Polarity-charged-hydrophobicity

The definition of pharmacophores is done manually by applying so-called schemes using a Pharmacophore Query Editor. A template molecule is generally used for this purpose. In the MOE environment, a scheme is a collection of functions that define how each ligand is annotated. This is accessed via an SVL function. The default scheme is called PCH (Polarity-Charged-Hydrophobicity). New schemes can be created to represent certain molecules better, e.g. Planar-Polar-Charged- Hydrophobiaty [91]. 

The basic assembly kit of 20 amino acids (Table 4.1) can be divided notionally into those which have non-polar, uncharged and generally hydrophobic side chains those which have polar, but uncharged side chains and those which have polar, charged side chains. 

All of these models predict that the hydrophobic effect provides a significant driving force for the exclusion of even highly polar, charged peptides from an aqueous environment to the nonpolar environment of the RPC sorbent. According to the solvophobic model, in order to place a peptide into a mobile phase, a cavity of the same molecular dimensions must first be created. The energy required to create this cavity is related to the cohesive energy density or the surface tension of the mobile phase. Conceptually, each solvent-accessible unit... 

Strikingly, the solvation dynamics for all mutants are nearly the same. All correlation functions can be best described by a double exponential decay with time constants of 0.67 ps with 68% of the total amplitude and 13.2 ps (32%) for D60, 0.47 ps (67%) and 12.7 (33%) for D60G, and 0.53 ps (69%) and 10.8 ps (31%) for D60N. Relative to SNase above, the solvation dynamics are fast, which reflects the neighboring hydrophobic environment. We also measured the anisotropy dynamics and, as shown in the inset of Fig. 33, the local structure is very rigid in the time window of 800 ps. This observation is consistent with the inflexible turn (-T30W31-) in the transition from the second /1-sheet and the second x-helix (Fig. 31). Thus, the three mutants, with a charged, polar, or hydrophobic reside around the probe (Fig. 34) but with the similar time scales of... 

ProTherm (16) is a large collection of thermodynamic data on protein stability, which has information on 1) protein sequence and stmcture (2) mutation details (wild-type and mutant amino acid hydrophobic to polar, charged to hydrophobic, aliphatic to aromatic, etc.), 3) thermodynamic data obtained from thermal and chemical denaturation experiments (free energy change, transition temperature, enthalpy change, heat capacity change, etc.), 4) experimental methods and conditions (pH, temperature, buffer and ions, measurement and method, etc.), 5) functionality (enzyme activity, binding constants, etc.), and 6) literature. 

For the mutations on the surface of the protein, the classifications based on the chemical nature of amino acids, such as hydrophobic amino acids (Ala, Cys, Phe, Gly, He, Leu, Met, Val, Trp, and Tyr), amino acid side chains that can form hydrogen bonds (Asp, Cys, Glu, His, Lys, Met, Asn, Gin, Arg, Ser, Thr, Trp, and Tyr), and so forth, improved the correlation between amino acid properties and protein mutant stability. Furthermore, the inclusion of neighboring and surrounding residues remarkably improved the correlation in all the subgroups of mutations. This result indicates that the information from nearby polar/charged amino acid residues and/or the aliphatic and aromatic residues that are close in space is important for the stability of exposed mutations. 

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