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Keywords:

  • Proteins;
  • Protein–pigment complexes;
  • Dyes/Pigments;
  • Dynamics;
  • X-ray structure analysis

Abstract

Proteins may be rigid or flexible to various degrees as required for optimal function. Flexibility of large parts of a protein, which rearrange or move, is particularly interesting and will be discussed in this article. We differentiate between several categories, although the boundaries between them are diffuse: flexibility of peptide segments, order–disorder transitions of spatially contiguous regions, and domain motions. The domains may be flexibly linked to allow rather unrestricted motions or the motions may be constrained to certain modes. The various categories of large-scale flexibility will be illustrated with the following examples: (1) Small protein proteinase inhibitors are rather rigid molecules which provide binding surfaces complementary to their cognate proteases but show also limited segmental flexibility and adaptation. (2) Large plasma proteinase inhibitors exhibit large conformational changes after interaction with proteases probably for regulatory purposes. (3) Pancreatic serine proteases employ a disorder–order transition of their activation domain as a means to regulate enzymic activity. (4) Immunoglobulins show rather unrestricted and also hinged domain motions in different parts of the molecule probably to allow binding to antigens in different arrangements. (5) Citrate synthase adopts open and closed forms by a hinged domain motion to bind substrates and release products and to perform the catalytic condensation reaction, respectively. (6) Riboflavin synthase, a bifunctional multienzyme complex, catalyzes two consecutive reactions by means of two subunits, α and β. The β-subunits form a shell, in which the α-subunits are enclosed. Diffusional motion of the catalytic intermediates is therefore restricted. In addition, rearrangement of the N-terminal segment occurs during the assembly of the β-subunit. In contrast, rigidity is dominant in the structures of the light-harvesting complexes and the photosynthetic reaction centers involved in photosynthetic light reactions. These are large protein–pigment complexes in which the proteins serve as matrices to hold the pigments in the appropriate conformation and relative arrangement. Since motion would contribute to deactivation of the photoexcited states of the pigments and diminish the efficiency of light-energy and electron transfer, the functional role of rigidity is easy to rationalize for these proteins.