Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations.

We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on time scales faster than conformational transitions but describe a path of least resistance toward structural change. A key challenge is that harmonic approximations are ill-suited to characterize these vibrations, which are observed at far-infrared frequencies and are easily excited by thermal collisions at room temperature. Here, we approached this problem with a frequency-selective anharmonic (FRESEAN) mode analysis that does not rely on harmonic approximations and successfully isolates anharmonic low-frequency vibrations from short molecular dynamics simulation trajectories. We applied FRESEAN mode analysis to simulations of alanine dipeptide, a common test system for enhanced sampling simulation protocols, and compared the performance of isolated low-frequency vibrations to conventional user-defined collective variables (here backbone dihedral angles) in enhanced sampling simulations. The comparison shows that enhanced sampling along anharmonic low-frequency vibrations not only reproduces known conformational dynamics but can even further improve the sampling of slow transitions compared to user-defined collective variables. Notably, free energy surfaces spanned by low-frequency anharmonic vibrational modes exhibit lower barriers associated with conformational transitions relative to representations in backbone dihedral space. We thus conclude that anharmonic low-frequency vibrations provide a promising path for highly effective and fully automated enhanced sampling simulations of conformational dynamics in biomolecules.

Conformational Properties of Aß Peptide Oligomers in Aqueous Ionic Liquid Solution: Insights from Molecular Simulation Studies.

Alzheimer's disease is a progressive irreversible neurological disorder with abnormal extracellular deposition of amyloid ß (Aß) peptides in the brain. We have carried out atomistic molecular dynamics simulations to investigate the size-dependent conformational properties of aggregated Aß oligomers of different orders, namely, pentamer [O(5)], decamer [O(10)], and hexadecamer [O(16)] in aqueous solutions containing the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]). The calculations revealed reduced peptide conformational fluctuations in O(5) and O(10) in the presence of the IL. In contrast, the higher order oligomer [O(16)] has been found to exhibit greater structural distortion due to enhanced flexibilities of its peptide units in the presence of the IL. Based on the distributions of the solvent (water) and the cosolvent (IL) components, it is demonstrated that exchange of water by the IL ion pairs at the exterior surface of the oligomers primarily occurs beyond the first layer of surface-bound water molecules. Importantly, a reduced number of relatively weaker peptide salt bridges have been found in O(16) in binary water-IL solution as compared to the other two smaller-sized oligomers [O(5) and O(10)]. Such differential influence of the IL on peptide salt bridges results in less favorable binding free energies of peptide monomers to O(16), which leads to its greater structural distortion and reduced stability compared to those of O(5) and O(10).

What Determines the District-Level Disparities in Immunization Coverage in India: Findings from Five Rounds of the National Family Health Survey.

India's Universal Immunization Programme has been performing at a sub-optimal level over the past decade, with there being a wide disparity in terms of immunization coverage between states. This study investigates the covariates that affect immunization rates and inequality in India at the individual and district levels. We used data from the five rounds of the National Family Health Survey (NFHS), conducted from 1992-1993 to 2019-2021. We used multilevel binary logistic regression analysis to examine the association between demographic, socio-economic and healthcare factors and a child's full immunization status. Further, we used the Fairlie decomposition technique to understand the relative contribution of explanatory variables to a child's full immunization status between districts with different immunization coverage levels. We found that 76% of children received full immunization in 2019-2021. Children from less wealthy families, urban backgrounds, Muslims, and those with illiterate mothers were found to have lower chances of receiving full immunization. There is no evidence that gender and caste disparities have an impact on immunization coverage in India. We found that having a child's health card is the most significant contributor to reducing the disparities that exist regarding children's full immunization between mid- and low-performing districts. Our study suggests that healthcare-related variables are more crucial than demographic and socio-economic variables when determining ways in which to improve immunization coverage in Indian districts.

Microscopic Understanding of the Conformational Stability of the Aggregated Nonamyloid ß Components of α-Synuclein.

Self-association of α-synuclein peptides into oligomeric species and ordered amyloid fibrils is associated with Parkinson's disease, a progressive neurodegenerative disorder. In particular, the peptide domain formed between the residues Glu-61 (or E61) and Val-95 (or V95) of α-synuclein, typically termed the "nonamyloid ß component" (NAC), is known to play critical roles in forming aggregated structures. In this work, we have employed molecular dynamics simulations to explore the conformational properties and relative stabilities of aggregated protofilaments of different orders, namely, tetramer (P(4)), hexamer (P(6)), octamer (P(8)), decamer (P(10)), dodecamer (P(12)), and tetradecamer (P(14)), formed by the NAC domains of α-synuclein. Besides, center-of-mass pulling and umbrella sampling simulation methods have also been employed to characterize the mechanistic pathway of peptide association/dissociation and the corresponding free energy profiles. Structural analysis showed that the disordered C-terminal loop and the central core regions of the peptide units lead to more flexible and distorted structures of the lower order protofilaments (P(4) and P(6)) as compared to the higher order ones. Interestingly, our calculation shows the presence of multiple distinctly populated conformational states for the lower order protofilament P(4), which may drive the oligomerization process along multiple pathways to form different polymorphic α-synuclein fibrillar structures. It is further observed that the nonpolar interaction between the peptides and the corresponding nonpolar solvation free energy play a dominant role in stabilizing the aggregated protofilaments. Importantly, our result showed that reduced cooperativity during the binding of a peptide unit beyond a critical size of the protofilament (P(12)) leads to less favorable binding free energy of a peptide.

Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies.

Ionic liquids (ILs) are known to modify the structural stability of proteins. The modification of the protein conformation is associated with the accumulation of ILs around the amino acid (AA) side chains and the nature of interactions between them. To understand the microscopic picture of the structural arrangements of ILs around the AA side chains, room temperature molecular dynamics (MD) simulations have been carried out in this work with a series of hydrophobic, polar and charged AAs in aqueous solutions containing the IL 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) at 2 M concentration. The calculations revealed distinctly nonuniform distribution of the IL components around different AAs. In particular, it is demonstrated that the BMIM+ cations preferentially interact with the aromatic AAs through favorable stacking interactions between the cation imidazolium head groups and the aromatic AA side chains. This results in preferential parallel alignments and enhanced population of the cations around the aromatic AAs. The potential of mean force (PMF) calculations revealed that such favorable stacking interactions provide greater stability to the contact pairs (CPs) formed between the aromatic AAs and the IL cations as compared to the other AAs. It is further quantified that for most of the AAs (except the cationic ones), a favorable enthalpy contribution more than compensates for the entropy cost to form stable CPs with the IL cations. These findings are likely to provide valuable fundamental information toward understanding the effects of ILs on protein conformational stability.

Truth-Telling to Terminal Stage Cancer Patients in India: A Study of the General Denial to Disclosure.

Telling the truth to the terminal-stage cancer patients differs socio-culturally based on the priorities assigned to patients' autonomy and the principles of beneficence and non-maleficence. After conducting in-depth interviews with 108 terminal-stage adult cancer patients, 306 family members, and 25 physicians, in private and public hospitals in both rural and urban areas, in the state of West Bengal, India it has been found that even though 85.60% of the patients prefer full disclosure, only 22.03% are actually informed. Though demographic characteristics, like age, gender, education etc., have marginal influences over the pattern of truth-telling, the main factor behind non-disclosure is the family members' preference for principles of beneficence and non-maleficence over patient autonomy. Hence, only 9.32% of those 118 patients' family members have agreed to full disclosure. Physicians comply with this culture of non-disclosure as family, in India, is the centre of decision-making and acts as the primary unit of care.

In Silico Studies to Predict the Role of Solvent in Guiding the Conformations of Intrinsically Disordered Peptides and Their Aggregated Protofilaments.

The formation of amyloids due to the self-assembly of intrinsically disordered proteins or peptides is a hallmark for different neurodegenerative diseases. For example, amyloids formed by the amyloid beta (Aß) peptides are responsible for the most devastating neuropathological disease, namely, Alzheimer's disease, while aggregation of α-synuclein peptides causes the etiology of another neuropathological disease, Parkinson's disease. Characterization of the intermediates and the final amyloid formed during the aggregation process is, therefore, crucial for microscopic understanding of the origin behind such diseases, as well as for the development of proper therapeutics to combat those. However, most of the research activities reported in this area have been directed toward examining the early stages of the aggregation process, including probing the conformational characteristics of the responsible protein/peptide in the monomeric state or in small oligomeric forms. This is because the small soluble oligomers have been found to be more deleterious than the final insoluble amyloids. This review discusses some of the recent findings obtained from our simulation studies on Aß and α-synuclein monomers and small preformed Aß aggregates. A molecular-level insight of the aggregation process with a special emphasis on the role of water in inducing the aggregation process has been provided.

Dynamic Heterogeneity at the Interface of an Intrinsically Disordered Peptide.

It is believed that water around an intrinsically disordered protein or peptide (IDP) in an aqueous environment plays an important role in guiding its conformational properties and aggregation behavior. However, despite its importance, only a handful of studies exploring the correlation between the conformational motions of an IDP and the microscopic properties of water at its surface are reported. Attempts have been made in this work to study the dynamic properties of water present in the vicinity of α-synuclein, an IDP associated with Parkinson's disease (PD). Room temperature molecular dynamics (MD) simulations of eight α-synuclein1-95 peptides with a wide range of initial conformations have been carried out in aqueous media. The calculations revealed that due to solid-like caging motions, the translational and rotational mobility of water molecules near the surfaces of the peptide repeat unit segments R1 to R7 are significantly restricted. A small degree of dynamic heterogeneity in the hydration environment around the repeat units has been observed with water near the hydrophobic R6 unit exhibiting relatively more restricted diffusivity. The time scales involving the overall structural relaxations of peptide-water and water-water hydrogen bonds near the peptide have been found to be correlated with the time scale of diffusion of the interfacial water molecules. We believe that the relatively more hindered dynamic environment near R6 can help create water-mediated contacts centered around R6 between peptide monomers at a higher concentration, thereby enhancing the early stages of peptide aggregation.

Importance of Solvent in Guiding the Conformational Properties of an Intrinsically Disordered Peptide.

Aggregated form of α-synuclein in the brain has been found to be the major component of Lewy bodies that are hallmarks of Parkinson's disease (PD), the second most devastating neurodegenerative disorder. We have carried out room-temperature all-atom molecular dynamics (MD) simulations of an ensemble of widely different α-synuclein1-95 peptide monomer conformations in aqueous solution. Attempts have been made to obtain a generic understanding of the local conformational motions of different repeat unit segments, namely R1-R7, of the peptide and the correlated properties of the solvent at the interface. The analyses revealed relatively greater rigidity of the hydrophobic R6 unit as compared to the other repeat units of the peptide. Besides, water molecules around R6 have been found to be less structured and weakly interacting with the peptide. These are important observations as the R6 unit with reduced conformational motions can act as the nucleation site for the aggregation process, while less structured weakly interacting water around it can become displaced easily, thereby facilitating the hydrophobic collapse of the peptide monomers and their association during the nucleation phase at higher concentrations. In addition, we demonstrated presence of doubly coordinated highly ordered as well as triply coordinated relatively disordered water molecules at the interface. We believe that while the ordered water molecules can favor water-mediated interactions between different peptide monomers, the randomly ordered ones on the other hand are likely to be expelled easily from the interface, thereby facilitating direct peptide-peptide interactions during the aggregation process.

MRI-negative myeloradiculoneuropathy following Covid-19 infection: An index case.

Covid-19 associated several neurological manifestation in the form of Post-infectious transverse myelitis(TM) and para-infectious TM has been reported. A 54 years old female patient presented to us with acute retention of urine and upper motor neuron type of bilateral lower limb weakness in shock stage, after 12 days of covid-19 infection. MRI (3T) brain and spine showed no abnormality and Nerve conduction study showed acquired motor axonal polyradiculoneuropathy in bilateral lower limbs. We herein present an index case of MRI-negative myeloradiculoneuropathy following covid-19 infection.

Contrasting Effects of Ionic Liquids of Varying Degree of Hydrophilicity on the Conformational and Interfacial Properties of a Globular Protein.

Ionic liquids (ILs), depending on their cation-anion combinations, are known to influence the conformational properties and activities of proteins in a nonuniform manner. To obtain microscopic understanding of such influence, it is important to characterize protein-IL interactions and explore the modified solvation environment around the protein. In this work, molecular dynamics (MD) simulations of the globular protein α-lactalbumin have been carried out in aqueous IL solutions containing 1-butyl-3-methylimidazolium cations (BMIM+) in combination with a series of anions with varying degree of hydrophilicity, namely, hexafluorophosphate (PF6-), ethyl sulfate (ETS-), acetate (OAc-), chloride (Cl-), dicyanamide (DCA-), and nitrate (NO3-) . The calculations revealed that ILs with hydrophobic and hydrophilic anions have contrasting influence on conformational flexibility of the protein. It is further observed that the BMIM+ cations exhibit site-specific orientations at the interface depending on the hydrophilicity of the anion component. Most importantly, the results demonstrated enhanced propensity of hydrophilic ILs to replace relatively weaker protein-water hydrogen bonds by stronger protein-IL hydrogen bonds at the protein surface as compared to the hydrophobic ILs. Such breaking of protein-water hydrogen bonds at a greater extent leads to greater loss of water hydrating the protein in the presence of hydrophilic ILs, thereby reducing the protein's stability.

Effects of Metal Ions on Aß42 Peptide Conformations from Molecular Simulation Studies.

In this study, we investigate the conformational characteristics of full-length Aß42 peptide monomers in the presence of Na+ and Zn2+ metal ions using atomistic molecular dynamics (MD) simulations with an aim to explore the possible driving forces behind enhanced aggregation rates of the peptides in the presence of salts. The calculations reveal that the presence of metal ions shifts the conformational equilibrium more toward the compact ordered Aß structures. Such compact ordered structures stabilized by distant nonlocal contacts between two crucial hydrophobic segments, hp1 and hp2, primarily through two important hydrophobic aromatic residues, Phe-19 and Phe-20, are expected to trigger the aggregation process at a faster rate by populating and stabilizing the aggregation prone structures. Formation of a significant number of such distant contacts in the presence of Na+ ions has also been found to result in breaking of the N-terminal helix. On the contrary, binding of Zn2+ ion to Aß peptide is highly specific, which stabilizes the N-terminal helix instead of breaking it. This explains why the aggregation rate of Aß peptides is higher in the presence of divalent Zn2+ ions than monovalent Na+ ions. Relatively higher overall stability of the most populated Aß peptide monomers in the presence of Zn2+ ions has been found to be associated with specific Zn2+-Aß binding and significant free energy gain.

Nonequilibrium steady states in a closed inhomogeneous asymmetric exclusion process with generic particle nonconservation.

We study the totally asymmetric exclusion process (TASEP) on a nonuniform one-dimensional ring consisting of two segments having unequal hopping rates, or defects. We allow weak particle nonconservation via Langmuir kinetics (LK), which are parametrized by generic unequal attachment and detachment rates. For an extended defect, in the thermodynamic limit the system generically displays inhomogeneous density profiles in the steady state-the faster segment is either in a phase with spatially varying density having no density discontinuity, or a phase with a discontinuous density changes. Nonequilibrium phase transitions between the above phases are controlled by the inhomogeneity and LK. The slower segment displays only macroscopically uniform bulk density profiles in the steady states, reminiscent of the maximal current phase of TASEP but with a bulk density generally different from half. With a point defect, there are spatially uniform low- and high-density phases as well, in addition to the inhomogeneous density profiles observed for an extended defect. In all the cases, it is argued that the mean particle density in the steady state is controlled only by the ratio of the LK attachment and detachment rates.

Caspase mediated beclin-1 dependent autophagy tuning activity and apoptosis promotion by surface modified hausmannite nanoparticle.

Hidden effects of nano-materials to induced autophagy, a lysosomal degradative pathway, remain an exciting topic, in the level of material-protein interaction and subsequent cellular signaling features. Here, our studies show that surface modified hausmannite nanoparticles (Mn3 O4 NPs) can uniformly cleave/splice Beclin-1 protein and alter cellular mechanism on the emphasis of tuning autophagy and subsequently promote enhancement of apoptosis. Details investigation of Beclin-1 dependency and its uniform cleavage/splice pattern by surface modified Mn3 O4 NPs, shows tuning of cellular mechanism on emphasis of caspase mediated autophagy tuning. Our findings will also clarify the conflict between apoptosis-autophagy on the basis of its unique property derived from surface chemistry modulation, in context of Beclin-1 eminent cleavage/splice which remarks novel effect of Beclin-1 dependent tuning of autophagosomes formation and switch to enhance apoptotic index, mediates by PI3KC3 cleavage and caspase activation. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1299-1310, 2017.

Effects of supplemental exogenous emulsifier on performance, nutrient metabolism, and serum lipid profile in broiler chickens.

The effects of an exogenous emulsifier, glyceryl polyethylene glycol ricinoleate, on performance and carcass traits of broiler chickens were assessed. The emulsifier was added to the diet at dose rates of 0 (control), 1 (E1) and 2 (E2) % of added fat (saturated palm oil). Live weight gain (P < .07) and feed conversion ratio (P < .05) in 39 days were higher in the E1 dietary group. Gain: ME intake and gain: protein intake during the grower phase improved quadratically (P < .05). Gross carcass traits were not affected. Body fat content and fat accretion increased (P < .05) and liver fat content decreased (P < .05) linearly with the level of emulsifier in diet. Fat excretion decreased (P < .001) leading to increased ileal fat digestibility (P < .06) in the E1 group (quadratic response). Metabolizable intake of N (P < .1) and fat (P < .05) increased quadratically due to supplementation of emulsifier in diet. Metabolism of trace elements and serum lipid profiles were not affected. The study revealed that supplementation of exogenous emulsifiers in diets containing moderate quantities of added vegetable fats may substantially improve broiler performance.

Performance traits and metabolic responses in goats (Capra hircus) supplemented with inorganic trivalent chromium.

The effects of supplemental chromium (Cr) as chromic chloride hexahydrate in incremental dose levels (0, 0.5, 1.0, and 1.5 mg/day for 240 days) on metabolism of nutrients and trace elements were determined in dwarf Bengal goats (Capra hircus, castrated males, average age 3 months, n = 24, initial mean body weight 6.4 +/- 0.22 kg). Live weight increased linearly (p < 0.05) with the level of supplemental Cr. Organic matter and crude protein digestibility, intake of total digestible nutrients, and retention of N (g/g N intake) increased (p < 0.05) in a dose-dependent linear manner. Serum cholesterol and tryacylglycerol concentrations changed inversely with the dose of supplemental Cr (p < 0.01). Supplemental Cr positively influenced retention of copper and iron (p < 0.05) causing linear increase (p < 0.01) in their serum concentrations. It was concluded that Cr supplementation may improve utilization of nutrients including the trace elements and may also elicit a hypolidemic effect in goats. However, further study with regards to optimization of dose is warranted.