We have used the occluded surface algorithm to estimate the packing of both buried and exposed amino acid residues in protein structures. This method works equally well for buried residues and solvent-exposed residues in contrast to the commonly used Voronoi method that works directly only on buried residues. The atomic packing of individual globular proteins may vary significantly from the ave...

A detailed understanding of the ion and counterion distribution and its effect on protein-protein interactions are essential for many biological systems. We have performed normal SAXS studies on a model globular protein, bovine serum albumin (BSA) in solution as a function of protein concentration, ionic strength and also the nature of the added salt [1,2]. We recently observed a reentrant cond...

RD1 is a 7-kDa globular protein from the Antarctic eel pout Lycodichthys dearborni. It belongs to type III of the four types of antifreeze proteins (AFPs) found in marine fishes living at subzero temperatures. For type III AFP, a potential ice-binding flat surface has been identified and is imbedded with side chains capable of making hydrogen bonds with a specific lattice plane on ice. So far, ...

The human rhinovirus 14 (HRV14) protomer, with or without the antiviral compound WIN 52084s, was simulated using molecular dynamics and rotational symmetry boundary conditions to model the effect of the entire icosahedral capsid. The protein asymmetrical unit, comprising four capsid proteins (VP1, VP2, VP3, and VP4) and two calcium ions, was solvated both on the exterior and the interior to fil...

Tiam1 and Tiam2 (Tiam1/2) are guanine nucleotide-exchange factors that possess the PH-CC-Ex (pleckstrin homology, coiled coil and extra) region that mediates binding to plasma membranes and signalling proteins in the activation of Rac GTPases. Crystal structures of the PH-CC-Ex regions revealed a single globular domain, PHCCEx domain, comprising a conventional PH subdomain associated with an an...

Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric for...

We discuss the statistical mechanical foundation for the two-state transition in the protein folding of small globular proteins. In the standard arguments of protein folding, the statistical search for the ground state is carried out from astronomically many conformations in the configuration space. This leads us to the famous Levinthal’s paradox. To resolve the paradox, Gō first postulated tha...

There has been a great deal of interest in proteins over the last century because fibrous proteins are structurally central in muscle, skin and hair, while globular proteins catalyze most biological reactions, are involved in the control of gene expression, facilitate transport of other molecules, and control signaling across cell membranes. Most proteins in all organisms can be described as he...

ABSTRACT Lipid droplets (LDs) are globular subcellular structures that store neutral lipids. LDs closely associated with the endoplasmic reticulum (ER) and limited by a phospholipid monolayer harboring specific set of proteins. Most these proteins associate through either an amphipathic helix or membrane-embedded hairpin motif. Here, we address question whether integral membrane can localize to...

in this article we introduce the notion of textit{fractal $omega$-operad} emerging from  a natural $omega$-operad associated to any coglobular object in the category of higher operads in batanin's sense, which in fact is a coendomorphism $omega$-operads. we have in mind coglobular object of higher operads which algebras are kind of higher transformations. it follows that this natural $omega$-op...