The plastid is an organelle vital to all photosynthetic and some non-photosynthetic eukaryotes. In the model plant Arabidopsis thaliana, a number of nuclear genes encoding plastid proteins have been found to be necessary for embryo development. However, the exact roles of plastids in this process remain largely unknown. Here we use publicly available datasets to obtain insights into the relevan...

When purified without the use of ionic detergents, both OmpA and OprF proteins contained nearly 20% alpha-helical structures, which disappeared completely upon the addition of sodium dodecyl sulfate. This result suggests that the proteins fold in a similar manner, with an N-terminal, membrane-spanning beta-barrel domain and a C-terminal, globular, periplasmic domain.

β-barrel membrane proteins (TMBs) perform a variety of functions in living organisms and these proteins contain β-strands as their membrane spanning segments. The membrane spanning segments of TMBs contain several charged and polar residues in contrast with a stretch of hydrophobic amino acid residues in transmembrane helical (TMH) proteins. Hence, most predictive schemes, which are successful ...

The score matrix from a structure comparison program (SAP) was used to search for repeated structures using a Fourier analysis. When tested with artificial data, a simple Fourier transform of the smoothed matrix provided a clear signal of the repeat periodicity that could be used to extract the repeating units with the SAP program. The strength of the Fourier signal was calibrated against the s...

There is a growing recognition for the importance of proteins with large intrinsically disordered (ID) segments in cell signaling and regulation. ID segments in these proteins often harbor regions that mediate molecular recognition. Coupled folding and binding of the recognition regions has been proposed to confer high specificity to interactions involving ID segments. However, researchers rece...

The GraphiteLifeExplorer tool enables biologists to reconstruct 3D cellular complexes built from proteins and DNA molecules. Models of DNA molecules can be drawn in an intuitive way and assembled to proteins or others globular structures. Real time navigation and immersion offer a unique view to the reconstructed biological machinery.

abstract adsorption of proteins on inorganic surfaces may lead to structural and functional changes that are dependent on both the nature of the adsorbed proteins and the physicochemical properties of the inorganic surfaces. chicken egg white lysozyme (e.c 3.2.1.17, mw=14.6 kda) is a small globular protein, that consists of 129 amino acid residues with four disulfide bonds. the aim of this stud...

Understanding the sequence-structure relationships in globular proteins is important for reliable protein structure prediction and de novo design. Using a database of 1131 alpha-helices with nonidentical sequences from 205 nonhomologous globular protein chains, we have analyzed structural and sequence characteristics of alpha-helices. We find that geometries of more than 99% of all the alpha-he...

Dynamic Monte Carlo studies have been performed on various diamond lattice models of 8-proteins. Unlike previous work, no bias toward the native state is introduced; instead, the protein is allowed to freely hunt through all of phase space to find the equilibrium conformation. Thus, these systems may aid in the elucidation of the rules governing protein folding from a given primary sequence; in...

1. Correlation between elution volume, V(e), and molecular weight was investigated for gel filtration of proteins of molecular weights ranging from 3500 (glucagon) to 820000 (alpha-crystallin) on Sephadex G-200 columns at pH7.5. 2. Allowing for uncertainties in the molecular weights, the results for most of the carbohydrate-free globular proteins fitted a smooth V(e)-log(mol.wt.) curve. In the ...