A novel conjugate of a cell-penetrating peptide and a ferrocenyl amino acid: a potential electrochemical sensor for living cells?

The conjugation of a ferrocenyl amino acid to the cell-penetrating peptide hCT(9-32) does not impair its ability to efficiently translocate into cells. Furthermore, the bioconjugate does not induce any cytotoxicity, thus presenting a potential electrochemical sensor suitable for the detection of living cells.     

How and how much can Hoechst 33258 cause unwinding in a DNA duplex?

The effect of Hoechst 33258 binding on the geometry of a DNA duplex (plasmid pBR322) has been examined using topoisomerase II relaxation followed by gel electrophoresis. Of this drug-DNA system, fluorescence, optical absorption, and calorimetric measurements were also made at various drug and DNA concentrations and in the same buffer as that for the topoisomerase reaction. It has been confirmed that there are two modes of drug-DNA interaction. When the drug concentration is much lower than the DNA base pair concentration, the Hoechst 33258 molecule binds in the minor groove of the DNA duplex and occupies a site formed of five continuous base pair sequences that contain no G.C pair. Here, the equilibrium constant K1 is 1.8 x 10(7) M-1 (at 37 degrees C), and the enthalpy of binding delta H1 is -865 cal/mol. When the drug concentration is much higher, on the other hand, it shows another binding mode which is much weaker, so that K2 = 2.25 x 10(4) M-1 and delta H2 is -464 cal/mol, which gives fluorescence quenching, which has no base pair preference, and which causes an unwinding of the duplex by 1 degree.     

Prediction of the reduction potential in transition‐metal containing complexes: How expensive? For what accuracy?

Accurate computationally derived reduction potentials are important for catalyst design. In this contribution, relatively inexpensive density functional theory methods are evaluated for computing reduction potentials of a wide variety of organic, inorganic, and organometallic complexes. Astonishingly, SCRF single points on B3LYP optimized geometries with a reasonably small basis set/ECP combination works quite well‐‐B3LYP with the BS1 [modified‐LANL2DZ basis set/ECP (effective core potential) for metals, LANL2DZ(d,p) basis set/LANL2DZ ECP for heavy nonmetals (Si, P, S, Cl, and Br), and 6‐31G(d') for other elements (H, C, N, O, and F)] and implicit PCM solvation models, SMD (solvation model based on density) or IEFPCM (integral equation formalism polarizable continuum model with Bondi atomic radii and α = 1.1 reaction field correction factor). The IEFPCM‐Bondi‐B3LYP/BS1 methodology was found to be one of the least expensive and most accurate protocols, among six different density functionals tested (BP86, PBEPBE, B3LYP, B3P86, PBE0, and M06) with thirteen different basis sets (Pople split‐valence basis sets, correlation consistent basis sets, or Los Alamos National Laboratory ECP/basis sets) and four solvation models (SMD, IEFPCM, IPCM, and CPCM). The MAD (mean absolute deviation) values of SCRF‐B3LYP/BS1 of 49 studied species were 0.263 V for SMD and 0.233 V for IEFPCM‐Bondi; and the linear correlations had respectable R ² values (R ² = 0.94 for SMD and R ² = 0.93 for IEFPCM‐Bondi). These methodologies demonstrate relatively reliable, convenient, and time‐saving functional/basis set/solvation model combinations in computing the reduction potentials of transition metal complexes with moderate accuracy. © 2017 Wiley Periodicals, Inc.     

How simple can a thermotropic mesogenic molecule be? Supramolecular layers through a network of hydrogen bonds

The supramolecular approach was applied to obtain a thermotropic liquid crystalline phase from the smallest possible molecules. Diaminobenzene derivatives are able to form smectic layers through a network of interconnected hydrogen bonded rings. The observed smectic A phase exhibits unusually small optical birefringence, comparable with that of lyotropic lamellar phases.     

How many dimensions are required to approximate the potential energy landscape of a model protein?

A scheme to approximate the multidimensional potential energy landscape in terms of a minimal number of degrees of freedom is proposed using a linear transformation of the original atomic Cartesian coordinates. For one particular off-lattice model protein the inherent frustration can only be reproduced satisfactorily when a relatively large number of coordinates are employed. However, when this frustration is removed in a Go-type model, the number of coordinates required is significantly lower, especially around the global potential energy minimum. To aid our interpretation of the results we consider modified disconnectivity graphs where a measure of the structural diversity and a metric relation between the stationary points are incorporated.     

Critical chromatography of macromolecules as a tool for reading the amino acid sequence of biomacromolecules: Reality or science fiction?

The capabilities of critical chromatography to study the amino acid sequences in biopolymer, peptide, and protein macromolecules are discussed. The rearrangement of two or more amino acid residues and the occurrence and location of modified residues in a chain are considered. The mechanism of an inversion in the order of peptide elution under changes in the gradient of the solvent composition is discussed.     

Is it possible to predict the average surface hydrophobicity of a protein using only its amino acid composition?

Hydrophobicity is one of the most important physicochemical properties of proteins. Moreover, it plays a fundamental role in hydrophobic interaction chromatography, a separation technique that, at present time, is used in most industrial processes for protein purification as well as in laboratory scale applications. Although there are many ways of assessing the hydrophobicity value of a protein, recently, it has been shown that the average surface hydrophobicity (ASH) is an important tool in the area of protein separation and purification particularly in protein chromatography. The ASH is calculated based on the hydrophobic characteristics of each class of amino acid present on the protein surface. The hydrophobic characteristics of the amino acids are determined by a scale of aminoacidic hydrophobicity. In this work, the scales of Cowan-Whittaker and Berggren were studied. However, to calculate the ASH, it is necessary to have the three-dimensional protein structure. Frequently this data does not exist, and the only information available is the amino acid sequence. In these cases it would be desirable to estimate the ASH based only on properties extracted from the protein sequence. It was found that it is possible to predict the ASH from a protein to an acceptable level for many practical applications (correlation coefficient > 0.8) using only the aminoacidic composition. Two predictive tools were built: one based on a simple linear model and the other on a neural network. Both tools were constructed starting from the analysis of a set of 1982 non-redundant proteins. The linear model was able to predict the ASH for an independent subset with a correlation coefficient of 0.769 for the case of Cowan-Whittaker and 0.803 for the case of Berggren. On the other hand, the neural model improved the results shown by the linear model obtaining correlation coefficients of 0.831 and 0.836, respectively. The neural model was somewhat more robust than the linear model particularly as it gave similar correlation coefficients for both hydrophobicity scales tested, moreover, the observed variabilities did not overcome 6.1% of the mean square error. Finally, we tested our models in a set of nine proteins with known retention time in hydrophobic interaction chromatography. We found that both models can predict this retention time with correlation coefficients only slightly inferior (11.5% and 5.5% for the linear and the neural network models, respectively) than models that use the information about the three-dimensional structure of proteins.     

Is X-ray absorption spectroscopy sensitive to the amino acid composition of functional proteins?

We report, compare, and analyze near-edge X-ray absorption fine structure (NEXAFS) spectra of powder samples of four different functional proteins, namely, lysozyme, ovalbumin, bovine serum albumin, and type-I collagen, at all relevant absorption edges. The spectra of all of the above proteins were found to be quite similar and to exhibit minor differences only. Nevertheless, despite the general similarity, the spectra of the individual proteins are distinguishable, and some of the respective differences clearly correlate with their amino acid compositions. Further factors affecting the NEXAFS spectra of proteins beyond the building block approach are discussed.     

How large a 3JHCCH coupling can be? Prediction of giant vicinal couplings in quinonoid systems

Second-order polarization propagator approximation (SOPPA) and density functional theory (DFT) B3LYP computations revealed the presence of giant ³J_HCCH couplings, up to more than 60 Hz, in conjugated quinonoid systems, very far above the typical limit of ~15 Hz. Strong hyperconjugative interactions of the C–H σ orbitals with the quinonoid 8-e⁻ π system, which allows effective propagation of the spin polarization, seem to be responsible for those extraordinarily large couplings. Computation on several model systems showed the additive nature of the contributions from the available coupling paths to the total coupling.     

BINOL-derived phosphoramidites in asymmetric hydrogenation: can the presence of a functionality in the amino group influence the catalytic outcome?

In discovering the remarkable catalytic properties of BINOL-derived phosphoramidites (binoP-NR(2)), Dutch researchers recently achieved a long-awaited breakthrough in asymmetric catalysis. For the first time, easily accessible monodentate chiral P(III) ligands turned out to provide high enantioselectivities when used in rhodium-catalysed olefin hydrogenation. The simplest ligand representative of this family is MonoPhos, which can be made straightforwardly from BINOL and hexamethylphosphorous triamide. Since the first publication dealing with such catalysts (J. Am. Chem. Soc., 2000), a variety of binoP-NRR' ligands have been reported in which the amino group bears a functional substituent or a stereogenic centre. This critical review examines the impact of the presence of such a functionality in the amino group on catalytic olefin hydrogenation reactions.     

How dominant is the most efficient pathway through the potential energy landscape of a slowly diffusing disordered system?

It has been suggested that the most-efficient pathway taken by a slowly diffusing many-body system is its geodesic path through the parts of the potential energy landscape lying below a prescribed value of the potential energy. From this perspective, slow diffusion occurs just because these optimal paths become particularly long and convoluted. We test this idea here by applying it to diffusion in two kinds of well-studied low-dimensional percolation problems: the 2d overlapping Lorentz model, and square and simple-cubic bond-dilute lattices. Although the most efficient path should be at its most dominant with the high-dimensional landscapes associated with many-body problems, it is useful to examine simpler, low-dimensional, constant-potential-energy problems such as these ones, both because the simpler models lend themselves to more accurate geodesic-path-finding approaches, and because they offer a significant contrast to many of the models used in the traditional energy-landscape literature. Neither the continuum nor the lattice percolation examples are adequately described by our geodesic-path formalism in the weakly disordered (relatively-fast-diffusion) limit, but in both cases the formalism successfully predicts the existence of the percolation transition and (to a certain extent) the slow diffusion characteristic of near-percolation behavior. The numerical results for these models are not nearly accurate enough near their transitions to describe critical exponents, but the models do showcase the qualitative validity of the geodesic perspective in that they allow us to see explicitly how tortuous and sparse the optimal pathways become as the diffusion constants begin to vanish.     

How many proteins can be identified in a 2DE gel spot within an analysis of a complex human cancer tissue proteome?

Two‐dimensional gel electrophoresis (2DE) in proteomics is traditionally assumed to contain only one or two proteins in each 2DE spot. However, 2DE resolution is being complemented by the rapid development of high sensitivity mass spectrometers. Here we compared MALDI‐MS, LC‐Q‐TOF MS and LC‐Orbitrap Velos MS for the identification of proteins within one spot. With LC‐Orbitrap Velos MS each Coomassie Blue‐stained 2DE spot contained an average of at least 42 and 63 proteins/spot in an analysis of a human glioblastoma proteome and a human pituitary adenoma proteome, respectively, if a single gel spot was analyzed. If a pool of three matched gel spots was analyzed this number further increased up to an average of 230 and 118 proteins/spot for glioblastoma and pituitary adenoma proteome, respectively. Multiple proteins per spot confirm the necessity of isotopic labeling in large‐scale quantification of different protein species in a proteome. Furthermore, a protein abundance analysis revealed that most of the identified proteins in each analyzed 2DE spot were low‐abundance proteins. Many proteins were present in several of the analyzed spots showing the ability of 2DE‐MS to separate at the protein species level. Therefore, 2DE coupled with high‐sensitivity LC‐MS has a clearly higher sensitivity as expected until now to detect, identify and quantify low abundance proteins in a complex human proteome with an estimated resolution of about 500 000 protein species. This clearly exceeds the resolution power of bottom‐up LC‐MS investigations.     

Optimization of enzymatic biochemical logic for noise reduction and scalability: how many biocomputing gates can be interconnected in a circuit?

We report an experimental evaluation of the "input-output surface" for a biochemical AND gate. The obtained data are modeled within the rate-equation approach, with the aim to map out the gate function and cast it in the language of logic variables appropriate for analysis of Boolean logic for scalability. In order to minimize "analog" noise, we consider a theoretical approach for determining an optimal set for the process parameters to minimize "analog" noise amplification for gate concatenation. We establish that under optimized conditions, presently studied biochemical gates can be concatenated for up to order 10 processing steps. Beyond that, new paradigms for avoiding noise buildup will have to be developed. We offer a general discussion of the ideas and possible future challenges for both experimental and theoretical research for advancing scalable biochemical computing.     

Palladium-catalyzed C–H alkenylation of quinoxaline N-oxide enabled by a mono-N-protected amino acid

The efficient alkenylation of quinoxaline N-oxide was achieved via Pd-catalyzed C–H activation, using the assistance of a mono-N-protected amino acid. Further deoxygenation of the 2-styrylquinoxaline-N-oxides yielded the corresponding styrylquinoxaline derivatives.     

NMR crystallography of zeolites: How far can we go without diffraction data?

Nuclear magnetic resonance (NMR) crystallography—an approach to structure determination that seeks to integrate solid-state NMR spectroscopy, diffraction, and computation methods—has emerged as an effective strategy to determine structures of difficult-to-characterize materials, including zeolites and related network materials. This paper explores how far it is possible to go in determining the structure of a zeolite framework from a minimal amount of input information derived only from solid-state NMR spectroscopy. It is shown that the framework structure of the fluoride-containing and tetramethylammonium-templated octadecasil clathrasil material can be solved from the 1D ²⁹Si NMR spectrum and a single 2D ²⁹Si NMR correlation spectrum alone, without the space group and unit cell parameters normally obtained from diffraction data. The resulting NMR-solved structure is in excellent agreement with the structures determined previously by diffraction methods. It is anticipated that NMR crystallography strategies like this will be useful for structure determination of other materials, which cannot be solved from diffraction methods alone.     

How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?

We estimate the statistical distribution of relative orientations between contacting residues from a database of protein structures and evaluate the potential of mean force for relative orientations between contacting residues. Polar angles and Euler angles are used to specify two degrees of directional freedom and three degrees of rotational freedom for the orientation of one residue relative to another in contacting residues, respectively. A local coordinate system affixed to each residue based only on main chain atoms is defined for fold recognition. The number of contacting residue pairs in the database will severely limit the resolution of the statistical distribution of relative orientations, if it is estimated by dividing space into cells and counting samples observed in each cell. To overcome such problems and to evaluate the fully anisotropic distributions of relative orientations as a function of polar and Euler angles, we choose a method in which the observed distribution is represented as a sum of delta functions each of which represents the observed orientation of a contacting residue, and is evaluated as a series expansion of spherical harmonics functions. The sample size limits the frequencies of modes whose expansion coefficients can be reliably estimated. High frequency modes are statistically less reliable than low frequency modes. Each expansion coefficient is separately corrected for the sample size according to suggestions from a Bayesian statistical analysis. As a result, many expansion terms can be utilized to evaluate orientational distributions. Also, unlike other orientational potentials, the uniform distribution is used for a reference distribution in evaluating a potential of mean force for each type of contacting residue pair from its orientational distribution, so that residue-residue orientations can be fully evaluated. It is shown by using decoy sets that the discrimination power of the orientational potential in fold recognition increases by taking account of the Euler angle dependencies and becomes comparable to that of a simple contact potential, and that the total energy potential taken as a simple sum of contact, orientation, and (phi,psi) potentials performs well to identify the native folds.     

Playing with podands based on cone-shaped cavities. How can a cavity influence the properties of an appended metal centre?

The potential of molecules that combine the properties of a conical cavity with those of a covalently-linked transition-metal centre is highlighted through the assessment of cyclodextrin- and calixarene-derived podands ("cavitand" ligands) in coordination chemistry and catalysis. Metallocavitands with coordination sites directed towards the interior of the generic cavity provide interesting systems for studying host-guest complexation processes, their enhanced strength of metal-ion binding allowing for regioselective catalysis in a confined environment, and stabilisation of coordination complexes of unusual forms. Where cavitands have exo-oriented podand arms, the intrinsic dynamics of the cavity can dramatically modify metal chelation behaviour and the catalytic properties of the complexes. Such functionalised cavities are also useful as metal-ion transporters.     

Mediated spectroelectrochemical determination of holo-transferrin reduction potential using a flow cell with disposable screen-printed indium‑tin oxide electrode

A convenient spectroelectrochemical method for the determination of holo-transferrin reduction potential is described. All materials and accessories are commercially available and the results are in agreement with previous reports that required custom-built hardware. The method requires minimal preparation with simple sample handling, small solution volume, cost-effective electrode replacement and automated measurement. This method can easily be applied to the study of similar systems in aqueous media and might be of particular importance in the momentous field of glycomics, where large numbers of protein isoforms need to be characterized.