Fast random opposition-based learning Aquila optimization algorithm

Meta-heuristic algorithms are usually employed to address a variety of challenging optimization problems. In recent years, there has been a continuous effort to develop new and efficient meta-heuristic algorithms. The Aquila Optimization (AO) algorithm is a newly established swarm-based method that mimics the hunting strategy of Aquila birds in nature. However, in complex optimization problems, the AO has shown a sluggish convergence rate and gets stuck in the local optimal region throughout the optimization process. To overcome this problem, in this study, a new mechanism named Fast Random Opposition-Based Learning (FROBL) is combined with the AO algorithm to improve the optimization process. The proposed approach is called the FROBLAO algorithm. To validate the performance of the FROBLAO algorithm, the CEC 2005, CEC 2019, and CEC 2020 test functions, along with six real-life engineering optimization problems, are tested. Moreover, statistical analyses such as the Wilcoxon rank-sum test, the t-test, and the Friedman test are performed to analyze the significant difference between the proposed algorithm FROBLAO and other algorithms. The results demonstrate that FROBLAO achieved outstanding performance and effectiveness in solving an extensive variety of optimization problems.

IMPETUS Stroke: Assessment of hospital infrastructure and workflow for implementation of uniform stroke care pathway in India

BACKGROUND

India accounts for 13.3% of global disability-adjusted life years (DALYs) lost due to stroke with a relatively younger age of onset compared to the Western population. In India's public healthcare system, many stroke patients seek care at tertiary-level government-funded medical colleges where an optimal level of stroke care is expected. However, there are no studies from India that have assessed the quality of stroke care, including infrastructure, imaging facilities, or the availability of stroke care units in medical colleges.

AIM

This study aimed to understand the existing protocols and management of acute stroke care across 22 medical colleges in India, as part of the baseline assessment of the ongoing IMPETUS stroke study.

METHODS

A semi-structured quantitative pre-tested questionnaire, developed based on review of literature and expert discussion, was mailed to 22 participating sites of the IMPETUS stroke study. The questionnaire assessed comprehensively all components of stroke care, including human resources, emergency system, in-hospital care, and secondary prevention. A descriptive analysis of their status was undertaken.

RESULTS

In the emergency services, limited stroke helpline numbers, 3/22 (14%); prenotification system, 5/22 (23%); and stroke-trained physicians were available, 6/22 (27%). One-third of hospitals did not have on-call neurologists. Although non-contrast computed tomography (NCCT) was always available, 39% of hospitals were not doing computed tomography (CT) angiography and 13/22 (59%) were not doing magnetic resonance imaging (MRI) after routine working hours. Intravenous thrombolysis was being done in 20/22 (91%) hospitals, but 36% of hospitals did not provide it free of cost. Endovascular therapy was available only in 6/22 (27%) hospitals. The study highlighted the scarcity of multidisciplinary stroke teams, 8/22 (36%), and stroke units, 7/22 (32%). Lifesaving surgeries like hematoma evacuation, 11/22 (50%), and decompressive craniectomy, 9/22 (41%), were performed in limited numbers. The availability of occupational therapists, speech therapists, and cognitive rehabilitation was minimal.

CONCLUSION

This study highlighted the current status of acute stroke management in publicly funded tertiary care hospitals. Lack of prenotification, limited number of stroke-trained physicians and neurosurgeons, relatively lesser provision of free thrombolytic agents, limited stroke units, and lack of rehabilitation services are areas needing urgent attention by policymakers and creation of sustainable education models for uniform stroke care by medical professionals across the country.

Molecular dynamics simulations for the study of chromatin biology

The organization of Eukaryotic DNA into chromatin has profound implications for the processing of genetic information. In the past years, molecular dynamics (MD) simulations proved to be a powerful tool to investigate the mechanistic basis of chromatin biology. We review recent all-atom and coarse-grained MD studies revealing how the structure and dynamics of chromatin underlie its biological functions. We describe the latest method developments; the structural fluctuations of nucleosomes and the various factors affecting them; the organization of chromatin fibers, with particular emphasis on its liquid-like character; the interactions and dynamics of transcription factors on chromatin; and how chromatin organization is modulated by molecular motors acting on DNA.

Structural-Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble

The functioning of proteins is intimately tied to their fluctuations in the native ensemble. The structural-energetic features that determine fluctuation amplitudes and hence the shape of the underlying landscape, which in turn determine the magnitude of the functional output, are often confounded by multiple variables. Here, we employ the FF1 domain from human p190A RhoGAP protein as a model system to uncover the molecular basis for phosphorylation of a buried tyrosine, which is crucial to the transcriptional activity associated with transcription factor TFII-I. Combining spectroscopy, calorimetry, statistical-mechanical modeling, molecular simulations, and in vitro phosphorylation assays, we show that the FF1 domain samples a diverse array of conformations in its native ensemble, some of which are phosphorylation-competent. Upon eliminating unfavorable charge-charge interactions through a single charge-reversal (K53E) or charge-neutralizing (K53Q) mutation, we observe proportionately lower phosphorylation extents due to the altered structural coupling, damped equilibrium fluctuations, and a more compact native ensemble. We thus establish a conformational selection mechanism for phosphorylation in the FF1 domain with K53 acting as a "gatekeeper", modulating the solvent exposure of the buried tyrosine. Our work demonstrates the role of unfavorable charge-charge interactions in governing functional events through the modulation of native ensemble characteristics, a feature that could be prevalent in ordered protein domains.

Folding Intermediates, Heterogeneous Native Ensembles and Protein Function

Single domain proteins fold via diverse mechanisms emphasizing the intricate relationship between energetics and structure, which is a direct consequence of functional constraints and demands imposed at the level of sequence. On the other hand, elucidating the interplay between folding mechanisms and function is challenging in large proteins, given the inherent shortcomings in identifying metastable states experimentally and the sampling limitations associated with computational methods. Here, we show that free energy profiles and surfaces of large systems (>150 residues), as predicted by a statistical mechanical model, display a wide array of folding mechanisms with ubiquitous folding intermediates and heterogeneous native ensembles. Importantly, residues around the ligand binding or enzyme active site display a larger tendency to partially unfold and this manifests as intermediates or excited states along the folding coordinate in ligand binding domains, transcription repressors, and representative enzymes from all the six classes, including the SARS-CoV-2 receptor binding domain (RBD) of the spike protein and the protease M^pro. It thus appears that it is relatively easier to distill the imprints of function on the folding landscape of larger proteins as opposed to smaller systems. We discuss how an understanding of energetic-entropic features in ordered proteins can pinpoint specific avenues through which folding mechanisms, populations of partially structured states and function can be engineered.

Tetracyanonickelate (II)/KOH/reduced graphene oxide fabricated carbon felt for mediated electron transfer type electrochemical sensor for efficient detection of N2O gas at room temperature

N₂O is the most significant anthropogenic greenhouse gas, which cause the ozone depletion. Hence, the room temperature detection of N₂O is highly desirable. In this work, The TCN(II)-KOH-rGO/CF modified electrode was successfully fabricated by drop coating method. The synthesized electrode was successfully characterized by SEM, TEM, FT-IR and XRD. The sensor electrode was used to detect different N₂O concentration in flow conditions at room temperature. TCN(II)-KOH-rGO/CF modified electrode showed high sensitivity towards N₂O, a wide range from 1ppm to 16 ppm and low detection of 1 ppm N₂O were achieved for the TCN(II)-KOH-rGO/CF modified electrode. The limit of detection and the response towards this nitrogen oxide is competitive to other sensing methods. In addition, the sensitivity of the electrochemical sensor electrode was compared with the online Gas Chromatography. Additionally, the selectivity of the working electrode was analyzed and specified. The working electrode stability was analyzed for more than 30 days shows good stability. The fabricated TCN(II)-KOH-rGO/CF electrode is easier to prepare to get excellent analytical performance towards N₂O. Hence, the proposed TCN(II)-KOH-rGO/CF electrode could be the suitable material for detection of N₂O in the real site process.

Tumescent Local Anesthesia in Parotid Abscess - Novel Application of Old Technique

Tumescent local anesthesia (TLA) is a regional anesthetic technique in which the diluted local anesthetic drug (commonly lidocaine) and epinephrine solution in large volume is injected subcutaneously around the site of incision. The main advantages of TLA are excellent bloodless field and longer duration of analgesia because of addition of epinephrine. Although TLA was used in various surgical procedures, there is no literature to date that has reported its use in the parotid region. Hence, we present an interesting case where this old technique found a novel application in avoiding general anesthesia and its sequelae. We also believe that it provides valuable information to doctors of various categories such as surgeons, Anesthesiologists and general practitioners/family physicians.

Dynamic association of the H3K64 trimethylation mark with genes encoding exported proteins in Plasmodium falciparum

Epigenetic modifications have emerged as critical regulators of virulence genes and stage-specific gene expression in Plasmodium falciparum. However, the specific roles of histone core epigenetic modifications in regulating the stage-specific gene expression are not well understood. In this study, we report an unconventional trimethylation at lysine 64 on histone 3 (H3K64me3) and characterize its functional relevance in P. falciparum. We show that PfSET4 and PfSET5 proteins of P. falciparum methylate H3K64 and that they prefer the nucleosome as a substrate over free histone 3 proteins. Structural analysis of PfSET5 revealed that it interacts with the nucleosome as a dimer. The H3K64me3 mark is dynamic, being enriched in the ring and trophozoite stages and drastically reduced in the schizont stages. Stage-specific global chromatin immunoprecipitation –sequencing analysis of the H3K64me3 mark revealed the selective enrichment of this methyl mark on the genes of exported family proteins in the ring and trophozoite stages and a significant reduction of the same in the schizont stages. Collectively, our data identify a novel epigenetic mark that is associated with the subset of genes encoding for exported proteins, which may regulate their expression in different stages of P. falciparum.

Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains

Native states of folded proteins are characterized by a large ensemble of conformations whose relative populations and interconversion dynamics determine the functional output. This is more apparent in transcription factors that have evolved to be inherently sensitive to small perturbations, thus fine-tuning gene expression. To explore the extent to which such functional features are imprinted on the folding landscape of transcription factor ligand-binding domains (LBDs), we characterize paralogous LBDs of the nuclear receptor (NR) family employing an energetically detailed and ensemble-based Ising-like statistical mechanical model. We find that the native ensembles of the LBDs from glucocorticoid receptor, PPAγ, and thyroid hormone receptor display a remarkable diversity in the width of the native wells, the number and nature of partially structured states, and hence the degree of conformational order. Monte Carlo simulations employing the full state representation of the ensemble highlight that many of the functional conformations coexist in equilibrium, whose relative populations are sensitive to both temperature and the strength of ligand binding. Allosteric modulation of the degree of structure at a coregulator binding site on ligand binding is shown to arise via a redistribution of populations in the native ensembles of glucocorticoid and PPAγ LBDs. Our results illustrate how functional requirements can drive the evolution of conformationally diverse native ensembles in paralogs.

Surface-tuned hierarchical ɤ-Fe2O3-N-rGO nanohydrogel for efficient catalytic removal and electrochemical sensing of toxic nitro compounds

4- Nitrophenol (4-NP) is a top rated hazardous environmental pollutant and secondary explosive chemicals. For the sake of ecology and environment safety, the catalytic reduction and detection of 4-NP is highly important. In this work, ɤ-Fe₂O₃-nitrogen doped rGO (ɤ-Fe₂O₃-N-rGO) nanohydrogel was synthesized by green hydrothermal method. The morphology and phase purity of prepared ɤ-Fe₂O₃-N-rGO nanohydrogel were confirmed by various analytical (SEM, TEM, XRD, and XPS) and electrochemical techniques. The morphological structure of ɤ-Fe₂O₃-N-rGO nanohydrogel confirmed that the nanocrystals are well covered over the 2D N-rGO layer. Further, ɤ-Fe₂O₃-N-rGO nanohydrogel was applied for the catalytic reduction and electrochemical detection of ecotoxic 4-NP. A low cost, ɤ-Fe₂O₃-N-rGO nanohydrogel displayed an excellent catalytic activity, high recyclability (>5 cycles) and high conversion efficiency of 4-NP to 4-Aminophenol (4-AP). In addition, ɤ-Fe₂O₃-N-rGO nanohydrogel modified GCE displayed a wide linear sensing range (0.1-1000 μM), and a low detection limit (LOD) of 0.1 μM with excellent sensitivity, high selectivity (<1.2%) and good stability (>4 weeks). The developed sensor electrode shows the low reduction potential of -0.3 V and -0.60 V for the determination of 4-NP. The proposed ɤ-Fe₂O₃-N-rGO nanohydrogel is promising catalyst for the detection and removal of toxic aromatic nitro compounds in real site applications.

A facile synthesis of metal ferrites and their catalytic removal of toxic nitro-organic pollutants

Nitrocompounds are the major prime water contaminants. In this investigative study, toxic nitrocompounds (4-nitrophenol, 2,4-dinitrophenol, 2,4,6-trinitrophenol) were removed by using magnetic CuFe₂O₄, CoFe₂O₄, and NiFe₂O₄ material systems. The metal ferrites were synthesized through hydrothermal method and also followed with calcination process. The properties of metal ferrites were confirmed through using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and field emission scanning electron microscopy (FE-SEM) studies and results there on were presented. For the first time, the synthesized CuFe₂O₄, CoFe₂O₄, and NiFe₂O₄ material systems were used for the reduction of 4-nitrophenol (NP), 2,4-dinitrophenol (DNP), and 2,4,6-trinitrophenol (TNP) in aqueous medium. The UV-visible spectrometry was employed to monitor the removal of nitro compounds and formation of aminophenol. Among, the three catalysts, the CuFe₂O₄ displayed excellent removal activity for nitrocompounds. The CuFe₂O₄ nanoparticles completely removed the NP, DNP and TNP within 2, 5, 10 min, respectively. The NP reduction reaction follows the pseudo-first-order kinetics. Further, the investigated and proposed CuFe₂O_4, catalyst has given and demonstrated excellent kinetic rate constants 0.990, 0.317, 0.184 min^-1 for 4-NP, DNP and TNP respectively, which was very fast kinetic than the already published reports. Also, the aminophenol formation was confirmed for the above mentioned and select nitrocompounds. The obtained results confirm suggest that CuFe₂O₄ nanoparticles based material system could be one of the promising catalysts for nitro compounds removal process.

Preparation, Characterization and Processing of PCL/PHO Blends by 3D Bioplotting

Blends of polycaprolactone (PCL) and poly(3-hydroxyoctanoate) P(3HO) were prepared by melt compounding. These immiscible blends exhibited droplet-matrix morphology at compositions up to 30 wt% P(3HO). Even though the addition of amorphous P(3HO) decreased the crystallinity of PCL, the crystallization temperature of the blends increased by 6 to 7 8C. Blends containing up to 30 wt% P(3HO) had higher crystallization rates, and lower crystallization half-times compared to neat PCL. The viscosity of PCL decreased upon addition of P(3HO), making the blends suitable for processing using a 3D bioplotter. Compositions with 10 to 30 wt% P(3HO) were ideal for processing, because of their improved crystallization kinetics, reduced stickiness and good flow properties. Estimation of the interfacial tension by fitting the Palierne model to the linear viscoelastic properties of the blends revealed good compatibility, which gave rise to synergistic effects in the thermal and mechanical properties. The fibres prepared by 3D bioplotting maintained droplet matrix morphology, with finer particle size than the original compounded material. In addition to favourable viscosity and thermal properties, the extruded fibres containing 30 wt% P(3HO) had comparable modulus to the neat PCL, while exhibiting good ductility. These blends may be suitable alternatives to PCL for biomedical applications, because they provide a range of crystallinities, crystallization rates and viscosities.

Brown-Vialetto-Van Laere syndrome: A rare case report of MND mimic

Brown-Vialetto-Van Laere Syndrome (BVVLS) is a rare disorder characterized by progressive neuropathy, optic atrophy, hearing loss, bulbar dysfunction, and respiratory insufficiency associated with mutations in SLC52A2 and SLC52A3 genes that code for human riboflavin transporters RFVT2 and RFVT3, respectively. Nearly 70 cases have been reported by molecular diagnosis.^[2],[3] The majority of familial cases are autosomal recessive^[2],[4] with female to male ratio of 3:1.^[5] We describe the clinical course of a 16-year-old boy with BVVLS who presented with 6 years duration of insidious onset gradually progressive sensory neural hearing loss, optic atrophy, amyotrophy of both upper limbs, and wasting of the tongue with fasciculations. Novel homozygous mutation c.1245C>T in the SLC52A2 gene was identified. At times, the clinical spectrum mimics the juvenile onset motor neuron disease (MND) as in this case. It was important to identify the BVVLS that can respond to high doses of riboflavin.

A Disordered Loop Mediates Heterogeneous Unfolding of an Ordered Protein by Altering the Native Ensemble

The high flexibility of long disordered or partially structured loops in folded proteins allows for entropic stabilization of native ensembles. Destabilization of such loops could alter the native ensemble or promote alternate conformations within the native ensemble if the ordered regions themselves are held together weakly. This is particularly true of downhill folding systems that exhibit weak unfolding cooperativity. Here, we combine experimental and computational methods to probe the response of the native ensemble of a helical, downhill folding domain PDD, which harbors an 11-residue partially structured loop, to perturbations. Statistical mechanical modeling points to continuous structural changes on both temperature and mutational perturbations driven by entropic stabilization of partially structured conformations within the native ensemble. Long time-scale simulations of the wild-type protein and two mutants showcase a remarkable conformational switching behavior wherein the parallel helices in the wild-type protein sample an antiparallel orientation in the mutants, with the C-terminal helix and the loop connecting the helices displaying high flexibility, disorder, and non-native interactions. We validate these computational predictions via the anomalous fluorescence of a native tyrosine located at the interface of the helices. Our observations highlight the role of long loops in determining the unfolding mechanisms, sensitivity of the native ensembles to mutational perturbations and provide experimentally testable predictions that can be explored in even two-state folding systems.

Non-specific DNA-driven quinary interactions promote structural transitions in proteins

The nature and distribution of charged residues on the surface of proteins play a vital role in determining the binding affinity, selectivity and kinetics of association to ligands. When it comes to DNA-binding domains (DBDs), these functional features manifest as anisotropic distribution of positively charged residues on the protein surface driven by the requirement to bind DNA, a highly negatively charged polymer. In this work, we compare the thermodynamic behavior of nine different proteins belonging to three families - LacR, engrailed and Brk - some of which are disordered in solution in the absence of DNA. Combining detailed electrostatic calculations and statistical mechanical modeling of folding landscapes at different distances and relative orientations with respect to DNA, we show that non-specific electrostatic interactions between the protein and DNA can promote structural transitions in DBDs. Such quinary interactions that are strictly agnostic to the DNA sequence induce varied behaviors including folding of disordered domains, partial unfolding of ordered proteins and (de-)population of intermediate states. Our work highlights that the folding landscape of proteins can be tuned as a function of distance from DNA and hints at possible reasons for DBDs exhibiting complex kinetic-thermodynamic behaviors in the absence of DNA.

Disease Severity Assessment and Short-Term Outcome in Patients with Myasthenia Gravis

Background

Myasthenia gravis (MG) is an autoimmune disorder with a chronic fluctuating course. The outcome measures encapsulate disease severity, functional impact at diagnosis, and objective evaluation of clinical benefit from therapeutic interventions.

Aims and Objective

To assess the disease severity, correlation between various outcome measures, and to evaluate the short-term outcome at 3 months and 6 months in a cohort of MG patients.

Materials and Methods

Quantitative myasthenia gravis (QMG) score, myasthenia gravis composite (MGC) score, and myasthenia gravis quality of life-15 (MG-QoL-15) score were applied to 54 patients at first visit, 3 months and 6 months follow-up.

Results

Mean quality of life-15 (QoL-15) score at base line was 15.241. Mean QMG and MGC scores at baseline were 14.63 ± 8.37 and 15.87 ± 9.14, respectively. QMG score showed a strong positive correlation with both MGC and MG-QoL-15 scores. QMG and MGC scores showed a moderate correlation with acetylcholine receptor antibody (AChR Ab) titers. Mean QMG at follow-up was 9.95 ± 5.49 at 3 months and 6.74 ± 4.74 at 6 months. Mean MGC at follow-up was 10.75 ± 5.58 at 3 months and 6.51 ± 4.36 at 6 months.

Conclusion

The combination of physician-evaluated and patient-reported outcome measures provided a more discerning picture of patient status and response to treatment. Incorporating MG outcome measures into clinical practice would aid in modulating therapies.

pPerturb: A Server for Predicting Long-Distance Energetic Couplings and Mutation-Induced Stability Changes in Proteins via Perturbations

The strength of intraprotein interactions or contact network is one of the dominant factors determining the thermodynamic stabilities of proteins. The nature and the extent of connectivity of this network also play a role in allosteric signal propagation characteristics upon ligand binding to a protein domain. Here, we develop a server for rapid quantification of the strength of an interaction network by employing an experimentally consistent perturbation approach previously validated against a large data set of 375 mutations in 19 different proteins. The web server can be employed to predict the extent of destabilization of proteins arising from mutations in the protein interior in experimentally relevant units. Moreover, coupling distances-a measure of the extent of percolation on perturbation-and overall perturbation magnitudes are predicted in a residue-specific manner, enabling a first look at the distribution of energetic couplings in a protein or its changes upon ligand binding. We show specific examples of how the server can be employed to probe for the distribution of local stabilities in a protein, to examine changes in side chain orientations or packing before and after ligand binding, and to predict changes in stabilities of proteins upon mutations of buried residues. The web server is freely available at http://pbl.biotech.iitm.ac.in/pPerturb and supports recent versions of all major browsers.

Thermodynamics and folding landscapes of large proteins from a statistical mechanical model

Statistical mechanical models that afford an intermediate resolution between macroscopic chemical models and all-atom simulations have been successful in capturing folding behaviors of many small single-domain proteins. However, the applicability of one such successful approach, the Wako-Saitô-Muñoz-Eaton (WSME) model, is limited by the size of the protein as the number of conformations grows exponentially with protein length. In this work, we surmount this size limitation by introducing a novel approximation that treats stretches of 3 or 4 residues as blocks, thus reducing the phase space by nearly three orders of magnitude. The performance of the 'bWSME' model is validated by comparing the predictions for a globular enzyme (RNase H) and a repeat protein (IκBα), against experimental observables and the model without block approximation. Finally, as a proof of concept, we predict the free-energy surface of the 370-residue, multi-domain maltose binding protein and identify an intermediate in good agreement with single-molecule force-spectroscopy measurements. The bWSME model can thus be employed as a quantitative predictive tool to explore the conformational landscapes of large proteins, extract the structural features of putative intermediates, identify parallel folding paths, and thus aid in the interpretation of both ensemble and single-molecule experiments.

Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA

The amplitude of thermodynamic fluctuations in biological macromolecules determines their conformational behavior, dimensions, nature of phase transitions and effectively their specificity and affinity, thus contributing to fine-tuned molecular recognition. Unique among large-scale conformational changes in proteins are temperature-induced collapse transitions in intrinsically disordered proteins (IDPs). Here, we show that CytR DNA-binding domain, an IDP that folds on binding DNA, undergoes a coil-to-globule transition with temperature in the absence of DNA while exhibiting energetically decoupled local and global structural rearrangements, and maximal thermodynamic fluctuations at the optimal bacterial growth temperature. The collapse is shown to be a continuous transition through a combination of statistical-mechanical modeling and all-atom implicit solvent simulations. Surprisingly, CytR binds single-site cognate DNA with negative cooperativity, described by Hill coefficients less than one, resulting in a graded binding response. We show that heterogeneity arising from varying binding-competent CytR conformations or orientations at the single-molecular level contributes to negative binding cooperativity at the level of bulk measurements due to the conflicting requirements of collapse transition, large fluctuations and folding-upon-binding. Our work reports strong evidence for functionally driven thermodynamic fluctuations in determining the extent of collapse and disorder with implications in protein search efficiency of target DNA sites and regulation.

Tunable order-disorder continuum in protein-DNA interactions

DNA-binding protein domains (DBDs) sample diverse conformations in equilibrium facilitating the search and recognition of specific sites on DNA over millions of energetically degenerate competing sites. We hypothesize that DBDs have co-evolved to sense and exploit the strong electric potential from the array of negatively charged phosphate groups on DNA. We test our hypothesis by employing the intrinsically disordered DBD of cytidine repressor (CytR) as a model system. CytR displays a graded increase in structure, stability and folding rate on increasing the osmolarity of the solution that mimics the non-specific screening by DNA phosphates. Electrostatic calculations and an Ising-like statistical mechanical model predict that CytR exhibits features of an electric potential sensor modulating its dimensions and landscape in a unique distance-dependent manner, while DNA plays the role of a non-specific macromolecular chaperone. Accordingly, CytR binds its natural half-site faster than the diffusion-controlled limit and even random DNA conforming to an electrostatic-steering binding mechanism. Our work unravels for the first time the synergistic features of a natural electrostatic potential sensor, a novel binding mechanism driven by electrostatic frustration and disorder, and the role of DNA in promoting distance-dependent protein structural transitions critical for switching between specific and non-specific DNA-binding modes.

pStab: prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration

Summary

We present a web-server for rapid prediction of changes in protein stabilities over a range of temperatures and experimental conditions upon single- or multiple-point substitutions of charged residues. Potential mutants are identified by a charge-shuffling procedure while the stability changes (i.e. an unfolding curve) are predicted employing an ensemble-based statistical-mechanical model. We expect this server to be a simple yet detailed tool for engineering stabilities, identifying electrostatically frustrated residues, generating local stability maps and in constructing fitness landscapes.

Availability and implementation

The web-server is freely available at http://pbl.biotech.iitm.ac.in/pStab and supports recent versions of all major browsers.

Contact

athi@iitm.ac.in.

Supplementary information

Supplementary data are available at Bioinformatics online.

Extracting the Hidden Distributions Underlying the Mean Transition State Structures in Protein Folding

The inherent conflict between noncovalent interactions and the large conformational entropy of the polypeptide chain forces folding reactions and their mechanisms to deviate significantly from chemical reactions. Accordingly, measures of structure in the transition state ensemble (TSE) are strongly influenced by the underlying distributions of microscopic folding pathways that are challenging to discern experimentally. Here, we present a detailed analysis of 150,000 folding transition paths of five proteins at three different thermodynamic conditions from an experimentally consistent statistical mechanical model. We find that the underlying TSE structural distributions are rarely unimodal, and the average experimental measures arise from complex underlying distributions. Unfolding pathways also exhibit subtle differences from folding counterparts due to a combination of Hammond behavior and native-state movements. Local interactions and topological complexity, to a lesser extent, are found to determine pathway heterogeneity, underscoring the importance of the balance between local and nonlocal energetics in protein folding.

Toward a quantitative description of microscopic pathway heterogeneity in protein folding

Experimentally consistent statistical modeling of protein folding thermodynamics reveals unprecedented complexity with numerous parallel folding routes in five different proteins.

Energetic and topological determinants of a phosphorylation-induced disorder-to-order protein conformational switch

We show that the phosphorylation of 4E-BP2 acts as a triggering event to shape its folding-function landscape that is delicately balanced between conflicting favorable energetics and intrinsically unfavorable topological connectivity. We further provide first evidence that the fitness landscapes of proteins at the threshold of disorder can differ considerably from ordered domains.

Quantifying Protein Disorder through Measures of Excess Conformational Entropy

Intrinsically disordered proteins (IDPs) and proteins with a large degree of disorder are abundant in the proteomes of eukaryotes and viruses, and play a vital role in cellular homeostasis and disease. One fundamental question that has been raised on IDPs is the process by which they offset the entropic penalty involved in transitioning from a heterogeneous ensemble of conformations to a much smaller collection of binding-competent states. However, this has been a difficult problem to address, as the effective entropic cost of fixing residues in a folded-like conformation from disordered amino acid neighborhoods is itself not known. Moreover, there are several examples where the sequence complexity of disordered regions is as high as well-folded regions. Disorder in such cases therefore arises from excess conformational entropy determined entirely by correlated sequence effects, an entropic code that is yet to be identified. Here, we explore these issues by exploiting the order-disorder transitions of a helix in Pbx-Homeodomain together with a dual entropy statistical mechanical model to estimate the magnitude and sign of the excess conformational entropy of residues in disordered regions. We find that a mere 2.1-fold increase in the number of allowed conformations per residue (∼0.7kBT favoring the unfolded state) relative to a well-folded sequence, or ∼2(N) additional conformations for a N-residue sequence, is sufficient to promote disorder under physiological conditions. We show that this estimate is quite robust and helps in rationalizing the thermodynamic signatures of disordered regions in important regulatory proteins, modeling the conformational folding-binding landscapes of IDPs, quantifying the stability effects characteristic of disordered protein loops and their subtle roles in determining the partitioning of folding flux in ordered domains. In effect, the dual entropy model we propose provides a statistical thermodynamic basis for the relative conformational propensities of amino acids in folded and disordered environments in proteins. Our work thus lays the foundation for understanding and quantifying protein disorder through measures of excess conformational entropy.

Protective Effect of Emblica officinalis Against Alcohol-Induced Hepatic Injury by Ameliorating Oxidative Stress in Rats

The effect of Emblica officinalis fruit extract (EFE) against alcohol-induced hepatic damage in rats was investigated in the present study. In vitro studies showed that EFE possesses antioxidant as well nitric oxide (NO) scavenging activity. In vivo administration of alcohol (5 g/kg b.wt/day) for 60 days resulted increased liver lipid peroxidation, protein carbonyls, nitrite plus nitrate levels. Alcohol administration also significantly lowers the activities of superoxide dismutase, catalase, glutathione peroxidase, glutathione S-transferase and reduced glutathione as compared with control rats. Administration of EFE (250 mg/kg body weight) to alcoholic rats significantly brought the plasma enzymes towards near normal level and also significantly reduced the levels of lipid peroxidation, protein carbonyls and restored the enzymic and non-enzymatic antioxidants level. This observation was supplemented by histopathological examination in liver. Our data indicate that the tannoid, flavonoid and NO scavenging compounds present in EFE may offer protection against free radical mediated oxidative stress in rat hepatocytes of animals with alcohol-induced liver injury.

Beneficial effect of the administration of Hemidesmus indicus against bromobenzene induced oxidative stress in rat liver mitochondria

AIM OF THE STUDY

To study the beneficial effect of the prior administration of an aqueous extract of Hemidesmus indicus against bromobenzene induced oxidative damage in rat liver mitochondria.

MATERIALS AND METHODS

Oxidative stress was induced in rats with bromobenzene (10 mmol/kg body wt.). The rate of respiration, P/O ratios, lipid peroxides, protein carbonyls and sulphydryls were studied.

RESULTS

When the rats were administered with bromobenzene, the rate of respiration was decreased significantly and the P/O ratio was completely abolished. There was a significant increase on the levels of lipid peroxide and protein carbonyl and a significant decrease on total sulphydryl groups when compared with control. Administration of rats with an aqueous extract (100mg/kg) prior to bromobenzene administration showed significant beneficial effects like, stimulation in respiration, prevented the rise in lipid peroxides and protein carbonyls, increased the level of sulphydryl groups back to control level. Administration of vitamin E could not reverse as effectively as Hemidesmus indicus.

CONCLUSIONS

This study demonstrates a good protective effect of Hemidesmus indicus against the bromobenzene induced oxidative stress.