Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations

Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.     

Diagnosing the Protonation Site of <Emphasis Type="BoldItalic">b</Emphasis><Subscript><Emphasis Type="BoldItalic">2</Emphasis></Subscript> Peptide Fragment Ions using IRMPD in the X–H (X = O,N, and C) Stretching Region

Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b ₂ ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800–3800 cm^–1 range acquired on a table-top laser system. Combining this tunable laser with a high power CO₂ laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm^–1, corresponding to the asymmetric N–H stretch of the (nonprotonated) N-terminal NH₂ group, is a distinct vibrational signature of the ring-protonated oxazolone structure.     

2-(2-Pyridyl) benzimidazole based Co(II) complex as an efficient fluorescent probe for trace level determination of aspartic and glutamic acid in aqueous solution: a displacement approach

A weakly fluorescent cobalt(II) complex is synthesized using 2-(2-pyridyl)-benzimidazole (PBI) as a chelating fluorescent ligand and characterized by single crystal X-ray structure. This complex serves as an efficient fluorescent probe for trace level determination of aspartic acid (AspA) and glutamic acid (GluA) in aqueous solution. Rest of the naturally occurring amino acids did not interfere. Both aspartic acid and glutamic acid replaces PBI from the coordination sphere of Co(II)-PBI complex resulting appearance of strong fluorescence signal for the released free PBI. The signal response is very fast and the interaction of both the AspA and GluA with the Co(II) is strong enough as evident from their displacement equilibrium constant values, viz. 4357.8 M(-1) and 8333.33 M(-1) respectively.     

Naked five-coordinate Fe(III)(NO) porphyrin complexes: vibrational and reactivity features

Model ferric heme nitrosyl complexes, [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+), where TPP is the dianion of 5,10,15,20-tetrakis-phenyl-porphyrin and TPFPP is the dianion of 5,10,15,20-tetrakis-pentafluorophenyl-porphyrin, have been obtained as isolated species by the gas phase reaction of NO with [Fe(III)(TPP)](+) and [Fe(III) (TPFPP)](+) ions delivered in the gas phase by electrospray ionization, respectively. The so-formed nitrosyl complexes have been characterized by vibrational spectroscopy also exploiting (15)N-isotope substitution in the NO ligand. The characteristic NO stretching frequency is observed at 1825 and 1859 cm(-1) for [Fe(III)(TPP)(NO)](+) and [Fe(III)(TPFPP)(NO)](+) ions, respectively, providing reference values for genuine five-coordinate Fe(III)(NO) porphyrin complexes differing only for the presence of either phenyl or pentafluorophenyl substituents on the meso positions of the porphyrin ligand. The vibrational assignment is aided by hybrid density functional theory (DFT) calculations of geometry and electronic structure and frequency analysis which clearly support a singlet spin electronic state for both [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+) complexes. Both TD-DFT and CASSCF calculations suggest that the singlet ground state is best described as Fe(II)(NO(+)) and that the open-shell AFC bonding scheme contribute for a high-energy excited state. The kinetics of the NO addition reaction in the gas phase are faster for [Fe(III)(TPFPP)](+) ions by a relatively small factor, though highly reliable because of a direct comparative evaluation. The study was aimed at gaining vibrational and reactivity data on five-coordinate Fe(III)(NO) porphyrin complexes, typically transient species in solution, ultimately to provide insights into the nature of the Fe(NO) interaction in heme proteins.     

Self‐Healing Reduced Graphene Oxide Films by Supersonic Kinetic Spraying

The industrial scale application of graphene and other functional materials in the field of electronics has been limited by inherent defects, and the lack of simple deposition methods. A simple spray deposition method is developed that uses a supersonic air jet for a commercially available reduced graphene oxide (r‐GO) suspension. The r‐GO flakes are used as received, which are pre‐annealed and pre‐hydrazine‐treated, and do not undergo any post‐treatment. A part of the considerable kinetic energy of the r‐GO flakes entrained by the supersonic jet is used in stretching the flakes upon impact with the substrate. The resulting “frozen elastic strains” heal the defects (topological defects, namely Stone‐Wales defect and C₂ vacancies) in the r‐GO flakes, which is reflected in the reduced ratio of the intensities of the D and G bands in the deposited film. The defects can also be regenerated by annealing.     

Crystal Structure and Interaction of 6-Amino Coumarin with Nitrite Ion for Its Selective Fluorescence Detection

ABSTRACT

6-Amino coumarin has been established as an efficient nitrite ion selective fluorescent sensor. The developed method shows linearity up to 1.6 × 10^?6 mol L^?1 of nitrite ion concentration. Interference from other common anions is almost negligible. The reagent shows strong binding affinity towards nitrite ion as evident from its binding constant value (5.8 × 10⁴), estimated by Stern-Volmer method. Some real samples were analyzed. Single crystal X-ray structure of the reagent is reported. Preliminary computational studies on the molecular level interaction between the reagent and nitrite ion were performed by density functional theory (DFT, B3LYP) method.     

A microfocus X‐ray fluorescence beamline at Indus‐2 synchrotron radiation facility

A microfocus X‐ray fluorescence spectroscopy beamline (BL‐16) at the Indian synchrotron radiation facility Indus‐2 has been constructed with an experimental emphasis on environmental, archaeological, biomedical and material science applications involving heavy metal speciation and their localization. The beamline offers a combination of different analytical probes, e.g. X‐ray fluorescence mapping, X‐ray microspectroscopy and total‐external‐reflection fluorescence characterization. The beamline is installed on a bending‐magnet source with a working X‐ray energy range of 4–20 keV, enabling it to excite K‐edges of all elements from S to Nb and L‐edges from Ag to U. The optics of the beamline comprises of a double‐crystal monochromator with Si(111) symmetric and asymmetric crystals and a pair of Kirkpatrick–Baez focusing mirrors. This paper describes the performance of the beamline and its capabilities with examples of measured results.     

Design of a Hybrid Fiber-Optic Network Using 3-D Optical Code Sequences

We present the design of a 3-dimensional (3-D) noncoherent optical hybrid network. We also report the design of a new family of 3-D codes for fiber optic hybrid networks. We show that the hybrid network allows for shorter bit times and a higher number of users, given a set chip rate, compared to previously conceived networks. These newly designed hybrid single-pulse-per-row (HSPR) codes have very low autocorrelation side-lobes and very small cross-correlation peaks. We compare the performance of our hybrid model using our codes with the Optical Orthogonal Codes (OOCs) and Temporal/Spatial (T/S) codes and show that the new network can support a greater number of users and higher data rates than those using OOCs and T/S codes.     

Hedging Uncertainty: Approximation Algorithms for Stochastic Optimization Problems

We study two-stage, finite-scenario stochastic versions of several combinatorial optimization problems, and provide nearly tight approximation algorithms for them. Our problems range from the graph-theoretic (shortest path, vertex cover, facility location) to set-theoretic (set cover, bin packing), and contain representatives with different approximation ratios. The approximation ratio of the stochastic variant of a typical problem is found to be of the same order of magnitude as its deterministic counterpart. Furthermore, we show that common techniques for designing approximation algorithms such as LP rounding, the primal-dual method, and the greedy algorithm, can be adapted to obtain these results.