tall oil biodiesel with Mg and Mo based fuel additives on diesel engine performance and emission

The purpose of this study is to investigate influences of tall oil biodiesel with Mg and Mo based fuel additives on diesel engine performance and emission. Tall oil resinic acids were reacted with MgO and MoO(2) stoichiometrically for the production of metal-based fuel additives (combustion catalysts). The metal-based additives were added into tall oil biodiesel (B60) at the rate of 4 micromol/l, 8 micromol/l and 12 micromol/l for preparing test fuels. In general, both of the metal-based additives improved flash point, pour point and viscosity of the biodiesel fuel, depending on the rate of additives. A single cylinder DI diesel engine was used in the tests. Engine performance values did not change significantly with biodiesel fuels, but exhaust emission profile was improved. CO emissions and smoke opacity decreased by 56.42% and by 30.43%, respectively. In general, low NO(x) and CO(2) emissions were measured with the biodiesel fuels.     

Salivary detection of periodontopathic bacteria in periodontally healthy children

BACKGROUND: Salivary occurrence of periodontopathic bacteria is of interest especially in children as a risk indicator for the transmission, development and control of periodontal disease. We assessed the prevalence of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia, Prevotella nigrescens and Treponema denticola as microbial complexes in the saliva of children with mixed dentition and healthy gingiva. MATERIALS AND METHODS: Paraffin-stimulated saliva samples were collected from 41 children (22 boys and 19 girls), aged 6-13 years old. Gingival health was determined during the initial screening exam. The test bacteria were identified using a 16S rRNA-based PCR analysis. RESULTS: P. nigrescens was the most frequent species (80%), followed by T. denticola (32%), A. actinomycetemcomitans (24%) and P. gingivalis (12%). P. intermedia and T. forsythia were not detected. P. nigrescens was also common species in combinations. Paired and triple bacterial combinations were found in 24% and 20% of all children, respectively. There was no positive association between bacterial combinations in colonization and subject's gender (P>0.05, Fisher exact test). CONCLUSION: The salivary presence of P. nigrescens, T. denticola, A. actinomycetemcomitans and P. gingivalis but not P. intermedia and T. forsythia can occur in childhood without clinical signs of gingival disease. Thus, the possible risk of bacterial transmissions through saliva and, the need to screen for periodontal pathogens should be considered before mixed dentition.     

Predicting tropospheric ozone concentrations in different temporal scales by using multilayer perceptron models

This study encompasses ozone modeling in the lower atmosphere. It was aimed to develop an appropriate neural network model in order to predict ozone concentrations in various temporal scales as a function of meteorological variables and air quality parameters. All data were collected from Dilovasi, Turkey as this site represents typical industrial regions with major air pollution problems. In the study performance of the multilayer perceptron models were tested for both annual and seasonal periods as meteorological conditions highly influence the ozone levels. Among the various architectures, a network of two hidden layers with fifteen neurons was found to give successful predictions. Modeling efficiency of the developed network was also evaluated for day light and night time data of warming season exhibiting highest ozone levels. Furthermore, principle component analysis was performed by using annual data in order to reduce the number of input variables describing ozone formation. Model run with principle components has also provided satisfying performance.