domains for reordering CLP(RLin) programs V. Ramachandran, P. Van Hentenryck, A. Cortesi* a Brown University, Computer Science Department, Box 1910, Providence, RI 02912, USA b Universite Catholique de Louvain, 2 Place Sainte-Barbe, B-1348 Louvain-la-Neuve, Belgium c Universit a Ca' Foscari, Dipartimento di Informatica, via Torino 155, 1-30170 Venezia, Italy Received 8 November 1997; received ...

We present a three-dimensional model of the rat type 1 receptor (AT1) for the hormone angiotensin II (Ang II). Ang II and the AT1 receptor play a critical role in the cell-signaling process responsible for the actions of renin-angiotensin system in the regulation of blood pressure, water-electrolyte homeostasis and cell growth. Development of improved therapeutics would be significantly enhance...

Helicobacter pylori is the major causative agent of Gastric carcinoma. Significance of the urease accessory interaction proteins are emphasized in colonization of human gastric mucosa and efficient infection of H. pylori. Here an attempt is made to explore the structure and properties of urease accessory interaction proteins from Helicobacter pylori J 99. The proteins chosen for the study are u...

During protein folding and as part of some conformational changes that regulate protein function, the polypeptide chain must traverse high-energy barriers that separate the commonly adopted low-energy conformations. How distortions in peptide geometry allow these barrier-crossing transitions is a fundamental open question. One such important transition involves the movement of a non-glycine res...

Homology modeling and structural analysis of human glutamate cysteine ligase catalytic subunit (hGCLC) were performed with a software package the Molecular Operating Environment. A yeast GCLC (yGCLC; PDB code: 3LVV) was selected as a template for the 3D structure modeling of hGCLC. The modeled hGCLC showed significant 3D similarities at the ligand biding site (LBS) to the yGCLC structure. The c...

In the study of the conformational behavior of complex systems, such as proteins, several related statistical measures are commonly used to compare two different potential energy functions. Among them, the Pearson's correlation coefficient r has no units and allows only semiquantitative statements to be made. Those that do have units of energy and whose value may be compared to a physically rel...

A protein can fold efficiently with high fidelity if on average native contacts survive longer than non-native ones. If native contacts survive long enough to obtain a certain level of probability that other native contacts form before the first interacting unit dissociates this provides the folding process with directionality towards the native state and no particular pathway is needed. Intera...

The impact of pressure on the backbone (15) N, (1) H and (13) C chemical shifts in N-terminally acetylated α-synuclein has been evaluated over a pressure range 1-2500 bar. Even while the chemical shifts fall very close to random coil values, as expected for an intrinsically disordered protein, substantial deviations in the pressure dependence of the chemical shifts are seen relative to those in...

P. A. Jarzyna, L. H. Deddens, B. H. Kann, S. Ramachandran, C. Calcagno, W. Chen, A. Gianella, R. M. Dijkhuizen, A. W. Griffioen, Z. A. Fayad, and W. J. Mulder Translational and Molecular Imaging Institute, Radiology, Mount Sinai School of Medicine, New York, NY, United States, Image Sciences Institute, University Medical Center Utrecht, Utrecht, Netherlands, Angiogenesis Laboratory, Department ...

We present a new algorithm for performing ab initio solution phase geometry optimizations. The procedure is based on the self consistent-reaction-field method developed in our laboratory which combines electronic structure calculations with a finite element formulation of the continuum electrostatics problem. A gradient for the total solution phase free energy is obtained by combining different...