Tertiary structure of protein molecules

On a larger scale, the unique folding and structure of one complete polypeptide chain is termed the tertiary structure of protein molecules. The difference between local secondary structure and complete polypeptide tertiary structure is arbitrary and sometimes of little practical difference. 

Torrens, F. (2002) Fractal hybrid orbitals analysis of the tertiary structure of protein molecules. Molecules, 7, 26-37. 

The surface activity of proteins (as well as many of their other functions) depends on the so-called tertiary structure of protein molecules, which is determined by the spatial arrangement of their polypeptide chains. This tertiary molecular structure depends in turn on the primary protein structure - the aminoacid sequence, which is determined by the genetic code of a cell. The surface of a protein globule is mosaic-like it contains both polar... 

DENATURATION A physical change in the tertiary structure of protein molecules, resulting in the destruction of their conformation. This disrupts the structure they form or the function they perform. 

The use of periodate as a cleavage agent does have advantages, however. Unlike the use of cleavable crosslinkers that contain disulfide bonds which require a reductant to break the conjugate, cleavage of diol-containing crosslinks with periodate typically preserves the indigenous disulfide bonds and tertiary structure of proteins and other molecules. As a result, with most proteins bioactivity usually remains unaffected after mild periodate treatment. 

The history of molecular biology has been a history of technological developments for determining the primary and tertiary structures of protein and nucleic acid molecules. Once the molecular structure is known, it provides clues to molecular functions. This is the principle of the structure-function relationship. Based on this principle the analysis of the amino acid sequence is performed to decipher the functional information from the sequence information. The analysis usually involves detection and prediction of empirical sequence—function relationships with additional consideration of known or predicted three-dimensional (3D) structures. Thus, the process can be represented schematically as ... 

It is helpful to know the chemistry of fixatives in order to understand their action and avoid artifacts (4). Most commonly studied antigens are either proteins or carbohydrates. Many of these molecules are soluble in aqueous solutions and need to be fixed in place in cells. Insoluble antigens also need to be structurally preserved (/). All chemical fixatives will cause chemical and conformational changes in the protein structure of cells with lesser changes noted for carbohydrate antigens (5). Secondary and tertiary structures of proteins are the most important for eliciting antigenicity and chemical fixatives usually disturb these conformations (3). 

The stereochemical specificity of enzymes depends on the existence of at least three different points of interaction, each of which must have a binding or catalytic function. A catalytic site on the molecule is known as an active site or active centre of the enzyme. Such sites constitute only a small proportion of the total volume of the enzyme and are located on or near the surface. The active site is usually a very complex physico-chemical space, creating micro-environments in which the binding and catalytic areas can be found. The forces operating at the active site can involve charge, hydrophobicity, hydrogen-bonding and redox processes. The determinants of specificity are thus very complex but are founded on the primary, secondary and tertiary structures of proteins (see Appendix 5.1). 

Abstract Now an incisive probe of biomolecular structure, Raman optical activity (ROA) measures a small difference in Raman scattering from chiral molecules in right- and left-circularly polarized light. As ROA spectra measure vibrational optical activity, they contain highly informative band structures sensitive to the secondary and tertiary structures of proteins, nucleic acids, viruses and carbohydrates as well as the absolute configurations of small molecules. In this review we present a survey of recent studies on biomolecular structure and dynamics using ROA and also a discussion of future applications of this powerful new technique in biomedical research. 

The order of amino acids in protein molecules, and the resulting three-dimensional structures that form, provide an enormous variety of possibilities for protein structure. This is what makes life so diverse. Proteins have primary, secondary, tertiary, and quaternary structures. The structures of protein molecules determine the behavior of proteins in crucial areas such as the processes by which the body s immune system recognizes substances that are foreign to the body. Proteinaceous enzymes depend on their structures for the very specific functions of the enzymes. 

Hydrophobic interactions are formed when two or more hydrophobic groups (for example, side chains of valine, leucine, phenylalanine, and so on) in an aqueous environment find themselves sufficiently close to exclude water molecules from their vicinity. These interactions are primarily a result of entropy effects and are believed to be of major importance in the maintenance of the tertiary structures of proteins. Scheraga and coworkers have also proposed that hydrophobic interactions may be involved in the stabilization of the a helix and the pleated sheet structures. 

The stereochemical shape concept covers a wide range of possible resolutions, from the details of electron density distributions between pairs of nuclei in relatively small molecules to the structural organization of the tertiary structure of proteins [201-203], the architecture of supramolecular assemblies [204-230], the problems of shape selectivity in reactions of large molecules [231-233], and the intriguing shape features of self-replicating chemical systems [234-239]. In the following chapters we shall discuss various topological shape analysis techniques, suitable for the relevant level of resolution. 

The tertiary structure of proteins, also called the super-secondary structure, denotes the way in which the secondary structures are assembled in the biologically active molecule, (Figure 7.27b). These are described in terms of motifs3, that consist of a small number of secondary structure elements linked by turns, such as (oc-helix - turn -a-helix). Motifs are further arranged into larger arrangements called folds, which can be, for example, a collection of / -sheets arranged in a... 

Introducing intramolecular amide bonds into synthetic polypeptides produces organized spatial structure which makes these polymers good models for the tertiary structure of proteins. The transition temperature, which measures the organized internal structure of the molecule, increases as the number of cross-links increases. The amount of internal structure has little effect on the over-all rigidity of the molecule until six cross-links have been introduced into the polymer. On the other hand, the over-all hydrodynamic domain of the molecule decreases to the same extent whether one, four, or six intramolecular cross-links are present. 

Bovine Pancreatic Trypsin Inhibitor (BPTI) is one of the smallest and simplest globular proteins. BPTI s sole function is to bind to and inhibit proteolytic enzymes like trypsin. BPTI contains both ot helical and sheet regions, as well as three disulfide bonds, which help to stabilize the tertiary structure of the molecule. 

We have shown that the morphology of the adsorbed individual molecule and the protein film is dependent upon the surface to which the protein is adsorbed and the wall shear rate at which the protein solution contacts the surface. We have studied the interaction of proteins with surfaces from two approaches the first involved observations of the tertiary structures of individual molecules, and the second involved the use of a flow cell and the exposure of test materials to flowing, dilute, purified human plasma protein solutions. On the hydrophobic surfaces of polystyrene and polycarbonate, albumin and fibrinogen films form networks. On the surface of the hard segment model polyurethane, the morphology of the adsorbed film is very similar to that formed on the hydrophobic polystyrene and polycarbonate surfaces. On the peu-2000, the lowest... 

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