Protein Structure and Function

Tissue hypoxia results from an inadequate supply of oxygen (O2) that compromises biological functions. Structural and functional abnormalities of the tumour vasculature together with altered diffusion conditions inside the tumour seem to be the main causes of tumour hypoxia. Evidence from experimental and clinical studies points to a role for tumour hypoxia in tumour propagation, resistance to therapy and malignant

One of the primary tools for raising awareness on biological invasions has been the publication of species accounts of the most prominent alien invaders. Until now such compilations have been available only for particular taxa, biomes and/or regions (Cronk and Fuller 2001; Weber 2003; Weidema 2000). In Europe, species accounts for selected invasive species have been published for a few countries or

We combine data on international trade linkages with network methods to examine the global trading system as an interdependent complex network. We map the topology of the international trade network and suggest new network based measures of international economic integration, at both a global system-wide level and a local country-level. We develop network based measures that incorporate not only the

The entire pathway of palmitate synthesis from malonyl-CoA in mammals is catalyzed by a single, homodimeric, multifunctional protein, the fatty acid synthase. Each subunit contains three N-terminal domains, the β-ketoacyl synthase, malonyl/acetyl transferase and dehydrase separated by a structural core from four C-terminal domains, the enoyl reductase, β-ketoacyl reductase, acyl carrier protein and thiosterase. The kinetics and specificities of the substrate loading reaction catalyzed by the malonyl/acetyl transferase, the condensation reaction catalyzed by β-ketoacyl synthase and chain-terminating reaction catalyzed by the thioesterase ensure that intermediates do not leak off the enzyme, saturated chains exclusively are elongated and palmitate is released as the major product. Only in the fatty acid synthase dimer do the subunits adopt conformations that facilitate productive coupling of the individual reactions for fatty acid synthesis at the two acyl carrier protein centers. Introduction of a double tagging and dual affinity chromatographic procedure has permitted the engineering and isolation of heterodimeric fatty acid synthases carrying different mutations on each subunit. Characterization of these heterodimers, by activity assays and chemical cross-linking, has been exploited to map the functional topology of the protein. The results reveal that the two acyl carrier protein domains engage in substrate loading and condensation reactions catalyzed by the malonyl/acetyl transferase and β-ketoacyl synthase domains of either subunit. In contrast, the reactions involved in processing of the β-carbon atom, following each chain elongation step, together with the release of palmitate, are catalyzed by the cooperation of the acyl carrier protein with catalytic domains of the same subunit. These findings suggest a revised model for the fatty acid synthase in which the two polypeptides are oriented such that head-to-tail contacts are formed both between and within subunits.

 Campanula spatulata is represented on Mt Olympos (2917 m) by two subspecies: the lowland spruneriana, from 400 to 1100 m, and the upland spatulata, from 1700 m to 2500 m. Spatulata populations significantly differed from those of spruneriana in the following features: (i) they consisted of shorter individuals with smaller flowers and lower flower production, (ii) they allocated more energy and resources below ground, (iii) they flowered much later in the year, had longer duration of flowering, and longer flower life span, (iv) they produced smaller fruits with fewer but heavier seeds, (v) they received lower numbers of insect visits for fewer hours per day, and (iv) they were pollinated by smaller insects. Between and within subspecies comparisons showed that in most cases the patterns of character change were neither gradual nor monotonous all along the elevation gradient. The differences in phenological characters are in agreement with patterns associated so far with elevation change. The taxonomic and biometric differences of the insect pollinators as well as the temporal separation of the flowering periods provide substantial evidence of reproductive isolation of the two C. spatulata subspecies on Mt Olympos.

The effects of short- versus long-term alpha tocopherol administration on oxidative stress and survival of dorsal random flaps were studied in diabetic rats. Seven groups, with 20 rats in each, were constructed: (1) control, (2) noncontrolled diabetes, (3) noncontrolled diabetes+short-term alpha tocopherol, (4) noncontrolled diabetes+long-term alpha tocopherol, (5) insulin treatment, (6) insulin+short-term alpha tocopherol, and (7) insulin+long-term alpha tocopherol. After 3 months of diabetes, dorsal McFarlane flaps were raised. Flap viability and free-radical measurements with histopathological examination were investigated. Mean flap survival in Groups I to VII were 84.0+/-2.2%, 55.0+/-2.4%, 57.0+/-2.5%, 57.8+/-3.7%, 64.1+/-4.1%, 70.0+/-4.9%, and 77.0+/-6.6%, respectively. Free-radical concentration, as assessed with luminol- and lucigenin-enhanced chemiluminiscence, was inversely correlated with flap survival. The results for viability and free-radical concentrations were significant between Groups 1, 2, 5, 6, and 7. Random flaps in diabetic animals showed significantly greater necrosis compared with controls. Among the diabetic animals, group receiving combination of insulin and long-term alpha tocopherol treatment had the greatest flap viability and least tissue free-radical concentration. Histopathological studies showed a hyalinization of arterioles in diabetics with long-term alpha tocopherol treatment protecting the vessel wall. In conclusion, random flaps in experimental diabetes mellitus show greater tissue oxidative stress and necrosis, which is only partially corrected with insulin treatment. Long-term antioxidant supplementation as an adjunct to insulin further lowers the oxidative stress, protects vessel structure and function, and therefore increases flap survival.

The analysis of brain network topological features has served to better understand these networks and reveal particular characteristics of their functional behavior. The distribution of brain network motifs is particularly useful for detecting and describing differences between brain networks and random and computationally optimized artificial networks. In this paper we use a multi-objective evolutionary optimization approach to generate optimized artificial

The relative importance of regional, watershed, and in-stream environmental factors on fish assemblage structure and function was investigated in western Lake Superior tributaries. We selected 48 second- and third-order watersheds from two hydrogeomorphic regions to examine fish assemblage response to differences in forest fragmentation, watershed storage, and a number of other watershed, riparian, and in-stream habitat conditions. Although a variety of regional, fragmentation, and storage-related factors had significant influences on the fish assemblages, water temperature appeared to be the single most important environmental factor. We found lower water temperatures and trout–sculpin assemblages at lower fragmentation sites and higher temperatures and minnow–sucker–darter assemblages as storage increased. Factors related to riparian shading and flow separated brook trout streams from brown trout (Salmo trutta) – rainbow trout (Oncorhynchus mykiss) streams. Functionally, fish asse...

Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo-(or other) stability to specific requested reactions such as protein–protein binding, enzymatic reactions, or nanotech-nology applications. The design scheme may encompass small regions of the proteins or the entire protein. In either case, the design may aim at the side-chains or at the full backbone conformation. Herein, the main framework for the process is outlined highlighting key elements in the CPD iterative cycle. These include the very definition of CPD, the diverse goals of CPD, components of the CPD protocol, methods for searching sequence and structure space, scoring functions, and augmenting the CPD with other optimization tools. Taken together, this chapter aims to introduce the framework of CPD.

The purpose of this paper is to determine the effects of usage of sequential teaching method on the academic achievement and retention level of students. Three student groups of biology students in University “Goce Delcev”, Faculty of Natural and Technical Sciences, Institute of Biology, - Stip, R. Macedonia were offered a topic on general characteristics of Proteins: Their Biological Functions and Primary Structure with different sequences of 3 teaching methods. The teaching methods were Laboratory method (student experiment), slide demonstration and lecture method. The first group started to course with experiments in the laboratory, then the relevant theory of proteins was given lecture method, and then the slides was shown (Group I). The sequence of these three teaching methods used in the first group was changed in both second and third group as follow: The lecture methods, slide show and experiment in Group II, and slide show, experiment and lecture method in Group III, respectively. Laboratory method used in the study was focused on the topic of This diversity and abundance reflect the central role of proteins in virtually all aspects of cell structure and function. An extraordinary diversity of cellular activity is possible only because of the versatility inherent in proteins, each of which is specifically tailored to its biological role. The pattern by which each is tailored resides within the genetic information of cells, encoded in a specific sequence of nucleotide bases in DNA proteins activity, a student experiment was designed for this reason, and including to examine its features, effective factors, and relation between the structure and function of the proteins. This experiment was carried out by students. Slide demonstration method included slides about protein structure and function. The slides were shown by teachers. Lecture method was performed by teachers as usual. Effectiveness of different sequential teaching methods was measured quantitatively by an achievement test. Achievement test contained 20 questions, testing the knowledge of facts as well as the ability to transfer the knowledge and problem solving ability. This test was used as pre-test before methods’ application, post-test after the methods’ application and retention test after 30 days from methods’ applied.

Peptides that bind either U1 small nuclear RNA (U1 snRNA) or the anticodon stem and loop of yeast tRNA(Phe) (tRNA(ACPhe)) were selected from a random-sequence, 15-amino acid bacteriophage display library. An experimental system, including an affinity selection method, was designed to identify primary RNA-binding peptide sequences without bias to known amino acid sequences and without incorporating nonspecific binding of the anionic RNA backbone. Nitrocellulose binding assays were used to evaluate the binding of RNA by peptide-displaying bacteriophage. Amino acid sequences of RNA-binding bacteriophage were determined from the foreign insert DNA sequences, and peptides corresponding to the RNA-binding bacteriophage inserts were chemically synthesized. Peptide affinities for the RNAs (Kd approximately 0.1-5.0 microM) were analyzed successfully using fluorescence and circular dichroism spectroscopies. These methodologies demonstrate the feasibility of rapidly identifying, isolating, and...