Structurefunction Relationships

Structural changes of food proteins usually take place during processing. Because the structure closely relates to food quality, optimization of processing conditions to obtain the best quality is one of the most important objectives of food protein research. From the aspect of structure-function relationships of food proteins, there are three categories of structure changes. (J) The purpose of processing is not for changing structures, but the processing results in structure changes. An example is pasteurization or sterilization. (2) The structural changes are the main purpose of processing, such as in breadmaking. (3) A new type of structure change to be introduced, including chemical, enzymatic, and genetic changes of protein structure, optimizes these changes to achieve the best functions. The functions include all the chemical, physical, and biological properties of protein molecules. The use of bioactive peptides or proteins found in natural resources as ingredients in food is quickly becoming a new trend for contributing to human health. A new concept of chemopreventive agents is being introduced into diet to prevent diseases (59).

Meanwhile, a new paradigm is being discussed for protein research. A novel concept of protein substructure based on a knot-matrix construction principle revealed a much more powerful paradigm for protein research than that based on protein secondary structures (60). For mac-romolecular crystal structure analysis, the simple Debye-Waller model has been widely used. In this treatment of atomic motion, the probability of finding an atom in a given distance x from its equilibrium position Xq IS Gaussian. If it is assumed that the motion is isotropic, the model states that the motion in any direction can be characterized in terms of a mean-square vibration amplitude, (x2), also termed the mean-square displacement. The X-ray scattering from each atom is modified by a Gaussian function that is related to the mean-square displacement of that atom. The form of the Gaussian is exp(-£ sinW)

where 6 is the Bragg angle, A is the wavelength of the incident radiation, and B is related to the mean-square displacement by

B is called Debye-Waller factor (59). The B factor provides useful information about conformational dynamics, which is calculated for each nonhydrogen atom.

Three groups of B factors are distinguished: group I, from 2 to 8 A2; group II, 8-14 A2; and group III, all higher values. Functional domains consist of one group I substructure (knot) to which is tethered most of the group II atoms (matrices) of the domain. Group III atoms are restricted to surface. In the knot-matrix construction principle, which explains properties of protein molecules, especially functions, knots determine palindromic B factor patterns and matrices put them to work. Palindromic patterns can be found on B factor vs atom-number plots as two functional domains against the residue lying halfway between them. The palindromic patterns control specificity of proteins such as enzymes and antibodies (60).

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