Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain
Water molecules, rigidly associated to protein surfaces, play a key role in stabilizing biomolecules and participating in their biological functions. Recent studies on the solvation properties of the carbohydrate recognition domain of Galectin-1 by means of molecular dynamic simulations have reveale...
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todo:paper_00222860_v978_n1-3_p220_DiLella2023-10-03T14:30:42Z Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain Di Lella, S. Petruk, A.A. De Armiño, D.J.A. Álvarez, R.M.S. Binding energies Galectin-1 Hydrogen-bonding interactions Quantum chemical calculations Amino acids Binding energy Bins Carbohydrates Chemical bonds Crystal structure Hydrogen bonds Ligands Methanol Molecular biology Molecular dynamics Proteins Quantum chemistry Quantum theory Bound water molecules Carbohydrate-recognition domains Galectin-1 Hydrogen bonding interactions Intermolecular interactions Quantum chemical calculations Quantum mechanical method Solvation properties Biological functions Molecules Water molecules, rigidly associated to protein surfaces, play a key role in stabilizing biomolecules and participating in their biological functions. Recent studies on the solvation properties of the carbohydrate recognition domain of Galectin-1 by means of molecular dynamic simulations have revealed the existence of several water sites which were well correlated to both the bound water molecules observed in the crystal structure of the protein in the free state and to some of the hydroxyl groups of the carbohydrate ligand observed in the crystal structure of the complexed protein. In this work, we present a study using quantum mechanical methods (B3LYP/6-311++G(3df,3dp)//B3LYP/6-31+G(d)) to determine the energy involved in the binding of these water molecules to specific amino acids in the carbohydrate recognition domain of the protein. By modeling the hydroxyl groups of the carbohydrate by methanol, the energies associated to the local interactions between the ligand and the protein have been evaluated by replacing specific water molecules with methanol. The values of the binding energies have been compared to those previously obtained by the molecular dynamic method. © 2010 Elsevier B.V. All rights reserved. Fil:Petruk, A.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_00222860_v978_n1-3_p220_DiLella |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
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R-134 |
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Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Binding energies Galectin-1 Hydrogen-bonding interactions Quantum chemical calculations Amino acids Binding energy Bins Carbohydrates Chemical bonds Crystal structure Hydrogen bonds Ligands Methanol Molecular biology Molecular dynamics Proteins Quantum chemistry Quantum theory Bound water molecules Carbohydrate-recognition domains Galectin-1 Hydrogen bonding interactions Intermolecular interactions Quantum chemical calculations Quantum mechanical method Solvation properties Biological functions Molecules |
| spellingShingle |
Binding energies Galectin-1 Hydrogen-bonding interactions Quantum chemical calculations Amino acids Binding energy Bins Carbohydrates Chemical bonds Crystal structure Hydrogen bonds Ligands Methanol Molecular biology Molecular dynamics Proteins Quantum chemistry Quantum theory Bound water molecules Carbohydrate-recognition domains Galectin-1 Hydrogen bonding interactions Intermolecular interactions Quantum chemical calculations Quantum mechanical method Solvation properties Biological functions Molecules Di Lella, S. Petruk, A.A. De Armiño, D.J.A. Álvarez, R.M.S. Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain |
| topic_facet |
Binding energies Galectin-1 Hydrogen-bonding interactions Quantum chemical calculations Amino acids Binding energy Bins Carbohydrates Chemical bonds Crystal structure Hydrogen bonds Ligands Methanol Molecular biology Molecular dynamics Proteins Quantum chemistry Quantum theory Bound water molecules Carbohydrate-recognition domains Galectin-1 Hydrogen bonding interactions Intermolecular interactions Quantum chemical calculations Quantum mechanical method Solvation properties Biological functions Molecules |
| description |
Water molecules, rigidly associated to protein surfaces, play a key role in stabilizing biomolecules and participating in their biological functions. Recent studies on the solvation properties of the carbohydrate recognition domain of Galectin-1 by means of molecular dynamic simulations have revealed the existence of several water sites which were well correlated to both the bound water molecules observed in the crystal structure of the protein in the free state and to some of the hydroxyl groups of the carbohydrate ligand observed in the crystal structure of the complexed protein. In this work, we present a study using quantum mechanical methods (B3LYP/6-311++G(3df,3dp)//B3LYP/6-31+G(d)) to determine the energy involved in the binding of these water molecules to specific amino acids in the carbohydrate recognition domain of the protein. By modeling the hydroxyl groups of the carbohydrate by methanol, the energies associated to the local interactions between the ligand and the protein have been evaluated by replacing specific water molecules with methanol. The values of the binding energies have been compared to those previously obtained by the molecular dynamic method. © 2010 Elsevier B.V. All rights reserved. |
| format |
JOUR |
| author |
Di Lella, S. Petruk, A.A. De Armiño, D.J.A. Álvarez, R.M.S. |
| author_facet |
Di Lella, S. Petruk, A.A. De Armiño, D.J.A. Álvarez, R.M.S. |
| author_sort |
Di Lella, S. |
| title |
Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain |
| title_short |
Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain |
| title_full |
Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain |
| title_fullStr |
Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain |
| title_full_unstemmed |
Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain |
| title_sort |
specific intermolecular interactions of conserved water molecules with amino acids in the galectin-1 carbohydrate recognition domain |
| url |
http://hdl.handle.net/20.500.12110/paper_00222860_v978_n1-3_p220_DiLella |
| work_keys_str_mv |
AT dilellas specificintermolecularinteractionsofconservedwatermoleculeswithaminoacidsinthegalectin1carbohydraterecognitiondomain AT petrukaa specificintermolecularinteractionsofconservedwatermoleculeswithaminoacidsinthegalectin1carbohydraterecognitiondomain AT dearminodja specificintermolecularinteractionsofconservedwatermoleculeswithaminoacidsinthegalectin1carbohydraterecognitiondomain AT alvarezrms specificintermolecularinteractionsofconservedwatermoleculeswithaminoacidsinthegalectin1carbohydraterecognitiondomain |
| _version_ |
1807322809734529024 |