Empirical conformational parameters

A simple and popular method for the prediction of conformation is the application of empirical conformational parameters. From the study of numerous protein structures determined by x-ray crystallography it became obvious that certain amino acids are frequent constituents of helical portions while others are more likely to occur in j -sheets and still others are often found in reverse turns. Statistical treatment of such frequencies (Chou and Fasman 1978) produced sets of conformational parameters (Table 5) which were applied for the prediction of conformation in proteins with considerable success. A cluster of four helical residues (P > 1.00) in a six residue stretch of a chain is predictive for a helical region that can be extended in both directions until a... 

Self-avoiding random walks statistics for intertwining polymeric chains and based on it thermodynamics of their conformational state in m-ball permitted to obtain the theoretical expressions for elasticity modules and main tensions appearing at the equilibrium deformation of /n-ball. Calculations on the basis of these theoretical expressions without empirical adjusting parameters are in good agreement with the experimental data. 

Some of the parameters that are used in the computer program ecepp (empirical conformational energy program for peptides) of Momany et al. (J. Phys. Chem. 1975, 79, 2361) are updated. The changes are based on experimental information that has become available since 1975,... 

Molecular mechanics calculations14 ) of the strain in adamantane support this interpretation. Since such calculations are based on empirically derived parameters, however, a unique set of parameters for the representation of physical reality cannot be derived. Nevertheless, all available conformational analysis calculations demonstrate that the strain in adamantane may be quantitatively accounted for in terms of angle strain, which implicitly includes strain due to... 

Following the empirical trends offered in the previous two sections, it might be expected that the role of intracomplex steric factors for such complexes would be intermediate between those for a cis-bis(N(7)-bound gtianine) complex and those for a cis-bis(N(3)-bound cytosine) complex. The conformational parameters displayed in Figure 5 seem to be in accord with this... 

The conclusion from these extensive elegant stereochemical studies is that in five-membered ring systems the apicophilicity of endocyclic ligands does not conform to Trippett s relative apicophilicity scale nor to Holmes s preference rules. Clearly, apicophilicity is a redundant term in such species. Relative apicophilicity is an empirically derived parameter formulated for universal application to phosphorus TBP species. The apicophilicity of a particular ligand is independent of the other phosphorus substituents and the nature of the TBP and is a transferable parameter. Since this definition of apicophilicity breaks down in five-membered TBP intermediates. Hall and Inch defined the alternative term apical potentiality . Thus, in the... 

Calibration curves, such as those shown in Fig. 7, are extremely important for qualitative studies of chain conformation using a probe such as Raman scattering. The experimentally obtained microscopic order parameter,R, is not related to the real order parameter,% trans, in a known or simple manner thus, in order to establish comparisons with theoretical predictions, it is imperative that a one-to-one correspondence be formed between empirical variables and actual chain conformation parameters. 

The localization of secondary structures in protdns can be predicted by means of empirical rules making use of these conformation parameters. For example, a segment consisting of n residues (n Q is predicted to adopt a helical conformation if

S 1,03 and

> . However, additional conditions with regard to... 

Mark-Houwink values confirm that for these conditions gelatin is behaves rod-hke conformation. Such of empirical equations can be relating the parameters of Mark-Houwink with T, which ultimately describe this type of thermodynamic parameters are relations between properties the solute with the solvent and temperature dependence. 

In general terms, it has been seen here that the parameter curves are almost always more stmctured than p parameter curves. The latter are known from years of study to broadly conform to a pattern (in the absence of resonances) that starts from a small value at threshold and over a span of a few tens of electronvolts approaches the positive limit (p = +2), essentially monotonically. Empirically, small distinctions between a and n orbital ionizations can be discussed, and of course there are many significant exceptions to such broad expectations. In contrast, there is clearly far more variability, and much less inmitive predictabihty in the detail of the curves we have seen. That being the case, while suggested shape resonant features in a and p parameter curves can sometimes apparently map onto features in the curves [55, 57, 60] these are no more prominent than other structure and seem unlikely, by themselves, to provide visual clues to the presence of a resonance. 

There has been considerable recent activity developing appropriate parameters to allow semi-empirical methods to describe a variety of biologically important systems, and their related properties, such as (i) enzyme reactivity, including both over- and through-barrier processes, (ii) conformations of flexible molecules such as carbohydrates, (iii) reactivity of metalloenzymes and (iv) the prediction of non-covalent interactions by addition of an empirical dispersive correction. In this review, we first outline our developing parameterisation strategy and then discuss progress that has been made in the areas outlined above. 

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