Structure, tertiary

Tertiary structure is the overall folding of the protein molecules, in contrast to the secondary structure, which is the local folding (e.g., a-helix, p-sheets). Tertiary structure makes the protein compact and globular in shape. It may be divided into units called domains. A simple domain contains 100-150 amino acid residues and is about 25 A in diameter. The light chain of IgGl, immunoglobulin, for example, consists of two domains and its heavy chain consists of four domains. In the same molecule, the domains may or may not have the same functions. 

A domain can sometimes be isolated as a fragment by limited proteolysis under appropriate conditions. Each fragment has the same conformation in the native protein molecule. A fragment is also stable and can be refolded spontaneously from the unfolded state under native conditions. 

In conclusion, a protein may be characterized by its structure in four different aspects  

Primary structure Secondary structure Tertiary structure Quaternary stmcture 

Graphic representations of protein stractures are carried out using computer programs and have become an essential part of understanding the molecule. They are often printed in several colors such as red, blue, green, yeUow, and purple to indicate different parts of the molecule for clarity. They have become part of the protein language for show and discussion. 

The tertiary protein structure consists of the large-scale bends and folds due to 

Information concerning the tertiary structure of the proteins has been obtained from fluorometry, proton magnetic resonance spectroscopy, limited proteolysis, and X-ray analysis of protein crystals. 

The NMR spectrum given by a globular protein with a well-defined tertiary structure differs from that of the same protein under denaturing conditions in two respects. First, the reduction in mobility of residues when the protein folds into a stable tertiary structure produces a broadening of resonances. Second, alterations in resonances caused by chemical shifts arise due to the stable placement of specific protons in unique chemical environments which leads to the appearance of resonances in new positions. 

The PMR spectrum of protein SI suggests that the protein has considerable tertiary structure in physiological buffer and is more flexible than normal globular proteins of its molecular weight (Moore and Laughrea, 1979). No difference was observed when the protein was prepared in the presence or absence of urea at neutral pH. The spectra obtained in this study resemble those previously obtained with salt-extracted SI by Little-child and Malcolm (1978). 

PMR studies have been performed on a number of other ribosomal proteins isolated by the acetic acid/urea method (Morrison etal., 1977a). The results of these studies have shown that acedc acid/urea-extracted proteins contain little tertiary structure. However, some structure was seen in protein S4 and especially in protein S16 as indicated by the appearance of ring-current shifted resonances in the apolar region of the spectrum (Morrison et al., 1977b). These are due to the interaction of apolar methyl groups with aromatic amino acids in the tertiary structure of the protein. The PMR spectra were recorded either in water or in dilute phosphate buffer at pH 7.0—conditions under which the proteins were soluble. 

When urea-denatured preparations of protein Lll are introduced into physiological buffers, two different conformations occur as shown by NMR studies (Kime et al., 1980). One form is distinctly folded while 

By far the most complex and technically demanding predictive method based on protein sequence data has to do with structure prediction. The importance of being able to adequately and accurately predict structure based on sequence is rooted in the knowledge that, whereas sequence may specify conformation, the same conformation may be specified by multiple sequences. The ideas that structure is conserved to a much greater extent than sequence and that there is a limited number of backbone motifs (Chothia and Lesk, 1986 Chothia, 1992) indicate that similarities between proteins may not necessarily be detected through traditional, sequence-based methods only. Deducing the relationship between sequence and structure is at the root of the protein-folding problem, and current research on the problem has been the focus of several reviews (Bryant and Altschul, 1995 Eisenhaber et al., 1995 Lemer et al., 1995). 

The most robust of the structure prediction techniques is homology model building or threading (Bryant and Lawrence, 1993 Fetrow and Bryant, 1993 Jones and Thornton, 1996). The threading methods search for structures that have a similar 

The second approach compares structures with structures, in the same light as the vector aligmnent search tool (VAST) discussed in Chapter 5 does. The DALI algorithm looks for similar contact patterns between two proteins, performs an optimization, and returns the best set of structure alignment solutions for those proteins (Holm and Sander, 1993). The method is flexible in that gaps may be of any length. 

IIFJL 0 KQRRS RTTFSASQLD ELERAPERTQ YPDIYTREEL AQRTNLTEAR 

21FJL 1 QRRS RTTFSASQLD ELERAFERTQ YPDIYTREEL AQRTNLTEAR 

The folding of the secondary structure into a macrostructure such as globules is called the tertiary structure of proteins. A given protein in a physiological environment can have a complex three-dimensional strnctnre. The amino acid backbone of a protein can rotate freely, allowing amino acids from distal protein domains to come into close contact with each other. As these regions of the protein interact 

If one of the amino acid residues in a reverse turn has a configuration different from that of the other residues, then the hydrogen bond formed is more kable. In proteins and in the majority of biologically active peptides (which are usually cleavage products of proteins) only L-residues are present, but in microbial peptides D-residues are quite common. It is not surprising, therefore, that most of them have cyclic structures ring closure is very much facilitated by reverse turns. 

Well defined folding of a peptide chain is called its tertiary structure. Hydrogen bond-stabilized reverse turns can contribute to folding but they are not its primary cause. A more important factor in folding was recognized in non-polar interaction, often described as hydrophobic bond (Kauzmann 1959). 

The importance of non-polar interaction can not be overemphasized. Hydrogen bonds which stabilize secondary structures should not exist in aqueous solutions of peptides and proteins. In the presence of a large number of water molecules the equilibrium 

A similar limited role can be assigned to polar coulombic) interaction. Ion pair formation between basic and acidic side chains is quite commonly observed 

1 Stereo ribbon diagram of human CDK2 with bound ATP (IHCK.PDB). Structural elements are colored as follows, glycine-rich loop in dark blue, N-terminal beta sheet 

Despite technical difficulties, a number of ABC transporters have now been over- 

Transmission electron microscopy (TEM) studies of ABC proteins have also 

The ModBC structure (right) has a more open structure on the cytoplasmic side. The lower panels show a simplified representation of the MalG (left) and ModB (right) subunits in the same orientation as in the upper panels, illustrating the similarity in the folds of the two proteins when aligned on the basis of the EAA loop (arrow). 

Circular dichroism spectra for polypeptides with different conformations. Note that for a-helix conformations, a characteristic dip is observed in the region of 210 nm. 

Three-dimensional tertiary structure in proteins is maintained by ionic bonds, hydrogen bonds, -S-S- bridges, van der Waals forces, and hydrophobic interactions. 

Myoglobin is an extremely compact molecule with very little empty space, accommodating only a small number of water molecules within the overall molecular dimensions of 4.5 x 3.5 x 2.5 nm. All of the peptide bonds are planar with the carbonyl and amide groups in trans configurations to each 

Eight right-handed a-helical segments involve approximately 75% of the chain. Five nonhelical regions separate the helical segments. There are two nonhelical regions, one at the N terminus and another at the C terminus. 

Eight terminations of the a-helices occur in the molecule, four at the four prolyl residues and the rest at residues of isoleucine and serine. 

Gimelli, Salvatore Paul (2001). Aroma Science. Port Washington, NY Micelle Press. 

Maarse, Henk, ed. (1991). Volatile Compounds in Foods and Beverages. New York Marcel Dekker. 

The tertiary structure is the complete three-dimensional structure of a polypeptide chain. Many polypeptides fold into compact, globular structures in which amino acid residues that are distant from each other in primary structure come into close proximity in the folded structure. Because of efficient packing, most water molecules are excluded from the protein s interior. It is the different interactions between the side chains of the amino acids that stabiUze the tertiary structure. A major force stabiUzing the tertiary strucmre is the hydrophobic interaction among nonpolar side chains in the core of the protein. 

The Conditions During the Preparation of the Polymer Film. Electro-polymerized PT films have a more compact morphology in contrast to chemically synthesized PT films [146]. Poly[l,2-bis(3-alkyl-2-thienyl)ethylene] prepared chemically is a bulk powder, in contrast to electrochemically prepared polymers which form homogeneous films (see also Sect. 5.3) [147]. The surface of elec-tropolymerized PTT films is also influenced by the current density. PTT films prepared at a current density of 0.4 mA cm (7.5 min) have typically rough surfaces. PTT films prepared at a current density of 0.05 mA cm (60 min), with the same quantity of electricity, have a compact homogeneous surface [146,148]. These characteristics are independent of the material of the electrodes. PTT films electrochemically prepared at room temperature have a more homogeneous and more compact and smooth surface than at — 5 °C, independently of the current density, with the same quantity of electricity [148]. 

A more homogeneous and compact surface of PT, PBT, and PTT films is achieved on Ni electrodes covered with Au [146]. The morphology of several conducting poly(heterolene) films synthesized galvanostatically on optically transparent SnO, electrodes shows substantial differences as compared with films formed on Pt surfaces [149]. 

The electrode rotation inffuences the morphology of PMT (cf. Sect. 5.2.2). Porous materials suitable for application in batteries and electrocatalysis can be prepared on a stationary or slowly rotating electrode, while much less permeable compact films (for analytical applications) can be prepared at high rotation rates [151]. 

The Thickness of the Film. Thin polymer films (about 10 to 2 x 10 A thick) have a very homogeneous surface, but with increasing thickness of the film the surface is no longer homogeneous. A granular structure and defects appear 

Forced Rayleigh scattering can be used to measure the z-average diffusion coefficient of a PAT in dilute solution. For POT in trichlorobenzene, the diffusion coefficient D = 8 x 10 cm s and hence the hydrodynamic radius of POT is about 130 A [156]. For copolymers of bithiophene and pyrrole, cyclic voltammetry (cf. Sect. 3.2.1) and UV/vis data support the formation of copolymers, which consist of three distinct oxidizable (dopable) units (i) short blocks of bithiophene units, (ii) short blocks of pyrrole units, (iii) random and alternating groupings of bithiophene and pyrrole [157]. 

---

Scott T W and Friedman J M 1984 Tertiary-structure relaxation in haemoglobin—a transient Raman-study J. Am. Chem. Soc. 106 5677-87... 

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... 

Keywords, protein folding, tertiary structure, potential energy surface, global optimization, empirical potential, residue potential, surface potential, parameter estimation, density estimation, cluster analysis, quadratic programming... 

Unfortunately, the approach of determining empirical potentials from equilibrium data is intrinsically limited, even if we assume complete knowledge of all equilibrium geometries and their energies. It is obvious that statistical potentials cannot define an energy scale, since multiplication of a potential by a positive, constant factor does not alter its global minimizers. But for the purpose of tertiary structure prediction by global optimization, this does not not matter. 

S. Sun, Reduced representation approach to protein tertiary structure prediction statistical potential and simulated annealing, J. Theor. Biol. 172 (1995), 13-32. 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

Figure 7-16. Superimpasition of the X-ray structure of the tetracycline repressor class D dimer (dark, protein database entry 2TRT) with the calculated geometrical average of a 3 ns MD simulation (light trace). Only the protein backbone C trace Is shown, The secondary structure elements and the tertiary structure are almost perfectly reproduced and maintained throughout the whole production phase of the calculation,...

Cohen F E, M J E Sternberg and W R Taylor 1982 Analysis and Prediction of the Paclung oi. i-E a iinst a /3-Sheet in the Tertiary Structure of Globular Proteins. Journal of AdoljcuLir E 156 821-862. 

Mosimann S, S Meleshko and M N G Jones 1995. A Critical Assessment of Comparative Molecular Modeling of Tertiary Structures of Proteins. Proteins Structure, Function and Genetics 23 301-317. 

Backbone generation is the first step in building a three-dimensional model of the protein. First, it is necessary to find structurally conserved regions (SCR) in the backbone. Next, place them in space with an orientation and conformation best matching those of the template. Single amino acid exchanges are assumed not to affect the tertiary structure. This often results in having sections of the model compound that are unconnected. 

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 shape of a large protein is influenced by many factors including of course Its primary and secondary structure The disulfide bond shown m Figure 27 18 links Cys 138 of carboxypeptidase A to Cys 161 and contributes to the tertiary structure Car boxypeptidase A contains a Zn " ion which is essential to the catalytic activity of the enzyme and its presence influences the tertiary structure The Zn ion lies near the cen ter of the enzyme where it is coordinated to the imidazole nitrogens of two histidine residues (His 69 His 196) and to the carboxylate side chain of Glu 72... 

Protein tertiary structure is also influenced by the environment In water a globu lar protein usually adopts a shape that places its hydrophobic groups toward the interior with Its polar groups on the surface where they are solvated by water molecules About 65% of the mass of most cells is water and the proteins present m cells are said to be m their native state—the tertiary structure m which they express their biological activ ity When the tertiary structure of a protein is disrupted by adding substances that cause the protein chain to unfold the protein becomes denatured and loses most if not all of Its activity Evidence that supports the view that the tertiary structure is dictated by the primary structure includes experiments m which proteins are denatured and allowed to stand whereupon they are observed to spontaneously readopt their native state confer matron with full recovery of biological activity... 

Section 27 20 The folding of a peptide chain is its tertiary structure The tertiary struc ture has a tremendous influence on the properties of the peptide and the biological role it plays The tertiary structure is normally determined by X ray crystallography... 

A single helix is a coil a double helix is two nested coils The tertiary structure of DNA in a nucleosome is a coiled coil Coiled coils are referred to as supercoils and are quite common... 

Tertiary structure (Section 27 20) A description of how a pro tein chain is folded... 

Tertiary structure also refers to the overall shape of a molecule, especially to structures stabilized by disulfide bridges (cystine) formed by the oxidation of cysteine mercapto groups. 

The three levels of structure listed above are also useful categories for describing nonprotein polymers. Thus details of the microstructure of a chain is a description of the primary structure. The overall shape assumed by an individual molecule as a result of the rotation around individual bonds is the secondary structure. Structures that are locked in by chemical cross-links are tertiary structures. 

Equation (8.97) shows that the second virial coefficient is a measure of the excluded volume of the solute according to the model we have considered. From the assumption that solute molecules come into surface contact in defining the excluded volume, it is apparent that this concept is easier to apply to, say, compact protein molecules in which hydrogen bonding and disulfide bridges maintain the tertiary structure (see Sec. 1.4) than to random coils. We shall return to the latter presently, but for now let us consider the application of Eq. (8.97) to a globular protein. This is the objective of the following example. 

Tertiary structure Tertran Terylene Teslac TestBench Testing... 

N Srimvasan, TL Blundell. An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure. Protein Eng 6 501-512, 1993. 

MI Sutcliffe, CM Dobson, RE Oswald. Solution structure of neuronal bungarotoxm determined by two-dimensional NMR spectroscopy Calculation of tertiary structure using systematic homologous model building, dynamical simulated annealing, and restrained molecular dynamics. Biochemistry 31 2962-2970, 1992. 

S Mosimann, R Meleshko, MNG lames. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 23 301-317, 1995. 

DM Standley, JR Gunn, RA Friesner, AE McDermott. Tertiary structure prediction of mixed alpha/beta proteins via energy minimization. Proteins 33 240-252, 1998. 

A Monge, R Friesner, B Elonig. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. Proc Natl Acad Sci USA 91 5027-5029, 1994. 

A Caflisch, M Karplus. Molecular dynamics studies of protein and peptide folding and unfolding. In K Merz Jr, S Le Grand, eds. The Protein Eoldmg Problem and Tertiary Structure Prediction. Boston Birkhauser, 1994, pp 193-230. 

BR Gelm, M Karplus. Mechanism of tertiary structural change m hemoglobin. Proc Natl Acad Sci USA 74 801-805, 1977. 

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. 

---