Protein Ordered structure

In addition to being a remarkable demonstration of the power of computer-based combinatorial design of a protein fold, this designed peptide is the shortest known peptide consisting entirely of naturally occurring amino acids that folds into a well-ordered structure without metal binding, oligomerization or disulfide bond formation. 

The atoms of a protein s structure are usually defined by four parameters, three coordinates that give their position in space and one quantity, B, which is called the temperature factor. For well refined, correct structures these B-values are of the order of 20 or less. High B-values, 40 or above, in a local region can be due to flexibility or slight disorder, but also serve as a warning that the model of this region may be incorrect. 

The biological function of biopolymers such as polypeptides, proteins, nucleic acids etc. depends strongly on their ordered structure which is determined by the pattern of inter- and intramolecular interactions given by the primary structure. 

Fig. 7. Scheme of the intermolecular forces stabilizing ordered structures in polypeptides and proteins m... 

Figure 3 Examples of higher-order structure in proteins the a-helix and P-sheet.

The essential distinction between the approaches used to formulate and evaluate proteins, compared with conventional low molecular weight drugs, lies in the need to maintain several levels of protein structure and the unique chemical and physical properties that these higher-order structures convey. Proteins are condensation polymers of amino acids, joined by peptide bonds. The levels of protein architecture are typically described in terms of the four orders of structure [23,24] depicted in Fig. 2. The primary structure refers to the sequence of amino acids and the location of any disulfide bonds. Secondary structure is derived from the steric relations of amino acid residues that are close to one another. The alpha-helix and beta-pleated sheet are examples of periodic secondary structure. Tertiary... 

An advantage of NMR spectroscopy is the analysis of protein dynamics. Measurement and analysis of the relaxation parameters R1 R2, and the 15N NOE of 15N-labeled proteins leads to an order parameter (S2) that can describe the relative mobility of the backbone of the protein. Both collagenase-1 and stromelysin-1 have been studied either as inhibited complexes or the free protein [19, 52], Stromleysin-1 was studied with inhibitors binding to prime or nonprime subsites. Presence or absence of inhibitors in the nonprime sites had minor effects on the highly ordered structure of residues in these subsites, which are in contact with the... 

Three groups of disordered proteins have been assembled, with the groups defined by the experimental method used to characterize the lack of ordered structure. Because the focus has been on long regions of disorder, an identified disordered protein or region was not included in these groups if it failed to contain 40 or more consecutive residues. Disordered regions from otherwise ordered proteins as well as wholly disordered proteins were identified. Table I summarizes the collection of sequences in this database. 

A change in the environment of a protein molecule, e.g. adsorption from aqueous solution onto a sorbent surface, may lead to a partial breakdown of its ordered structure, resulting in an increase of conformational entropy. This is a fundamental difference between protein adsorption and the adsorption of flexible polymers, for which attachment to a surface implies a loss of conformational entropy. 

Based on these contributions (a-d), we may arrive at the predictive scheme presented in Table 1. Because of the relatively large contribution from dehydration, essentially all proteins adsorb from an aqueous environment on apolar surfaces, even under electrostatically adverse conditions. With respect to polar surfaces, distinction may be made between proteins having a strong internal coherence ( hard proteins) and those having a weak internal coherence ( soft proteins). The hard proteins adsorb at polar surfaces only if they are electrically attracted, whereas the structural rearrangements (i.e., reductions in ordered structure) in the soft proteins lead to a sufficiently large increase in conformational entropy to make them adsorb at a polar, electrostatically repelling surface. 

The influence of adsorption on the structure of a -chymotrypsin is shown in Fig. 10, where the circular dichroism (CD) spectrum of the protein in solution is compared with that of the protein adsorbed on Teflon and silica. Because of absorbance in the far UV by the aromatic styrene, it is impossible to obtain reliable CD spectra of proteins adsorbed on PS and PS- (EO)8. The CD spectrum of a protein reflects its composition of secondary structural elements (a -helices, / -sheets). The spectrum of dissolved a-chymotrypsin is indicative of a low content of or-helices and a high content of //-sheets. After adsorption at the silica surface, the CD spectrum is shifted, but the shift is much more pronounced when the protein was adsorbed at the Teflon surface. The shifts are in opposite directions for the hydrophobic and hydrophilic surfaces, respectively. The spectrum of the protein on the hydrophilic surface of silica indicates a decrease in ordered secondary structure, i.e., the polypeptide chain in the protein has an increased random structure and, hence, a larger conformational entropy. Adsorption on the hydrophobic Teflon surface induces the formation of ordered structural elements, notably an increase in the content of O -helices (cfi, the discussion in Sect. 3.1.4). 

Therefore, in order to identify copolymers possessing a protein-like structure, it is necessary to choose a property with which one can distinguish them unambiguously from random copolymers or alternating block-copolymers. 

For proteins the X-ray structures usually are not determined at high enough resolution to use anisotropic temperature factors. Average values for B in protein structures range from as low as a few A2 for well-ordered structures to 30 A2 for structures involving flexible surface loops. Using equation 3.6, one can calculate the root mean square displacement fu2 for a well-ordered protein structure at approximately 0.25 A (for B = 5 A2) and for a not-so-well-ordered structure at... 

AFM imaging of the protein A array deposited on an HOPG plate showed an ordered alignment of protein molecules when the measurement was made in a pH 7.0 lOmM phosphate buffer at a controlled force of 4 X 10"H N and a scanning rate of 0.6 Hz. However, an ordered structure was not observed unless the protein A molecules were not cross-linked by glutaraldehyde. 

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