2012
SiteBinder: An improved approach for comparing multiple protein structural motifs
SEHNAL, David, Radka SVOBODOVÁ VAŘEKOVÁ, Heinrich J. HUBER, Stanislav GEIDL, Crina-Maria IONESCU et. al.Základní údaje
Originální název
SiteBinder: An improved approach for comparing multiple protein structural motifs
Autoři
SEHNAL, David (203 Česká republika, domácí), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, domácí), Heinrich J. HUBER (40 Rakousko), Stanislav GEIDL (203 Česká republika, domácí), Crina-Maria IONESCU (642 Rumunsko, domácí), Michaela WIMMEROVÁ (203 Česká republika, domácí) a Jaroslav KOČA (203 Česká republika, garant, domácí)
Vydání
Journal of Chemical Information and Modeling, 2012, 1549-9596
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10403 Physical chemistry
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Impakt faktor
Impact factor: 4.304
Kód RIV
RIV/00216224:14310/12:00057316
Organizační jednotka
Přírodovědecká fakulta
UT WoS
000300650400009
Klíčová slova anglicky
protein structural motifs; superimposition; comparison; lectins; apoptosis
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 27. 7. 2014 18:56, RNDr. Stanislav Geidl, Ph.D.
Anotace
V originále
There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. Our benchmarking analysis has shown the robustness, efficiency, and versatility of our methodology and its implementation by the successful superimposition of 1000 experimentally determined structures for each of 32 eukaryotic linear motifs. We also demonstrate the applicability of SiteBinder using three case studies. We first compared the structures of 61 PA-IIL sugar binding sites containing nine different sugars, and we found that the sugar binding sites of PA-IIL and its mutants have a conserved structure despite their binding different sugars. We then superimposed over 300 zinc finger central motifs and revealed that the molecular structure in the vicinity of the Zn atom is highly conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic proteins. Our findings come to support the hypothesis that there is a structural basis for the functional segregation of BH3-only proteins into activators and enablers.
Návaznosti
| GD301/09/H004, projekt VaV |
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| ME08008, projekt VaV |
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| MUNI/A/0914/2009, interní kód MU |
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