Protein , association 1960 Volume

Here,. Ai(X) is the partial SASA of atom i (which depends on the solute configuration X), and Yi is an atomic free energy per unit area associated with atom i. We refer to those models as full SASA. Because it is so simple, this approach is widely used in computations on biomolecules [96-98]. Variations of the solvent-exposed area models are the shell model of Scheraga [99,100], the excluded-volume model of Colonna-Cesari and Sander [101,102], and the Gaussian model of Lazaridis and Karplus [103]. Full SASA models have been used for investigating the thermal denaturation of proteins [103] and to examine protein-protein association [104]. 

Combination of the Perrin function, p often referred as the frictional ratio due to shape with the frictional ratio (f/fo) enables the degree of expansion of the molecule (vh/ w ) to be estimated, where Vh, (cw / g) is the volume of the swollen molecule (Polysaccharide or protein + associated solvent) per unit mass of polysaccharide and v is the partial specific volume (essentially the anhydrous molecule) ... 

Protein Subunit Dissociation-Association Volumes and Protein Denaturation Volumes ... 

Assessment of protein-associated activity with trichloroacetic acid precipitation a. Dilute a small volume of the pooled radiolabeled streptavidin with saline solution such that 50 pL of the diluted solution has 104—106 cpm. b Add 50 pL of the diluted streptavidin solution to a 12 x 75-mm glass tube, followed by 500 pL of a 0.1% BSA solution in saline, c. For precipitating the proteins, add 500 pL of 10% (w/v) TCA solution in saline. 

The main protein component of chromatin is histones, which are basic proteins associated with the DNA in the form of structures called nucleosomes (Fig. 6.3) (12). The DNA can be stored in very small, compact forms called condensed DNA, which is 10 - to 106-fold less in volume than uncondensed DNA. The main force that must be overcome in the condensation process is charge repulsion because of the negatively charged phosphates in the polyanion. This repulsion may be overcome by DNA interaction with multivalent organic and inorganic cations. The histones, which are the major components of the nucleosome, are cationic organic proteins that interact with DNA in the compact nucleosome structure. 

This Advances in Protein Chemistry volume on Proteins in Eukaryotic Transcription seeks to provide an up-to-date account of the proteins and mechanisms of eukaryotic transcription and to illuminate the intimate cross-talk among eukaryotic RNA polymerases, their transcription factors, and the enzymes that expedite their journeys through chromatin. The first three chapters are devoted to Pol II and its associated transcription factors. Chapter 1 by Cramer describes the structure and function of Pol II, with special emphasis on the recent landmark high-resolution crystal resolutions of the enzyme. Chapter 2 provides an account by Bjorklund and... 

Prior to the availability of time-resolved measurements, such so-called Perrin plots were used extensively to determine the apparent hydrodynamic volume of proteins [129—131]. Since protein association reactions usually affect the rotational correlation time of the protein label, such reactions have been characterized by steady state anisotropy measurements [132, 133]. 

One general benefit of subunit association is a favorable reduction of the protein s surface-to-volume ratio. The surface-to-volume ratio becomes smaller as the radius of any particle or object becomes larger. (This is because surface area is a function of the radius squared and volume is a function of the radius cubed.) Because interactions within the protein usually tend to stabilize the protein energetically and because the interaction of the protein surface with... 

The cytoskeleton also contains different accessory proteins, which, in accordance with their affinities and functions, are designated as microtubule-associated proteins (MAPs), actin-binding proteins (ABPs), intermediate-filament-associated proteins (IFAPs), and myosin-binding proteins. This chapter is focused on those parts of the cytoskeleton that are composed of microfilaments and microtubules and their associated proteins. The subject of intermediate filaments is dealt with in detail in Volume 2. 

Both of the above approaches rely in most cases on classical ideas that picture the atoms and molecules in the system interacting via ordinary electrical and steric forces. These interactions between the species are expressed in terms of force fields, i.e., sets of mathematical equations that describe the attractions and repulsions between the atomic charges, the forces needed to stretch or compress the chemical bonds, repulsions between the atoms due to then-excluded volumes, etc. A variety of different force fields have been developed by different workers to represent the forces present in chemical systems, and although these differ in their details, they generally tend to include the same aspects of the molecular interactions. Some are directed more specifically at the forces important for, say, protein structure, while others focus more on features important in liquids. With time more and more sophisticated force fields are continually being introduced to include additional aspects of the interatomic interactions, e.g., polarizations of the atomic charge clouds and more subtle effects associated with quantum chemical effects. Naturally, inclusion of these additional features requires greater computational effort, so that a compromise between sophistication and practicality is required. 

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