Tertiary Motifs

There are a few examples of three-helix bundles, notably the protein A fragment 

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Costa, M., and Michel, P. (1995). Frequent use of the same tertiary motif by self-folding RNAs. EMBOJ. 14, 1276-1285. 

RNA motifs refer to the small, finite and natmaUy occurring structmal elements of RNAs that are present abundantly as non-canonical bps in hairpins/loops (loop motifs) and sequences involved in tertiary interactions (tertiary motifs). The most important secondary structural element in RNA is the A-form double helix (A-helix). However, motifs. 

A key prerequisite for obtaining statistically meaningful averages and fluctuations from molecular dynamics simulations is a proper equilibration of the system. Several measures have been suggested to test if the system is near equilibrium [1]. First, the overall dynamically averaged structure may be compared with the X-ray structure as shown in Figure 7.1. A system far removed from equilibrium is likely to display considerable structural deviation (e.g. denatured), and as is evident from the figure, this is not the case. The overall three-dimensional structure and tertiary motif is essentially preserved in the simulations. 

A common tertiary motif composed of p-sheets is the p-barrd. A p-barrel is a large p-sheet that twists and coils to form a dosed stmcture in which the first strand is hydrogen bonded to the last, as depicted in Figure 4. p-Strands are typically antiparalld, with hydrophobic residues oriented in the interior of the band to form a hydrophobic core and the polar residues oriented toward the exterior of the band. Membrane protdns containing p-bands reverse this pattern, with hydrophobic residues oriented toward the exterior where they interact with sunotmd-ing lipids, and hydrophilic residues oriented toward the interior. 

For example, a polypeptide is synthesized as a linear polymer derived from the 20 natural amino acids by translation of a nucleotide sequence present in a messenger RNA (mRNA). The mature protein exists as a weU-defined three-dimensional stmcture. The information necessary to specify the final (tertiary) stmcture of the protein is present in the molecule itself, in the form of the specific sequence of amino acids that form the protein (57). This information is used in the form of myriad noncovalent interactions (such as those in Table 1) that first form relatively simple local stmctural motifs (helix... 

Fig. 5. Protein folding. The unfolded polypeptide chain coUapses and assembles to form simple stmctural motifs such as -sheets and a-hehces by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) stmcture in this way. Larger proteins and multiple protein assembhes aggregate by recognition and docking of multiple domains (eg, -barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further stmctural...

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

Several motifs usually combine to form compact globular structures, which are called domains. In this book we will use the term tertiary structure as a common term both for the way motifs are arranged into domain structures and for the way a single polypeptide chain folds into one or several domains. In all cases examined so far it has been found that if there is significant amino acid sequence homology in two domains in different proteins, these domains have similar tertiary structures. 

These predictive methods are very useful in many contexts for example, in the design of novel polypeptides for the identification of possible antigenic epitopes, in the analysis of common motifs in sequences that direct proteins into specific organelles (for instance, mitochondria), and to provide starting models for tertiary structure predictions. 

Upon mutagenesis of the monoamine oxidase from Aspergillus niger (MAO-N) within several rounds of directed evolution [65], variant biocatalysts were identified with largely expanded substrate acceptance, enabling also the deracemization of tertiary amines incorporating straight-chain and cyclic structural motifs [66]. 

Pt(en)(N03)2] and [Pt(OTf)2L2] (L = mono- or 1/2 bidentate tertiary phosphine) or dinuclear complexes of the type [Pt2(OTf)2(/i-monodentate tertiary phosphine cr-aryl = 4, -biphenyl, / -terphenyL 4,4 -benzophenone, etc.) other structural motifs employing platinum(II) have also been reported.2 0 The addition of bridging, multidentate N-donor ligands of various shapes and sizes to the labile complexes in a suitable solvent system has afforded several classes of discrete, plat-inum(II)-containing polygons, polyhedra, and catenanes. 

The second mode of toxicity is postulated to involve the direct interaction of the epidithiodiketopiperazine motif with target proteins, forming mixed disulfides with cysteine residues in various proteins. Gliotoxin, for example, has been demonstrated to form a 1 1 covalent complex with alcohol dehydrogenase [13b, 17]. Epidithiodi-ketopiperazines can also catalyze the formation of disulfide bonds between proxi-mally located cysteine residues in proteins such as in creatine kinase [18]. Recently, epidithiodiketopiperazines have also been implicated in a zinc ejection mechanism, whereby the epidisulfide can shuffle disulfide bonds in the CHI domain of proteins, coordinate to the zinc atoms that are essential to the tertiary structure of that domain, and remove the metal cation [12d, 19],... 

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