WIMMEROVÁ, Michaela, Stanislav KOZMON, Ivona NEČASOVÁ, Sushil Kumar MISHRA, Jan KOMÁREK and Jaroslav KOČA. Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods. Plos One. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2012, vol. 7, No 10, p. "nestránkováno", 9 pp. ISSN 1932-6203. doi:10.1371/journal.pone.0046032.
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Basic information
Original name Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods
Authors WIMMEROVÁ, Michaela (203 Czech Republic, guarantor, belonging to the institution), Stanislav KOZMON (703 Slovakia, belonging to the institution), Ivona NEČASOVÁ (203 Czech Republic, belonging to the institution), Sushil Kumar MISHRA (356 India, belonging to the institution), Jan KOMÁREK (203 Czech Republic, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, belonging to the institution).
Edition Plos One, SAN FRANCISCO, PUBLIC LIBRARY SCIENCE, 2012, 1932-6203.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10600 1.6 Biological sciences
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 3.730
RIV identification code RIV/00216224:14740/12:00057813
Organization unit Central European Institute of Technology
Doi http://dx.doi.org/10.1371/journal.pone.0046032
UT WoS 000309831500025
Keywords in English SMALL MOLECULAR-INTERACTIONS; DENSITY-FUNCTIONAL THEORY; SEPARATE TOTAL ENERGIES; INTERACTIONS AB-INITIO; DOT-PI-INTERACTIONS; O HYDROGEN-BONDS; AROMATIC INTERACTIONS; RALSTONIA-SOLANACEARUM; STRUCTURAL BASIS; EXCHANGE-ENERGY
Tags ok, rivok
Tags International impact, Reviewed
Changed by Changed by: Olga Křížová, učo 56639. Changed: 16. 11. 2012 12:03.
Abstract
Carbohydrate - receptor interactions are an integral part of biological events. They play an important role in many cellular processes, such as cell-cell adhesion, cell differentiation and in-cell signaling. Carbohydrates can interact with a receptor by using several types of intermolecular interactions. One of the most important is the interaction of a carbohydrate's apolar part with aromatic amino acid residues, known as dispersion interaction or CH/pi interaction. In the study presented here, we attempted for the first time to quantify how the CH/pi interaction contributes to a more general carbohydrate - protein interaction. We used a combined experimental approach, creating single and double point mutants with high level computational methods, and applied both to Ralstonia solanacearum (RSL) lectin complexes with alpha-L-Me-fucoside. Experimentally measured binding affinities were compared with computed carbohydrate-aromatic amino acid residue interaction energies. Experimental binding affinities for the RSL wild type, phenylalanine and alanine mutants were -8.5, -7.1 and -4.1 kcal.mol(-1), respectively. These affinities agree with the computed dispersion interaction energy between carbohydrate and aromatic amino acid residues for RSL wild type and phenylalanine, with values -8.8, -7.9 kcal.mol(-1), excluding the alanine mutant where the interaction energy was -0.9 kcal.mol(-1). Molecular dynamics simulations show that discrepancy can be caused by creation of a new hydrogen bond between the alpha-L-Me-fucoside and RSL. Observed results suggest that in this and similar cases the carbohydrate-receptor interaction can be driven mainly by a dispersion interaction.
Links
ED1.1.00/02.0068, research and development projectName: CEITEC - central european institute of technology
GA303/09/1168, research and development projectName: Lektiny z lidských patogenů - struktura, funkce, inženýrství
Investor: Czech Science Foundation, Standard Projects
GD301/09/H004, research and development projectName: Molekulární a strukturní biologie vybraných cytostatik. Od mechanistických studií k chemoterapii rakoviny
Investor: Czech Science Foundation, Doctor grants
2SGA2747, internal MU codeName: Saccharide - protein dispersion interactions involved in the bacterial recognition processes (Acronym: SaProDI)
Investor: South-Moravian Region, SoMoPro, Incoming grants
286154, internal MU codeName: SYLICA - Synergies of Life and Material Sciences to Create a New Future (Acronym: SYLICA)
Investor: European Union, 7th Specific RTD Programme, Capacities
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