References of "Roterman-Konieczna, I"
     in
Bookmark and Share    
Peer Reviewed
See detailStructural information involved in the interpretation of the stepwise protein folding process
Alejster, P.; Jurkowski, Wiktor UL; Roterman-Konieczna, I.

in Protein folding in silico : protein folding versus protein structure prediction (2012)

Calculating the quantity of information present in each step of the protein folding process suggests that the multistep approach requires less information than the one-step model. Quantitative analysis ... [more ▼]

Calculating the quantity of information present in each step of the protein folding process suggests that the multistep approach requires less information than the one-step model. Quantitative analysis reveals that the amino acids present in the polypeptide chain do not carry enough information to accurately predict the values of the angles Φ and Ψ in folded proteins. This conclusion results from comparing the amount of information carried by amino acids with the quantity of information necessary to determine Φ and Ψ, taking the complete Ramachandran map as the conformational space. It is shown that the two-step model (comprising two stages, the ES and LS) requires less information, owing to the fact that the final predictions of the angles Φ and Ψ can be based on a preexisting ES structure. Analysis based on information theory points to particular zones of the Ramachandran map that appear to play an important role in the context of protein structure prediction. [less ▲]

Detailed reference viewed: 77 (1 UL)
See detailThe early-stage intermediate
Jurkowski, Wiktor UL; Baster, Z.; Dulak, D. et al

in Roterman-Konieczna, I. (Ed.) Protein Fold Silico Protein Fold Versus Protein Struct Predict (2012)

The multistep polypeptide chain folding model presented in this chapter involves several intermediates, the first of which is called the early-stage (ES) intermediate. This intermediate is assumed to be ... [more ▼]

The multistep polypeptide chain folding model presented in this chapter involves several intermediates, the first of which is called the early-stage (ES) intermediate. This intermediate is assumed to be defined solely on the basis of the backbone conformation and does not take side chains into account. The geometric principles that guide the backbone alignment process and its quantitative influence on the structural arrangement of the folded chain can be expressed by means of a contingency table, linking known structural motifs to specific polypeptide sequences. The basic unit of this algorithm is the tetrapeptide, and the corresponding ES conformational subspace is assumed to consist of seven types of motifs. This limited subspace represents a subset of the full conformational space (i.e., the Ramachandran plot). The volumetric structure of the ES intermediate corresponds to the output of the early folding stage and, simultaneously, provides input for further stages of the folding process. [less ▲]

Detailed reference viewed: 72 (2 UL)