A critical evaluation of the performance of X-ray refinement protocols using various energy functions is presented using the bovine pancreatic trypsin inhibitor (BPTI) protein. The four potential energy functions we explored include: (1) fully quantum mechanical calculations; (2) one based on an incomplete molecular mechanics (MM) energy function employed in the Crystallography and NMR System (...

Pairwise interaction models to recognize native folds are designed and analyzed. Different sets of parameters are considered but the focus was on 20 x 20 contact matrices. Simultaneous solution of inequalities and minimization of the variance of the energy find matrices that recognize exactly the native folds of 572 sequences and structures from the protein data bank (PDB). The set includes man...

Canonical cap-dependent translation initiation requires a large number of protein factors that act in a stepwise assembly process. In contrast, internal ribosomal entry sites (IRESs) are cis-acting RNAs that in some cases completely supplant these factors by recruiting and activating the ribosome using a single structured RNA. Here we present the crystal structures of the ribosome-binding domai...

Characterization of aerosol optical properties, such as aerosol optical depth, Angstrom exponent, and volume size distribution at the semiarid site of Tombstone Arizona (31823VN, 110805VW, 1408 m) will be presented for one annual cycle. In this region, extensive observations of selected optical parameters such as aerosol optical depth (AOD) have been made in the past and reported on in the lite...

We introduce a minimally invasive technique for optoacoustic imaging of turbid media using optical interferometric detection of surface displacement produced by thermoelastic stress transients. The technique exploits endogenous or exogenous optical contrast of heterogeneous tissues and the low attenuation of stress wave propagation to localize and image subsurface absorbers in optically turbid ...

Atomic force microscopes employ stacked or cylindrical piezoceramic actuators to achieve sub-angstrom resolution. While these devices produce excellent set-point accuracy, they exhibit hysteresis and constitutive nonlinearities even at low drive levels. Feedback mechanisms can mitigate the deleterious effects of these nonlinearities for low frequency operation but such techniques fail at higher...

Abstract Cracks are formed along the photolithographically pre-determined lines with extremely high yield and repeatability, when Cu clusters introduced between planarized Au thin films sequentially deposited on a PET substrate. These act as nanometer-sized spacers preventing formation of contiguous metallic bond adjacent layers which will render prepatterned-cracking impossible. While effectiv...

Background. HNF-1a is a transcription factor that regulates glucose metabolism by expression in various tissues. Aim. To dock potential ligands of HNF-1a using docking software in silico. Methods. We performed in silico studies using HNF-1a protein 2GYP·pdb and the following softwares: ISIS/Draw 2.5SP4, ARGUSLAB 4.0.1, and HEX5.1. Observations. The docking distances (in angstrom units: 1 angstr...

During protein synthesis, translational release factors catalyze the release of the polypeptide chain when a stop codon on the mRNA reaches the A site of the ribosome. The detailed mechanism of this process is currently unknown. We present here the crystal structures of the ribosome from Thermus thermophilus with RF1 and RF2 bound to their cognate stop codons, at resolutions of 5.9 Angstrom and...