Conformation of a macromolecule

P. Corradini. Observation of different conformations of a macromolecule in the crystalline state , J. Polym. Sci., Polym. Symp. 51, 1 (1975). 

While the number of possible conformers of a macromolecule is practically unlimited, it is a common observation that macromolecules in biological systems occupy only an extremely limited portion of the conformational hyperspace open to them. As a result, they exhibit well-defined shapes which confer upon them the emergent property of functionality (see Section 2.3.3). 

The chain conformation of a macromolecule is determined by the torsional angles assumed by the backbone bonds. By convention, the angles 0°, 0° are used to define a trans-trans-planar conformation as shown in Figure 3.9a. Torsion (rotation) of bonds 2 and 4 in Figure 3.9a by 180° generates the cis-trans-plmar conformation (Figure 3.9b). 

Here, H and C are symmetric matrices whose elements are the partial total hap(r) and direct cap,(r) pair correlation functions a,ft = A,B) W is the matrix of intramolecular correlation functions wap r) that characterize the conformation of a macromolecule and its sequence distribution and p is the average number density of units in the system. Equation 17 is complemented by the closure relation corresponding to the so-called molecular Percus-... 

Although a network is not present in a concentrated solution, there exists a characteristic length, which had earlier been assumed the distance between neighbouring network sites. The characteristic length is a dynamic one. There are no temporary knots in a polymer system, though there is a characteristic time, which is the lifetime of the frozen large-scale conformation of a macromolecule in the system. So, the conceptions of intermediate length and characteristic time are based on deeper ideas and are reflected in the theory. 

The conformation of a macromolecule consisting of N independent subchains (or segments) can be considered as the result of a random walk of a Brownian particle after N independent steps (Flory 1953). 

The conformation of a macromolecule of given constitution and configuration specifies the spatial arrangements of the various atoms in the molecule that may occur because of rotations about single bonds. Molecules with different conformations are called conformational isomers, rotamers, or conformers. 

The disordered state of a statistical coil is what is displayed by polymers in the molten and amorphous states and also in solution. To describe the conformation of a macromolecule consisting of a main chain N +l atoms, the positions of all them have to be determined. Using vectorial... 

Thus, it may seem that the probability of ring closure should not be higher than calculated on a theoretical basis, already including the assumption of a lack of ring strain. The theory requires, however, that all possible conformations of a macromolecule be equally probable. If we assume that, due to the interaction between substituents or electron pairs or to the presence of certain bonds in eclipsed position, some conformations are excluded, and if these factors do not operate in the conformations leading to ring closure, then the formation of this particular ring will be favoured. 

The molecular conformation of a macromolecule is one of the fundamental physical properties of polymers, since it controls macroscopic properties, such as viscosity or solubility. There have been many attempts to stimulate reversible changes in polymer conformation under controlled and reproducible conditions in order to create responsive polymers. One approach is to induce a structural change in photosensitive groups incorporated into the polymer chains, such as a trans-cis isomerization. Another method is to generate ionic charges along the polymer chains. The repulsive interactions thus created force the chain to adopt a different conformation. 

The Influence of Changes in Conformation of a Macromolecule on Reaction Rates... 

The solution conformation of a macromolecule under deformation, and therefore its stability, is not always predictable, particularly for carbohydrate polymers. This aspect of carbohydrate polymer stability has been investigated and related to the DUEVs of the aqueous solutions (iO). Increasing entanglements at higher concentrations and higher shear deformations can also result in mechanical degradation (ii). 

There are many different ways in which the changes in conformation of a macromolecule or binding of ligands can be observed experimentally. Some of these methods, such as the calorimetric techniques described above, give thermodynamic information directly. Other methods, many of them based on spectroscopic changes (see Chapter 2), are more indirect, but we can still obtain useful thermodynamic data provided we have a reasonable idea about what is going on in the process. 

Energy minimum The native conformation of a macromolecule is the one with the lowest overall potential energy. Therefore energy minimization is applied to search for the native/most stable conformation of a biomacromolecule. 

Molecular simulations include the application of FF to model the lowest potential energy of a conformation (energy minimization, EMin), the dynantic properties of macromolec-ular structure (molecular dynamics, MoID) and search for the optimum conformation of a macromolecule (conformation search). In all these techniques, the positions of atoms are perturbed in small increments, and it is difficult to sample all of the possible arrangements of atoms in conformational space. The successful simulation is the one that reproduces the experimentally observed properties of the molecule. It is essential to incorporate as much empirical information as possible into the initial model for simulation. While the overall system must be accurately defined, it is important to understand the limitations of FF since a choice of FF may affect the outcome of the simulation results. 

The geometrical equivalence of structural units along an axis allows defining types of geometrical symmetry that a linear macromolecule may achieve in the crystalline sate. The conformation of a macromolecule is generally defined in terms of its symmetry and, precisely, of the hne repetition symmetry group [65,67-69]. 

The conformation of a macromolecule is its shape in space that alters as a result of thermal motion without breaking of bonds. 

At the end of Chapter 2 is given a version of the general mean-field theory to account for the correlations of order parameter fluctuations. 1 he hypothesis of similarity (scaling) and the hypothesis of universality are considered. Table 2.5 contains a summary of physical systems whose properties arc successfully studied by means of the field theory methods, including the conformations of a macromolecule coil in a good solvent. 

To a first approximation the exponential constant, a, in the Mark-Houwink equation reflects the solution conformation of a macromolecule. The exponential constants for the carbohydrate polymers studied, excluding the cellulose sulfate ester, are listed in Table I. Generally a value of 0.7-0.8 reflects a random coil conformation as the constant approaches or exceeds 1.0 the conformation approaches a rod-like shape. 

Figure 19 Coil conformation of a macromolecule in solution. The distance between chain ends and the radius of gyration are indicated.

The effect of the solid surface on the transition layers in the polymers case is manifested both spatially and energetically. From the geometric point of view, the substrate imposes restrictions to the material in contact with it, which are manifested at three structural levels, namely chain segment level, macromolecular, and supramolecular level, respectively. From energetic viewpoint, the substrate role consists in the modification of the interphasic interaction character. Consequently, the motility of the structural elements into the transition layers is well impeded, by comparison with the material volume, due to the decrease of the number of possible conformations of a macromolecule in contact with a solid surface [1239,1240],... 

These symmetry elements may be combined into the chain repetition symmetry groups. Thirteen chain repetition groups, indicated in Table 2.1, have been defined [1] and the conformation of a macromolecule is generally defined in terms of its chain repetition symmetry group [1,16,26]. 

The conformation of a macromolecule was reversibly regulated by a photo-induced change of the binding properties of a photochromic ligand (Section 3). 

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