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In this work, we have explored the interaction of three different polyphenols with the food protein β-lactoglobulin. Antioxidant activities of polyphenols are influenced by complexation with the protein. However, studies have shown that polyphenols after complexation with the protein can be more beneficial due to enhanced antioxidant activities. We have carried out molecular docking, molecular dynamics (MD) simulation, and quantum mechanics/molecular mechanics (QM/MM) studies on the three different protein-polyphenol complexes. We have found from molecular docking studies that apigenin binds in the internal cavity, luteolin binds at the mouth of the cavity, and eriodictyol binds outside the cavity of the protein. Docking studies have also provided binding free energy and inhibition constant values that showed that eriodictyol and apigenin exhibit better binding interactions with the protein than luteolin. For eriodictyol and luteolin, van der Waals, hydrophobic, and hydrogen bonding interactions are the main interacting forces, whereas for apigenin, hydrophobic and van der Waals interactions play major roles. We have calculated the root mean square deviation (RMSD), root mean square fluctuations (RMSF), solvent-accessible surface area (SASA), interaction energies, and hydrogen bonds of the protein-polyphenol complexes. Results show that the protein-eriodictyol complex is more stable than the other complexes. We have performed ONIOM calculations to study the antioxidant properties of the polyphenols. We have found that apigenin and luteolin act as better antioxidants than eriodictyol does on complexation with the protein, which is consistent with the results obtained from MD simulations.

Alpha glucosidase inhibitors reduce post prandial hyperglycemia and are the drugs of choice for the treatment of type 2 diabetes. As synthetic α-glucosidase inhibitors often produce undesirable side effects, less toxic inhibitors from natural sources are in high demand.

Homopolar quadruple bonding in first row p-block elements is expected due to the presence of four valence orbitals accessible for bonding. Although quadruple bonding in C2 has been proposed, no such proposal exists for B2. Here we report the unprecedented B–B quadruple bonding in Li3B2− and Li4B2 clusters based on high level theoretical calculations. The quadruple bonding is omnipresent in the global minimum, its nearest energy isomer and the transition states connecting them. Various bonding analyses reveal the unprecedented nature of the BB quadruple bonding interaction.

High-level quantum-chemical calculations have been used to predict a cationic ternary NBe5H4+ cluster containing a planar pentacoordinate nitrogen atom. The proposed cluster has pseudo dual aromaticity and is kinetically and thermodynamically very stable.

Plants inherently show resistance to pathogen attack but are susceptible to multiple bacteria, viruses, fungi, and phytoplasmas. Diseases as a result of such infection leads to the deterioration of crop yield. Several pathogen-sensitive gene activities, promoters of such genes, associated transcription factors, and promoter elements responsible for crosstalk between the defense signaling pathways are involved in plant resistance towards a pathogen. Still, only a handful of genes and their promoters related to plant resistance have been identified to date. Such pathogen-sensitive promoters are accountable for elevating the transcriptional activity of certain genes in response to infection. Also, a suitable promoter is a key to devising successful crop improvement strategies as it ensures the optimum expression of the required transgene. The study of the promoters also helps in mining more details about the transcription factors controlling their activities and helps to unveil the involvement of new genes in the pathogen response. Therefore, the only way out to formulate new solutions is by analyzing the molecular aspects of these promoters in detail. In this review, we provided an overview of the promoter motifs and cis-regulatory elements having specific roles in pathogen attack response. To elaborate on the importance and get a vivid picture of the pathogen-sensitive promoter sequences, the key motifs and promoter elements were analyzed with the help of PlantCare and interpreted with available literature. This review intends to provide useful information for reconstructing the gene networks underlying the resistance of plants against pathogens.

Chlorpyrifos is an extensively used organophosphate pesticide showing broad-spectrum effectiveness on various target pests. Long-term sublethal exposure to this pesticide is reported to produce detrimental effects on sex hormone metabolism and nervous system functioning. It is a suspected endocrine-disrupting chemical and causes abnormal developmental patterns, gonadal atrophy, and neurodevelopmental problems. The degradation products formed during environmental degradation of chlorpyrifos are also capable of binding with steroid hormone receptors such as estrogen receptor alpha (ER-α) and can disrupt estrogen signaling in humans. In the present study, chlorpyrifos and four of its degradation products viz. CPYO, DEC, TCP, and TMP were chosen to study their ability to bind with estrogen receptors. The molecular docking and dynamics simulation carried out to understand the molecular interaction of chlorpyrifos and its environmental degradation products with human ER reveal the risk of potential disruption in estrogen signaling in humans by these compounds.

Major abiotic stress factors such as drought, salinity, hypoxia, and extreme temperatures along with rapid global climate change have had a huge negative impact on agricultural productivity. Understanding the abiotic stress-responsive molecular mechanisms and its associated proteins is extremely important to advance our knowledge towards developing multiple abiotic stress tolerance in plants. Firstly, basic understanding at transient level would be a vital foundation to accomplish this goal. Therefore, our present study aimed at understanding the sub-cellular localization of Eukaryotic Initiation Factor 4A-III (AteIF4A-III), a key DEAD-box RNA helicase, and Always Early 4 (AtALY4), an mRNA export factor, and their in vivo protein-protein interaction with major abiotic stress–associated proteins under control and multiple abiotic stress conditions. AteIF4A-III and AtALY4 were localized to the nucleus as evident by transient protoplast assay. AteIF4A-III has shown strong interaction with a negative regulator of multiple abiotic stresses, Stress Response Suppressor 1 (AtSTRS1) in Bi-FC assay. Further, the flow cytometry analysis has shown the strong interaction between them. Interestingly, under multiple abiotic stress treatment, the interacting partners were rapidly re-localized from nucleus to cytoplasm and cytoplasmic space. Similar results were observed when N- and C-terminal fusions of AteIF4A-III and AtALY4 treated under multiple abiotic stresses. Our study reveals that AteIF4A-III, AtALY4, and abiotic stress–associated protein AtSTRS1 are among the key proteins associated with multiple abiotic stress responses in plants.

Planar hypercoordinate structures are gaining immense attention due to the shift from common paradigm. Herein, our high level ab initio calculations predict that planar pentacoordinate aluminium and gallium centres in Cu5Al2+ and Cu5Ga2+ clusters are global minima in their singlet ground states. These clusters are thermodynamically and kinetically very stable. Detailed electronic structure analyses reveal the presence of both σ and π aromaticity which is the driving force for the stability of the planar form.

Planar pentacoordinate zinc group elements, (M = Zn, Cd, Hg) were computationally found to be at a global minimum in Li

Homopolar quadruple bonding in first row p-block elements is expected due to the presence of four valence orbitals accessible for bonding. Although quadruple bonding in C

Sandwich complexes find their interests among the chemists after the breakthrough discovery of ferrocene. Since then, a number of sandwich and half sandwich complexes were predicted and synthesized. Herein, we have theoretically proposed a series of half-sandwich complexes involving a neutral Be3 ring and transition metal. Quantum chemical calculations have shown that the proposed complexes are quite stable involving high bond dissociation energies. The thermodynamics of their formation is also favorable. The Be3 ring in all cases posses dual aromaticity which has been ascertained based on magnetic as well as topological feature of electron density.

This article reports the interaction between a synthetic statin, fluvastatin with bovine milk protein, β-lactoglobulin (BLG) through docking, constant pH molecular dynamics simulation (cpHMD) and binding free energy calculations. Docking provides the best fitted binding mode of the ligand with the receptor. We have carried out MD simulations of the protein and protein-ligand complex at two different pH viz. 7.0 and 1.5. We have found that the protein shows more compact behavior at pH 1.5 and this behavior is more prominent on complexation with the ligand. In support of this we have utilized the properties viz. root mean square deviations, root mean square fluctuations, radius of gyration, protein-ligand hydrogen bond and binding free energy calculations. Calculation of radius of gyration shows that the value decreases from 14.51 A to 14.03 A on complexation at pH 1.5. Calculations of hydrogen bonds at pH 1.5 confirms that hydrogen bonding interactions of the binding residues of the protein with the ligand provides stability to the complex. We have used molecular mechanics-generalized Born surface area (MMGBSA) method to estimate binding free energies of the protein with the ligand. MMGBSA calculations suggest that there is favorable binding interactions between the protein and the ligand with major contributions from Van der Waals interactions. We have found that the net average binding free energy is −29.394 kcal/mol that reveals a favorable binding interactions of BLG with the ligand. This study suggests that in spite of the acidic environment in the stomach BLG can act as a carrier for the acid-sensitive drug molecules such as fluvastatin because of its highly stable conformational behavior in the acidic pH.

Quadruple bonding in heavier main group elements is not known albeit having four valence orbitals accessible for bonding. Here we report the unprecedented quadruple bonding between a silicon atom and a transition metal fragment in the 1A1 electronic ground state of C3v symmetric SiRu(CO)3 based on high level theoretical calculations. Various bonding analyses reveal the nature of the Si[quadruple bond, length as m-dash]Ru quadruple bonding interaction, which involves one usual Si-Ru σ bond, two usual Si-Ru π bonds and one additional Si → Ru dative σ bond.

Unsupported donor-acceptor complexes of noble gases (Ng) with group 13 elements have been theoretically studied using density functional theory. Calculations reveal that heavier noble gases form thermodynamically stable compounds. The present study reveals that no rigid framework is necessary to stabilize the donor-acceptor complexes. Rather, prepyramidalization at the Lewis acid center may be an interesting alternative to stabilize these complexes. Detailed bonding analyses reveal the formation of two-center-two-electron dative bonding, where Ng atoms act as a donor.

In silico search for planar hexacoordinate silicon center has been initiated by global minimum screening with density functional theory and energy refinement using coupled cluster theory. The search resulted in a local minimum of SiAl3Mg3H2+ structure which contains a planar hexacoordinate silicon center (phSi). The phSi structure is 5.8 kcal/mol higher in energy than the global minimum. However, kinetic studies reveal that the local minimum structure has enough stability to be detected experimentally. Born-Oppenheimer molecular dynamics (BOMD) simulations reveal that the phSi structure can be maintained up to 400 K. The formation of multiple bonds between the central silicon atom and framework aluminium atom is the key stabilizing factor for the planar structure.

Rice is one of the widely popular staple foods across the globe. Abiotic stress is known for its devastating effect on crop plants. Drought amid the other abiotic factors has received constant attention as it causes loss in productivity and thus disrupts the efforts toward food security. Drought stress causes havoc in rice productivity as it harms the rice plants at all the developmental stages and the reproductive stages. Concurrently, the effective measures to reduce the loss in yield and development in rice due to drought conditions mostly consist of long-term research efforts. Therefore, it has become an utmost necessity to search for convenient alternatives that are efficient, less time-consuming, cost-effective, and environment friendly. Thus, attention has been paid to Plant growth-promoting rhizobacteria (PGPRs), which stands out as an excellent measure to reduce the stress posed by drought. PGPR could be used for increasing the tolerance mechanisms in drought-affected rice crops and could be established as an excellent choice of the mitigation strategy. We aim to summarize the research efforts of this field in this chapter.

High-level quantum-chemical calculations have been used to predict a cationic ternary NBe

An extended computational approach has been utilized to explore the reactions of acids with carbonyl oxide, also known as Criegee intermediate (CI). The reactions were explored inside water cluster containing 50 water molecules. All possibilities of product formation were considered. Among the considered acids, the rate of 1,4-insertion follows the order - HCOO < HCl < HNO3. The most stable products of the reactions between the considered acids and CI have been identified.

Abiotic stresses are the key factors which negatively influence plant development and productivity and are the main cause of extensive agricultural production losses worldwide. Brassica napus is an oilseed crop of global economic significance and major contributor to the total oilseed production, quite often encounters abiotic stresses, resulting in reduced agricultural productivity. Hence, there is an immediate need being felt to raise B. napus cultivars which would be more suitable for various abiotic stress conditions presently and in the years to come. Biotechnology and molecular plant breeding has emerged as an important tool for molecular understanding of plant response to various abiotic stresses. Currently, various stress-responsive genes and mechanisms have been identified and functionally characterized in model plant Arabidopsis and other major crop plants such as Oryza sativa and Zea mays. However, very inadequate success has been achieved in this direction in a major oilseed crop such as B. napus. In this review, we present the latest methods and approaches of studying abiotic stress in B. napus. In this review, we describe the genes functioning as markers for crop breeding and discuss the recent progress and advances in genome editing by break through CRISPR/Cas9 multigene–multiplex approaches for developing multiple abiotic stress tolerance with our on-going research as a scheme. We also throw some light on molecular genetics, plant breeding and abiotic stress biotechnology of B. napus which offer a new prospective on the research directions for the practical plant breeding and functional genomics of B. napus in response to different abiotic stress conditions.

Agriculture is the key to a stable civilization, and it applies to the whole world. The most important factor for stable agricultural productivity is the delivery of healthy and shockproof seeds. Seeds are encapsulated form of gene pools as well as an integral part of the basis for plant life on earth. As there is a vivid change in the environmental conditions and change in farming procedures, the seeds also need to be competent enough to be able to withstand the harsh alterations in the environment and perform well with better production level. Therefore, there is an urgent need for reviewing the measures taken to uplift the production level by enhancing the seed quality and productivity. In this chapter, we have taken into consideration the role of application of different tools of agricultural biotechnology in augmentation of seed quality and prospects in the agricultural scenario.

Catalytic CO2 reduction mediated by Ru-PNP pincer complexes has been studied using density functional theory (DFT). Calculations clearly reveal that modification of the PNP pincer framework by introducing planar conjugation in the backbone improves the catalytic efficiency. Activation strain model reveals that reduction of strain in the transition states with modified PNP framework associated with the insertion of CO2 molecule is responsible for lowering the activation barrier. Calculations also reveal that electron withdrawing substituents at the PNP ligand improves the catalytic performance.

In the present study we have tried to explore the effect of static external electric field of strength 3.0 V/nm on the conformational changes adopted by the protein β-lactoglobulin. We have chosen different temperatures viz. 300 K, 400 K and 450 K to evaluate the temperature dependent effect of electric field. We have observed that combined effect of high temperature and static external electric field show significant changes on the structural conformation of the protein which in turn may affect the functional properties of the protein. Calculations of root mean square deviations reveal that both helical and β-sheet regions of the protein are noticeably affected at high temperature. We have used solvent accessible surface area (SASA) and dipole moment values to explain that there is changes in hydrophobicity of the protein surface due to presence of external electric field. The study reveals that electric field in combination with high temperature can be used to alter the conformation of the protein and the effect of external electric field is more pronounced at high temperature than that of low temperature. The study provides a better understanding of the conformational changes adopted by the protein under the stress of external electric field and high temperature and provide guidance to choose optimum conditions for processing without loss of nutritional properties.

Drought, salinity, and extreme temperatures are the key abiotic stress factors that negatively influence plant growth, leading to loss of agricultural productivity worldwide. Plants during the course of their evolution develop biochemical and physiological mechanisms to withstand different abiotic stresses. This book chapter describes the plant response to abiotic stress in developing tolerance through stress signaling molecules such as late embryogenesis abundant proteins, HSPs, methylglyoxyl, HyPRPs, aquaporins, and protein kinases. Various genetic engineering approaches to modulate the abiotic stress signaling process in crop plants are also discussed along with recent case studies on transgenics, plant transcription factors, and molecular chaperones. The topic emphasizes ubiquitination pathway genes, epigenetic regulation, small RNAs, and helicases in modulating signaling processes in abiotic stress tolerance. The chapter also focuses on the huge potential of breakthrough CRISPR-Cas9 and CRISPR-Cpf1 genome editing systems in developing sustainable multiple abiotic stress tolerance in crop plants.

The Indian subcontinent is considered to be the major centre of hybridization of the wild Musa progenies, as it forms the centre of secondary origin of the taxa and therefore expected to exhibit a high degree of diversity. Musa balbisiana Colla is known to be one of the wild progenitors of cultivated bananas and plantains. Knowledge of genetic variability is very important for contemplating any conservation and management programmes. Single Primer Amplification Reaction (SPAR) approach i.e., a combination of random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and directed amplification of minisatellites DNA (DAMD) markers function as important tools for analyzing genetic variation in plants. They collectively provide a comprehensive description of the nature and the extent of existing natural genetic diversity, as the primers target different regions of the genome. A total of 47 SPAR primers (RAPD-25, ISSR-12 and DAMD-10) with high reproducibility were used for analysis of intraspecific genetic variation of the 12 genotypes of M. balbisiana, which yielded 331 polymorphic bands. The RAPD, ISSR and DAMD markers revealed 82.63 %, 90.36 % and 84.72 % of polymorphic bands respectively. The polymorphic information content (PIC) values were almost identical for each marker system while the resolving power (Rp) was found to be highest in DAMD (4.10). The dendrogram obtained showed the presence of two main clusters in all the analyses, with some genotypes (MB10-MB11 and MB5-MB7) always maintaining and manifesting their strong genetic relationship by clustering together in almost all the analyses. Combinations of such markers can be considered as more effective and promising tool for assessing genetic variation in other Musa species as well.