Secondary and tertiary structure

The lack of secondary and tertiary structures is probably significant for the following reasons  

The caseins are readily susceptible to proteolysis, in contrast to globular proteins, e.g. whey proteins, which are usually very resistant in their 

The caseins adsorb readily at air-water and oil-water interfaces due to their open structure, relatively high content of apolar amino acid residues and the uneven distribution of amino acids. This gives the caseins very good emulsifying and foaming properties, which are widely exploited in the food industry. 

The lack of higher structures probably explains the high stability of the caseins to denaturing agents, including heat. 

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Beratan D N, Betts J N and Onuchic J N 1991 Protein electron transfer rates set by the bridging secondary and tertiary structure Science 252 1285-8... 

Model optimization is a further refinement of the secondary and tertiary structure. At a minimum, a molecular mechanics energy minimization is done. Often, molecular dynamics or simulated annealing are used. These are frequently chosen to search the region of conformational space relatively close to the starting structure. For marginal cases, this step is very important and larger simulations should be run. 

The Danish biochemist Kai Linderstrom-Lang coined the terms "primary," "secondary," and "tertiary" structure to emphasize the structural hierarchy in... 

Figure 18.17 Two-dimensional NMR spectnim of the C-terminal domain of a cellulase. The peaks along the diagonal correspond to the spectrum shown in Figure 18.16b. The off-diagonal peaks in this NOE spectrum represent interactions between hydrogen atoms that are closer than 5 A to each other in space. From such a spectrum one can obtain information on both the secondary and tertiary structures of the protein. (Courtesy of Per Kraulis, Uppsala.)...

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). 

In contrast, RNA occurs in multiple copies and various forms (Table 11.2). Cells contain up to eight times as much RNA as DNA. RNA has a number of important biological functions, and on this basis, RNA molecules are categorized into several major types messenger RNA, ribosomal RNA, and transfer RNA. Eukaryotic cells contain an additional type, small nuclear RNA (snRNA). With these basic definitions in mind, let s now briefly consider the chemical and structural nature of DNA and the various RNAs. Chapter 12 elaborates on methods to determine the primary structure of nucleic acids by sequencing methods and discusses the secondary and tertiary structures of DNA and RNA. Part rV, Information Transfer, includes a detailed treatment of the dynamic role of nucleic acids in the molecular biology of the cell. 

Denaturation (Section 26.9) The physical changes that occur in a protein when secondary and tertiary structures are disrupted. 

Kurian, E., Fisher, P. J., Ward, W. W., and Prendergast, F. G. (1994). Characterization of secondary and tertiary structure of the green fluorescent protein from A. victoria. J. Biolumin. Chemilumin. 9 333. 

A problem with employment of ASON in a larger clinical setting is their poor uptake and inappropriate intracellular compartmentalization, e.g., sequestration in endosomal or lysosomal complexes. In addition, there is a need for a very careful selection of the ASON-mRNA pair sequences that would most efficiently hybridize. To date, several computer programs are used to predict the secondary and tertiary structures of the target mRNA and, in turn, which of the mRNA sequences are most accessible to the ASON. However, even with this sophisticated techniques, the choice of base-pairing partners still usually includes a component of empiricism. Despite these principal limitations, it has become clear that ASON can penetrate into cells and mediate their specific inhibitory effect of the protein synthesis in various circumstances. 

Proteins derive their powerful and diverse capacity for molecular recognition and catalysis from their ability to fold into defined secondary and tertiary structures and display specific functional groups at precise locations in space. Functional protein domains are typically 50-200 residues in length and utilize a specific sequence of side chains to encode folded structures that have a compact hydrophobic core and a hydrophilic surface. Mimicry of protein structure and function by non-natural ohgomers such as peptoids wiU not only require the synthesis of >50mers with a variety of side chains, but wiU also require these non-natural sequences to adopt, in water, tertiary structures that are rich in secondary structure. 

It is important to note that the secondary and tertiary structure of peptides to which they are attached may subsequently help in controUing the reactivity of... 

Figure 5-10. Primary, secondary, and tertiary structures of collagen.

The properties of individual hemoglobins are consequences of their quaternary as well as of their secondary and tertiary structures. The quaternary structure of hemoglobin confers striking additional properties, absent from monomeric myoglobin, which adapts it to its unique biologic roles. The allosteric (Gk alios other, steros space ) properties of hemoglobin provide, in addition, a model for understanding other allosteric proteins (see Chapter 11). 

Myoglobin the p Subunits of Hemoglobin Share Almost Identical Secondary and Tertiary Structures... 

Amino acid sequences of eleven homologous sea anemone polypeptides have been elucidated. All possess three disulfide bonds. The six half-cysteine residues always occur in the same positions (7,8). Initial studies concerning the toxin secondary and tertiary structures relied upon circular dichroism, laser Raman, and, to a lesser extent, fluorescence spectral measurements (15—18). The circular dichroism spectra of the four toxins so far examined are essentially superimpos-able and thus indicate a common secondary structure. The only peak observed, a negative ellipticity at 203 nm, largely results from a non-regular ("random")... 

Some chemical modification studies on the sea anemone toxins have unfortunately been less than rigorous in analyzing the reaction products. Consequently, results from many of these studies can only provide suggestions, rather than firm conclusions, regarding the importance of particular sidechains. Many such studies also have failed to determine if the secondary and tertiary structures of the toxin products were affected by chemical modification. 

We have sequenced RpII and studied the structures of RpII and RpIII in solution by 2D-NMR and distance geometry methods. The resonances are almost completely assigned, and secondary and tertiary structures have been determined. Our results indicate that Rp toxins have a four strand anti-parallel )9-sheet and no a-helix. Functionally important residues are found to be located in looped regions of the... 

C13-0031. Define primary, secondary, and tertiary structure. Give examples of each type of structure for a protein and for DNA. 

Enzymes frequently lose their activity and secondary and tertiary structural integrity immediately upon incorporation into w/o-MEs, particularly for systems containing ionic surfactants such as AOT [61-67], It is the author s belief that this occurs if INJ is not conducted quickly because of the exposure of biomolecules to macroscopic interfaces... 

Amongst the secretions of specialised exocrine complexes, the ancillary products which act as sticky compounds are large, often proteinaceous, molecules. Their primary, secondary and tertiary structures being inherently complex are now seen as ideal informational vehicles — alone or in combination with volatile molecules. Much recent work (Sec. 3.2, below) has identified them as the key components involved in close range transmission, and in intra-nasal peri-receptor events. Proteins are semiochemically implicated when their selective removal or presentation alters responsiveness (Belcher et al., 1990 Mucignat-Caretta et al, 1995). 

Cross-links, which impose strong conformational constraints on the intervening segment of the chain, generally are not classified as elements of secondary or tertiary structure. Disulfide cross-links in protein may certainly stabilize both secondary and tertiary structure, and such cross-links have the... 

The denaturation of proteins generally involves at least partial unfolding, with the loss of secondary and tertiary structure. In the present context, we are interested in the end point of this process — proteins that are unfolded to the maximal extent by various agents heat, cold, acid, urea, Gdm-HCl.1 Three major questions concerning unfolded proteins are of interest in the present chapter. Do different unfolding agents... 

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