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Thermodynamics (4):
Recent article
Thermodynamics
Abstract
We present six design rules that can be used to deliberately prepare nine distinct colloidal crystal structures, with control over lattice parameters on the 25- to 150-nanometer length scale. These design rules outline a strategy to independently adjust each of the relevant crystallographic paramete...
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PMID: 21998382
PDF is available here.
PDF is available here.
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Abstract
The influence of temperature and relative air humidity on the stability of omeprazole (OME) in solid state was studied. Changes in the concentration were monitored by HPLC with UV detection. The method was validated; its selectivity, range of linearity, precision, limit of detection (LOD) and limit o...
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PMID: 21928721
PDF is available here.
PDF is available here.
Abstract
The influence of temperature and relative air humidity on the stability of the novel derivative of daunorubicin: [(N-morpholine)metylene]daunorubicin hydrochloride was investigated. The process of degradation was studied by using high-performance liquid chromatography with ultraviolet (UV) detection....
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PMID: 21928722
PDF is available here.
PDF is available here.
Abstract
We show that molecular interactions, e.g., protein-DNA interactions, can be analyzed in a directly analogous manner and with similarly remarkable results. Specifically, mesoscopic molecular interactions act as incoherent sensors that measure the energies of microscopic interactions between atoms. We...
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PMID: 21825146
PDF is available here.
PDF is available here.
Nature Reviews: Genetics (12)9 2011
Abstract
RNA structure is crucial for gene regulation and function. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational pred...
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PMID: 21850044
PDF is available here.
PDF is available here.
Abstract
We recently introduced the enhanced aromatic sequon as a family of portable structural motifs that are stabilized upon glycosylation in specific reverse turn contexts: a five-residue type I β-turn harboring a G1 β-bulge (using a Phe-Yyy-Asn-Xxx-Thr sequon) and a type II β-turn within a six-residu...
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PMID: 21825145
PDF is available here.
PDF is available here.
Abstract
We show that enzymes can also be extremely efficient electrocatalysts (catalysts of redox reactions at electrodes). Despite being large and electronically insulating through most of their volume, some enzymes, when attached to an electrode, catalyze electrochemical reactions that are otherwise extre...
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PMID: 21844379
PDF is available here.
PDF is available here.
Abstract
A new reactive force field to describe proton diffusion within the solid oxide fuel cell material BaZrO(3) has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO(3) ha...
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PMID: 21813946
PDF is available here.
PDF is available here.
Abstract
Our analysis demonstrated that dispersion was the largest correction term that influenced the magnitude of BDE. Previous studies have shown that B3LYP significantly underestimates BDE, whereas BP86 gives BDE values that are fairly close to the experimental values (36-37 kcal/mol). The same trend in...
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PMID: 21806069
PDF is available here.
PDF is available here.
Abstract
We describe the potential of estimating melting temperature (T(m)) for nonstandard oligonucleotides by using the correlation of the experimental T(m) with the calculated duplex binding energy (BE) for oligonucleotides of a given length. This method has been automated into a standardized molecular dy...
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PMID: 21702481
PDF is available here.
PDF is available here.
Abstract
We address this challenge, developing a new methodology for analysing and quantifying image data and its integration with biophysical models. Specifically we fit a binding kinetics model to 2 colour fluorescence data for cytoskeleton independent synapses (2 and 3D) and test whether the observed inve...
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PMID: 21829338
PDF is available here.
PDF is available here.
Ukrainskij biokhimicheskij zhurnal/Ukrayins'kij biokhimichnij zhurnal/Ukrainian biochemical journal (82)6 2011
Abstract
The conformational analysis of the DNA structural unit--the nucleotide with thymine base and electroneutral phosphate group at 5'-position-has been carried out with the applied quantum mechanics methods at the MP2/6-311++G(d,p) // B3LYP/6-31G(d,p) theory level. As many as 660 conformations with relat...
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PMID: 21805865
PDF is available here.
PDF is available here.
Abstract
A series of conformationally flexible bicyclic N-arylimides were employed as molecular balances to study the weak aliphatic CH-π interaction between alkyl and arene groups. The formation of intramolecular CH-π interactions in the folded conformers was characterized by X-ray crystal...
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PMID: 21797218
PDF is available here.
PDF is available here.
Abstract
Our results demonstrate that recording amplitude and noise are relatively independent of microelectrode size, but instead are primarily affected by the selected recording bandwidth, impedance of the electrode-tissue interface and the density and firing rates of neurons surrounding the recording elec...
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PMID: 21775783
PDF is available here.
PDF is available here.
Abstract
The two isomers of 6-stilbene-amide-α-CD (6-StiNH-α-CD) exhibit different inclusion behaviors upon complexation with an alkyl chain bearing pyridinium end caps. Photoisomerization of the stilbene moiety of the CD derivative affects threading due to complexation between the axle and...
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PMID: 21774508
PDF is available here.
PDF is available here.
Scientific American (305)1 2011
Abstract
Abstract
We reassessed this question by performing a global investigation of a genome-scale human metabolic network, which had been reconstructed on the basis of experimental results. By elementary flux pattern analysis, we found numerous pathways on which gluconeogenesis from fatty acids is feasible in huma...
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PMID: 21814506
PDF is available here.
PDF is available here.
Abstract
We have performed fluorescence polarisation assays to indirectly measure relative binding affinity, and applied computational simulations to interrogate the behaviour of the eight human BRC-RAD51 complexes, as well as a suite of BRC cancer-associated mutations. Our computational approaches encompass...
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PMID: 21789034
PDF is available here.
PDF is available here.
Abstract
We use molecular simulations of a coarse-grained model, which reproduces most of the salient features of the experimental melting profiles of PK and HP, to show that crowding enhances the stability of PK relative to HP in the wild type and in a mutant associated with dyskeratosis congenita. In monod...
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PMID: 21736319
PDF is available here.
PDF is available here.
Abstract
We combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry...
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PMID: 21829336
PDF is available here.
PDF is available here.
Abstract
We built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without...
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PMID: 21760760
PDF is available here.
PDF is available here.
Abstract
Polyethylene terephthalate (PET) is a widely used thermoplastic. PET residues represent on average 7.6 wt% of the different polymer wastes in Europe. Pyrolysis of these wastes is attracting increasing interest, and PET is a potential candidate for this thermal process. The paper measures and discusse...
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PMID: 21850826
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1807)11 2011
Abstract
We employed a simple algorithm for calculation of the medium reorganization energy using the numerical solution of the Poisson-Boltzmann equation. Namely, the reaction field energy was computed in two versions - all media having optical dielectric permittivity, and all the media with the static one;...
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PMID: 21777562
PDF is available here.
PDF is available here.
Abstract
The Hepatitis Delta Virus (HDV) ribozyme, which is well adapted to the environment of the human cell, is an excellent candidate for the future development of gene-inactivation systems. On top of this, a new generation of HDV ribozymes now exists that benefits from the addition of a s...
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PMID: 21793786
PDF is available here.
PDF is available here.
Abstract
We applied molecular dynamics simulations and potential of mean force calculations to examine the structures and the free energies associated with these putative drug binding sites in an M2-lipid bilayer system. We found that, at biological pH (∼7.4), the pore binding site is more thermodynamicall...
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PMID: 21711026
PDF is available here.
PDF is available here.
Abstract
Nitrosamines are a class of carcinogenic, mutagenic, and teratogenic compounds generally produced from the nitrosation of amine. This paper investigates the mechanism for the formation of nitrosodimethylamine (NDMA) from the nitrosation of dimethylamine (DMA) by four common nitrosating agents (NO(2)(...
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PMID: 21667950
PDF is available here.
PDF is available here.
Abstract
We have studied the L24A mutant that has been shown previously to form non-native interactions in the folding transition state. A suite of Carr-Purcell-Meiboom-Gill relaxation dispersion NMR experiments have been used to measure backbone chemical shifts and amide bond vector orientations of the invi...
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PMID: 21639149
PDF is available here.
PDF is available here.
Abstract
We have investigated complexes of CK2 protein kinase with halogenated inhibitors by means of the advanced semiempirical quantum mechanical (SQM) PM6 method (called PM6-DH2X), which describes various types of noncovalent interactions including halogen bonding well. The PM6-DH2X method provides reliab...
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PMID: 21648479
PDF is available here.
PDF is available here.
Abstract
Base pairs formed by the inosine nucleoside (I) play an important role in many physiological processes as well as in various DNA technologies. Relative stabilities and favored base pair geometries of free inosine wobble base pairs in aprotic solvents have been determined through (1)H NMR measurements...
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PMID: 21644523
PDF is available here.
PDF is available here.
Abstract
The conformational space of 1H-Indole-3-Acetic Acid (IAA) was scanned using molecular dynamics at semiempirical level, and complemented with functional density calculations at B3LYP/6-31G** level, 14 conformers of lowest energy were obtained. Electronic distributions were analyzed at...
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PMID: 20706854
PDF is available here.
PDF is available here.
Abstract
Magnesium dimers play important roles in inorganic and organometallic chemistry. This study evaluates the inherent bridging ability of a range of different ligands in magnesium dimers. In the first part, the Cambridge Structural Database is interrogated to establish the frequency of...
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PMID: 20820825
PDF is available here.
PDF is available here.
Abstract
Topological analysis based on DFT calculations regarding proton transfer reaction in salicylideneaniline (SA) was performed to scrutinize possible changes in the intramolecular H-bond, pi-electron delocalization and aromaticity levels of certain fragments. Quantum chemical calculatio...
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PMID: 20820826
PDF is available here.
PDF is available here.
Abstract
Quantum chemical methods have been used to study the conformational and electronic properties of sulfanilamide and derivatives with antibacterial activity. Calculations at B3LYP/6-311++G(3df,2p) level of theory predict the existence of four conformers for sulfanilamide depending on t...
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PMID: 20820828
PDF is available here.
PDF is available here.
Abstract
Receptor proteins at the cell surface regulate the ability of natural killer cells to recognize and kill a variety of aberrant target cells. The structural features determining the function of natural killer receptor proteins 1 (NKR-P1s) are largely unknown. In the present work, refi...
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PMID: 20839018
PDF is available here.
PDF is available here.
Abstract
Our analysis showed that dimeric forms predicted theoretically contribute distinctively to the assignments of experimental results. These structures are defined by the orientation of the acetyl moieties with respect to the plane of indole ring. The dimers are formed by two symmetrical IAA monomers (...
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PMID: 20839020
PDF is available here.
PDF is available here.
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis of large, flexible molecules, such as the dopamine reuptake inhibitor GBR 12909 (1), is complicated by the fact that they can take on a wide range of closely-related conformations. The first step in the...
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PMID: 20839021
PDF is available here.
PDF is available here.
Abstract
The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employin...
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PMID: 20842396
PDF is available here.
PDF is available here.
Abstract
Enoyl-acyl carrier protein (ACP) reductase (ENR) is an attractive and potential target for developing selective antibacterial agents. Recent studies showed that FabK is the sole isoform of ENR in Streptococcus pneumoniae, and at the same time an X-ray crystallographic study of FabK f...
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PMID: 20862594
PDF is available here.
PDF is available here.
Abstract
Our simulations suggest the mechanism of acid-induced apatite decomposition to i) require a considerable degree of protonation of the apatite surface. The first ion dissociation step ii) involves calcium ions which electrostatic binding has been locally destabilized through phosphate and hydroxide p...
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PMID: 20886246
PDF is available here.
PDF is available here.
Abstract
Our results make the case that these two strategies greatly enhance the sampling of the conformational space near the native state. A detailed comparative analysis shows that our approach performs as well as state-of-the-art ab initio structure prediction protocols....
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PMID: 21714131
PDF is available here.
PDF is available here.
Abstract
The paper presents the results of viscosity determinations on aqueous solutions of different mammalian serum albumins at a wide range of concentrations and at temperatures ranging from 278 K to 318 K. On the basis of these measurements and a modified Arrhenius equation, the functiona...
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PMID: 21613666
PDF is available here.
PDF is available here.
Abstract
We studied the phase transition behaviors of dipalmitoylphosphatidylcholine (DPPC) by differential scanning calorimetry, synchrotron X-ray scattering, Fourier transform infrared spectroscopy, and image analysis. We found that different parts (head, interface, and tail) of DPPC molecules all exhibit...
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PMID: 21634795
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1807)9 2011
Abstract
We assessed ΔG'(ATP) hydrolysis, cytosolic [ADP], and the rate of phosphocreatine recovery using Phosphorus Magnetic Resonance Spectroscopy in the calf muscle of a group of patients affected by glycogen myo-phosphorylase deficiency (McArdle disease). The goal was to ascertain whether and to what ex...
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PMID: 21722623
PDF is available here.
PDF is available here.
Abstract
For the first time it is shown that exceptionally electron-rich arene rings can be fluorinated exclusively during the reductive elimination reactions of diaryliodonium fluorides. The 5-methoxy[2.2]paracyclophan-4-yl directing group simultaneously reduces unproductive aryne chemistry...
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PMID: 21591627
PDF is available here.
PDF is available here.
Abstract
Core-level X-ray photoemission and near-edge X-ray absorption fine structure spectra of 5-methylcytosine, 5-fluorocytosine, and isocytosine are presented and discussed with the aid of high-level ab initio calculations. The effects of the methylation, halogenation, and isomerization on the relative st...
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PMID: 21591661
PDF is available here.
PDF is available here.
Abstract
Experimental and theoretical studies based on mass spectrometry, collision-induced dissociation, and ab initio calculations are performed on the formation and stability of FeO(n)(+) clusters, as well as on their structural, electronic, and magnetic properties. In the mass spectra, clusters with an ev...
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PMID: 21615142
PDF is available here.
PDF is available here.
Abstract
A constraint-based modeling approach was developed to investigate the metabolic response of the eukaryotic microalgae Chlamydomonas reinhardtii under photoautotrophic conditions. The model explicitly includes thermodynamic and energetic constraints on the functioning metabolism. A mi...
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PMID: 21567987
PDF is available here.
PDF is available here.
Abstract
Simulated annealing of chemical potential located the highest affinity positions of eight organic probes and water on eight static structures of hen egg white lysozyme (HEWL) in various conformational states. The location of the highest affinity binding site for at least six of the o...
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PMID: 21682273
PDF is available here.
PDF is available here.
Abstract
The torquoselectivity of the 4π electrocyclic ring-opening reaction of 2-azetines can be controlled by the Brønsted acidity of the catalyst and the polarity of the solvent. DFT calculations provided insight into the mechanism of this remarkable switch. Anti and syn stereoisomers of α,β-unsaturate...
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PMID: 21557577
PDF is available here.
PDF is available here.
Abstract
We found several well-known inactive Zf cores containing Cys ligands with no H-bonding interactions. Here, we show that H bonds from the peptide backbone or bonds from a second Zn cation to Zn-bound S atoms suppress the reactivity not only of these S atoms, but also of Zn-bound S* atoms with no inte...
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PMID: 21574548
PDF is available here.
PDF is available here.
Abstract
We show that the competition between Mg(2+) and Li(+) depends on the net charge of the metal complex, which is determined by the numbers of metal cations and negatively charged ligands, as well as the relative solvent exposure of the metal cavity. The protein itself is found to select Mg(2+) over th...
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PMID: 21595457
PDF is available here.
PDF is available here.
Abstract
We study a model describing the stochastic dynamics of a group of coupled molecular motors (CMMs). Using two independent numerical methods, one based on the stationary velocity distribution of the motors and the other one on the local increments (also known as the Kramers-Moyal coefficients) of the...
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PMID: 21728577
PDF is available here.
PDF is available here.
Abstract
We established the molecular basis for this model for the archetypal signaling adaptor protein Crk-II by measuring the thermodynamics and kinetics of the equilibrium between autoinhibited and activated-like states. We used fluorescence and NMR spectroscopies together with segmental isotopic labeling...
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PMID: 21532593
PDF is available here.
PDF is available here.
Physical Chemistry (62)1 2011
Abstract
We show that a variety of theoretical approaches, ranging from scaling arguments to minimal models to atomistic simulations, are needed as a complement to experimental studies probing the principles governing protein aggregation....
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PMID: 21219143
PDF is available here.
PDF is available here.
Abstract
We provide the first rationale, at the molecular level, of the regulatory mechanism mediated by casein kinase 2 (CK2) phosphorylation of E2 Cdc34-like enzymes. In particular, we identify two co-evolving signature elements in one of the larger families of E2 enzymes: an acidic insertion in β4α2 loo...
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PMID: 21637798
PDF is available here.
PDF is available here.
Abstract
PX-18 and PX-13 are secretory phospholipase A2-IIA (sPLA2-IIA) inhibitors. An increased expression of sPLA2 in psoriatic skin has been reported. The selective inhibition of this enzyme is a new therapeutic approach. For dermal application PX-18 and PX-13 have been loaded to Nanostructured lipid carri...
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PMID: 21699069
PDF is available here.
PDF is available here.
Abstract
We present what we believe to be a novel procedure, based on combinations of multistep trajectories, that was used to estimate the binding free energy (ΔG) of each disaccharide. The computed binding free energy differences show excellent correlation with experimental values determined previously. T...
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PMID: 21539798
PDF is available here.
PDF is available here.
Abstract
We examine the extent to which the molecular mechanics force field used in such simulations might influence the observed folding pathways. To that end, we performed equilibrium simulations of a fast-folding variant of the villin headpiece using four different force fields. In each simulation, we obs...
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PMID: 21539772
PDF is available here.
PDF is available here.
Abstract
We used atomistic molecular-dynamics simulation to examine the thermodynamic stability of a amyloid fibrils in different polymorphic forms by performing a systematic investigation of sequence and symmetry space for a series of peptides with a range of physicochemical properties. We show that the sta...
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PMID: 21539792
PDF is available here.
PDF is available here.
Abstract
We theoretically modeled the interactions between phospholipid membranes and compared this model with our experimental results on membranes doped with Le(X) lipids. We demonstrated that the bending rigidity, extracted from the off-specular scattering signals, is not significantly influenced by the m...
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PMID: 21539782
PDF is available here.
PDF is available here.