Secondary structure packing

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

Level 1 Class. Three major classes — namely, mainly a, mainly /1, and both a. and f— are recognized by considering composition or residues in a. helix, /1-strand and the secondary structure packing, plus class 4 for few secondary structures,... 

Once the physico-chemical basis of secondary structure packing is determined, and once the local interactive forces that give rise to secondary structure are known, it vrill be possible to predict both the folding pathway and the final stable conformation of a protein from its amino-add sequence. There are three approaches to these problems, (a) One can correlate sequence and structure using data from as many proteins as possible and derive empirical probabilities for any particular sequence-forming secondary structure, (b) One can derive semi-empirical energy functions for amino-add sequences based on allowed conformation around the... 

BVB Reddy TL Blundell. Packing of secondary structural elements m proteins. Analysis and prediction of mter-helix distances. J Mol Biol 233 464-479, 1993. 

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

Secondary structure occurs mainly as a helices and p strands. The formation of secondary structure in a local region of the polypeptide chain is to some extent determined by the primary structure. Certain amino acid sequences favor either a helices or p strands others favor formation of loop regions. Secondary structure elements usually arrange themselves in simple motifs, as described earlier. Motifs are formed by packing side chains from adjacent a helices or p strands close to each other. 

Figure 6.2 The molten globule state is an important intermediate in the folding pathway when a polypeptide chain converts from an unfolded to a folded state. The molten globule has most of the secondary structure of the native state but it is less compact and the proper packing interactions in the interior of the protein have not been formed.

During this process of designing sequence changes, models were built and assessed to ensure that there were no obvious steric clashes and that the hydrophobic core was well packed. Furthermore, secondary structure prediction was also used to monitor the progress of change and to choose among different possible substitutions. The final sequence (see Table 17.3) contains 28 changes it had 50% identity to B1 and the similarity to Rop had increased from 5.4% identity to 41%. 

Proteins are polymers made of amino acid units. The primary structure of a polypeptide is the sequence of amino acid residues secondary structure is the formation of helices and sheets tertiary structure is the folding into a compact unit quaternary structure is the packing of individual protein units together. 

Such differences in the secondary structure behavior with respect to temperature can be explained by suggesting that molecular close packing of proteins in the film is the main parameter responsible for the thermal stability. In fact, as in the case of BR, we have close packing of molecules even in the solution (membrane fragments) there are practically no differences in the CD spectra of BR solution at least tiU 75°C (denaturation takes place only for the sample heated to 90°C). RC in solution begins to be affected even at 50°C and is completely denatured at 75°C, for the solution contains separated molecules. 

Comparative study of LB films of cytochrome P450 wild type and recombinant revealed similar surface-active properties of the samples. CD spectra have shown that the secondary structure of these proteins is practically identical. Improved thermal stability is also similar for LB films built up from these proteins. Marked differences for LB films of wild type and recombinant protein were observed in surface density and the thickness of the deposited layer. These differences can be explained by improved purity of the recombinant sample. In fact, impurity can disturb layer formation, preventing closest packing and diminishing the surface density and the average monolayer thickness. Decreased purity of... 

M. Vieth, A. Kolinsky, J. Skolnicek, and A. Sikorski, Prediction of protein secondary structure by neural networks, encoding short and long range patterns of amino acid packing. Acta Biochim. Pol., 39 (1992) 369-392. 

Polyacrylamide gel electrophoresis results suggest that p-LG undergoes a greater conformational loss as a fimction of extrusion temperature than a-LA, presumably due to intermolecular disulfide bond formation. Atomic force microscopy indicates that texturization results in a loss of secondary structure of aroimd 15%, total loss of globular structure at 78 °C, and conversion to a random coil at 100 °C (Qi and Onwulata, 2011). Moisture has a small effect on whey protein texturization, whereas temperature has the largest effect. Extrusion at or above 75 °C leads to a uniform densely packed polymeric product with no secondary structural elements (mostly a-helix) remaining (Qi and Onwulata, 2011). 

The principal defining properties of the molten globule are as follows (Arai and Kuwajima, 2000) (1) substantial secondary structure (2) no significant tertiary structure (3) structure only slightly expanded from the native state (10—30% increase in radius of gyration) (4) a loosely packed hydrophobic core with increased solvent accessibility. The first two criteria are readily assessed by far- and near-UV CD, respectively. Therefore, CD has been extensively applied to the detection and characterization of molten globules. 

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