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.     

Sequential ortho effects: characterization of novel [M - 35]+ fragment ions in the mass spectra of 2-alkyl-4, 6-dinitrophenols

High-resolution mass spectrometry (HRMS), hybrid tandem mass spectrometry (MS/MS) (EBqQ), and photoelectron-photoion coincidence (PEPICO) experiments were conducted to examine a possible ortho-ortho effect resulting in a novel [M - 35]⁺ fragment ion in 2-alkyl-4, 6-dinitrophenols. For compounds having ethyl or larger alkyl substituents, [M35]⁺ was observed only when [M - 18]⁺ ions were present, with the ortho nitro group being involved in the reaction to [M- 35]⁺. For [M - 18]⁺ and [M - 35]⁺, HRMS results were consistent with losses of H₂O and H₂O + OH, respectively, whereas MS/MS results indicated a sequential reaction due to metastable dissociations. The appearance energy determined by PEPICO for [M - 35]⁺ was found to be greater than the appearance energy for [M - 18]⁺, thus supporting a sequential reaction. 69–75).     

ABSORPTION SPECTRAL SHIFTS OF CAROTENOIDS RELATED TO MEDIUM POLARIZABILITY

Abstract–Solvent induced absorption spectral shifts of the electronic transition from ground 1 A_g state to the excited 1B_u state in carotenoids have been studied. It is shown that the shift depends only on dispersion interactions in non-polar solvents. In polar media there is just a small extra contribution to the red-shift, due to other forms of interactions. The spectral shifts are well described by the theory, which expresses the shift relative to the gas phase value, as a function of solvent polarizability. The main conclusion is that the dominating mechanism behind the large red-shifted absorbance of carotenoids in the proteinacous environment, in vivo, is the mutual polarizability interactions between the carotenoids and the surrounding medium. The solution-phase values of the dipole moments of the lA_g to 1B_u transitions and the differences of isotropic polarizability between 1B_u and lA_g states of carotenoids in non-polar solvents are calculated and found to be around 13 D and 360 ų respectively. From the great overlap of absorption spectra between carotenoids in quinoline and carotenoids in vivo in purple bacterial antenna complexes, it can be expected that the carotenoids are surrounded by several aromatic amino acids in vivo. Comparisons have been done between the exicted states in carotenoids and in linear conjugated polyenes.     

Challenges for impedimetric affinity sensors targeting protein detection

The review provides articles discussing big challenges behind successful design of impedimetric biosensors and the way such challenges were/could be addressed for highly sensitive affinity detection of proteins. In particular, the effect of gold etching by chloride ions or by CN^? ions (released from the redox probe [Fe(CN)₆]^3-/4-), the effect of ionic strength of the assay buffer; the effect of initial interfacial properties (capacitance) and the effect of the high analyte:bioreceptor ratio on electrochemical impedance spectroscopy–based biosensing are discussed. The review provides also short discussion related to other factors, which can significantly affect operational performance of electrochemical impedance spectroscopy–based biosensing including novel conductive interfaces, small bioreceptors, strategies for improved selectivity (nonbiofouling interfaces) and sensitivity (use of nanoparticles).     

Design and synthesis of two epoxide derivatives from 3-ethynylaniline

For several years ago, several epoxide derivatives have been prepared using different methods; however, some protocols use reagents which could be expensive and require specials conditions. The aim of this investigation was to prepare two new epoxide-derivatives from 3-ethynylaniline using some reactions such as oximation, acetylation, 2 + 2 addition, functionalized chloroamides, and epoxidation via Darzens reaction. The chemical characteristics of epoxide derivatives were determinate through a spectroscopic and spectrometric analysis. In conclusion, it is noteworthy that the reactions used in this study do not involve expensive reagents or special conditions for the synthesis of epoxide derivatives.     

Light-Responsive Elastin-Like Peptide-Based Targeted Nanoparticles for Enhanced Spheroid Penetration

We describe here a near infrared light-responsive elastin-like peptide (ELP)-based targeted nanoparticle (NP) that can rapidly switch its size from 120 to 25 nm upon photo-irradiation. Interestingly, the targeting function, which is crucial for effective cargo delivery, is preserved after transformation. The NPs are assembled from (targeted) diblock ELP micelles encapsulating photosensitizer TT1-monoblock ELP conjugates. Methionine residues in this monoblock are photo-oxidized by singlet oxygen generated from TT1, turning the ELPs hydrophilic and thus trigger NP dissociation. Phenylalanine residues from the diblocks then interact with TT1 via π-π stacking, inducing the re-formation of smaller NPs. Due to their small size and targeting function, the NPs penetrate deeper in spheroids and kill cancer cells more efficiently compared to the larger ones. This work could contribute to the design of “smart” nanomedicines with deeper penetration capacity for effective anticancer therapies.     

An alternating method for Cauchy problems for Helmholtz-type operators in non-homogeneous medium

Kozlov & Maz'ya (1989, Algebra Anal., 1, 144–170)proposed an alternating iterative method for solving Cauchyproblems for general strongly elliptic and formally self-adjointsystems. However, in many applied problems, operators appearthat do not satisfy these requirements, e.g. Helmholtz-typeoperators. Therefore, in this study, an alternating procedurefor solving Cauchy problems for self-adjoint non-coercive ellipticoperators of second order is presented. A convergence proofof this procedure is given.