Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods

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 interact...

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Main Authors:	Wimmerová, Michaela, Kozmon, Stanislav, Nečasová, Ivona, Mishra, Sushil Kumar, Komárek, Jan, Koča, Jaroslav
Format:	Online
Language:	English
Published:	Public Library of Science 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3466270/

id	pubmed-3466270
recordtype	oai_dc
spelling	pubmed-34662702012-10-10 Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods Wimmerová, Michaela Kozmon, Stanislav Nečasová, Ivona Mishra, Sushil Kumar Komárek, Jan Koča, Jaroslav Research Article 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/π interaction. In the study presented here, we attempted for the first time to quantify how the CH/π 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 α-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 α-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. Public Library of Science 2012-10-08 /pmc/articles/PMC3466270/ /pubmed/23056230 http://dx.doi.org/10.1371/journal.pone.0046032 Text en © 2012 Wimmerová et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Wimmerová, Michaela Kozmon, Stanislav Nečasová, Ivona Mishra, Sushil Kumar Komárek, Jan Koča, Jaroslav
spellingShingle	Wimmerová, Michaela Kozmon, Stanislav Nečasová, Ivona Mishra, Sushil Kumar Komárek, Jan Koča, Jaroslav Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods
author_facet	Wimmerová, Michaela Kozmon, Stanislav Nečasová, Ivona Mishra, Sushil Kumar Komárek, Jan Koča, Jaroslav
author_sort	Wimmerová, Michaela
title	Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods
title_short	Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods
title_full	Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods
title_fullStr	Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods
title_full_unstemmed	Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods
title_sort	stacking interactions between carbohydrate and protein quantified by combination of theoretical and experimental methods
description	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/π interaction. In the study presented here, we attempted for the first time to quantify how the CH/π 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 α-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 α-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.
publisher	Public Library of Science
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3466270/
_version_	1611914406674825216

Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods

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