NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES

The allowed and the ``disallowed'' regions in the celebrated Ramachandran map (phi-psi] map) was elegantly deduced by Ramachandran, Ramakrishnan and Sasisekharan even before the protein crystal structures became available. This powerful map was derived based on rigid geometry of the peptide group and later several investigations on protein crystal structures reported the occurrence of a small fraction of the phi-psi] torsion angles in the disallowed region. The question is what factors make these residues adopt disallowed conformations? Is it driven by the necessity to maintain the overall topology or is it associated with function or is it just that the disallowed conformations are extreme limits of the allowed conformations? Today, with the availability of a large number of high resolution crystal structures, we have revisited this problem. Apart from validating some of the earlier findings such as residue propensities, preferred location in the secondary structure, we have explored their spatial neighborhood preferences using the protein structure network PSN] approach developed in our lab. Finally, the structural and functional implications of the disallowed conformations are examined.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Field induced domain switching as the origin of anomalous lattice strain along non-polar direction in rhombohedral BiScO3-PbTiO3 close to the morphotropic phase boundary

The lattice strain and domain switching behavior of xBiScO(3)-(1-x) PbTiO3 (x = 0.40) was investigated as a function of cyclic field and grain orientation by in situ X-ray diffraction during application of electric fields. The electric field induced 200 lattice strain was measured to be five times larger than the 111 lattice strain in pseudorhombohedral xBiScO(3)-(1-x) PbTiO3 (x = 0.40). It is shown that the anomalous 200 lattice strain is not an intrinsic phenomenon, but arises primarily due to stress associated with the reorientation of the 111 domains in dense polycrystalline ceramic. (C) 2015 AIP Publishing LLC.

A coupling model for terrestrial processes in arid areas and its application

In this paper, the importance of investigation on terrestrical processes in arid areas for mankind's living environment protection and local economy development as well as its present state of the art are elucidated. A coupling model, which evaluates heat, mass, momentum and radiative fluxes in the SPAC system, is developed for simulating microclimate over plant and bare soil. Especially, it is focussed on the details of turbulence transfer. For illustration, numerical simulation of the water-heat exchange processes at Shapotou Observatory, GAS, Ninxia Province are conducted, and the computational results show that the laws of land-surface processes are rather typical in the arid areas.

Packet error rate and bit error rate non-deterministic relationship in optical network applications

The non-deterministic relationship between Bit Error Rate and Packet Error Rate is demonstrated for an optical media access layer in common use. We show that frequency components of coded, non-random data can cause this relationship. © 2005 Optical Society of America.

Studies on terrestrial interface processes in arid areas, China

In the present paper, we have elucidated the importance of energy and water cycling in arid areas to investigate global climate and local economics. Then, we were concerned with the physical arguments as how to stratify the soil, and the stability of the numerical scheme in the mathematical model for predicting temperature variation and water motion. Furthermore, we discuss the methods to estimate evaporation in arid areas. Numerical simulation of energy and water cycling at the Acsu Observatory, CAS, Xinjiang province and Shapuotou Observatory, CAS, Ningxia Province are conducted as case studies. The results show that the laws of terrestrial processes are rather typical in these arid areas. Planting drought-endurable trees can alleviate unfavourable conditions to a certain extent. (C) 1997 Academic Press Limited.

Non-Stationary Demand in a Durable Goods Monopoly

In a context where demand for the services of a durable good changes over time, and this change may be uncertain, the paper shows that social welfare may be higher when the monopolist seller can commit to any future price level she wishes than when she cannot. Moreover, the equilibrium under a monopolist with commitment power may Pareto-dominate the equilibrium under a monopolist without commitment ability. These results affect the desired regulation of a durable goods monopolist in this context.

Mapping and Distribution of Torpedograss and Evaluating the Effectiveness of Torpedograss Management Activities in Lake Okeechobee, Florida

Thousands of hectares of native plants and shallow open water habitat have been displaced in Lake Okeechobee’s marsh by the invasive exotic species torpedograss ( Panicum repens L.). The rate of torpedograss expansion, it’s areal distribution and the efficacy of herbicide treatments used to control torpedograss in the lake’s marsh were quantified using aerial color infra red (IR) photography.(PDF has 6 pages.)

Breed effect on quality veal production in mountain areas: Emphasis on meat

This study was designed to compare the quality of veal produced from ‘Tudanca x Charolais’ cross (n=6) and Limousin (n=6) breeds when allowed to feed freely on mountain pastures and suckle naturally from birth to 7 months of age. After 80 days of age calves also had access to concentrate (maximum of 3 Kg/day), while mothers did not. At slaughter, Limousin calves were heavier (P<0.01) and provided better carcass yield (P<0.05) and conformation (P<0.001) than Tudanca calves. Tudanca beef provided higher fat content (P<0.05) was less tough (P<0.05), and was scored as more tender and juicy (P<0.1) with higher acceptability than Limousin beef (P<0.1). In general, Tudanca had a better fatty acid profile than Limousin beef, especially in terms of the content of polyunsaturated (P<0.05), long-chain polyunsaturated fatty acids (P<0.05) and their n-6/n-3 ratios (P<0.1), as well as vaccenic acid (P<0.1) and the overall trans-18:1 isomer profile.