PloS one

The HIV-1 nucleocapsid protein (NC) is a small basic protein containing two zinc fingers (ZF) separated by a short linker. It is involved in several steps of the replication cycle and acts as a nucleic acid chaperone protein in facilitating nucleic acid strand transfers occurring during reverse transcription. Recent analysis of three-dimensional structures of NC-nucleic acids complexes established a new property: the unpaired guanines targeted by NC are more often inserted in the C-terminal zinc finger (ZF2) than in the N-terminal zinc finger (ZF1). Although previous NMR dynamic studies were performed with NC, the dynamic behavior of the linker residues connecting the two ZF domains remains unclear. This prompted us to investigate the dynamic behavior of the linker residues. Here, we collected 15N NMR relaxation data and used for the first time data at several fields to probe the protein dynamics. The analysis at two fields allows us to detect a slow motion occurring between the two domains around a hinge located in the linker at the G35 position. However, the amplitude of motion appears limited in our conditions. In addition, we showed that the neighboring linker residues R29, A30, P31, R32, K33 displayed restricted motion and numerous contacts with residues of ZF1. Our results are fully consistent with a model in which the ZF1-linker contacts prevent the ZF1 domain to interact with unpaired guanines, whereas the ZF2 domain is more accessible and competent to interact with unpaired guanines. In contrast, ZF1 with its large hydrophobic plateau is able to destabilize the double-stranded regions adjacent to the guanines bound by ZF2. The linker residues and the internal dynamics of NC regulate therefore the different functions of the two zinc fingers that are required for an optimal chaperone activity

Unprocessed Viral DNA Could Be the Primary Target of the HIV-1 Integrase Inhibitor Raltegravir

Integration of HIV DNA into host chromosome requires a 3′-processing (3′-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 3′-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 5′C4pA33′ step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance

The HIV-1 Integrase α4-Helix Involved in LTR-DNA Recognition Is also a Highly Antigenic Peptide Element

Monoclonal antibodies (MAbas) constitute remarkable tools to analyze the relationship between the structure and the function of a protein. By immunizing a mouse with a 29mer peptide (K159) formed by residues 147 to 175 of the HIV-1 integrase (IN), we obtained a monoclonal antibody (MAba4) recognizing an epitope lying in the N-terminal portion of K159 (residues 147–166 of IN). The boundaries of the epitope were determined in ELISA assays using peptide truncation and amino acid substitutions. The epitope in K159 or as a free peptide (pep-a4) was mostly a random coil in solution, while in the CCD (catalytic core domain) crystal, the homologous segment displayed an amphipathic helix structure (α4-helix) at the protein surface. Despite this conformational difference, a strong antigenic crossreactivity was observed between pep-a4 and the protein segment, as well as K156, a stabilized analogue of pep-a4 constrained into helix by seven helicogenic mutations, most of them involving hydrophobic residues. We concluded that the epitope is freely accessible to the antibody inside the protein and that its recognition by the antibody is not influenced by the conformation of its backbone and the chemistry of amino acids submitted to helicogenic mutations. In contrast, the AA →Glu mutations of the hydrophilic residues Gln148, Lys156 and Lys159, known for their interactions with LTRs (long terminal repeats) and inhibitors (

Allelopathic Effects of Chinaberry, Silk Tree and Iranian Pine on some Growth Traits of Lolium prene and Festuca arundinaceae

Introduction As the population grows and cities expand, the demand for more green spaces has also increased. Grass is widely recognized as one of the most important ground covers in the world. However, the development of green spaces is hindered by a severe shortage of water resources and challenges associated with managing and maintaining grass. The composition of trees and plants may cause to inhibitory or stimulation effects on crops, called allopathic effects. Therefore, understanding the allopathic effects is important to determine appropriate methods of cultivation and product management to prevent interference of allopathic substances in the growth and production of products. Materials and Methods  This study was performed in two separate experiments as a factorial based on completely randomized design at Ferdowsi University of Mashhad. In the first experiment, the effect of three different levels of plant residue powder (zero, 0.46 and 1 g) of three types of trees (Pine, Silk and Chinaberry) on germination and growth of Lolium prenne and Festuca arundinaceae grasses with four replications in the greenhouse was investigated.  The second experiment, the effect of 5 ml of aqueous extract prepared from plant residues of the mentioned trees on germination and growth of the mentioned grasses in three replications in the laboratory was investigated. At the end of both experiments, some of morophology traits (weight, length, germination index) were measured. Minitab software was used to analyze the data obtained from both experiments. Results and Discussion  According to the analysis of variance table of the first experiment, the results show that the simple effect of grass treatment on plant and root length, fresh weight, germination percentage and rate are significantly different. In the simple effect of treatment the quantity of plant residues, all traits have a significant difference. Also, in the simple effect of treatment of plant residue kind, plant length, root length, fresh and dry weight, germination percentage and rate were significantly different. Interaction grass and the quantity of plant residues treatment and the interaction of grass and kind of plant residues treatment, all measured traits had a significant difference. The interaction triple treatments plant length, root length, dry weight, germination percentage and rate differences were observed. Therefore, in the interaction triple treatments, the most and least plant lengths were observed related to the treatment of Lolium grass with 0.46 gr of Pine residue powder and the treatment of Festuca with 1 gr of Chinaberry residue powder. Also, the most and least root lengths were related to Lollium grass with 0.46 gr of Pine plant residue powder and Festuca grass with 1 gr of Pine plant residue powder. In the triple of dry weight the most amount was related to Festuca with 1 gr of Chinaberry residue powder and the least was related to Lolium control. The most and least germination percentages belonged to the control Festuca and lollium with 0.46 gr of pine plant residue powder respectively, and in the trait of germination rate, the most amount belonged to the control Festuca and the least to the control lollium has been observed. The results of the second experiment demonstrated a significant difference in all measured traits including grass treatment, plant length, fresh and dry weight, germination percentage and rate, and simple effect of plant extract. Moreover, the interaction of grass treatment and plant residue extract showed significant differences in root length, plant length, fresh weight, dry weight, and germination rate and percentage. Comparison of the mean interaction of grass treatment and type of plant residues revealed that the control Festuca had the highest plant length, while Lolium with Silk residue extract had the lowest. The longest and shortest root lengths were observed in control Lolium and Lolium with Silk residues, respectively. The highest and lowest fresh weight were recorded in Lolium control and Lolium grass along with Silk residue extract, respectively. For the dry weight trait, the highest amount was related to the treatment of Lolium grass with pine residue extract, while the lowest dry weight was observed in Festuca grass and Lolium grass with Silk residue extract. In terms of the germination percentage trait, control Festuca and Festuca with pine residue extract had the highest germination percentage, while Lolium with Chinaberry residue extract and Lolium with Silk residue extract had the lowest.  The most and least germination rates belonged to Festuca control and Lolium with Chinaberry residue extract. From these discussions, it can be concluded that the allelchemicals in the powder extract of plant residues have had a significant effect on the yield of these two grasses and have reduced growth and germination. Decreased germination due to allelopathic stress can be due to different abnormalities in metabolic activity, seed saturation potential, death of some dividing cells and embryonic abnormalities. Conclusion  Based on the results of both experiments, it can be concluded that Chinaberry and Silk trees have a stronger allelopathic effect compared to Pine. Additionally, the performance of both grasses in response to residues and extracts containing allelochemicals was slightly different. For instance, in the second experiment, the impact of Chinaberry extract reduced plant length by 28%, root length by 89%, dry weight by 16%, germination percentage by 75%, and germination rate by 85% compared to the Festuca control treatment. Similarly, the effect of Chinaberry extract on Lolium grass resulted in a 96% reduction in plant growth, 97% reduction in root length, 98% reduction in wet weight, 50% reduction in dry weight, 89% reduction in germination percentage, and 89% reduction in germination rate compared to the Lollium control treatment

Artificial neural network potential in yield prediction of lentil (Lens culinaris L.) influenced by weed interference

This study was conducted to predict the yield and biomass of lentil (Lens culinaris L.) af- fected by weeds using artificial neural network and multiple regression models. Systematic sampling was done at 184 sampling points at the 8-leaf to early-flowering and at lentil maturity. The weed density and height as well as canopy cover of the weeds and lentil were measured in the first sampling stage. In addition, weed species richness, diversity and even- ness were calculated. The measured variables in the first sampling stage were considered as predictive variables. In the second sampling stage, lentil yield and biomass dry weight were recorded at the same sampling points as the first sampling stage. The lentil yield and biomass were considered as dependent variables. The model input data included the total raw and standardized variables of the first sampling stage, as well as the raw and stan- dardized variables with a significant relationship to the lentil yield and biomass extracted from stepwise regression and correlation methods. The results showed that neural network prediction accuracy was significantly more than multiple regression. The best network in predicting yield of lentil was the principal component analysis network (PCA), made from total standardized data, with a correlation coefficient of 80% and normalized root mean square error of 5.85%. These values in the best network (a PCA neural network made from standardized data with significant relationship to lentil biomass) were 79% and 11.36% for lentil biomass prediction, respectively. Our results generally showed that the neural net- work approach could be used effectively in lentil yield prediction under weed interference conditions

Aloe vera incorporated biomimetic nanofibrous scaffold: A regenerative approach for skin tissue engineering

10.1007/s13726-013-0219-2Iranian Polymer Journal (English Edition)233237-248IPJO