Medium-range interactions

Zimmerman and Scheraga, 1977a) can reproduce the observed distribution in most respects, in spite of omission of all long-range and medium-range interactions. 

Simulations relying on realistic medium-range interactions 305... 

Medium-range interactions can be defined as those which dominate the dynamics when atoms interact with energies within a few eV of their molecular binding energies. These forces determine a majority of the physical and chemical properties of surface reactions which are of interest, and so their incorporation in computer simulations can be very important. Unfortunately, they are usually many-body in nature, and can require complicated functional forms to be adequately represented. This means that severe approximations are often required when one is interested in performing molecular dynamics simulations. Recently, several potentials have been semi-empirically developed which have proven to be sufficiently simple to be useful in computer simulations while still capturing the essentials of chemical bonding. 

The remainder of this chapter is devoted to describing the results of computer simulations which have used the ideas discussed above. The overall goal of these studies is to describe and understand phenomena which depend for the most part on bonding ( medium-range ) interactions. For example, simulations of the reaction of small molecules on metal surfaces are discussed in section 3.1, where bond formation occurs at thermal energies. The major drawback for using simulations to study these types of processes is that the... 

Hydrophobic periodicity can have such a large influence on the formation of secondary structure that it dominates over short- and medium-range interactions (DeGrado and Lear, 1985). This has been demonstrated recently, using a set of designed peptides with leucyl and lysyl residues in identical ratios but with different hydrophobic periodicities. 

H. Wako, N. Saito, and H. A. Scheraga, J. Protein Chem., 2,221 (1983). Statistical Mechanical Treatment of a-Helices and Extended Structures in Proteins with Inclusion of Short- and Medium-Range Interactions. 

S. Loughran, Secondary stmcture predictions and medium range interactions, Biochim. Biophys. Acta 1987, 936, 200-204. 

Luijten, E., Blote, H.W.J., and Binder, K. (1996) Medium-range interactions and crossover to classic d critic d behavior, Phys. Rev. E 54, 4626-4636. 

With the experiments it was possible to underscore the relevance of stereochemical criteria, i.e. medium-range interactions, for the stability of P-structures. The prediction of P-sheets on the exclusive basis of algorithms of the kind described above must necessarily be of inferior quality. 

In our Molecular Dynamics simulations we adopted a coarse-grained polymer melt + substrate system [29]. Here N-beads chains interact via a sum of bead-bead Lennard-Jones (LJ) interactions truncated and shifted at tcutoff = 2.3o, combining repulsive (short range) and attractive (medium range) interactions. 

Some of the different theoretical approaches, prediction methods, and simulation of protein folding are briefly introduced here. The methods for evaluating, first the conformational preferences of a single peptide unit, and second the conformational preferences of a polypeptide chain, are discussed. Models that use short- and medium-range interactions are briefly analyzed. The results of these different predictive methods of secondary structures are compared. Actually the refinements of these predictive methods are under study in the main laboratories of this field of study. It is evidently of great... 

In this category of methods the frequency of occurrence of each amino acid in a defined conformational state is deduced from the observation of X-ray structures of many proteins. Several algorithms for the prediction of protein folding based on short- and medium-range interactions have been developed during the 1970s. Many of the earlier studies were based on only a few... 

Some of the methods used for prediction of ordered regions in proteins based on short- and medium-range interactions have been described. This rapid and certainly incomplete survey indicates the variety of the procedures. Burgess and co-workers (1974) emphasized the necessity of having some criteria by which one can evaluate the ability of any predictive algorithm for accurate assignment of the conformational state of each residue. Otherwise the algorithm cannot be used to predict the native conformation of a protein from the sequence of the polypeptide chain. The authors proposed the use of an index of prediction P define as follows ... 

Fig.4.11. (A) Spatial structure of BPTI computed by the procedure described in Fig. 4.10 taking into account short- and medium-range interactions (according to Burgess and Scheraga, 1975b). (B) Spatial structure as determined by X-ray crystallography. (C and D) Distance contour maps between C related to (A) and (B) structures, respectively (according to Ooi and Nishikawai 1973).

It is generally accepted that the formation of ordered backbone structures is dominated by short- and medium-range interactions. It is supported by the rather good agreement between experimental data and predictions... 

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