How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP,TP2 and ONEG?

Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) ¹H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.

A protocol for simulating intrinsically disordered peptides in aqueous and hydrophobic solvents is proposed. Results from four force fields are compared with experiment. CHARMM36m performs the best for the simulated IDPs in all environments.     

In memory of Professor Ali H. Nayfeh

Nonlinear Dynamics - In this paper, we propose and numerically study a nonlinear, asymmetric, passive metamaterial that achieves giant non-reciprocity with (i) broadband frequency operation and...     

Lossy mode resonance-based uniform core tapered fiber optic sensor for sensitivity enhancement

A lossy mode resonance (LMR)-supported fiber optic sensor in which a uniform fiber core is placed among two identical tapered regions, is investigated numerically. Indium tin oxide (ITO) and aluminum-doped zinc oxide (AZO) are considered as LMR active materials used to excite several lossy modes and gold and silver are used as surface plasmon resonance (SPR) active materials. In this probe design, a central uniform core coated with ITO/AZO is the active sensing region, whereas tapered regions are meant for bringing the incident angle close to the critical angle. The sensitivity of the present fiber optic bio-sensor is evaluated for first two LMRs utilizing both ITO and AZO separately, along with its variation with the taper ratio (TR). For ITO, the maximum sensitivity values are observed to be 18.425 μm RIU⁻¹ (refractive index unit) and 0.825 μm RIU⁻¹, corresponding to the first and second LMRs, respectively, at a TR of 1.6 and for AZO, equivalent values are 0.79 μm RIU⁻¹ and 0.35 μm RIU⁻¹, respectively, at a TR of 2.0. The results illustrate that the first LMR is more sensitive than the second LMR and the ITO-coated probe possesses greater sensitivity than the AZO-coated probe for both LMRs. Similarly, for the fiber optic SPR sensor, the maximum value of sensitivity is 5.6425 μm RIU⁻¹, in the case of gold and 5.0615 μm RIU⁻¹ in the case of silver, at a TR of 1.6. Hence, the result shows that the sensor with the present fiber optic probe design has around a 3-fold enhancement in sensitivity compared with conventional SPR sensors. This study will have applications in many sensing schemes where the requirement of large sensitivity is vital.     

Decay of Hot and Rotating $${}^{\boldsymbol{88}}$$ Mo $${}^{\boldsymbol{*}}$$ at Incident Energies of 300, 450, and 600 MeV

Physics of Atomic Nuclei - The reaction mechanism for the decay of the hot and rotating compound system $${}^{88}$$ Mo $${}^{*}$$ formed in $${}^{48}\textrm{Ti}+^{40}$$ Ca reaction and the time for...     

Biofortification—A Frontier Novel Approach to Enrich Micronutrients in Field Crops to Encounter the Nutritional Security

Globally, many developing countries are facing silent epidemics of nutritional deficiencies in human beings and animals. The lack of diversity in diet, i.e., cereal-based crops deficient in mineral nutrients is an additional threat to nutritional quality. The present review accounts for the significance of biofortification as a process to enhance the productivity of crops and also an agricultural solution to address the issues of nutritional security. In this endeavor, different innovative and specific biofortification approaches have been discussed for nutrient enrichment of field crops including cereals, pulses, oilseeds and fodder crops. The agronomic approach increases the micronutrient density in crops with soil and foliar application of fertilizers including amendments. The biofortification through conventional breeding approach includes the selection of efficient genotypes, practicing crossing of plants with desirable nutritional traits without sacrificing agricultural and economic productivity. However, the transgenic/biotechnological approach involves the synthesis of transgenes for micronutrient re-translocation between tissues to enhance their bioavailability. Soil microorganisms enhance nutrient content in the rhizosphere through diverse mechanisms such as synthesis, mobilization, transformations and siderophore production which accumulate more minerals in plants. Different sources of micronutrients viz. mineral solutions, chelates and nanoparticles play a pivotal role in the process of biofortification as it regulates the absorption rates and mechanisms in plants. Apart from the quality parameters, biofortification also improved the crop yield to alleviate hidden hunger thus proving to be a sustainable and cost-effective approach. Thus, this review article conveys a message for researchers about the adequate potential of biofortification to increase crop productivity and nourish the crop with additional nutrient content to provide food security and nutritional quality to humans and livestock.     

A Novel and Efficient One Pot Synthesis of 2,4‐Disubstituted Thiazoles and Oxazoles Using Phenyltrimethylammoniumtribromide in Ionic Liquid

A novel and efficient one‐pot procedure has been described for synthesis of 2,4‐disubstituted thiazoles and oxazoles from substituted ketones using phenyltrimethylammoniumtribromide as in situ brominating agent followed by reaction with thioamide/thiourea and amides/ureas, respectively in [bmim][BF₄] ionicliquid. The advantages of the procedure include avoiding the handling of lacrymetric compounds, hazardous and toxic organic solvents along with good to excellent yield of the products.     

Terahertz radiation generation by beating of two spatial-Gaussian lasers

Terahertz radiation generation is proposed based on beating of two spatial-Gaussian lasers in a periodic density plasma, where a transverse component of current is realized that resonantly excites the radiation with efficiency ∼10⁻³. Importance of laser-beam-width, amplitude and periodicity of density structure is discussed for the efficient THz generation.     

XNBR/LDH nanocomposites: Effect of vulcanization and organic modifier on nanofiller dispersion and strain‐induced crystallization

In elastomer/organo clay nanocomposites, the morphological characteristics, and hence the mechanical properties, of the vulcanizates are strongly influenced by the organic modifier and the vulcanization process. When the elastomer itself undergoes strain‐induced crystallization, both the organic modifier and the dispersed filler particles could significantly influence the crystallization process. These phenomena are very common in case of natural rubber‐based vulcanizates. In this study, the similar effects have been demonstrated with carboxylated nitrile rubber (XNBR) and organically modified layered double hydroxide (O‐LDH)‐based nanocomposites. The effect of size of the organic modifier was obviously visible on the interlayer distance of O‐LDH and also on the morphological reorganization of the dispersed O‐LDH particles during vulcanization process. The strain‐induced crystallization of the XNBR was found to be strongly dependent on the morphological change that occurs during vulcanization process. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2010