A Comparative Analysis of Interhelical Polar Interactions of Various α-Helix Packings in Proteins

One hundred twenty globular proteins and forty five leucine zippers representing all types of packing of long -helices were studied in terms of revealing and comparing their interhelical hydrogen and salt bonds. Many previous studies of leucine zippers and their analogs showed that interhelical interactions between polar groups could impart specificity to packing of an -helix. The current comparison demonstrated that basically, globular proteins and leucine zippers had similar interhelical polar interactions with presumably a similar structural role. However, depending on the packing of -helices, the networks of interhelical polar bonds were shown to be distinct and determined both by physicochemical properties of involved amino acid residues and by the relative positions of hydrophobic and hydrophilic residues on the surface of -helices. The revealed distinction is probably crucial for selecting the unique packing of an -helix.     

Does Tenure Matter? A Comparative Analysis of Agricultural Expansion in the Mosquitia Forest Corridor

This article compares how public protection of forests and common-property forest institutions serve to control outside encroachment into frontier forests in Honduras and Nicaragua. The article combines institutional analysis with ethnographically based fieldwork and analysis of land-cover images to evaluate how property-rights arrangements influence monitoring, enforcement, and compliance with rules to restrict agricultural expansion in two biosphere reserves in the Mosquitia Corridor. Findings show that territorial demarcation and common-property rights are important components for frontier forest conservation. In areas with weak enforcement mechanisms and heavy reliance on social norms over official regulatory measures, the findings suggest that the perceived legitimacy of tenure arrangements and their respective land-use rules are fundamental to controlling the agricultural frontier.

The “Intrinsic” Thermal Conductivity of Some Wet Proteins in Relation to Their Hydrophobicity: Analysis on Gelatin Gel

Since the intrinsic thermal conductivity of protein cannot be measured directly, the apparent “intrinsic” thermal conductivity of gelatin was estimated on the basis of the most suitable heat conduction model. Among four models of heat conduction through heterogeneous material, the series layers model best described the experimental results for frozen gelatin gels of different concentrations. Then, the “intrinsic” thermal conductivity of frozen wet gelatin was estimated to be 0.61 [W/m·°C]. The “intrinsic” thermal conductivity of unfrozen wet gelatin was estimated on the basis of Filippov’s equation to be 0.38 [W/m·°C], since the unfrozen gelating gel seemed to be as homogeneous as the solution.     

Does ADP-Ribosylation of Proteins in Nuclei Contribute to Ectoderm Cell Differentiation in Sea Urchin Embryos?

In nuclei of sea urchin embryos, marked increase in ADP-ribosyltransferase activity followed by its decrease occurrs in the pre-hatching and post-hatching periods with peaks of activity at the morula and gastrula stages. Increase in its activity was blocked by cycloheximide in the pre- and post-hatching periods and by actinomycin D only in the post-hatching period. Embryo wall cells (ectoderm cells) isolated from gastrulae exhibited markedly higher activity of this enzyme than archenteron cells and mesenchyme cells. Probably, the increase in the activity of this enzyme in the post-hatching period results from expression of the gene for this enzyme mainly in ectoderm cells. In the post-hatching period, the activity increased more in animalized embryos than in normal ones, and increased little in vegetalized embryos. 3-Aminobenzamide (3-ABA), as well as luminol and nicotinamide, inhibited formation of ectoderm structures more than that of endoderm structures, such as the archenteron, in normal and animalized embryos, but had no appreciable effect on morphogenesis in vegetalized embryos. The reaction catalyzed by ADP-ribosyltransferase probably contributes to ectoderm cell differentiation. Treatment of embryos with 3-ABA in the pre-hatching period had little inhibitory effect on the morphogenesis in the post-hatching period, though it caused death of many embryos.     

A Systematic Analysis of Buried Polar Side Chains and Their Interactions in α-Helical Proteins

Examination of 80 -helical proteins and domains demonstrates that they contain from 1 to more than 20 completely buried (water-inaccessible) polar side chains. As a rule the latter have partners for H-bonding but the resulting H-bond system is often not saturating. Basing on statistical analysis, we determined the optimal number of H-bonds for every type of polar side chain, and discuss the structural role of vacant donors and acceptors. About half of the H-bonds formed by buried side chains pertain to interhelix contacts of the (side chain)–(side chain) and (side chain)–(main chain) types. Such interactions appear to be a most important factor determining the mutual arrangement of -helices in proteins. Analysis of the frequency of occurrence of various interacting pairs reveals that these interactions are selective.     

Do Pheromone Binding Proteins Converge in Amino Acid Sequence When Pheromones Converge?

Convergence in amino acid sequences between proteins can be strong evidence for selection. Here, I look for evidence of convergence in the amino acid sequences of pheromone binding protein (PBP) in response to convergence in pheromones. PBPs are involved in sex pheromone reception by the antennae of male moths. In this role PBPs may selectively bind pheromone components and experience convergent selection in response to convergence in pheromone components. However, examination of the PBPs of the taxa that have converged upon the use of (E)- or (Z)-11-tetradecenyl acetate as their major pheromone component reveals little evidence for convergence in the PBPs identified from these taxa. A few sites show a pattern consistent with convergence or parallelism; however, it cannot be ruled out that these sites share the ancestral state. Two of these sites fall within the proposed binding region of PBPs. These results suggest that PBPs either have not converged in sequence or have converged at very few sites in response to convergence on the same pheromone component. Received: 29 July 1999 / Accepted: 8 November 1999     

Structure–Function Analysis of the ADAM Family of Disintegrin-Like and Metalloproteinase-Containing Proteins (Review)

The ADAMs belong to a disintegrin-like and metalloproteinase-containing protein family that are zinc-dependent metalloproteinases. These proteins share all or some of the following domain structure: a signal peptide, a propeptide, a metalloproteinase, a disintegrin, a cysteine-rich, and an epidermal growth factor (EGF)-like domains, a transmembrane region, and a cytoplasmic tail. ADAMs are widely distributed in many organs, tissues, and cells, such as brain, testis, epididymis, ovary, breast, placenta, liver, heart, lung, bone, and muscle. These proteins are capable of four potential functions: proteolysis, adhesion, fusion, and intracellular signaling. Because the number of ADAM genes has grown rapidly and the biological functions of most members are unclear, this review analyzes the protein structures and functions, their activation and processing, their known and potential activities, and their evolutionary relationships. A sequence alignment of human ADAMs is compiled and their homology and physical data are calculated. The conceivable functions of ADAMs in reproduction, development, and diseases are also discussed.     

Analysis of Erythrocyte and Platelet Membrane Proteins in Various Forms of β-Thalassemia

Major membrane proteins have been quantitatively analyzed in erythrocytes and platelets from patients with homozygous (splenectomized and non-splenectomized) and heterozygous forms of beta-thalassemia depending on severity of clinical manifestation of this disease. Quantitative analysis of erythrocyte membrane proteins revealed increase in alpha- and beta-spectrin. (In non-splenectomized patients with homozygous beta-thalassemia the amount of this protein was lower than in corresponding controls.) Besides spectrin, the increase of 2.1-2.3 fractions of ankyrin, and the decrease of band 3 protein (anion-transport protein), 4.1, palladin, and glyceraldehyde-3-phosphate dehydrogenase were also found. Analysis of major platelet membrane proteins revealed significant increase in gelsolin. This increase was found in all forms of beta-thalassemia irrespective of gender. Significant changes in platelet membrane protein fractions were found in patients (especially non-splenectomized) with homozygous beta-thalassemia. These included significant decrease in myosin, profilin, and gamma-actin and increase in actin-binding protein in both male and female patients. The content of other protein fractions (alpha-actinin, tubulin, tropomyosin) remained unchanged. Changes in protein fractions of erythrocytes and platelets correlated with severity of clinical manifestation of the disease.     

A Genome-Wide Sequence–Structure Analysis Suggests Aggregation Gatekeepers Constitute an Evolutionary Constrained Functional Class

Protein aggregation is geared by aggregation-prone regions that self-associate by β-strand interactions. Charged residues and prolines are enriched at the flanks of aggregation-prone regions resulting in decreased aggregation. It is still unclear what drives the overrepresentation of these “aggregation gatekeepers”, that is, whether their presence results from structural constraints determining protein stability or whether they constitute a bona fide functional class selectively maintained to control protein aggregation. As functional residues are typically conserved regardless of their cost to protein stability, we compared sequence conservation and thermodynamic cost of these residues in 2659 protein families in Escherichia coli. Across protein families, we find gatekeepers to be under strong selective conservation while at the same time representing a significant thermodynamic cost to protein structure. This finding supports the notion that aggregation gatekeepers are not structurally determined but evolutionary selected to control protein aggregation.     

Structure of α-α-Hairpins with Short Connections in Globular Proteins

The analysis of conformations of more than 100 --hairpins with closely packed helical segments and connections up to four amino acid residues in length was carried out. Five types of the connections were revealed, and their and values on the Ramachandran map were found. Each type of --hairpins was shown to have a unique sequence pattern for hydrophobic and hydrophilic residues.     

Does Consolidation of Visuospatial Sequence Knowledge Depend on Eye Movements?

In the current study, we assessed whether visuospatial sequence knowledge is retained over 24 hours and whether this retention is dependent on the occurrence of eye movements. Participants performed two sessions of a serial reaction time (SRT) task in which they had to manually react to the identity of a target letter pair presented in one of four locations around a fixation cross. When the letter pair ‘XO’ was presented, a left response had to be given, when the letter pair ‘OX’ was presented, a right response was required. In the Eye Movements (EM) condition, eye movements were necessary to perform the task since the fixation cross and the target were separated by at least 9° visual angle. In the No Eye Movements (NEM) condition, on the other hand, eye movements were minimized by keeping the distance from the fixation cross to the target below 1° visual angle and by limiting the stimulus presentation to 100 ms. Since the target identity changed randomly in both conditions, no manual response sequence was present in the task. However, target location was structured according to a deterministic sequence in both the EM and NEM condition. Learning of the target location sequence was determined at the end of the first session and 24 hours after initial learning. Results indicated that the sequence learning effect in the SRT task diminished, yet remained significant, over the 24 hour interval in both conditions. Importantly, the difference in eye movements had no impact on the transfer of sequence knowledge. These results suggest that the retention of visuospatial sequence knowledge occurs alike, irrespective of whether this knowledge is supported by eye movements or not.     

Proteomic Analysis of PKCγ-Related Proteins in the Spinal Cord of Morphine-Tolerant Rats

Background

Morphine tolerance is a common drawback of chronic morphine exposure, hindering use of this drug. Studies have shown that PKCã may play a key role in the development of morphine tolerance, although the mechanisms are not fully known.

Methodology/Principal Findings

In a rat model of morphine tolerance, PKCã knockdown in the spinal cord was successfully carried out using RNA interference (RNAi) with lentiviral vector-mediated short hairpin RNA of PKCã (LV-shPKCã). Spinal cords (L4-L5) were obtained surgically from morphine-tolerant (MT) rats with and without PKCã knockdown, for comparative proteomic analysis. Total proteins from the spinal cords (L4-L5) were extracted and separated using two-dimensional gel electrophoresis (2DGE); 2D gel images were analyzed with PDQuest software. Seven differential gel-spots were observed with increased spot volume, and 18 spots observed with decreased spot volume. Among these, 13 differentially expressed proteins (DEPs) were identified with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), comparing between MT rats with and without PKCã knockdown. The DEPs identified have roles in the cytoskeleton, as neurotrophic factors, in oxidative stress, in ion metabolism, in cell signaling, and as chaperones. Three DEPs (GFAP, FSCN and GDNF) were validated with Western blot analysis, confirming the DEP data. Furthermore, using immunohistochemical analysis, we reveal for the first time that FSCN is involved in the development of morphine tolerance.

Conclusions/Significance

These data cast light on the proteins associated with the PKCã activity during morphine tolerance, and hence may contribute to clarification of the mechanisms by which PKCã influences MT.     

The Role of Intelligence in Posttraumatic Stress Disorder: Does it Vary by Trauma Severity?

Background

Only a small minority of trauma victims develops post-traumatic stress disorder (PTSD), suggesting that victims vary in their predispositions to the PTSD response to stressors. It is assumed that the role of predispositions in PTSD varies by trauma severity: when stressors are less severe, predispositions play a bigger role. In this study, we test whether the role of intelligence in PTSD varies by trauma severity. Specifically, does low intelligence plays a bigger part among victims of lower magnitude stressors than among victims of extreme stressors?

Methods

Data come from a longitudinal study of randomly selected sample in Southeast Michigan (n = 713). IQ was measured at age 6. PTSD was measured at age 17, using the NIMH-DIS for DSM-IV. Stressors were classified as extreme if they involved assaultive violence (e.g. rape, sexual assault, threatened with a weapon); other stressors in the list (e.g. disaster, accidents) were classified as lower magnitude. Assaultive violence victims had experienced assaultive violence plus other event types or only assaultive violence. Victims of other stressors were participants who had never experienced assaultive violence. We compared the influence of age 6 IQ on PTSD among persons exposed to assaultive violence vs. other stressors, using multinomial logistic regression.

Results

Relative risk ratio (RRR) for PTSD associated with a one point drop in age 6 IQ among victims of assaultive violence was 1.04 (95% CI 1.01, 1.06); among victims of other stressors, it was 1.03 (95% CI 0.99, 1.06). A comparison of the two RRRs indicates no significant difference between the two estimates (p = 0.652). IQ does not play a bigger role in PTSD among victims of other stressors than it does among victims of assaultive violence.

Conclusions

Lower IQ exerts an adverse PTSD effect on trauma victims, with no evidence of variability by the severity of trauma they have experienced.     

Genome-Wide Analysis of Simple Sequence Repeats in Marine Animals—a Comparative Approach

Tandem simple sequence repeats (SSRs) are one of the most popular molecular markers in genetic analysis owing to their ubiquitous occurrence,high reproducibility, multiallelic nature, and codominant mode. High mutability makes SSRs play a role in genome evolution and correspondingly show different patterns. Comparative analysis of genomic SSRs in different taxonomic groups usually focuses on land species, while marine animals have been neglected. This study examined the abundance of genomic SSRs with repeated unit lengths of 1–6 bp in 30 marine animals including nine taxonomic groups and further compared with the land species. More than thousands of SSRs were discovered in every organism which provided a huge resource for the development of molecular markers. Thirty marine animals showed profound differences in SSR characteristics, but some group-specific trends were also found. Both similarities and differences of repeat patterns were discovered between the land and marine species. Two taxon-specific SSR types were discovered: the pentanucleotides motif AGAGG in Euteleostei and the hexanucleotide repeats of ATGTAC in Porifera and Echinodermata. Gene ontology (GO) enrichment analysis of two representative species (Amphimedon queenslandica for Porifera and Strongylocentrotus purpuratus for Echinodermata) revealed functional preference of the ATGTAC motif associated genes, and this might hint at evolutionary significance.     

Molecular Cloning and Sequence Analysis of PGC-1α cDNA in Tibetan Antelope

以藏羚羊(Pantholops hodgsonii)及同海拔分布的藏系绵羊(Tibetan Sheep)的心肌组织为材料,提取总RNA,利用逆转录聚合酶链反应(RT-PCR)技术扩增出过氧化物酶体增生物激活受体γ辅激活因子-1α(PGC-1α)的基因编码区cDNA片段,与载体连接构建重组质粒,经转化、扩增培养、鉴定后测序.利用生物信息学方法分析显示,藏羚羊和藏系绵羊的PGC-1α基因编码区长度均为2 349 bp,编码797个氨基酸(GenBank登录号分别为:JF449959和JF449960);与其他脊椎动物PGC-1α基因的核苷酸及氨基酸序列相似性达到90％以上;其包含RNA/DNA结合位点、RNA识别基序(RRM)、与核呼吸因子1( NRF-1)及肌细胞增强因子2C(MEF2C)相互作用的区域、富含丝氨酸/精氨酸的结构域、负调节功能结构域、LXXLL模体以及TPPTTPP和DHDYCQ两个保守序列,14个氨基酸差异性位点位于以上部分功能结构域中;此外,磷酸化位点的预测提示藏羚羊可能存在一个潜在的蛋白激酶G的磷酸化位点(第329位的苏氨酸).本研究成功克隆出了藏羚羊PGC-1α基因的编码区序列,为从能量代谢角度深入探讨藏羚羊适应高原的分子生物学机制提供了新的思路.     

Does Simplicity Compromise Accuracy in ACS Risk Prediction? A Retrospective Analysis of the TIMI and GRACE Risk Scores

Background

The Thrombolysis in Myocardial Infarction (TIMI) risk scores for Unstable Angina/Non-ST–elevation myocardial infarction (UA/NSTEMI) and ST-elevation myocardial infarction (STEMI) and the Global Registry of Acute Coronary Events (GRACE) risk scores for in-hospital and 6-month mortality are established tools for assessing risk in Acute Coronary Syndrome (ACS) patients. The objective of our study was to compare the discriminative abilities of the TIMI and GRACE risk scores in a broad-spectrum, unselected ACS population and to assess the relative contributions of model simplicity and model composition to any observed differences between the two scoring systems.

Methodology/Principal Findings

ACS patients admitted to the University of Michigan between 1999 and 2005 were divided into UA/NSTEMI (n = 2753) and STEMI (n = 698) subpopulations. The predictive abilities of the TIMI and GRACE scores for in-hospital and 6-month mortality were assessed by calibration and discrimination. There were 137 in-hospital deaths (4%), and among the survivors, 234 (7.4%) died by 6 months post-discharge. In the UA/NSTEMI population, the GRACE risk scores demonstrated better discrimination than the TIMI UA/NSTEMI score for in-hospital (C = 0.85, 95% CI: 0.81–0.89, versus 0.54, 95% CI: 0.48–0.60; p<0.01) and 6-month (C = 0.79, 95% CI: 0.76–0.83, versus 0.56, 95% CI: 0.52–0.60; p<0.01) mortality. Among STEMI patients, the GRACE and TIMI STEMI scores demonstrated comparably excellent discrimination for in-hospital (C = 0.84, 95% CI: 0.78–0.90 versus 0.83, 95% CI: 0.78–0.89; p = 0.83) and 6-month (C = 0.72, 95% CI: 0.63–0.81, versus 0.71, 95% CI: 0.64–0.79; p = 0.79) mortality. An analysis of refitted multivariate models demonstrated a marked improvement in the discriminative power of the TIMI UA/NSTEMI model with the incorporation of heart failure and hemodynamic variables. Study limitations included unaccounted for confounders inherent to observational, single institution studies with moderate sample sizes.

Conclusions/Significance

The GRACE scores provided superior discrimination as compared with the TIMI UA/NSTEMI score in predicting in-hospital and 6-month mortality in UA/NSTEMI patients, although the GRACE and TIMI STEMI scores performed equally well in STEMI patients. The observed discriminative deficit of the TIMI UA/NSTEMI score likely results from the omission of key risk factors rather than from the relative simplicity of the scoring system.     

Yeast Two-Hybrid Analysis of PriB-Interacting Proteins in Replication Restart Primosome: A Proposed PriB–SSB Interaction Model

PriB is one of the components of the replication restart primosome. The activity mediated by the primosomal proteins, including PriB, is required for reinitiating chromosomal DNA replication in bacteria after DNA damage. As such, the study of the interactions between PriB and members in the primosome is essential to better understand their mechanism of action. In this study, we investigated PriB-interacting proteins in the primosome through the yeast two-hybrid system. Yeast two-hybrid analysis using two strains, Y187 and AH109, revealed that PriB interacts with PriA, DnaT, SSB, and itself and does not interact with DnaA, DnaB, DnaC, or DnaG. In addition, mutational analysis showed that PriB may bind to SSB via K82, K84, and K89 in the L₄₅ loop. Based on these preliminary data, we proposed a PriB–SSB interaction model. Further work can focus on determination of how PriB binds to the PriA–SSB complex in replication restart.