Protein globules

The length of monomer unit of MA is taken to be 0.25 nm [71]. The length of the polymer chain equal to the turn or the diameter of the protein globule is calculated taking into account the hydrodynamic size of the protein molecule via Stockes radius (Rsl). 

As a result of thermodynamic analysis it is shown that protein bonding to carboxylic CP exhibiting a local internal chain structure is determined by the entropy factor, whereas, if the arrangement of flexible chain parts on the protein globule is possible, the energetic component predominates. 

The enzymes are protein molecules having globular structure, as a rule. The molecular masses of the different enzymes have values between ten thousands and hundred thousands. The enzyme s active site, which, as a rule, consists of a nonproteinic organic compound containing metal ions of variable valency (iron, copper, molybdenum, etc.) is linked to the protein globule by covalent or hydrogen bonds. The catalytic action of the enzymes is due to electron transfer from these ions to the substrate. The protein part of the enzyme secures a suitable disposition of the substrate relative to the active site and is responsible for the high selectivity of catalytic action. 

Already at the very beginning of his studies in this field [ 1 ] I.M. Lifshitz insisted that the most important stage of the work to follow should be developing a theory of heteropolymers with a frozen (or quenched) disordered sequence of chemically different units. Many years passed before an essential progress was made in this direction despite the motivation originating from protein physics, that is the very problem of protein globules that I.M. Lifshitz had in mind while starting to study polymers. 

Molecular Relaxation and Dynamics of Dipoles in the Protein Globule... 

Martinek, K., Levashov, A. V, Pantin, V. I., and Berezin, I. V. (1978). Model of biological membranes or surface-layer (active center) of protein globules (enzymes) - reactivity of water solubilized by reversed micelles of aerosol OT in octane during neutral hydrolysis of picrylchloride. Doklady Akademii Nauk SSSR, 238, 626-9. 

Fig. 1. Subunit of GO from Aspergillus niger with FAD hidden inside the protein globule (left) and a FAD area of GO with amino acid residues in a 8.0 A vicinity from the N5 atom of FAD (right) (21).

A. niger, the structure of HRP has been established by X-ray crystallography (29,30). Most of the hemin is immersed into the protein globule. Only its edge is exposed to the surface (Scheme 3). 

The electron transport chains of these systems contain complex molecules whose reaction centres (donor and acceptor fragments) are immersed in. protein globules. The tunneling mechanism permits electron transfer to be performed between these active centres even in the cases when they are separated by distances of 10-20 A and screened from each other by protein chain fragments. 

The albumin/silica system is too large to model completely. Thus a small fragment of is selected to examine the main features of its adsorption. The helical section of human serum albumin (HSA) has been chosen as a model consisting of a 16 fragment amino acid chain placed at the periphery of a protein globule. 

In solving problems of enzyme catalysis, molecular biophysics of proteins, biomembranes and molecular biology it is necessary to know the spatial disposition of individual parts. One must also know the depth of immersion of paramagnetic centers in a biological matrix, i.e. the availability of enzyme sites to substrates, distance of electron tunneling between a donor and an acceptor group, position of a spin-label in a membrane and in a protein globule, distribution of the electrostatic field around the PC, etc. 

Concerning proteins, the X value is strongly dependent on local polarity, which differs in different portions of such a mosaic structure as a protein globule. Positions of the donor and acceptor centers relative to the protein-water interface, chemical nature and mobility of adjacent groups can drastically affect X values. Thus, the precise calculation of real X in biological objects requires special theoretical approaches. 

One of the most important factors providing acceleration of enzymatic reactions as compared to chemical reactions is drastic changes of chemical reactivity catalytic groups inside and outside the enzyme protein globule. Drawing the charges of metal ions, carboxylate and protonated residues into the protein interior is accompanied by essential alternation of its acid-base and redox properties. This effect can be illustrated by the reaction of cleavage and formation of an a-C-H bond in enzymatic reactions of racemization, transamination, and isomerization (Ha et al., 2000 and references therein). 

Recently the investigation of the structure, molecular dynamics and action mechanism of enzymes revealed that protein globules of many enzymes consist of two tightly packed knots (matrix, domains, blocks) tethered with a relatively flexible spacer. (Lumry, 1995a,b, 2002 and references herein) (See also Section 4.1). The enzyme active sites are most commonly located in a cleft between these domains. Binding of substrates and inhibitors depends on the extend of matrix contraction (Fersht, 1999). 

The anomalies pointed out above, including compensation effects, may be accounted for in general bases of the assumption that the chemical elementary steps on the enzyme are accompanied by the arrangement of the conformational structure of protein globules and surrounding water molecules. The kinetic and thermodynamic parameters of such structural rearrangements make a contribution to the experimentally measured and whose reflect cooperative properties of the water-protein matrix. 

The protein globule of cytochrome P450 from the adrenal cortex consists of two fragments. The hydrophilic fragment FI has a molecular mass of 27000 and contains a heme and an adrenodoxin-binding site. The hydrophobic fragment of molecular mass 22000 binds the enzyme to the biomemrane. The presence of extensive hydrophobic portions has also been detected in liver cytochrome. 

In the 1960 s and 1970 s, much indirect evidence was obtained in favour of protein intramolecular mobility, i.e. the entropy and energy specificity of enzyme catalysis (Likhtenshtein, 1966, 1976a, b, 1979, 1988 Lumry and Rajender, 1970 Lumry and Gregory, 1986). The first observations made concerned the transglobular conformational transition during substrate-protein interaction (Likhtenshtein, 1976), the reactivity of functional groups inside the protein globule, and proteolysis. 

From the late 1960 s to the early 1970 s, more direct approaches to the investigation of protein dynamics were intensively developed. Such investigations featured the application of physical methods, such as physical labeling, NMR, optical spectroscopy, fluorescence, differential scanning calorimetry, and X-ray and neutron scattering. The purposeful application of the approaches made it possible to obtain detailed information on the mobility of different parts of protein globules and to compare this mobility with both the functional characteristics and stability of proteins, and with results of the theoretical calculation of protein dynamics. 

---