Solvent exposed area

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]. 

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). 

Reactions done with NHS-PEG -biotin compounds typically are done with the reagent in molar excess over the amount of protein being modified. The efficiency of the reaction is dependent on the concentrations of reactants and the solvent exposed area of the amine groups on the protein. Reactions done with a 10-fold molar excess of NHS-PEG -biotin usually will result in at least 2-3 biotin labels per protein, while doubling the molar excess should provide 4-6 biotinylations. The optimal number of biotin groups added to a particular protein should be determined experimentally to provide the best performance in the intended application. 

How might one think about this energy as it is felt in the transition between the forms of hemoglobin with a difference of 60 associated water molecules and a 550-A difference in solvent exposed area Even if hydration energy of the exposed protein surface were only one-tenth of that for PC or DNA, the expected contribution would be... 

A. Wallqvistand D. G. Covell,y. Phys. Chem., 99,13118 (1995). Free-Energy Cost of Bending w-Dodecane in Aqueous Solution. Influence of the Hydrophobic Effect and Solvent Exposed Area. 

Due to its lipidic nature, anandamide is barely soluble in water. In this case, it is impossible for the neurotransmitter to bind to a solvent-exposed area of its receptor, as schematized for classical neurotransmitter/receptor couples (Fig. 5.5). Instead, the ligand-binding domain of anandamide receptors (e.g., the cannabinoid receptor CBl in the brain) is made from a cluster of transmembrane helices. To reach this intramembrane binding site, anandamide has to penetrate the lipid bilayer before binding to the transmembrane embedded helices of the receptor. The molecular details of this intriguing mechanism are described in Section 5.2. 

---