Proteins fold component structure

Because protein ROA spectra contain bands characteristic of loops and turns in addition to bands characteristic of secondary structure, they should provide information on the overall three-dimensional solution structure. We are developing a pattern recognition program, based on principal component analysis (PCA), to identify protein folds from ROA spectral band patterns (Blanch etal., 2002b). The method is similar to one developed for the determination of the structure of proteins from VCD (Pancoska etal., 1991) and UVCD (Venyaminov and Yang, 1996) spectra, but is expected to provide enhanced discrimination between different structural types since protein ROA spectra contain many more structure-sensitive bands than do either VCD or UVCD. From the ROA spectral data, the PCA program calculates a set of subspectra that serve as basis functions, the algebraic combination of which with appropriate expansion coefficients can be used to reconstruct any member of the... 

Quantitative analysis of protein IR and VCD spectra in terms of the fractional components (FC) of their secondary structure has taken different approaches, as noted earlier. The FTIR approach of assigning frequencies to specific components can, in principle, identify amounts of unordered structure in a protein fold. The viability of this approach... 

This discussion puts us in a position to define a set of structural and evolutionary objects the tracing of whose history via homology, as implied by sequence similarity, is the primary aim of sequence analyses. The simple view of protein folding produces a small set of structural components to consider. This is the set of regular secondary structures the amphipathic a helix, the transmembrane or hydrophobic a. helix, the... 

The linear polypeptide chains of a protein fold in a highly specific way that is determined by the sequence of amino acids in the chains. Many proteins are composed of two or more polypeptides. Certain proteins function in structural roles. Some structural proteins interact with lipids in membrane structures. Others aggregate to form part of the cytoskeleton that helps to give the cell its shape. Still others are the chief components of muscle or connective tissue. Enzymes constitute yet another major class of proteins, which function as catalysts that accelerate and direct biochemical reactions. 

Fig. 1. Domain structure of ionotropic glutamate receptors (iGluRs) showing the four major components of mammalian iGluRs and the transmembrane topology. Bacterial iGluRs do not have the ATD and the C-terminal domain, and kainate binding proteins from lower vertebrates do not have the ATD. Note that SI and S2 refer to segments of the primary sequence whereas, Lobes 1 and 2 refer to protein folding units. Both Lobes 1 and 2 are made up of pordons of both SI and S2.

It is interesting to note that although apparently unaware of the development of molecular imprinting, Pande et al. [28] proposed the use of thermodynamic control for the preparation of synthetic polymer systems with a memory for a template structure. Monte Carlo computer simulations were performed to validate their hypothesis. From these calculations they identified the formation of non-random polymer sequences arising from an evolution-like preferred selection of various monomer components by similar species. These studies have since been expanded upon using statistical mechanics to examine the consequences for protein folding [29]. 

---