Amino acid free energy change

Almost all problems that require knowledge of free energies are naturally formulated or can be framed in terms of (1.15) or (1.16). Systems 0 and 1 may differ in several ways. For example, they may be characterized by different values of a macroscopic parameter, such as the temperature. Alternatively, they may be defined by two different Hamiltonians, 3%o and 3%, as is the case in studies of free energy changes upon point mutation of one or several amino acids in a protein. Finally, the definitions of 0 and 1 can be naturally extended to describe two different, well-defined macroscopic states of the same system. Then, Q0 is defined as ... 

M. A. S. Saqi and J. M. Goodfellow, Free energy changes associated with amino acid... 

Fig. 12.5 Free energy change (expressed in kcal mol per amino acid) upon folding of hGH (a) at pH 7.0, and (b) at pH 2.6 [8]. Folding free energies are mapped on the X-ray structure (1 HCU) by colored segments according to the key at the right. Cray indicates residues that were not analyzed [34],...

Measured s values (helix propagation factor values) obtained by various groups110,12,24-311 for all the amino acids are listed in Table 1. Chakrabartty and Baldwin1281 have also compared free-energy changes and determined rank orders of helix propensities of all the amino acids as measured in various experimental peptide systems. 

Exercise 15-42 The amino acid methionine is a methyl donor in biological methyla-tion of hydroxyl groups. However, direct methylation has an unfavorable free energy change ... 

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. 

The hydrocarbon core of a membrane is typically 30 A wide, a length that can be traversed by an a helix consisting of 20 residues. We can take the amino acid sequence of a protein and estimate the free-energy change that takes place when a hypothetical a helix formed of residues 1 through 20 is transferred from the membrane interior to water. The same calculation can be made for residues 2 through 21,3 through 22, and so forth, until we reach the end of the sequence. 

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