Sulfonated molecules that bind a partially structured species of beta2-microglobulin also influence refolding and fibrillogenesis

Human beta2-microglobulin (beta2-m) is a small amyloidogenic protein responsible for dialysis-related amyloidosis, which represents a severe complication of long-term hemodialysis. A therapeutic approach for this amyloidosis could be based on the stabilization of beta2-m through the binding to a small molecule, to possibly inhibit protein misfolding and amyloid fibril formation. The search of a strong ligand of this protein is extremely challenging: by using CE in affinity and refolding experiments we study the effect that previously selected sulfonated molecules have on the equilibrium between the native form and an ensemble of conformers populating the slow phase of beta2-m folding. These data are correlated with the effect that the same molecules exert on in vitro fibrillogenesis experiments.     

Algorithmic dimensionality reduction for molecular structure analysis

Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation--a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.     

Sieve-based device for MALDI sample preparation. I. Influence of sample deposition conditions in oligonucleotide analysis to achieve significant increases in both sensitivity and resolution

Spraying of oligonucleotide-matrix solutions through a stainless steel (ss) sieve (38 microm, 450 mesh) leads to the formation, on the matrix-assisted laser desorption/ionization (MALDI) sample holder, of uniformly distributed microcrystals, well separated from each other. When the resulting sample holder surface is irradiated by laser, abundant molecular species form, with a clear increase in both intensity and resolution with respect to values obtained by 'Dried Droplet', 'Double Layer', and 'Sandwich' deposition methods. In addition, unlike the usual situation, the sample is perfectly homogeneous, and identical spectra are obtained by irradiating different areas. On one hand, the data indicate that this method is highly effective for oligonucleotide MALDI analysis, and on the other, that it can be validly employed for fully automated MALDI procedures.     

Rate constants for the gas-phase reactions of OH radicals with dimethyl phosphonate over the temperature range of 278-351 K and for a series of other organophosphorus compounds at approximately 280 K

Rate constants for the gas-phase reactions of OH radicals with dimethyl phosphonate [DMHP; (CH3O)2P(O)H] were measured over the temperature range of 278-351 K at atmospheric pressure of air using a relative rate method with 4-methyl-2-pentanone as the reference compound. The Arrhenius expression obtained was 1.01 x 10(-12) e((474 +/- 159)/T) cm(3) molecule(-1) s(-1), where the indicated error is two least-squares standard deviations and does not include uncertainties in the rate constants for the reference compound. Rate constants for the gas-phase reactions of OH radicals with dimethyl methylphosphonate [DMMP, (CH3O)2P(O)CH3], dimethyl ethylphosphonate [DMEP, (CH3O)2P(O)C2H5], diethyl methylphosphonate [DEMP, (C2H5O)2P(O)CH3], diethyl ethylphosphonate [DEEP, (C2H5O)2P(O)C2H5], and triethyl phosphate [TEP, (C2H5O)3PO] were also measured at 278 and/or 283 K for comparison with a previous study (Aschmann, S. M.; Long, W. D.; Atkinson, R. J. Phys. Chem. A, 2006, 110, 7393). With the experimental procedures employed, experiments conducted at temperatures below the dew point where a water film was present on the outside of the Teflon reaction chamber resulted in measured rate constants which were significantly higher than those expected from the extrapolation of rate data obtained at temperatures (283-348 K) above the dew point. Using rate constants measured at > or = 283 K, the resulting Arrhenius expressions (in cm(3) molecule(-1) s(-1) units) are 6.25 x 10(-14) e((1538 +/- 112)/T) for DMMP (283-348 K), 9.03 x 10(-14) e((1539 +/- 27)/T) for DMEP (283-348 K), 4.35 x 10(-13) e((1444 +/- 148)/T) for DEMP (283-348 K), 4.08 x 10(-13) e((1485 +/- 328)/T) for DEEP (283-348 K), and 4.07 x 10(-13) e((1448 +/- 145)/T) for TEP (283-347 K), where the indicated errors are as above. Aerosol formation at 296 +/- 2 K from the reactions of OH radicals with these organophosphorus compounds was relatively minor, with aerosol yields of < or = 8% in all cases.     

SCKs as nanoparticle carriers of doxorubicin: investigation of core composition on the loading, release and cytotoxicity profiles

SCK nanoparticles having differing core thermal characteristics were designed and evaluated as thermoresponsive drug delivery systems of doxorubicin for the killing of cancerous cells.     

Organic thin-film transistors based on carbonyl-functionalized quaterthiophenes: high mobility N-channel semiconductors and ambipolar transport

New carbonyl-functionalized quaterthiophenes, 5, 5' '-diheptanoyl-2,2':5',2' ':5' ',2' '-quaterthiophene (DHCO-4T), 5, 5' '-diperfluorohexylcarbonyl-2,2':5',2' ':5' ',2' '-quaterthiophene (DFHCO-4T), and 2,7-[bis-(5-perfluorohexylcarbonylthien-2-yl)]-4H-cyclopenta[2,1-b:3,4-b']-dithiophen-4-one (DFHCO-4TCO) have been synthesized and characterized. Field-effect transistors fabricated with these materials exhibit high electron mobilities both in a vacuum (up to 0.6 cm2 V-1 s-1) and in air (up to 0.02 cm2 V-1 s-1) and very high Ion:Ioff currents ratios (>107). DHCO-4T is the first organic material exhibiting excellent ambipolar transport (mue/muh up to 0.1/0.01 cm2 V-1 s-1, (Ion:Ioff)e/(Ion:Ioff)h up to 107/108 for the same device) over a broad range of deposition temperatures. These materials are therefore promising for organic complementary circuits.     

Homochiral conglomerates and racemic crystals in two dimensions: tartaric acid on Cu(110)

Two-dimensional lattice structures formed by racemic tartaric acid on a single crystalline Cu(110) surface have been studied and compared with the enantiopure lattices. At low coverage, the doubly deprotonated bitartrate species is separated into two-dimensional conglomerates showing opposite enantiomorphism. At higher coverage, however, a singly deprotonated monotartrate species forms a heterochiral, racemic crystal lattice. While the enantioseparated bitartrate system undergoes decomposition at the same temperature as the enantiopure system, the racemic monotartrate lattice has a lower thermal stability than the enantiopure lattice of identical periodicity and surface density. At monolayer saturation coverage, the pure enantiomers form a denser lattice than the racemate. This is in contrast to the three-dimensional tartaric acid crystals, where the racemate crystallizes in a lattice of higher density, which is also more thermally stable than the enantiopure tartaric acid crystals.     

Proteolytic cleavage reveals interaction patterns between silica nanoparticles and two variants of human carbonic anhydrase

To characterize the sites on the protein surface that are involved in the adsorption to silica nanoparticles and the subsequent rearrangements of the protein/nanoparticle interaction, a novel approach has been used. After incubation of protein with silica nanoparticles for 2 or 16 h, the protein was cleaved with trypsin and the peptide fragments were analyzed with mass spectrometry. The nanoparticle surface area was in 16-fold excess over available protein surface to minimize the probability that the initial binding would be affected by other protein molecules. When the fragment patterns obtained in the presence and absence of silica nanoparticles were compared, we were able to characterize the protein fragments that interact with the surface. This approach has allowed us to identify the initial binding sites on the protein structure and the rearrangement of the binding sites that occur upon prolonged incubation with the surface.