An Atom-Economic Method for 1,2,3-Triazole Derivatives via Oxidative [3 + 2] Cycloaddition Harnessing the Power of Electrochemical Oxidation and Click Chemistry

An electrochemical method was developed to accomplish the reagentless synthesis of 4,5-disubstituted triazole derivatives employing secondary propargyl alcohol as C-3 synthon and sodium azide as cycloaddition counterpart. The reaction was conducted at room temperature in an undivided cell with a constant current using a pencil graphite (C) anode and stainless-steel cathode in a MeCN solvent system. The proposed reaction mechanism was convincingly established by carrying out a series of control experiments and further supported by electrochemical and density functional theory (DFT) studies.

Structural impairment of p53 C-terminal due to the effect of phosphorylation and acetylation: a study on the interdependence of PTM

The C-terminal of tumor suppressor protein p53 is intrinsically disordered while unbound. This particular segment often shows structural plasticity when bound to other binding partners. The disordered component undergoes a disordered to ordered transition upon recognition. Post-translational modifications (PTMs), namely phosphorylation and acetylation, significantly alter the structural motifs of the segment. Among the various types of PTMs, phosphorylation, and acetylation of p53 at both N- and C- terminals lead to stabilization and activation. It has been noted experimentally that phosphorylation often regulates (enhances or reduces) the acetylation at specific sites. The phosphorylation of Thr377 and Ser378 reduces the acetylation of Lys373 and Lys382. Mutations of Thr377 and Ser378 to neutral Ala enhance and phospho mimic Asp reduce the acetylation of Lys373 and Lys382. Simulations of several single-point and pair-wise mutated systems have been generated to compare how the presence or absence of phosphorylation favors or disfavors the acetylation by thermodynamic and conformational analysis. We are using implicit solvent replica exchange molecular dynamics simulations to get 200 ns well-converged conformational ensembles of each system. Different sets of systems having both single and double PTMs are simulated. The results admit the appreciable change in the secondary structural level upon specific PTM. Also, the residual structure of the unbound p53 with single-point PTM varies significantly with pair-wise modifications. These observations further shed light on the relationship between the interdependencies of the specific PTM sites and the secondary structural levels.Communicated by Ramaswamy H. Sarma.

Interspecific variations in leaf litter decomposition and nutrient release from tropical mangroves

Efficient nutrient cycling through decomposition of leaf litter often regulates the high productivity and subsequent carbon sequestration of mangrove ecosystems along the land-ocean boundary. To understand the characteristics and the potentials of mangrove leaf litter in supplying organic carbon and nutrients to the coastal waters, four major mangrove species (A. officinalis, R. mucronata, H. littoralis and S. apetala) of Bhitarkanika mangrove forest, Odisha, India, were examined in controlled environmental conditions. Half-life time (t₀.₅), estimated for decomposition of those mangrove leaf litter materials ranged from 18 to 52 days. During the incubation experiment, organic carbon from mangrove leaf litter was released primarily through physical processes and was available for heterotrophic respiration. Among the four species, leaf litter of S. apetala with the lowest initial C/N ratios, released organic carbon with low molecular weight (labile substances) that has a relatively higher potential to support the aquatic food web. On the contrary, leaf litter of R. mucronata released organic material with relatively higher molecular weight (humic substances, higher aromaticity), which revealed its superior non-labile characteristics in this unique environment. The mean total heterotrophic bacterial (THB) population in the incubation was around nine-fold higher than the control. THB population growth and Chromophoric Dissolved Organic Matter (CDOM) spectral data further suggested the rapid release of highly labile and recalcitrant carbon from S. apetala and R. mucronata (between 7th and 21st day of incubation), respectively. The mean litter fall from the Bhitarkanika mangrove forest was estimated to be 11.32 ± 1.57 Mg ha^-1 y^-1 and its corresponding carbon content was 5.43 ± 0.75 Mg C ha^-1. The study revealed the role of leaf litter leachates as an important food source to microbial communities in the adjacent coastal waters, in addition to a potential carbon sequesterer through long-term burial in mangrove soil and export to the deep sea.

Structural modulation of p53TAD1-TAZ2 complex upon mutations and post-translational modification

The tumour suppressing p53 is a target for genetic alterations in human cancer. Native p53, found in latent state in cells, gets activated following various intracellular or extracellular responses. It plays imperative role in cell-cycle control, via growth-arrest, DNA repair and apoptosis, mainly regulated by post-translational modifications (PTM). However, the influence of PTMs on the activity of p53 is still under extensive experimental and computational study. There are numerous PTM sites in p53, which are reported to regulate its binding affinities with other proteins. Of the many, Thr18 at transactivational domain (TAD) of p53 is reported to amplify p53 activity upon phosphorylation. To understand the molecular basis of p53 recognition by its binding partner upon mutations and PTMs, we have exploited all atom molecular dynamic (MD) simulation of p53TAD1 bound to TAZ2 domain of p300. The MD simulation inferred that phosphorylated and mutated Thr18, as a phospho-mimic, bound with TAZ2, redistributed the charge environment of the interface, thereby modulating the stronger interactions with TAZ2 to enhance the binding efficiency. The electrostatic interactions due to different charge environment together with H-bonding and hydrophobic interaction dictate diverse binding approach between the two. The results of this computational study further explain the importance of the Thr18 as a PTM site in atomistic detail, hence shedding further light to the understanding of how PTMs are imperative for p53 activity to protect the cellular world.Communicated by Ramaswamy H. Sarma.

Microplastic pollution in fragile coastal ecosystems with special reference to the X-Press Pearl maritime disaster, southeast coast of India

Microplastics (MPs) are a global environmental concern and pose a serious threat to marine ecosystems. This study aimed to determine the abundance and distribution of MPs in beach sediments (12 beaches), marine biota (6 beaches) and the influence of microbes on MPs degradation in eco-sensitive Palk Bay and Gulf of Mannar coast. The mean MP abundance 65.4 ± 39.8 particles/m² in beach sediments; 0.19 ± 1.3 particles/individual fish and 0.22 ± 0.11 particles g^-1 wet weight in barnacles. Polyethylene fragments (33.4%) and fibres (48%) were the most abundant MPs identified in sediments and finfish, respectively. Histopathological examination of fish has revealed health consequences such as respiratory system damage, epithelial degradation and enterocyte vacuolization. In addition, eight bacterial and seventeen fungal strains were isolated from the beached MPs. The results also indicated weathering of MPs due to microbial interactions. Model simulations helped in tracking the fate and transboundary landfall of spilled MPs across the Indian Ocean coastline after the X-Press Pearl disaster. Due to regional circulations induced by the monsoonal wind fields, a potential dispersal of pellets has occurred along the coast of Sri Lanka, but no landfall and ecological damage are predicted along the coast of India.

A direct entry to polycyclic quinoxaline derivatives via I2-DMSO mediated oxidative decarboxylation of α-amino acids and the subsequent Pictet-Spengler cyclization reaction

A facile and highly efficient iodine-promoted strategy has been delineated for the synthesis of indolo and pyrrolo[1,2-a]quinoxaline derivatives via an oxidative Pictet-Spengler type amino cyclo-annulation reaction using ∝-amino acids as aldehyde surrogates. The concomitant benzylic oxidation and the compatibility of different starting materials under standard conditions made the current method versatile. The salient features of the protocol such as readily available starting materials, inexpensive promoters, environmental benignity, broad substrate scope, scalability, and good to excellent yield make the method more attractive to practitioners of organic synthesis.

A practical route to arylated dihydroacridine derivatives via nickel boride mediated intramolecular reductive cyclization-concomitant dehydration

A facile and highly efficient route towards 3-aryl-1,2-dihydroacridine derivatives from an aldol adduct of o-nitrobenzaldehyde and cyclohexenone derivatives has been described.

COVID-19 restrictions and their influences on ambient air, surface water and plastic waste in a coastal megacity, Chennai, India

Anthropogenic activities experienced a pause due to the nationwide lockdown, imposed to contain the rapid spread of COVID-19 in the third week of March 2020. The impacts of suspension of industrial activities, vehicular transport and other businesses for three months (25 March-30 June) on the environmental settings of Chennai, a coastal megacity was assessed. A significant reduction in the key urban air pollutants [PM_2.5 (66.5%), PM₁₀ (39.5%), NO₂ (94.1%), CO (29%), O₃ (45.3%)] was recorded as an immediate consequence of the reduced anthropogenic activities. Comparison of water quality of an urban river Adyar, between pre-lockdown and lockdown, showed a substantial drop in the dissolved inorganic N (47%) and suspended particulate matter (41%) during the latter period. During the pandemic, biomedical wastes in India showed an overall surge of 17%, which were predominantly plastic. FTIR-ATR analysis confirmed the polymers such as polypropylene (25.4%) and polyester (15.4%) in the personal protective equipment.

Single Amino-Acid Based Self-Assembled Biomaterials with Potent Antimicrobial Activity

The design and development of soft biomaterials based on amino acid and short-peptide have gained much attention due to their potent biomedical applications. A slight alteration in the side-chain of single amino acid in a peptide or protein sequence has a huge impact on the structure and function. Phenylalanine is one of the most studied amino acids, which contains an aromatic phenyl group connected through a flexible -CH₂ - unit. In this work, we have examined whether flexibility and aromatic functionality of phenylalanine (Phe) are important in gel formation of model gelator Fmoc-Phe-OH or not. To examine this hypothesis, we synthesized Fmoc-derivatives of three analogues unnatural amino acids including cyclohexylalanine, phenylglycine, and homophenylalanine; which are slightly varied from Phe. Interestingly, all these three new analogues formed hydrogels in phosphate buffer at pH 7.0 having different gelation efficacy and kinetics. This study suggests that the presence of aromatic side-chain and flexibility are not mandatory for the gelation of this model gelator. Newly synthesized unnatural amino acid derivatives have also exhibited promising antimicrobial activity towards gram-positive bacteria by inhibiting cellular oxygen consumption. We further determined the biocompatibility of these amino acid derivatives by using a hemolysis assay on human blood cells. Overall studies described the development of single amino acid-based new injectable biomaterials with improved antimicrobial activity by the slight alteration in the side-chain of amino acid.

Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19?

The dire need of effective preventive measures and treatment approaches against SARS-CoV-2 virus, causing COVID-19 pandemic, calls for an in-depth understanding of its evolutionary dynamics with attention to specific geographic locations, since lockdown and social distancing to prevent the virus spread could lead to distinct localized dynamics of virus evolution within and between countries owing to different environmental and host-specific selection pressures. To decipher any correlation between SARS-CoV-2 evolution and its epidemiology in India, we studied the mutational diversity of spike glycoprotein, the key player for the attachment, fusion and entry of virus to the host cell. For this, we analyzed the sequences of 630 Indian isolates as available in GISAID database till June 07, 2020 (during the time-period before the start of Unlock 1.0 in India on and from June 08, 2020), and detected the spike protein variants to emerge from two major ancestors – Wuhan-Hu-1/2019 and its D614G variant. Average stability of the docked spike protein – host receptor (S-R) complexes for these variants correlated strongly (R² = 0.96) with the fatality rates across Indian states. However, while more than half of the variants were found unique to India, 67% of all variants showed lower stability of S-R complex than the respective ancestral variants, indicating a possible fitness loss in recently emerged variants, despite a continuous increase in mutation rate. These results conform to the sharply declining fatality rate countrywide (>7-fold during April 11 – June 28, 2020). Altogether, while we propose the potential of S-R complex stability to track disease severity, we urge an immediate need to explore if SARS-CoV-2 is approaching mutational meltdown in India.

Holistic assessment of microplastics in various coastal environmental matrices, southwest coast of India

Plastics in the marine environment are introduced through multiple pathways, and pose serious threats to aquatic biota. Recently microplastic pollution and its possible consequences in India have been recognized by the scientific community, however the extent of the crisis has not yet been quantified. The present study attempted to ascertain the abundance, distribution and characteristics of microplastics in coastal waters (14 locations), beach sediments (22 locations) and marine fishes (11 locations) from the state of Kerala, southwest coast of India. The results showed that the mean microplastic abundance was 1.25 ± 0.88 particles/m³ in coastal waters and 40.7 ± 33.2 particles/m² in beach sediments with higher concentrations in the southern coast of the state. The abundance of microplastics, mostly contributed by fragments, fibre/line and foam, in both coastal waters and beach sediments, were highly influenced by river runoff and proximity to urban agglomeration. Fourier Transform Infrared Spectroscopy-Attenuated Total Reflection (FTIR-ATR) revealed that polyethylene (PE) and polypropylene (PP) were the dominant polymers in the marine environment. The digestive tracts of 15 out of 70 commercially important fishes studied, contained 22 microplastic particles. Polyethylene (PE; 38.46%) followed by cellulose (CE; 23.08%), rayon (RY; 15.38%), polyester (PL; 15.38%) and polypropylene (PP; 7.69%) were the major contributors in the fish ingested microplastic composition. A broad range of heavy metals, metalloids and other elements that are potentially indicative of hazardous chemicals were present in microplastics collected from the beaches of Kerala. These results enhance our understanding on the sources, transport pathways and the associated environmental risks of microplastics to marine ecosystems.

Microplastics along the beaches of southeast coast of India

Occurrence of microplastics (plastic debris <5 mm) along the coast is a growing concern worldwide, due to increased input of discarded wastes from various sources. In order to evaluate the extent of microplastic pollution on the sandy beaches (25 locations) along Tamil Nadu coast (1076 km), India, microplastic debris were quantified and categorized into four different size classes. The beaches were classified according to potential sources of pollution i.e. riverine, tourism and fisheries. Beach samples collected from the high tide line contained significantly higher abundance of microplastic than at the low tide line. Beaches adjacent to rivers exhibited relatively higher microplastic abundance compared to those influenced by tourism and fishing activities. Out of the total detected debris, plastic fragments were the maximum (47-50%), followed by line/fibres (24-27%) and foam (10-19%) materials. Fourier Transform Infrared Spectroscopy (FTIR) analysis revealed that polyethylene, polypropylene, and polystyrene were the main types of microplastics present in these beaches. Gut content analysis of commercially important fishes, collected from the coastal waters, revealed microplastics ingestion in 10.1% of fishes. The results indicate that microplastics accumulation in the coastal environment, especially close to the river mouths, may be a serious concern, due to its ability to enter into the marine food web and highlights the necessity of microplastics screening from estuarine, coastal waters and other potential sources.

Seagrass litter decomposition: an additional nutrient source to shallow coastal waters

Seagrass ecosystems are vital for its regulatory services yet, highly threatened by degradation due to human pressures. Decomposition of two tropical seagrass species (Cymodocea serrulata and Cymodocea rotundata) was studied and compared, to understand their potential in generating additional nutrients to coastal waters. Release of carbon, nitrogen and phosphorus during the decomposition process of seagrass wracks was estimated in bacteria-active (non-poisoned) and bacteria-inhibited (poisoned) conditions from shore-washed fresh seagrass, sampled from Palk Bay, India. Incubation experiments for 25 days indicated a near three times higher concentration of dissolved organic carbon (DOC) in bacteria-inhibited flasks compared to bacteria-active conditions for both species. The maximum leaching rates of DOC, TDN and TDP were found to be 294, 65.1 and 11.2 μM/g dry wt/day, respectively. Further, higher release of dissolved inorganic nitrogen (DIN) (> 1.3 times) was documented from the bacteria-active flask, highlighting the significance of microbial process in generating bio-available nutrients from decaying seagrass. Faster decomposition (0.014 ± 0.004 day^-1) in the initial stages (up to 8 days) compared to the later stages (0.005 ± 0.001 day^-1) indicated a rapid loss of biomass carbon during the initial leaching process and its relative importance in the decomposition pathway. The decomposition rate is best described by a single-stage exponential decay model with a half-life of 41 days. It is estimated that the total seagrass litter available along the Palk Bay coast is about ~ 0.3 Gg with high potential of additional nitrogen (0.9 ± 0.5 Mg) and phosphorus (0.3 ± 0.1 Mg) supply to the adjacent coastal waters.

C-terminal tail insertion of Bcl-xL in membrane occurs via partial unfolding and refolding cycle associating microsolvation

Insertion of the Bcl-x_L C-terminal into the mitochondrial outer membrane is found to be guided by the partial unfolding–refolding cycle, assisted by micro-solvation.

Conformational Flexibility and pH Effects on Anisotropic Growth of Sheet-Like Assembly of Amphiphilic Peptides

Peptide-based biomaterials have many potential applications in tissue engineering, drug delivery, surface engineering, and other areas. In this study, we exploited a series of amphiphilic diblock model peptides (L5K10, L5GSIIK10, and L5P(D)PK10) to understand how the supramolecular assembly morphology may be modulated by the physical properties of the peptide monomer and experimental conditions. A combination of experimentation and simulation revealed that although all three peptides lack stable structures as monomers, their levels of conformational heterogeneity differ significantly. Importantly, such differences appear to be correlated with the peptides' ability to form sheet-like assemblies. In particular, substantial conformational heterogeneity appears to be required for anisotropic growth of sheet-like materials, likely by reducing the peptide assembly kinetics. To test this hypothesis, we increased the pH to neutralize the lysine residues and promote peptide aggregation, and the resulting faster assembly rate hindered the growth of the sheet morphology as predicted. In addition, we designed and investigated the assembly morphologies of a series of diblock peptides with various lengths of polyglycine inserts, L5GxK10, x = 1, 2, 3, 4. The results further supported the importance of peptide conformational flexibility and pH in modulation of the peptide supramolecular assembly morphology.

Modulation of the disordered conformational ensembles of the p53 transactivation domain by cancer-associated mutations

Intrinsically disordered proteins (IDPs) are frequently associated with human diseases such as cancers, and about one-fourth of disease-associated missense mutations have been mapped into predicted disordered regions. Understanding how these mutations affect the structure-function relationship of IDPs is a formidable task that requires detailed characterization of the disordered conformational ensembles. Implicit solvent coupled with enhanced sampling has been proposed to provide a balance between accuracy and efficiency necessary for systematic and comparative assessments of the effects of mutations as well as post-translational modifications on IDP structure and interaction. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in implicit solvent. The simulations are critically assessed by quantitative comparisons with several types of experimental data that provide structural information on both secondary and tertiary levels. The results show that the calculated ensembles reproduce local structural features of wild-type p53-TAD and the effects of K24N mutation quantitatively. On the tertiary level, the simulated ensembles are overly compact, even though they appear to recapitulate the overall features of transient long-range contacts qualitatively. A key finding is that, while p53-TAD and its cancer mutants sample a similar set of conformational states, cancer mutants could introduce both local and long-range structural modulations to potentially perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The current study clearly demonstrates the promise of atomistic simulations for detailed characterization of IDP conformations, and at the same time reveals important limitations in the current implicit solvent protein force field that must be sufficiently addressed for reliable description of long-range structural features of the disordered ensembles.

Tumor suppressor p53 is the most frequently mutated protein in human cancers. Clinical studies have suggested that the type of p53 mutation can be linked to cancer prognosis, response to drug treatment, and patient survival. It is thus crucial to understand the molecular basis of p53 inactivation by various types of mutations, so as to understand the biological outcomes and assess potential cancer intervention strategies. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in an implicit solvent protein force field. The calculated ensembles are in quantitative agreement with several types of existing NMR data on the wild-type protein and the K24N mutant. The results suggest that, while all sequences sample a similar set of conformational substates, cancer mutants could introduce both local and long-range structural modulations and in turn perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The study also reveals important limitations in implicit solvent for simulations of disordered proteins like p53-TAD.

Electrostatically accelerated encounter and folding for facile recognition of intrinsically disordered proteins

Achieving facile specific recognition is essential for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regulation. Consideration of the physical time scales of protein folding and diffusion-limited protein-protein encounter has suggested that the frequent requirement of protein folding for specific IDP recognition could lead to kinetic bottlenecks. How IDPs overcome such potential kinetic bottlenecks to viably function in signaling and regulation in general is poorly understood. Our recent computational and experimental study of cell-cycle regulator p27 (Ganguly et al., J. Mol. Biol. (2012)) demonstrated that long-range electrostatic forces exerted on enriched charges of IDPs could accelerate protein-protein encounter via "electrostatic steering" and at the same time promote "folding-competent" encounter topologies to enhance the efficiency of IDP folding upon encounter. Here, we further investigated the coupled binding and folding mechanisms and the roles of electrostatic forces in the formation of three IDP complexes with more complex folded topologies. The surface electrostatic potentials of these complexes lack prominent features like those observed for the p27/Cdk2/cyclin A complex to directly suggest the ability of electrostatic forces to facilitate folding upon encounter. Nonetheless, similar electrostatically accelerated encounter and folding mechanisms were consistently predicted for all three complexes using topology-based coarse-grained simulations. Together with our previous analysis of charge distributions in known IDP complexes, our results support a prevalent role of electrostatic interactions in promoting efficient coupled binding and folding for facile specific recognition. These results also suggest that there is likely a co-evolution of IDP folded topology, charge characteristics, and coupled binding and folding mechanisms, driven at least partially by the need to achieve fast association kinetics for cellular signaling and regulation.

Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) are now recognized to be prevalent in biology, and many potential functional benefits have been discussed. However, the frequent requirement of peptide folding in specific interactions of IDPs could impose a kinetic bottleneck, which could be overcome only by efficient folding upon encounter. Intriguingly, existing kinetic data suggest that specific binding of IDPs is generally no slower than that of globular proteins. Here, we exploited the cell cycle regulator p27(Kip1) (p27) as a model system to understand how IDPs might achieve efficient folding upon encounter for facile recognition. Combining experiments and coarse-grained modeling, we demonstrate that long-range electrostatic interactions between enriched charges on p27 and near its binding site on cyclin A not only enhance the encounter rate (i.e., electrostatic steering) but also promote folding-competent topologies in the encounter complexes, allowing rapid subsequent formation of short-range native interactions en route to the specific complex. In contrast, nonspecific hydrophobic interactions, while hardly affecting the encounter rate, can significantly reduce the efficiency of folding upon encounter and lead to slower binding kinetics. Further analysis of charge distributions in a set of known IDP complexes reveals that, although IDP binding sites tend to be more hydrophobic compared to the rest of the target surface, their vicinities are frequently enriched with charges to complement those on IDPs. This observation suggests that electrostatically accelerated encounter and induced folding might represent a prevalent mechanism for promoting facile IDP recognition.

Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins

To understand the interplay of residual structures and conformational fluctuations in the interaction of intrinsically disordered proteins (IDPs), we first combined implicit solvent and replica exchange sampling to calculate atomistic disordered ensembles of the nuclear co-activator binding domain (NCBD) of transcription coactivator CBP and the activation domain of the p160 steroid receptor coactivator ACTR. The calculated ensembles are in quantitative agreement with NMR-derived residue helicity and recapitulate the experimental observation that, while free ACTR largely lacks residual secondary structures, free NCBD is a molten globule with a helical content similar to that in the folded complex. Detailed conformational analysis reveals that free NCBD has an inherent ability to substantially sample all the helix configurations that have been previously observed either unbound or in complexes. Intriguingly, further high-temperature unbinding and unfolding simulations in implicit and explicit solvents emphasize the importance of conformational fluctuations in synergistic folding of NCBD with ACTR. A balance between preformed elements and conformational fluctuations appears necessary to allow NCBD to interact with different targets and fold into alternative conformations. Together with previous topology-based modeling and existing experimental data, the current simulations strongly support an “extended conformational selection” synergistic folding mechanism that involves a key intermediate state stabilized by interaction between the C-terminal helices of NCBD and ACTR. In addition, the atomistic simulations reveal the role of long-range as well as short-range electrostatic interactions in cooperating with readily fluctuating residual structures, which might enhance the encounter rate and promote efficient folding upon encounter for facile binding and folding interactions of IDPs. Thus, the current study not only provides a consistent mechanistic understanding of the NCBD/ACTR interaction, but also helps establish a multi-scale molecular modeling framework for understanding the structure, interaction, and regulation of IDPs in general.

Intrinsically disordered proteins (IDPs) are now widely recognized to play fundamental roles in biology and to be frequently associated with human diseases. Although the potential advantages of intrinsic disorder in cellular signaling and regulation have been widely discussed, the physical basis for these proposed phenomena remains sketchy at best. An integration of multi-scale molecular modeling and experimental characterization is necessary to uncover the molecular principles that govern the structure, interaction, and regulation of IDPs. In this work, we characterize the conformational properties of two IDPs involved in transcription regulation at the atomistic level and further examine the roles of these properties in their coupled binding and folding interactions. Our simulations suggest interplay among residual structures, conformational fluctuations, and electrostatic interactions that allows efficient synergistic folding of these two IDPs. In particular, we propose that electrostatic interactions might play an important role in facilitating rapid folding and binding recognition of IDPs, by enhancing the encounter rate and promoting efficient folding upon encounter.

Pulmonary Hydatid : Diagnosis and Response to Hypertonic Saline Irrigation and Albendazole

BACKGROUND

Pulmonary hydatid is caused by larval stage of parasite Echinococcus granulosus. Although surgery still remains the definitive therapy, various workers have tried albendazole and sterilization of cysts with varying result.

METHODS

32 patients(21 males, 11 females) of pulmonary hydatid disease with average age 32.5 years(21-51 years) treated by us between Jan 97 to Apr 2001 were analysed. Diagnosis was established clinically, radiologically and by serological testing. 16 patients who had simple cyst were treated with 20 ml percutaneous hypertonic(20%) saline irrigation of the cyst along with albendazole (400 mg twice a day, 6 cycles of 4 weeks with 2 weeks drug free period between the cycles). 13 patients of complicated cysts were treated with 6 cycles of albendazole. All cases were followed up for one year. 16 patients including three fresh cases were subjected to surgical resection.

RESULTS

Pleural involvement was noted in 10 patients. On chest radiography 19 patients had homogenous oval or circular cysts, 6 patients had crescent sign and 10 had water lily sign. After percutaneous hypertonic saline irrigation all patients showed initial regression in size and developed complicated cysts with water lily sign but subsequently there was no regression. Of 13 patients treated with albendazole, 3 patients showed complete resolution and 2 patients showed regression of cyst. All these 5 patients had shown regression during first cycle of albendazole. 16 patients were subjected to surgery (6 after saline irrigation, 7 after albendazole course and 3 fresh cases). No difference was noted in these groups on histopathological examination.

CONCLUSION

From this study it was evident that those patients who demonstrate regression in size during first cycle of albendazole are likely to benefit and improve with further cycles of it. Those who do not respond should be subjected to surgery. Result of percutaneous hypertonicsaline irrigation as scolicidal was not encouraging.

Synergistic folding of two intrinsically disordered proteins: searching for conformational selection

Intrinsically disordered proteins (IDPs) lack stable structures under physiological conditions but often fold into stable structures upon specific binding. These coupled binding and folding processes underlie the organization of cellular regulatory networks, and a mechanistic understanding is thus of fundamental importance. Here, we investigated the synergistic folding of two IDPs, namely, the NCBD domain of transcription coactivator CBP and the p160 steroid receptor coactivator ACTR, using a topology-based model that was carefully calibrated to balance intrinsic folding propensities and intermolecular interactions. As one of the most structured IDPs, NCBD is a plausible candidate that interacts through conformational selection-like mechanisms, where binding is mainly initiated by pre-existing folded-like conformations. Indeed, the simulations demonstrate that, even though binding and folding of both NCBD and ACTR is highly cooperative on the baseline level, the tertiary folding of NCBD is best described by the "extended conformational selection" model that involves multiple stages of selection and induced folding. The simulations further predict that the NCBD/ACTR recognition is mainly initiated by forming a mini folded core that includes the second and third helices of NCBD and ACTR. These predictions are fully consistent with independent physics-based atomistic simulations as well as a recent experimental mapping of the H/D exchange protection factors. The current work thus adds to the limited number of existing mechanistic studies of coupled binding and folding of IDPs, and provides a first direct demonstration of how conformational selection might contribute to efficient recognition of IDPs. Interestingly, even for highly structured IDPs like NCBD, the recognition is initiated by the more disordered C-terminal segment and with substantial contribution from induced folding. Together with existing studies of IDP interaction mechanisms, this argues that induced folding is likely prevalent in IDP-protein interaction, and emphasizes the importance of understanding how IDPs manage to fold efficiently upon (nonspecific) binding. Success of the current study also further supports the notion that, with careful calibration, topology-based models can be effective tools for mechanistic study of IDP interaction and regulation, especially when combined with physics-based atomistic simulations and experiments.

Intrinsically disordered proteins in a physics-based world

Intrinsically disordered proteins (IDPs) are a newly recognized class of functional proteins that rely on a lack of stable structure for function. They are highly prevalent in biology, play fundamental roles, and are extensively involved in human diseases. For signaling and regulation, IDPs often fold into stable structures upon binding to specific targets. The mechanisms of these coupled binding and folding processes are of significant importance because they underlie the organization of regulatory networks that dictate various aspects of cellular decision-making. This review first discusses the challenge in detailed experimental characterization of these heterogeneous and dynamics proteins and the unique and exciting opportunity for physics-based modeling to make crucial contributions, and then summarizes key lessons from recent de novo simulations of the structure and interactions of several regulatory IDPs.

Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding

Intrinsically disordered proteins (IDPs) are a newly recognized class of functional proteins for which a lack of stable tertiary fold is required for function. Because of the heterogeneous and dynamical nature, molecular modeling is necessary to provide the missing details of disordered states of IDP that are crucial for understanding their functions. In particular, generalized Born (GB) implicit solvent, combined with replica exchange (REX), might offer an optimal balance between accuracy and efficiency for modeling IDPs. We carried out extensive REX simulations in an optimized GB force field to characterize the disordered states of a regulatory IDP, KID domain of transcription factor CREB, and its phosphorylated form, pKID. The results revealed that both KID and pKID, though highly disordered on the tertiary level, are compact and mainly occupy a small number of helical substates. Interestingly, although phosphorylation of KID Ser133 leads only to marginal changes in average helicities on the ensemble level, underlying conformational substates differ significantly. In particular, pSer133 appears to restrict the accessible conformational space of the loop region and thus reduces the entropic cost of KID folding upon binding to the KIX domain of CREB-binding protein. Such an expanded role of phosphorylation in the KID:KIX recognition was not previously recognized because of a lack of substantial conformational changes on the ensemble level and inaccessibility of the structural details from experiments. The results also suggest that an implicit solvent-based modeling framework, despite various existing limitations, might be feasible for accurate atomistic simulation of small IDPs in general.

Structural interpretation of paramagnetic relaxation enhancement-derived distances for disordered protein states

Paramagnetic relaxation enhancement (PRE) is a powerful technique for studying transient tertiary organizations of unfolded and partially folded proteins. The heterogeneous and dynamic nature of disordered protein states, together with the r(-6) dependence of PRE, presents significant challenges for reliable structural interpretation of PRE-derived distances. Without additional knowledge of accessible conformational substates, ensemble-simulation-based protocols have been used to calculate structure ensembles that appear to be consistent with the PRE distance restraints imposed on the ensemble level with the proper r(-6) weighting. However, rigorous assessment of the reliability of such protocols has been difficult without intimate knowledge of the true nature of disordered protein states. Here we utilize sets of theoretical PRE distances derived from simulated structure ensembles that represent the folded, partially folded and unfolded states of a small protein to investigate the efficacy of ensemble-simulation-based structural interpretation of PRE distances. The results confirm a critical limitation that, due to r(-6) weighting, only one or a few members need to satisfy the distance restraints and the rest of the ensemble are essentially unrestrained. Consequently, calculated structure ensembles will appear artificially heterogeneous no matter whether the PRE distances are derived from the folded, partially unfolded or unfolded state. Furthermore, the nature of the heterogeneous ensembles is largely determined by the protein model employed in structure calculation and reflects little on the true nature of the underlying disordered state. These findings suggest that PRE measurements on disordered protein states alone generally do not contain enough information for a reliable structural interpretation and that the latter will require additional knowledge of accessible conformational substates. Interestingly, when a very large number of PRE measurements is available, faithful structural interpretation might be possible with intermediate ensemble sizes under ideal conditions.

Biogeochemical controls of arsenic occurrence and mobility in the Indian Sundarban mangrove ecosystem

This study aims to investigate the control of arsenic distribution by biogeochemical processes in the Indian Sundarban mangrove ecosystem and the importance of this ecosystem as an arsenic source for surrounding coastal water. The As(V)/As(III) ratio was found to be significantly lower in both surface and pore waters compared to sea water, which could be attributed to biogeochemical interconversion of these arsenic forms. The biological uptake of arsenic due to primary and benthic production occurs during the post-monsoon season, and is followed by the release of arsenic during the biochemical degradation and dissolution of plankton in the pre-monsoon season. These results suggest that arsenic is immobilized during incorporation into the arsenic-bearing initial phase, and unlikely to be released into pore water until the complete microbial degradation of arsenic-bearing organic compounds.

Steered unfolding of ricin A and B chains

Highly toxic, heterodimeric protein ricin binds itself to the cell surface glycolipids or glycoproteins via its B-chain. The toxic A-chain halts protein synthesis by inactivating the ribosomes, leading to cell death. The translocation step requires partial unfolding of the protein. In this work mechanical unfolding of intact ricin as well as the individual A- and B-chains has been studied. A total of 110 ns simulation run has been performed to observe the unfolding of ricin dimer using steered molecular dynamics simulation. A gradual unfolding against a constant pulling velocity is observed for the ricin A-chain leaving the B-chain in its native-like structure. The breakage of the disulfide linkage connecting the two chains and reversal of the pulling ends of B-chain surprisingly reversed the picture as the B-chain starts to unfold from its N-terminal end. Due to the unfolding of B-chain from N-terminal end, the A-chain appears structurally rigid, which comes from the strong interfacial interactions (hydrophobic, hydrogen bonding, salt bridge). Mechanical unfolding of the individual monomers has also been performed to compare their stabilities in the monomeric and dimeric forms.

Extended binding site of ricin B lectin for oligosaccharide recognition

The plant lectin ricin B chain binds oligosaccharide with more affinity than the mono- or disaccharide ligands. The experiments indicated that a biantennary oligosaccharide could bind itself to any of the crystallographically established 1st or 2nd binding sites. After manual docking of either terminal galactose residues of the oligosaccharide in the 1st and 2nd binding sites of Ricin B and simulating the systems over nanosecond trajectories in implicit solvent, it was observed that the protein bound the oligosaccharide strongly through both its 1st and 2nd binding sites. Not only were the terminal galactose residues, several other residues of the oligosaccharide were involved in the binding scheme. Average gas phase energies were calculated molecular mechanically, solvation energies were calculated by Generalized Born model and the normal mode analysis was used to calculate the entropic contribution of binding. The entropy/enthalpy compensation has been observed for the protein-oligosaccharide interactions. The binding was found to be enthalpically favorable and compensating for the unfavorable entropic contribution. Comparison of the calculated free energy with the experimental data clearly suggests that binding is mono-dentate rather than bi-dentate through a single Gal-containing antenna.

Binding diversity of the two binding sites of ricin B lectin

Ricin B is a galactose-binding protein, which contains two binding sites. We have compared the binding properties of the two binding sites of ricin B chain toward different mono- and disaccharide ligands. The free energies of binding are calculated using the free energy perturbation simulation (thermodynamic integration method) and linear interaction energy approach using CHARMM force field. The second binding site of the protein was found to be weaker compared to the first. The details of the hydrogen-bonding scheme suggested the origin of the epimeric specificity of the protein. The reason for the weaker binding capacity of the second binding site has been addressed.

Smoking and tuberculosis: the epidemiological association and immunopathogenesis

There is increasing evidence of a link between tuberculosis and smoking. This paper reviews the epidemiological evidence from the UK, China, India and the USA, summarizing some of the main papers which indicate an association. Where an association has been found there seems to be an increase in tuberculosis case rates of between two- and four-fold for those smoking in excess of 20 cigarettes a day, but it may be difficult to control for other factors, particularly alcohol consumption. The final part of the paper reviews possible mechanisms. A likely possibility is that nicotine turns off the production of TNF-alpha by the macrophages in the lungs, rendering the patient more susceptible to the development of progressive disease from latent Mycobacterium tuberculosis infection.

Mediastinal cavernous haemangioma

A 44-year-old man presented with palpable right supraclavicular swelling having no symptoms pertaining to respiratory tract. A routine chest radiograph showed an anterior mediastinal mass. Computerised tomographic scan (CT-scan) of chest showed an enhancing and homogeneous mass in anterior mediastinal space with few tiny calcific specks within the mass. Biopsy of cervical swelling showed cavernous haemangioma with chronic non-specific lymphadenitis. A sternotomy was undertaken and an encapsulated 9x7.5x5 cm, dark purplish mass was seen in anteior mediastinum adherent to pericardium and right pleura. The cut-surface was elastic and soft. Histology confirmed cavernous haemangioma. Post-operative course was uneventful. Mediastinal cavernous haemangioma is extremely rare and surgical excision is the treatment of choice.

Synthetic studies on nogarol anthracyclines. Enantioselective total synthesis of an aminohydroxy epoxybenzoxocin

A chiral synthesis of the aminohydroxy expoxybenzoxocin 6 is described. Enantioselective Friedel-Crafts coupling using a chiral titanium catalyst was employed to produce the optically active atrolactic ester 16a from the phenol 11 and l-menthyl pyruvate (12). The phenolic group in 16a was protected as the benzyl ether and the t-alcohol functionality as the MEM ether to give 20, which after sequential reduction/oxidation provided the aldehyde 22. Addition of the acetylide anion of propargyl aldehyde diethyl acetal (23) to aldehyde 22, followed by oxidation of the resultant diastereoisomeric carbinols, gave the acetylenic ketone 24. Lindlar reduction of 24 afforded the trans-enone 26. Reaction of 26 with thiophenylate anion furnished 27, which was then cyclized to the alpha-methyl pyranoside 29. Oxidation of 29 to the sulfoxide and subsequent thermolysis afforded the hexenulose 30. Sequential epoxidation of 30, reduction of the keto epoxide 31, and reaction of the resultant epoxycarbinol 32 with dimethylamine produced the aminohydroxy pyranose 33a. Debenzylation of 33a to the phenol 33b, followed by intramolecular cyclization, completed the fabrication of the optically active aminohydroxy epoxybenzoxocin 6. The 17-step sequence from the phenol 11 to 6 was achieved in 22% overall yield.

Paediatric adrenocortical neoplasia - a study of 25 cases

We reviewed our experience of 25 children with adrenocortical tumours from January 1980 to December 1994. Their ages ranged from 7 months to 15 years; there were 16 girls and 9 boys. Truncal obesity, moon facies, hypertension, and virilisation were the most common clinical features. Establishment of the diagnosis of Cushing's syndrome was accomplished by hormonal and radiological studies. Eighteen patients had adrenocortical carcinomas, but 2 of them refused operation; 7 had adrenocortical adenomas. Twenty-three patients were treated by surgery; 6 with carcinomas are still alive after periods of 6 months to 3 years. The results of treatment of adrenocortical carcinoma have been poor, but the prognosis is excellent for benign lesions.

INTRACARDIAC TUMOURS - EXPERIENCE WITH 12 CASES

Twelve cases of intracardiac tumours operated during the period 1975 to 1994 are presented. There were 8 males and 4 females in the age range of 18 years to 64 years. Tumours were located in the left atrium in 10 patients and in the right atrium in 2 patients. Standard cardiopulmonary techniques were followed. The right atrial tumours were approached through a right atrial incision while the left atrial tumours were approached through a bi-atrial trans-septal approach. One patient underwent a perineal urethrolithotomy for an impacted urethral calculus at the same sitting. Eleven of the tumour masses excised were myxomas confirmed on histopathology. The last patient, operated for synovial sarcoma of the left knee 2 years before, presented with a metastatic tumour mass in the left atrium. No deaths occurred in the series.