Secondary protein structure methodology

Computation proteome annotation is the process of proteome database mining, which includes structure/fold prediction and functionality assignment. Methodologies of secondary structure prediction and problems of protein folding are discussed. Approaches to identify functional sites are presented. Protein structure databases are surveyed. Secondary structure predictions and pattern/fold recognition of proteins using the Internet resources are described. 

One widely used modem method is PHD." The program incorporates evolutionary information, in the form of mnltiple sequence alignments, to develop a neural network method that predicts secondary stmcture with an accuracy >70%. Knowledge of neural networks is not necessary for the practical user of this method, and the methodology is not discussed in detail here. Instead, the interested reader shonld consult reviews of the use of neural networks in protein structure prediction. ... 

One of the common ways of predicting protein tertiary structure assumes that the secondary structure has to be known before the prediction of a three-dimensional fold can be attempted [154-157]. While this view as a paradigm for protein structure prediction could be challenged, it certainly provides a straightforward framework that may sometimes prove to be useful. Indeed, there were a number of early attempts to apply such a methodology to low resolution protein fold predictions that were quite successful in some specific cases [154-157]. However, only recently has the problem of protein structure assembly, given its secondary structure, been more systematically addressed. 

Chi Z H, Chen X G, Holtz J S W and Asher S A 1998 UV resonance Raman-selective amide vibrational enhancement quantitative methodology for determining protein secondary structure Biochemistry 27 2854-64... 

Similarly to their (33-counterparts, short 32-peptides have been shown to exhibit extraordinary tendencies to adopt stable secondary structures. Again, interest has, to date, focused on those 32-amino acids which bear protein side chains.15 7 This interest has resulted in the development of methodology based on Evans work 18 for the synthesis of these (3-amino acids bearing a substituent on C2. 

Methodologies to assess interface properties of amphiphiles are surface tension measurements (Phan et al. 2006 Golding and Sein 2004 Miller et al. 2004), ellip-sometry (Dickinson 2003a Murray 2002) and Brewster angle microscopy (Grigoriev et al. 2006 Rodrguez Patino et al. 2001). Both and P NMR have been applied in order to study the conformation and dynamics of P-casein at the oil-water interface of emulsions (ter Beek et al. 1996). Their NMR results showed that the protein at the interface has mobile regions with httle secondary structure in which the motions are rather slow. 

This methodology has been used to predict the structure of loops of helical-bundle proteins, given the positions of the connection to the helices (372). Because of the uncertainties in secondary structure predictions that are used as inputs to constrain the search, any single prediction of the method must be viewed with skepticism. Development of scoring functions that discriminate between alternative models at the Ca level of resolution would complement this approach. 

When structural alignments do not reveal structural similarities that allow annotation transfer, other approaches can be used to obtain information about the function of the target protein. The analysis of the conservation of 3D patterns of functionally relevant residues and evolutionary trace analysis (described in section 2.3.3) are examples of these methodologies. Structural patterns consist of coordinate files in PDB format containing the spatial positions of functionally important residues without considering their positions on the primary or secondary structure. In fact, these patterns can correspond to functional sites present in proteins with completely different folds. The program PINTS (Patterns In Non-homologous Tertiary Structures)... 

This methodology was similarly applied to cold shock proteins (CSP) [81]. They are a family of small single domain proteins, with a highly conserved sequence identity [82,83]. The known structures of CSPs consist of a secondary structure of two amphipathic /3-sheets. The first /3-sheet is formed by three antiparallel /3-strands and the second contains two anti-parallel /3-strands. These two /3-sheets form a hydrophobic core and a predominantly hydrophilic surface [84]. Many mutational forms of these proteins have been studied experimentally and hence they can be used as a model to study the effects of mutations on folding stability and mechanisms. 

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