Tertiary structure, definition

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. 

The three-dimensional conformation of a protein is called its tertiary structure. An a-helix can be either twisted, folded, or folded and twisted into a definite geometric pattern. These structures are stabilized by dispersion forces, hydrogen bonding, and other intermo-lecular forces. 

In this chapter, it will be described how we have utilized endogenous and engineered Zn2+ binding sites to explore the structure and molecular function of Na+/Cl -depen-dent neurotransmitter transporters. The work has not only allowed the definition of the first structural constraints in the tertiary structure of this class of transporters, but also provided new insight into both conformational changes accompanying substrate translocation and mechanisms governing conformational isomerization in the translocation cycle. In the chapter, we will also review the theoretical and practical basis for... 

Fig. 7. Plot of main chain dihedral angles and (see Fig. 5 for definition) experimentally determined for approximately 1000 nonglycine residues in eight proteins whose structures have been refined at high resolution (chosen to be representative of all categories of tertiary structure).

It is worth to mention that this definition is not always consistent with the nature of the macromolecular assembly when applying to nucleic acids. For example, from all different types of quadruplex nucleic acids only quadruplex monomers are covered by lUPAC definition of tertiary structure being a single chain of DNA or RNA. However, also the quadruplexes with higher molecularity of the formed structures (dimers, tetramers) belong to this important tertiary structure family. 

T4 lysozyme 33,497 helix stability of 528, 529 hydrophobic core stability of 533, 544 Tanford j8 value 544, 555, 578, 582-Temperature jump 137, 138, 541 protein folding 593 Terminal transferase 408,410 Ternary complex 120 Tertiary structure 22 Theorell-Chance mechanism 120 Thermodynamic cycles 125-131 acid denaturation 516,517 alchemical steps 129 double mutant cycles 129-131, 594 mutant cycles 129 specificity 381, 383 Thermolysin 22, 30,483-486 Thiamine pyrophosphate 62, 83 - 84 Thionesters 478 Thiol proteases 473,482 TNfn3 domain O-value analysis 594 folding kinetics 552 Torsion angle 16-18 Tbs-L-phenylalanine chloromethyl ketone (TPCK) 278, 475 Transaldolase 79 Tyransducin-o 315-317 Transit time 123-125 Transition state 47-49 definition 55... 

As many B cell epitopes are described to be conformational (Aalberse, 2000), peptides identified by sequential approaches may render limited information and might exhibit reduced antibody-binding affinity. In a very stringent definition, conformational epitopes are composed of amino acids from different loci in the allergen sequence brought into proximity by the tertiary structure of the protein. Systematic characterization of conformational epitopes is much more difficult compared to linear epitopes, because it requires knowledge of the 3D structure, which is often limited. 

The term quaternary structure was proposed to supplement the terms primary, secondary, and tertiary structure, 9 and refers to the spatial arrangement of noncovalently linked polypeptides which we shall call subunits. Generally, a subunit is defined as a tertiary structural unit composed of a single polypeptide, but the definition is somewhat ambiguous. In aspartate transcarbamoylase from Escherichia coli, for example, tertiary structural units composed of three catalytic polypeptide chains are called catalytic subunits and those composed of two regulatory chains are called regulatory subunits.2)... 

Figure 1 Definitions of primary (left), secondary (center), and tertiary structures (right).

The position of several amino acid residues at certain definite sites of the chain suggests that these residues play a specific role in the formation of the secondary and tertiary structure (Watson and Kendrew, 1961). Thus, e.g., phenylalanines in positions 43 and 46 (a-chain) and histidine in position 87 (a-chain) obviously participate in the stabilization of the heme. The hydrogen bond linking tyrosine in position 42 and aspartic acid in position 94 stabilizes two sections of the o-helix. At those sites where the chains... 

In other instances—as this will be developed later in this book by Carpenter and Pikal—it appears essential to safeguard the glassy state, which is indeed an absolute prerequisite to secure the tertiary structure of active proteins. Here, again, a precise knowledge of the bounderies and sensitivities of this glass is definitely needed. 

Chart 1) have particular preferences for the formation of a 14-helix and a 12-helix, respectively. The crystal structure of oligomers 6 (based on the former monomer) indeed revealed a perfect 14-helix, but although strong indications for the presence of a similar structure in solution were obtained, no definitive solution data have been presented yet.29 For a hexamer (7a) and an octamer (7b) of the cyclopen-tane-derived /1-peptide, the solution structure was determined using NMR. This supported the existence of the 12-helix structure which was also found in the solid state.30 More recently also X-ray data on the packing of these helices in the solid state have become available, which may help to design tertiary structures based on these foldamers.31... 

The term stability can have different meanings in the context of protein formulations. A stable pharmaceutical product according to the U.S. Food and Drug Administration definition is one that deteriorates no more than 10% in 2 years [25], Conformational and physical stability of a protein are defined as the ability of the protein to retain its tertiary structure [6], Noncovalent degradation is relevant mainly for proteins having higher order structures, rather than peptides. Native structure is maintained by a balance of noncovalent interactions such as hydrogen bonds, 2005 by CRC Press LLC... 

Surface-active materials consist of molecules containing both polar and nonpolar portions, i.e., amphiphilic molecules. The proteins are typically amphiphilic, polymeric substances made of amino acid residues combined in definite sequences by peptide bonds (primary structure). In many cases polypeptide chains are present in helical or /3-sheet configuration (secondary structure) which are stabilized by intramolecular (S-S and hydrogen) bonding. The next structural level, the tertiary structure, is determined by the folding of the polypeptide chains to more or less compact globules, maintained by hy-... 

The antisense sequence contains the complementary bases in an antiparallel arrangement. Thus, the definition of antisense compounds refers to their interaction with transcribed RNA. In a broader sense the term antisense action is also used to describe inhibition of mRNA processing by molecules binding to sites formed by tertiary structures of single-stranded mRNA and interaction of molecules with duplex DNA by sequence specific insertion into the grooves. 

In the opinion of a maximalist, the folding problem is the one of prediction if we knew the primary structme, could we in principle predict the tertiary one As we mentioned before, the latter question is a practical one. If the answer were yes , we would no longer need complicated and expensive X-ray and NMR analysis of proteins. Unfortunately, the ideal full prediction is far from being true despite impressive achievements in some cases. At present, we can guess the secondary structure with decent accuracy (i.e. a- and /3-segments), but predicting the tertiary structure remains elusive. In this sense, protein folding is definitely not resolved. 

To perform activities, the protein units need a definite and stable 3D structure. When a protein folds to form a well-defined 3D structure, it exhibits primary, secondary, tertiary, and quaternary levels of structures. The genetically determined sequence of amino acids is the primary structure. The primary structure is often modeled as beads on a string, where each bead represents one amino acid unit. The intermediate level of protein structure is called secondary structure. This includes the a-heUces, -sheets, and turns that allow the amides to hydrogen bond very efhciently with one another. The tertiary structure might be modeled as a tightly packed snowball to form the well-defined 3D structure, where each atom in the protein has a well-defined... 

A more scientific definition is given by Veis [423] The gelatins are a class of proteinaceous substance that have no existence in nature, but are derived from the parent protein collagen, by any one of a number of procedures involving the destruction of the secondary structure of the collagen and, in most cases, some aspects of the primary and tertiary structures. Collagen is the principle proteinaceous component of the white fibrous connective tissues, which serve as the chief, tensile stress-bearing elements for all vertebrates, whereas related protons are found in any of the lower phyla . 

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