Accessible surface

IV. APPLICATIONS IN STRUCTURAL BIOLOGY A. Secondary Structure and Surface Accessibility... 

A common use of statistics in structural biology is as a tool for deriving predictive distributions of strucmral parameters based on sequence. The simplest of these are predictions of secondary structure and side-chain surface accessibility. Various algorithms that can learn from data and then make predictions have been used to predict secondary structure and surface accessibility, including ordinary statistics [79], infonnation theory [80], neural networks [81-86], and Bayesian methods [87-89]. A disadvantage of some neural network methods is that the parameters of the network sometimes have no physical meaning and are difficult to interpret. 

In its simplest form the competition model assumes the entire adsorbent surface is covered by a monolayer of solute and mobile phase molecules. Under normal chromatographic conditions, the concentration of sample molecules will be small and the adsorbed monolayer will consist mainly of mobile phase molecules. Retention of a solute molecule occurs by displacing a roughly equivalent volume of mobile phase molecules from the monolayer to make the surface accessible to the adsorbed solute aiolecule. For elution of the solute to occur -the above process must be reversible, and can be represented by the equilibrium depicted by equation (4.6)... 

In order to overcome some limitations of the adsorption process due to surface accessibility or diffusional hindering, immobilization of enzymes by direct in situ encapsulation has been investigated. When inorganic supports can be prepared in mild conditions compatible with the enzyme stability, then such processes allow... 

However, just considering the individual properties of each amino acid type is not enough to determine its accessibility to the surrounding aqueous environment. There have been many attempts at developing analytical models with predictive value for determining buried or surface accessible amino acids in a folded polypeptide chain. These studies have concluded fractional assignments for each residue that relate to its accessible surface area (ASA) or its solvent exposed area (SEA). 

For a solid-catalyzed gas-phase reaction, the catalyst is commonly in the form of particles or pellets of various possible shapes and sizes, and formed in various ways. Such particles are usually porous, and the interior surface accessible to the reacting species is usually much greater than the gross exterior surface. 

Affinity chromatography and related techniques (e.g., thiol chromatography and IMAC) are widely used for preparative isolation because they enable a single protein or class of proteins to be selectively purified from very complex mixtures. They may be occasionally used as analytical tools. For example, protein A affinity chromatography has been used for quantitative analysis of immunoglobulins in ascites fluid.45 Information about surface-accessible histidine and phosphate groups may be obtained using IMAC. 

Lynch JW, Reena Han N-L, Haddrill J, Pierce KD, Schofield PR. 2001. The surface accessibility of the glycine receptor M2-M3 loop is increased in the channel open state. J Neurosci 21 2589-2599. 

The C-curve isotherm is similar to the H-curve, being characterized by a linear increase, but also passing through the origin. This behavior may be due to a proportional increase of the adsorbing surface as well as to surface accessibility. 

Since peptides are amphoteric, Zt and Zc are expected to show nonlinear dependencies on pH. Similar behavior has been observed for various synthetic peptides separated on both strong anion and strong cation HP-IEX sorbents. As a consequence, the minima in the In /t iex i versus pH plots at a defined concentration of displacing salt will not usually occur at the predicted p/ value of the peptide, but rather at another pH value. Implementation of an optimized HP-IEX separation of peptides thus requires that the sequence microlocality and extent of ionization of the surface-accessible amino acid side chains, or the N- and C-terminal amino and carboxy groups, respectively, are taken into account. 

An alternative method to investigate DNA strand breakage by OH radicals considers the surface accessibility of hydrogen atoms of the DNA backbone [102]. The solvent accessibility is 80% for the sugar-phosphates and —20% for the bases. This method allows a more direct determination of reaction of OH radicals with the individual deoxyribose hydrogens [103,104]. Recent studies show trends in reactivity of OH radicals closely follow the accessibility of the solvent to various deoxyribose hydrogens [105,106]. 

The hydrophobic component (g23) contains a large entropy contribution, which becomes more significant when the adsorptive substance is a macromolecule such as protein. Peppas et al. regarded the quantity, N2S2, as the hydrophobic exposure area (S2) of the protein. Here, N2 is the total number of carbon atoms contained in the protein, and S2 is their surface accessibility. Thus, the fraction of the hydrophobic exposure area of protein, which is in contact with polymer surface, is expressed as K S2. 

To verify functional results using synthetic peptides, antipeptide antisera were produced [14]. All antipeptide antisera were reactive with the native molecule. Interestingly, antisera titers correlated with the hydropathic index of the peptide, rather than with the predicted surface accessibility of the specific region in the 3-D configuration. Consistent with the peptide studies, antisera against the same four regions of the molecule inhibited IFN- activity while antisera to other regions did not. 

The fact that different types of cell wall respond differently to the decay conditions is clear and extremely interesting. These differentiations no doubt arise partly from differences in the chemical nature of the substances in the walls and lumina. But could they not also arise in part from differences in physical structure—e.g., a porosity or surface accessibility to enzymes or other reaction-inducing substances ... 

The side chain Cotton effect in the 270-290-nm region clearly arises from the tyrosine residues. This effect disappears on denaturation. However, whether the effect is owing to the surface, accessible tyrosines, or... 

A more comprehensive introduction is Ref. [399], We restrict ourselves to uncharged species and dilute solutions (not binary mixtures). The important subject of polymer adsorption is described in Ref. [400], Adsorption of surfactants is discussed in Ref. [401], Adsorption of ions and formation of surface charges was treated in Chapter 5. In dilute solutions there is no problem in positioning the Gibbs dividing plane, and the analytical surface access is equal to the thermodynamic one, as occurs in the Gibbs equation. For a thorough introduction into this important field of interface science see Ref. [8],... 

In some of our earlier studies, we presented values of W [26-30]. MEP maps are usually obtained in terms of contours of equal potential. However, maps giving MEP values on van der Waals surfaces have been found to be more useful for structure-activity correlation [2]. For the same reason, it is preferable to have MEF maps giving values on van der Waals surfaces. Accessibility of atomic sites is an important aspect in connection with MEP studies [32], When MEP or MEF maps are obtained giving values on van der Waals surfaces, accessibility of sites is easily accounted for. We compute MEF at points which are at distances (R + Rj + A) from the atomic sites where R, and Rj are van der Waals radii of atoms of the molecule under study and those of the charged ends of the point dipole (taken to be 1 A each) respectively, and A is a parameter which can be fixed at suitable values in order to generate desired surfaces of closest distance of approach (CDA) between the dipole and atoms of the molecule. 

Induction of apoptosis in cultured cardiocytes results in surface accessibility of the Ro/La antigens (M17). 

PEPOP Clustering of surface accessible segments http //pepop.sysdiag.cnrs.fr/ PEPOP/ Moreau et al. (53)... 

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