Structures composing protein domains

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships.     

Cloning of the Lentinula edodes B mating-type locus and identification of the genetic structure controlling B mating

During the life cycle of heterothallic tetrapolar Agaricomycetes such as Lentinula edodes (Berk.) Pegler, the mating type system, composed of unlinked A and B loci, plays a vital role in controlling sexual development and resulting formation of the fruit body. L. edodes is produced worldwide for consumption and medicinal purposes, and understanding its sexual development is therefore of great importance. A considerable amount of mating type factors has been indicated over the past decades but few genes have actually been identified, and no complete genetic structures of L. edodes B mating-type loci are available. In this study, we cloned the matB regions from two mating compatible L. edodes strains, 939P26 and 939P42. Four pheromone receptors were identified on each new matB region, together with three and four pheromone precursor genes in the respective strains. Gene polymorphism, phylogenetic analysis and distribution of pheromone receptors and pheromone precursors clearly indicate a bipartite matB locus, each sublocus containing a pheromone receptor and one or two pheromone precursors. Detailed sequence comparisons of genetic structures between the matB regions of strains 939P42, 939P26 and a previously reported strain SUP2 further supported this model and allowed identification of the B mating type subloci borders. Mating studies confirmed the control of B mating by the identified pheromone receptors and pheromones in L. edodes.     

A fast approximate method of identifying paths of allosteric communication in proteins

Fluctuations of the distance between a pair of residues i and j may be correlated with the fluctuations of the distance between another pair k and l. In this case, information may be transmitted among these four residues. Allosteric activity is postulated to proceed through such correlated paths. In this short communication a fast method for calculating correlations among all possible pairs ij and kl leading to a pathway of correlated residues of a protein is proposed. The method is based on the alpha carbon centered Gaussian Network Model. The model is applied to Glutamine Amidotransferase and pathways of allosteric activity are identified and compared with literature. Proteins 2013; 81:1097–1101. © 2013 Wiley Periodicals, Inc.     

Cellulase–lignin interactions—The role of carbohydrate-binding module and pH in non-productive binding

Non-productive cellulase adsorption onto lignin is a major inhibitory mechanism preventing enzymatic hydrolysis of lignocellulosic feedstocks. Therefore, understanding of enzyme–lignin interactions is essential for the development of enzyme mixtures and processes for lignocellulose hydrolysis. We have studied cellulase–lignin interactions using model enzymes, Melanocarpus albomyces Cel45A endoglucanase (MaCel45A) and its fusions with native and mutated carbohydrate-binding modules (CBMs) from Trichoderma reesei Cel7A. Binding of MaCel45A to lignin was dependent on pH in the presence and absence of the CBM; at high pH, less enzyme bound to isolated lignins. Potentiometric titration of the lignin preparations showed that negatively charged groups were present in the lignin samples and that negative charge in the samples was increased with increasing pH. The results suggest that electrostatic interactions contributed to non-productive enzyme adsorption: Reduced enzyme binding at high pH was presumably due to repulsive electrostatic interactions between the enzymes and lignin. The CBM increased binding of MaCel45A to the isolated lignins only at high pH. Hydrophobic interactions are probably involved in CBM binding to lignin, because the same aromatic amino acids that are essential in CBM–cellulose interaction were also shown to contribute to lignin-binding.     

Importance of Dietary Cholesterol for the Maturation of Mouse Brain Myelin

The effect of nil (control), 1% (CH-l) and 5% (CH-5) dietary cholesterol on the myelination of mouse brain, and its deposition in the heart and liver were investigated during infancy. Swiss Webstar female mice were given formulated diets from early gestation, and their pups were weaned on the same diet as that of the individual mothers up to 60 days after birth. The test diets increased the liver weight and cholesterol content compared to the control even in suckling pups (20 days), but did not significantly influence the heart weight until 60 days. The cholesterol content of the heart was not increased by the CH-l diet throughout the feeding period, but it did increase the mole ratio of major myelin lipids and hastened its maturation. Myelin cholesterol was 10% higher in 20-day-old suckling pups in the CH-5 group compared to the control. Data indicate that dietary cholesterol altered the brain myelination rate of weaning mice, and that the mother’s dietary cholesterol influenced myelination of the suckling pups.     

Fungal response from oat (Avena sativa) plants and surface residue in relation to soil aggregation and organic carbon

Abstract

The influence of soil fungi on soil organic carbon (OC) from surface residue was tested in outdoor plots in southern Ontario, Canada, 2004. Fungal hyphal length, soil aggregation, OC and light and heavy fractions of organic matter were compared with factors of plant growth (with or without oat [Avena sativa]) and surface residue (no residue, oat straw (low C:N) or corn (Zea mays) stalks (high C:N)) in a factorial arrangement. Significant increases were observed in soil OC from the oat plants, and from corn stalks compared to straw residue, in the growing season with very moist, high OC, sandy soil. In treatments with corn stalk residue, fungal hyphal length was increased with interaction from the oat plants and residue and was positively correlated with the heavy fraction organic matter along with soil OC. Fungal hyphae, plant roots and high C:N residue were all factors in soil OC increases.     

Comprehensive Study of Mediterranean (Croatian) Propolis Peculiarity: Headspace,Volatiles, Anti‐Varroa‐Treatment Residue,Phenolics, and Antioxidant Properties

Eight propolis samples from Croatia were analyzed in detail, to study the headspace, volatiles, anti‐Varroa‐treatment residue, phenolics, and antioxidant properties. The samples exhibited high qualitative/quantitative variability of the chemical profiles, total phenolic content (1,589.3–14,398.3 mg GAE (gallic acid equivalent)/l EtOH extract), and antioxidant activity (11.1–133.5 mmol Fe²⁺/l extract and 6.2–65.3 mmol TEAC (Trolox^® equivalent antioxidant capacity)/l extract). The main phenolics quantified by HPLC‐DAD at 280 and 360 nm were vanillin, p‐coumaric acid, ferulic acid, chrysin, galangin, and caffeic acid phenethyl ester. The major compounds identified by headspace solid‐phase microextraction (HS‐SPME), simultaneous distillation extraction (SDE), and subsequent GC‐FID and GC/MS analyses were α‐eudesmol (up to 19.9%), β‐eudesmol (up to 12.6%), γ‐eudesmol (up to 10.5%), benzyl benzoate (up to 28.5%), and 4‐vinyl‐2‐methoxyphenol (up to 18.1%). Vanillin was determined as minor constituent by SDE/GC‐FID/MS and HPLC‐DAD. The identified acaricide residue thymol was ca. three times more abundant by HS‐SPME/GC‐FID/MS than by SDE/GC‐FID/MS and was not detected by HPLC‐DAD.     

Enhanced Immobilization of Cr(VI) in Soils by the Amendment of Rice Straw Char

This study investigated the effect of rice straw char (RSC) on the immobilization of Cr(VI) in soils. The Cr(VI) sorption experiments on the RSC and RSC-amended soils were conducted using the batch method. RSC exhibited Cr(VI) reduction capacity due to its black carbon content. The addition of RSC to the soils enhanced the overall Cr(VI) immobilization of the soils, which is primarily attributed to the Cr(VI) reduction capacity of RSC. The effects of RSC amendment on the Cr(VI) sorption of the soils increased with increasing RSC content in the soils and decreased with increasing pH or anion contents in the soil solutions. After Cr(VI) was sorbed by the soils, a portion of the Cr(VI) was converted to Cr(III) and the remainder was sorbed onto the soils. The presence of RSC in the soils decreased the portion of sorbed Cr(VI) in the soils and therefore lowered the potential remobilization of Cr(VI) from the soils. The results suggested that RSC amendment can be applied to develop a cost-effective method for immobilizing Cr(VI) in polluted soils, thus lowering the environmental risk from Cr(VI) toxicity.     

Role of lysine residues of the Magnaporthe oryzae effector AvrPiz-t in effector- and PAMP-triggered immunity

Magnaporthe oryzae is an important fungal pathogen of both rice and wheat. However, how M. oryzae effectors modulate plant immunity is not fully understood. Previous studies have shown that the M. oryzae effector AvrPiz-t targets the host ubiquitin-proteasome system to manipulate plant defence. In return, two rice ubiquitin E3 ligases, APIP6 and APIP10, ubiquitinate AvrPiz-t for degradation. To determine how lysine residues contribute to the stability and function of AvrPiz-t, we generated double (K1,2R-AvrPiz-t), triple (K1,2,3R-AvrPiz-t) and lysine-free (LF-AvrPiz-t) mutants by mutating lysines into arginines in AvrPiz-t. LF-AvrPiz-t showed the highest protein accumulation when transiently expressed in rice protoplasts. When co-expressed with APIP10 in Nicotiana benthamiana, LF-AvrPiz-t was more stable than AvrPiz-t and was less able to degrade APIP10. The avirulence of LF-AvrPiz-t on Piz-t:HA plants was less than that of AvrPiz-t, which led to resistance reduction and lower accumulation of the Piz-t:HA protein after inoculation with the LF-AvrPiz-t-carrying isolate. Chitin- and flg22-induced production of reactive oxygen species (ROS) was higher in LF-AvrPiz-t than in AvrPiz-t transgenic plants. In addition, LF-AvrPiz-t transgenic plants were less susceptible than AvrPiz-t transgenic plants to a virulent isolate. Furthermore, both AvrPiz-t and LF-AvrPiz-t interacted with OsRac1, but the suppression of OsRac1-mediated ROS generation by LF-AvrPiz-t was significantly lower than that by AvrPiz-t. Together, these results suggest that the lysine residues of AvrPiz-t are required for its avirulence and virulence functions in rice.     

All-atom contact potential approach to protein thermostability analysis

In this paper we use all-atom potential energy to define and analyze the inter-residue contacts in mesophilic and thermophilic proteins. Fifteen families of proteins are selected and each family has two representative proteins with greatly different preferred environmental temperatures. We find that both the number and energy of the contacts defined in this way show stronger correlations with the preferred temperatures of proteins than other factors used before. We also find that the charged-polar and charged-nonpolar residue contacts not only have larger contact numbers but also have lower single contact energies. Furthermore, the most important is that most of the thermophilic proteins have more charged-polar and charged-nonpolar residue contacts than their mesophilic counterparts. This suggests that they may play an important role in the thermostability of proteins, except usual charged-charged and nonpolar-nonpolar residue contacts. Charged residues may exert their profound influence by forming contacts not only with other charged residues but also with polar or nonpolar residues, thus further increasing the strength of contact network and then the thermostability of proteins.