Computational Studies on PA-IIL Lectin-Carbohydrate
Interactions

a 2007

Computational Studies on PA-IIL Lectin-Carbohydrate Interactions

MISHRA, Navnit Kumar, Petr KULHÁNEK, Zdenek KRIZ, Michaela WIMMEROVA, Jaroslav KOCA et. al.

Basic information

Original name

Computational Studies on PA-IIL Lectin-Carbohydrate Interactions

Authors

MISHRA, Navnit Kumar (356 India), Petr KULHÁNEK (203 Czech Republic), Zdenek KRIZ (203 Czech Republic), Michaela WIMMEROVA (203 Czech Republic) and Jaroslav KOCA (203 Czech Republic, guarantor)

Edition

Materials Structure in Chemistry, Biology, Physics and Technology, 2007

Other information

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL URL

RIV identification code

RIV/00216224:14310/07:00020642

Organization unit

Faculty of Science

ISSN

Keywords in English

Computational studies; Molecular modeling; Interaction energy calculation

Abstract

V originále

Lectins are proteins of nonimmune origin that non-enzymatically selectively bind to mono or oligosaccharides. Multifarious activity of carbohydrates in biophysiological pathway, such as immune activity, tumor metastasis, cell-cell recognition, bacterial pathogenecity, open an avenue for the lectin-carbohydrate interaction research, which is also a big challenge for theoretical modeling due to the polar flexible saccharide moiety. One of the lectins, PA-IIL that produced by Pseudomonas aeruginosa, which play significant role in cystic fibrosis disease, motivated our study on PA-IIL-carbohydrate interactions. The structure can provide a static view of the macromolecules, but for the full understanding of protein-ligand interactions it is necessary to know all the accessible spatial orientations of the ligand in the receptor binding pocket. It is often seen that the binding energy calculated over the sampled structure by molecular dynamics could give the insight of the interactions between protein and ligand.[1, 2] We used the MM/PBSA approach to calculate the binding free energy of the lectin-carbohydrate. The entropy contribution to the binding free energies was obtained by normal mode analysis. Unfortunately these conventional methods are not precise enough to accurately distinguish the binding order of saccharide series. Thus, to gain the insight of the spatial orientation of the monosaccharide and conversely the ligand induced fit in the receptor binding site, the binding energy and the pocket conform to the specific orientation of the saccharide was correlated. The spatial proximity of carbohydrate inside the binding domain is the key factor for the lectin-carbohydrate binding, which was identified by statistical clustering. One of the interesting finding was ions behavior, revealing their paramount significance for the binding.

Links

GD204/03/H016, research and development project

Name: Strukturní biofyzika makromolekul

Investor: Czech Science Foundation, Structural biophysics of macromolecules

Citovat

MISHRA, Navnit Kumar, Petr KULHÁNEK, Zdenek KRIZ, Michaela WIMMEROVA and Jaroslav KOCA. Computational Studies on PA-IIL Lectin-Carbohydrate Interactions. In Materials Structure in Chemistry, Biology, Physics and Technology. 2007. ISSN 1211-5894.

@proceedings{744323,
   author = {Mishra, Navnit Kumar and Kulhánek, Petr and Kriz, Zdenek and Wimmerova, Michaela and Koca, Jaroslav},
   booktitle = {Materials Structure in Chemistry, Biology, Physics and Technology},
   keywords = {Computational studies; Molecular modeling; Interaction energy calculation},
   language = {eng},
   title = {Computational Studies on PA-IIL Lectin-Carbohydrate Interactions},
   url = {http://www.xray.cz/ms},
   year = {2007}
}

TY  - CONF
ID  - 744323
AU  - Mishra, Navnit Kumar - Kulhánek, Petr - Kriz, Zdenek - Wimmerova, Michaela - Koca, Jaroslav
PY  - 2007
TI  - Computational Studies on PA-IIL Lectin-Carbohydrate Interactions
KW  - Computational studies
KW  - Molecular modeling
KW  - Interaction energy calculation
UR  - http://www.xray.cz/ms
N2  - Lectins are proteins of nonimmune origin that non-enzymatically selectively bind to mono or oligosaccharides. Multifarious activity of carbohydrates in biophysiological pathway, such as immune activity, tumor metastasis, cell-cell recognition, bacterial pathogenecity, open an avenue for the lectin-carbohydrate interaction research, which is also a big challenge for theoretical modeling due to the polar flexible saccharide moiety. One of the lectins, PA-IIL that produced by Pseudomonas aeruginosa, which play significant role in cystic fibrosis disease, motivated our study on PA-IIL-carbohydrate interactions. The structure can provide a static view of the macromolecules, but for the full understanding of protein-ligand interactions it is necessary to know all the accessible spatial orientations of the ligand in the receptor binding pocket. It is often seen that the binding energy calculated over the sampled structure by molecular dynamics could give the insight of the interactions between protein and ligand.[1, 2] We used the MM/PBSA approach to calculate the binding free energy of the lectin-carbohydrate. The entropy contribution to the binding free energies was obtained by normal mode analysis. Unfortunately these conventional methods are not precise enough to accurately distinguish the binding order of saccharide series. Thus, to gain the insight of the spatial orientation of the monosaccharide and conversely the ligand induced fit in the receptor binding site, the binding energy and the pocket conform to the specific orientation of the saccharide was correlated. The spatial proximity of carbohydrate inside the binding domain is the key factor for the lectin-carbohydrate binding, which was identified by statistical clustering. One of the interesting finding was ions behavior, revealing their paramount significance for the binding.
ER  -

MISHRA, Navnit Kumar, Petr KULHÁNEK, Zdenek KRIZ, Michaela WIMMEROVA and Jaroslav KOCA. Computational Studies on PA-IIL Lectin-Carbohydrate Interactions. In \textit{Materials Structure in Chemistry, Biology, Physics and Technology}. 2007. ISSN~1211-5894.

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