Tertiary structure parameters

All factors related to the arrangement of the polymer chain in space are classified as tertiary structure. Parameters measurable directly (the radius of gyration RG, the end-to end distance h, the hydrodynamical radius RH, and the asymmetry in light scattering intensity) or indirectly (interaction parameters, the second virial coefficient A2) are related to the dimensions, such as size and shape of the polymer chain in a specific solvent under given conditions of temperature and pressure. For the exact determination of the coil size of macromolecules, it is necessary to ensure that measure-... 

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

In an attempt to separate the domains from the cores, we used limited degradation with several proteases. CBH I (65 kda) and CBH II (58 kda) under native conditions could only be cleaved successfully with papain (15). The cores (56 and 45 kda) and terminal peptides (11 and 13 kda) were isolated by affinity chromatography (15,16) and the scission points were determined unequivocally. The effect on the activity of these enzymes was quite remarkable (Fig. 7). The cores remained perfectly active towards soluble substrates such as those described above. They exhibited, however, a considerably decreased activity towards native (microcrystalline) cellulose. These effects could be attributed to the loss of the terminal peptides, which were recognized as binding domains, whose role is to raise the relative concentration of the intact enzymes on the cellulose surface. This aspect is discussed further below. The tertiary structures of the intact CBH I and its core in solution were examined by small angle X-ray scattering (SAXS) analysis (17,18). The molecular parameters derived for the core (Rj = 2.09 mm, Dmax = 6.5 nm) and for the intact CBH I (R = 4.27 nm, Dmax = 18 nm) indicated very different shapes for both enzymes. Models constructed on the basis of these SAXS measurements showed a tadpole structure for the intact enzyme and an isotropic ellipsoid for the core (Fig. 8). The extended, flexible tail part of the tadpole should thus be identified with the C-terminal peptide of CBH I. 

Perfluoroalkylhalogenomercurates, 3 344-346 Perfluoroalkylmercuric iodides, 3 340 Perfluoroalkyl phosphorus acids, 3 382-387 Perfluoroalkyl tertiary amines, 16 26, 27 structural parameters, 16 27 Perfluoroamines preparation of, 3 356 properties of, 3 361-363 Perfluoro-/-butyl(fluorosulfuryl) peroxide, 16 126... 

Another important parameter is the acidity of the system. Since the relation between enzyme activity and pH often shows an optimum, buffers are regularly used in enzymatic derivatization to control the pH. Use of buffers, however, can cause increase of the ionic strength of the system, thus changing the tertiary structure of the enzyme and either making it more accessible for the substrate or blocking its active sites. Therefore, optimization of the chromatographic system is recommended for each specific system. 

Obviously the tertiary structure of the catalyst obtained by cold rolling is optimal and is least efficient for the plasma-sprayed coating. It should be stressed that by variation of the process parameters, also galvanically generated NiZn codeposits yield optimal performance, which is comparable to that of cold-rolled coatings (83). 

A series of enzyme-catalyzed reactions recently conducted in both conventional and supercritical fluid medium has shown that while no loss of enzyme activity was experimentally observed for the conventional medium, the same was no longer valid for supercritical C02 systems (1,4,10,11). For instance, Steinberger and Marr (12) have pointed out that the stability of an enzyme in supercritical C02 depends onboth its tertiary structure and several parameters during exposure to high-pressure fluid. They argued that high temperatures, the water content in C02 and pressurization/de-pressurization steps might cause enzyme inactivation. 

The tertiary structure of the protein induces a high energy transfer between the Trp residue and the neighboring amino acids. This induces low values in the fluorescence parameters of the Trp residue in the native state in comparison to those measured when the protein is denatured, and so the energy transfer is weak. 

Fig. 2.13. The probability distributions of four structural parameters calculated for the structures of each cluster [25]. (a) The fraction of the native tertiary contacts Q. (b) The RMSD value of Ca atoms between a pair of structures that belong to the same cluster. The SASA for (c) hydrophobic and (d) hydrophilic side chains. Reproduced with permission from [25]...

A large number of chemical and physical properties, manifest in the amino acid side chains, have been thoroughly examined by many investigators. Attempts have been made to correlate these properties with their relatedness among protein sequences. What is most relevant is how these side chains interact with the backbone and with one another and what roles they each play within particular types of secondary and tertiary structure. The parametric description of residue environments with the help of solvent accessibility, secondary structure, backbone torsion angles, pairwise residue-residue distances, or Ca positions is the comparison between amino acid types at protein sequence positions and residue locations in structural templates. A recent review has evaluated and quantified the extent to which the amino acid type-specific distributions of commonly used environment parameters discriminate with respect to the 20 amino acid types (Sunyaev et al., 1998). Some of the important amino acid properties and residue environments are discussed below. 

The secondary and tertiary structure of a partially purified 7S globulin was examined by Fukushima (7) based on optical rotatory dispersion, infrared and ultraviolet difference spectra. Antiparallel (5 -structure (352) and random coil (60%) predominated with only 5% helical structure present. The contribution of the three structures was calculated from molecular ellipticity values obtained by circular dichroism (11) and from the Moffitt parameters in ORD (11, 12). Between 210 and 250 nm, the experimental CD curve for the 7S protein was similar to the CD curve computed from ORD Moffitt parameters with the major dissimilarity occurring at 208-213 nm. 

Polyethylene is a man-made homopolymer. Its chemical synthesis is well understood. It is a random walk polymer with little secondary or tertiary structure. A batch can largely be characterised by its molecular weight distribution, and its rheology can be related to these parameters by developed rules of polymer behaviour. The action of specific chemicals as plasticisers can be used to modulate these bulk properties in a predictable way, allowing the nature and characterisation of its glass to fluid transition to be predicted. 

From this type of analysis, Leonard and Foster conclude that a change in the mean intrinsic residue coefficient best accounts for the lack of correlation between the monochromatic rotations and the dispersive parameters, and they tentatively ascribe this change to alterations in tertiary structure which might affect vicinal interactions, side-chain hydrogen bonds, and so... 

More recently, there has been direct observation of protein structural perturbation in the frozen state using phosphorescence lifetime measurements [62]. Reductions in this parameter indicated that freezing perturbed the tertiary structure (at a protein concentration of 3-5 pM) of azurin, ribonuclease, alcohol dehydrogenase, alkaline phosphatase, glyceraldehyde 3-phosphate dehydrogenase, and LDH. The cryoprotectants sucrose and glycerol were tested and were found to inhibit the freezing-induced structural perturbations, with almost complete protection noted at a 1 M concentration. 

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