Polypeptide approximate conformation

It may therefore be concluded that the asymmetric structure unit of the picornaviral capsid is composed of three polypeptides and conforms to the prediction of Finch and Klug. It has a molec]jlar mass of approximately 86,000 daltons, a diameter of about 68 A (35) and is repeated 60 times in the virus capsid. This corresponds to the simplest icosahedral lattice, with a triangulation number of 1 (57) Considering the I4S pentamers as capsomeres, there would be 12 capsomeres per virion. The location of the 6 (7P4) polypeptides in the capsid has not yet been established, but it is possible that they are distributed over the internal surface and in direct contact with the virion RNA (5Q, 39I see below). 

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). 

To the best of our knowledge, there is one host which conforms to the structure of an Archimedean dual. Harrison was the first to point out that the quaternary structure of ferritin, a major iron storage protein in animals, bacteria, and plants, corresponds to the structure of a rhombic dodecahedron. [45] This protein, which is approximately 12.5 nm in diameter, consists of 24 identical polypeptide subunits (Fig. 9.18), and holds up to 4500 iron atoms in the form of hydrated ferric oxide with... 

In Chapter B it has been shown that, if the restrictions that N> 1, a112 < 1, and No112 > 2 are imposed, very useful approximate expressions can be derived for the quantities characterizing the average conformation of a polypeptide molecule. Teramoto et al. (i4) have simplified Nagai s expressions for by imposing the same restrictions. Their results read... 

Wada 109, 110) pioneered studies of polypeptide conformation by the dielectric method. He found 110) a linear dependence of (ft2)1 2 on Mw for a series of PBLG samples (ranging from 7 x 104 to 18 x 104 in Mw) in EDC at 25° C and obtained 3.5 D for gh, where D stands for debye units. He computed (ft2) by the use of an approximate equation derived by himself 109) for rigid-rod molecules, which for very dilute solutions may be written... 

FIGURE 4-15 Globul ar protein structures are compact and varied. Human serum albumin (Mr 64,500) has 585 residues in a single chain. Given here are the approximate dimensions its single polypeptide chain would have if it occurred entirely in extended /3 conformation or as an a helix. Also shown is the size of the protein in its native globular form, as determined by X-ray crystallography the polypeptide chain must be very compactly folded to fit into these dimensions. 

Approximately one half of an average globular protein is organized into repetitive structures, such as the a-helix and/or 3-sheet. The remainder of the polypeptide chain is described as having a loop or coil conformation. These nonrepetitive secondary structures are not... 

Nuclease behaves like a typical globular protein in aqueous solution when examined by classic hydrodynamic methods (40) or by measurements of rotational relaxation times for the dimethylaminonaphth-alene sulfonyl derivative (48)- Its intrinsic viscosity, approximately 0.025 dl/g is also consistent with such a conformation. Measurements of its optical rotatory properties, either by estimation of the Moffitt parameter b , or the mean residue rotation at 233 nin, indicate that approximately 15-18% of the polypeptide backbone is in the -helical conformation (47, 48). A similar value is calculated from circular dichroism measurements (48). These estimations agree very closely with the amount of helix actually observed in the electron density map of nuclease, which is discussed in Chapter 7 by Cotton and Hazen, this volume, and Arnone et al. (49). One can state with some assurance, therefore, that the structure of the average molecule of nuclease in neutral, aqueous solution is at least grossly similar to that in the crystalline state. As will be discussed below, this similarity extends to the unique sensitivity to tryptic digestion of a region of the sequence in the presence of ligands (47, 48), which can easily be seen in the solid state as a rather anomalous protrusion from the body of the molecule (19, 49). 

Each molecule (molecular weight 30000) contains one zinc(II) atom, which is (approximately) tetrahedrally coordinated to two N atoms and one O atom from amino-acid residues plus a water molecule. The structures of both the enzyme and some enzyme-substrate complexes have been carefully studied and the detailed mechanism of the hydrolysis is now quite well understood. Without going into details, a crucial factor appears to be the pronounced distortion from regular tetrahedral coordination about the Zn(II), apparently imposed by the conformational requirements of the polypeptide chain. The conflict of interest between the needs of the Zn(II) atom - which, when four-coordinate, always assumes tetrahedral coordination - and the ligands induces an entatic state, a condition of strain and tension which enhances the reactivity at the active site. The Zn atom binds the substrate peptide via the O atom of the —CONH— peptide link, and the entatic state of the free enzyme facilitates formation of the enzyme-substrate complex. 

Many theoretical studies have predicted a significant dependence of a helix CD spectra upon chain length [37-40] which is supported by experimental investigations [41,42], Other calculations have found little or no dependence [43,44]. In particular, it is important to delineate two aspects of chain length dependence. First, it is of interest to know the minimal number of residues in an a-helical conformation which would produce an a helix-like CD spectrum. Second, it would be of importance to know the length of an a helix which would approximate an infinite polypeptide chain. 

The antibodies are similar in structure to other globulin proteins which are present in serum of vertebrates [9], The antibody molecule consists of two light polypeptide chains and two heavy polypeptide chains [10]. The amino acids are present in all the chains but the number of residues and the sequence will vary in different antibody multiforms [9], Light chains contain approximately 220 amino add residues and heavy chains about 450 residues. The complete sequence of the chains of human IgG myeloma protein has been determined by Edelman [11], The chains are held together in the unique conformational structure of the antibody molecule by a few covalent disulfide bonds between the chains and many electrostatic bonds between the amino groups of one chain and the hydroxyl groups of another chain. The covalent bonds are represented in Formula 1, 2 and 3 [peptide, disulfide and... 

For the sake of convenience, the different aspects of protein structure have been divided into four categories primary, secondary, tertiary, and quaternary structures. When we speak of the primary structure of a protein, we are concerned with the amino acid sequence of its component polypeptide chains. A protein may have a single polypeptide chain with one N and one C terminus, or it may have two or more polypeptide chains, often termed subunits, with multiple N and C termini. Secondary structure problems address themselves to whether the polypeptide chains of a protein exhibit any sort of periodicity of structure in three dimensions that is, is the polypeptide chain simply an extended ribbon, or is it present in the form of a spring or a folded structure Secondary structure has also been referred to as conformation. Tertiary structure is concerned with the overall three-dimensional appearance of the protein for example, is the shape of the protein molecule best approximated by a sphere or by a disk Last, quaternary structure refers to the number, size, and shape of component polypeptide chains in a protein. 

The animal fatty acid synthase (FAS EC 2.3.1.85) is one of the most complex multifunctional enzymes that have been characterized, as this single polypeptide contains all the catalytic components required for a series of 37 sequential transactions (Smith, 1994). The animal FAS consists of two identical polypeptides of approximately 2500 amino acid residues (MW, ca. 270 kDa), each containing seven catalytic subunits (1) ketoacylsynthase, (2) malonyl/acetyl transferase, (3) dehydrase, (4) enoyl reductase, (5) (3-kcto reductase, (6) acyl carrier protein (ACP), and (7) thioesterase. Although some components of the complex are able to carry out their respective catalytic steps in the monomeric form, only in the FAS dimer do the subunits attain conformations that facilitate coupling of the individual reactions of fatty acid synthesis to occur (Smith et al., 2003). 

Because of their structural and conformational complexity, polypeptides, proteins, and their feedstock contaminants thus represent an especially challenging case for the development of reliable adsorption models. Iterative simulation approaches, involving the application of several different isothermal representations8,367 369 enable an efficient strategy to be developed in terms of computational time and cost. Utilizing these iterative strategies, more reliable values of the relevant adsorption parameters, such as q, Kd, or the mass transfer coefficients (the latter often lumped into an apparent axial dispersion coefficient), can be derived, enabling the model simulations to more closely approximate the physical reality of the actual adsorption process. 

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