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Prediction of protein folding initiation sites with alpha-helix preferences


Jerončić, Ana; Juretić, Davor; Zucić, Damir
Prediction of protein folding initiation sites with alpha-helix preferences // Beyond the Genome: Understanding and Exploiting Molecules and Cells in the 3rd Millenium / 18th International Congress of Biochemistry and Molecular Biology
Birmingham: IUBMB, 2000. str. xx-xx (poster, međunarodna recenzija, sažetak, znanstveni)


Naslov
Prediction of protein folding initiation sites with alpha-helix preferences

Autori
Jerončić, Ana ; Juretić, Davor ; Zucić, Damir

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

Izvornik
Beyond the Genome: Understanding and Exploiting Molecules and Cells in the 3rd Millenium / 18th International Congress of Biochemistry and Molecular Biology / - Birmingham : IUBMB, 2000, Xx-xx

Skup
18th International Congress of Biochemistry and Molecular Biology

Mjesto i datum
Birminhgam, Velika Britanija, 16-20.07.2000

Vrsta sudjelovanja
Poster

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
Helix initiation

Sažetak
In view of hierarchical models of folding, protein folds through intermediate states of increasing level of order, starting with native-like secondary structure. If this is the case, then the local interactions are necessary prerequisite for both the formation of native secondary structure and foldability of proteins. In particular the formation of alpha-helices is thought to direct the folding. We analyzed the data from the literature concerning the existence and location of folding intermediates and initiation sites. The results have shown that folding initiation sites assuming helical structure are associated with the middle region of the corresponding native helices. A procedure for detection of folding initiation sites based on the use of middle helix preferences has been developed. The method utilizes preference functions [1], as well as position specific helix preferences, when searching for the segments with pronounced conformational bias towards mid alpha-helix. The tests performed on 100 proteins with the best known 3D structures and on 37 known folding initiation sites revealed that: a) preference-derived parameter is well suited for the detection of middle part of helices and b) strongly predicted middle helical segments correspond to protein folding initiation sites. Therefore, just by setting a high parameter threshold one can weed out helices that are not part of initiation sites. Prediction efficiency of 92% is reached with the threshold set at 3.6. The method is available via automatic server on the WWW site http://pref.etfos.hr/helix-start. [1] D. Juretic et al, J. Chem. Inf. Comput. Sci., 38, (1998) 575

Izvorni jezik
Engleski

Znanstvena područja
Fizika, Biologija



POVEZANOST RADA


Projekt / tema
177060

Ustanove
Prirodoslovno-matematički fakultet, Split