Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most ...important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.
Bitter gourd (Momordica charantia L.) is an economically important vegetable crop grown in tropical parts of the world. In this study, a high-density linkage map of M. charantia was constructed ...through genotyping-by-sequencing (GBS) technology using F
mapping population generated from the cross DBGy-201 × Pusa Do Mausami. About 2013 high-quality SNPs were assigned on a total of 20 linkage groups (LGs) spanning over 2329.2 CM with an average genetic distance of 1.16 CM. QTL analysis was performed for six major yield-contributing traits such as fruit length, fruit diameter, fruit weight, fruit flesh thickness, number of fruits per plant and yield per plant. These six quantitative traits were mapped with 19 QTLs (9 QTLs with LOD > 3) using composite interval mapping (CIM). Among 19 QTLs, 12 QTLs derived from 'Pusa Do Mausami' revealed a negative additive effect when its allele increased trait score whereas 7 QTLs derived from 'DBGy-201' revealed a positive additive effect when its allele trait score increased. The phenotypic variation (R
%) elucidated by these QTLs ranged from 0.09% (fruit flesh thickness) on LG 14 to 32.65% (fruit diameter) on LG 16 and a total of six major QTLs detected. Most QTLs detected in the present study were located relatively very close, maybe due to the high correlation among the traits. This information will serve as a significant basis for marker-assisted selection and molecular breeding in bitter gourd crop improvement.
The translocase of the outer membrane (TOM) mediates the membrane permeation of mitochondrial matrix proteins. Tom20 is a subunit of the TOM complex and binds to the N‐terminal region (ie, ...presequence) in mitochondrial matrix precursor proteins. Previous experimental studies indicated that the presequence recognition by Tom20 was achieved in a dynamic‐equilibrium among multiple bound states of the α‐helical presequence. Accordingly, the co‐crystallization of Tom20 and a presequence peptide required a disulfide‐bond cross‐linking. A 3‐residue spacer sequence (XAG) was inserted between the presequence and the anchoring Cys residue at the C‐terminus to not disturb the movement of the presequence peptide in the binding site of Tom20. Two crystalline forms were obtained according to Ala or Tyr at the X position of the spacer sequence, which may reflect the dynamic‐equilibrium of the presequence. Here, we have performed replica‐exchange molecular dynamics (REMD) simulations to study the effect of disulfide‐bond linker and single amino acid difference in the spacer region of the linker on the conformational dynamics of Tom20‐presequence complex. Free energy and network analyses of the REMD simulations were compared against previous simulations of non‐tethered system. We concluded that the disulfide‐bond tethering did not strongly affect the conformational ensemble of the presequence peptide in the complex. Further investigation showed that the choice of Ala or Tyr at the X position did not affect the most distributions of the conformational ensemble of the presequence. The present study provides a rational basis for the disulfide‐bond tethering to study the dynamics of weakly binding complexes.
Tim21, a subunit of a highly dynamic translocase of the inner mitochondrial membrane (TIM23) complex, translocates proteins by interacting with subunits in the translocase of the outer membrane (TOM) ...complex and Tim23 channel in the TIM23 complex. A loop segment in Tim21, which is in close proximity of the binding site of Tim23, has different conformations in X-ray, NMR and new crystal contact-free space (CCFS) structures. MD simulations can provide information on the structure and dynamics of the loop in solution.
The conformational ensemble of the loop was characterized using loop modeling and molecular dynamics (MD) simulations.
MD simulations confirmed mobility of the loop. Multidimensional scaling and clustering were used to characterize the dynamic conformational ensemble of the loop. Free energy landscape showed that the CCFS crystal structure occupied a low energy region as compared to the conventional X-ray crystal structure. Analysis of crystal packing indicates that the CCFS provides larger conformational space for the motions of the loop.
Our work reported the conformational ensemble of the loop in solution, which is in agreement with the structure obtained from CCFS approach. The combination of the experimental techniques and computational methods is beneficial for studying highly flexible regions of proteins.
Computational methods, such as loop modeling and MD simulations, have proved to be useful for studying conformational flexibility of proteins. These methods in integration with experimental techniques such as CCFS has the potential to transform the studies on flexible regions of proteins.
•Loop modeling was used to generate multiple conformations of a loop segment.•MD simulations confirmed highly dynamic nature of the flexible loop.•CCFS is a crystal contact-free space formed in designed MBP-Tim21 fusion crystals.•CCFS structure is consistent with solution conformational ensemble of the loop.•CCFS approach provides sufficient space for flexible loops to allow their motions.
•Structural topic modeling of 14,523 articles related to corporate social responsibility.•Identified 19 themes and their trends over 30 years.•Mapped themes to corporate social responsibility ...dimensions and plotted their trend.•The stakeholder dimension is the most researched dimension by a wide margin.•Primary stakeholders are more researched with the customer being the most researched.
This study provides a bird’s eye view of research on corporate social responsibility (CSR) by text-mining 14,523 articles published in reputed scholarly journals spanning the period from 1991 to 2020. This is the first study on CSR to use an unsupervised text-mining method (structural topic modeling) thereby overcoming several limitations of methods used in previous analyses. Aside from the methodological novelty, this study contributes to three distinct but related strands of literature. First, it contributes to efforts made in the prior literature to characterize the CSR concept in a novel way. Second, this study contributes to the debate on the dimensions that constitute CSR. Additionally, it provides evidence of how the focus on particular dimensions has varied over time. Third, it contributes to the debate on instrumental versus injunctive CSR by providing concrete evidence that the literature has shifted from injunctive to instrumental CSR.
We report coarse-grained Langevin dynamics simulations of homogeneous mixtures of lobed colloidal particles with opposite charges. We show that dumbbell, trigonal planar, tetrahedral, square planar, ...trigonal bipyramidal, and octahedral shaped particles form distinct self-assemblies including chains, sheets, crystalline, and spherical structures. The dumbbell and square planar particles predominantly form chains and sheets while other particles form network-like self-assembled morphologies. At higher temperatures and lower charges, non-planar particles form three-dimensional aggregates. We further report on packing arrangements of particles which lead to differences in porosities within self-assembled morphologies. Our results show that the trigonal planar particles form larger porous structures. The self-assembled structures that we report are potentially useful in designing porous biomaterials for biomedical applications.
In the present climate change scenario, controlling plant disease through exploitation of host plant resistance could contribute toward the sustainable crop production and global food security. In ...this respect, the identification of new sources of resistance and utilization of genetic diversity within the species may help in the generation of cultivars with improved disease resistance. Begomoviruses namely,
(TYLCV) and
(ChLCV) are known to cause major yield losses in several economically important crop plants of the family Solanaceae. Though co-occurrence, association and synergistic interactions among these viruses in the host plants is reported, whether orthologous genetic loci in related host plants could be responsible for conferring resistance to these viruses has not been investigated yet. Several loci including
, and
have been reported to confer resistance to leaf curl viruses in tomato. Here, we examined the pepper orthologous markers, corresponding to these QTL regions, for polymorphism between ChLCV susceptible and resistant genotypes of pepper. Further, to examine if the polymorphic markers are segregating with the disease resistance, Bulk Segregant Analysis (BSA) was performed on F
population derived from crosses between resistant and susceptible lines. However, none of the markers showed polymorphism in BSA suggesting that the tested markers are not linked to genes/QTLs responsible for conferring resistance to ChLCV in the selected genotypes.
analysis was performed to study the synteny and collinearity of genes located within these QTL regions in tomato and pepper genomes, which revealed that more than 60% genes located in
and
, 13.71% genes in
, 23.07% in
, and 44.77% genes located within
QTL region in tomato are conserved in pepper genome. However, despite such a high conservation in gene content, the linkage relationship in these regions seems to be greatly affected by gross rearrangements in both the species.
High temperatures present a formidable challenge to the cultivation of hot pepper, profoundly impacting not only vegetative growth but also leading to flower and fruit abscission, thereby causing a ...significant reduction in yield. To unravel the intricate genetic mechanisms governing heat tolerance in hot pepper, an F
2
population was developed through the crossing of two distinct genotypes exhibiting contrasting heat tolerance characteristics: DLS-161-1 (heat tolerant) and DChBL-240 (heat susceptible). The F
2
population, along with the parental lines, was subjected to comprehensive phenotyping encompassing diverse morphological, physiological, and biochemical heat-related traits under high temperature conditions (with maximum temperature ranging from 31 to 46.5°C and minimum temperature from 15.4 to 30.5°C). Leveraging the Illumina Nova Seq-6000 platform, Double digest restriction-site associated DNA sequencing (ddRAD-seq) was employed to generate 67.215 Gb data, with subsequent alignment of 218.93 million processed reads against the reference genome of
Capsicum annuum
. Subsequent variant calling and ordering resulted in 5806 polymorphic SNP markers grouped into 12 LGs. Further QTL analysis identified 64 QTLs with LOD values ranging from 2.517 to 11.170 and explained phenotypic variance ranging from 4.05 to 19.39%. Among them, 21 QTLs, explaining more than 10% phenotypic variance, were identified as major QTLs controlling 9 morphological, 3 physiological, and 2 biochemical traits. Interestingly, several QTLs governing distinct parameters were found to be colocalized, suggesting either a profound correlation between the QTLs regulating these traits or their significant genomic proximity. In addition to the QTLs, we also identified 368380 SSR loci within the identified QTL regions, dinucleotides being the most abundant type (211,381). These findings provide valuable insights into the genetics of heat tolerance in hot peppers. The identified QTLs and SSR markers offer opportunities to develop heat-tolerant varieties, ensuring better crop performance under high-temperature conditions.
Four cold tolerant hot pepper (Capsicum annuum L.) genotypes were identified at Division of Vegetable Science,ICAR-IARI, New Delhi which showed significantly better agronomic performance during the ...cold winter conditions ofDelhi during 2019–20 when most of other genotypes succumbed. Present investigations were carried out to understand the biochemical and molecular basis of cold tolerance in these genotypes for which they were compared with cold sensitive genotypes for various biochemical parameters as well as for expression of some cold inducible genes. The results indicated that the cold tolerant genotypes had inherent biochemical and molecular mechanism which helped them in cold acclimation. These genotypes had strong antioxidant defense and ROS (Reactive Oxygen Species) scavenging system as displayed by significantly high activities of guaiacol-peroxidase and superoxide dismutase and lower levels of lipid peroxidation in response to cold stress. They also accumulated higher concentration of proline to maintain their membrane fluidity and H2O2. Twelve of the fourteen cold inducible genes studied in the present investigations had significantly high expression in cold tolerant genotypes. However the expression profile of these genes differed in different genotypes indicating that mechanism of cold tolerance was not identical in all the genotypes. The confirmation of existence of innate cold tolerance mechanism in our test genotypes can pave a way for future utilization of these genotypes in cold stress breeding.
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