Global Changes in Local Protein Dynamics Reduce the Entropic Cost of Carbohydrate Binding in the Arabinose-binding Protein
Protein dynamics make important but poorly understood contributions to molecular recognition phenomena. To address this, we measure changes in fast protein dynamics that accompany the interaction of the arabinose-binding protein (ABP) with its ligand, d-galactose, using NMR relaxation and molecular dynamics simulation. These two approaches present an entirely consistent view of the dynamic changes that occur in the protein backbone upon ligand binding. Increases in the amplitude of motions are observed throughout the protein, with the exception of a few residues in the binding site, which show restriction of dynamics. These counter-intuitive results imply that a localised binding event causes a global increase in the extent of protein dynamics on the pico- to nanosecond timescale. This global dynamic change constitutes a substantial favourable entropic contribution to the free energy of ligand binding. These results suggest that the structure and dynamics of ABP may be adapted to exploit dynamic changes to reduce the entropic costs of binding.
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| Format: | artículo biblioteca |
| Language: | English |
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Elsevier
2007-05-04
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| Subjects: | Ligand binding, Thermodynamics, NMR relaxation, Molecular dynamics, Periplasmic binding protein, |
| Online Access: | http://hdl.handle.net/10261/213361 |
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dig-ipna-es-10261-2133612021-11-22T12:46:59Z Global Changes in Local Protein Dynamics Reduce the Entropic Cost of Carbohydrate Binding in the Arabinose-binding Protein MacRaild, Christopher A. Hernández Daranas, Antonio Bronowska, Agnieszka Homans, Steve W. Ligand binding Thermodynamics NMR relaxation Molecular dynamics Periplasmic binding protein Protein dynamics make important but poorly understood contributions to molecular recognition phenomena. To address this, we measure changes in fast protein dynamics that accompany the interaction of the arabinose-binding protein (ABP) with its ligand, d-galactose, using NMR relaxation and molecular dynamics simulation. These two approaches present an entirely consistent view of the dynamic changes that occur in the protein backbone upon ligand binding. Increases in the amplitude of motions are observed throughout the protein, with the exception of a few residues in the binding site, which show restriction of dynamics. These counter-intuitive results imply that a localised binding event causes a global increase in the extent of protein dynamics on the pico- to nanosecond timescale. This global dynamic change constitutes a substantial favourable entropic contribution to the free energy of ligand binding. These results suggest that the structure and dynamics of ABP may be adapted to exploit dynamic changes to reduce the entropic costs of binding. Peer reviewed 2020-06-04T10:56:13Z 2020-06-04T10:56:13Z 2007-05-04 artículo http://purl.org/coar/resource_type/c_6501 Journal of Molecular Biology 368(3): 822-832 (2007) 0022-2836 http://hdl.handle.net/10261/213361 10.1016/j.jmb.2007.02.055 1089-8638 17368482 en Postprint https://doi.org/10.1016/j.jmb.2007.02.055 No none Elsevier |
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Ligand binding Thermodynamics NMR relaxation Molecular dynamics Periplasmic binding protein Ligand binding Thermodynamics NMR relaxation Molecular dynamics Periplasmic binding protein |
| spellingShingle |
Ligand binding Thermodynamics NMR relaxation Molecular dynamics Periplasmic binding protein Ligand binding Thermodynamics NMR relaxation Molecular dynamics Periplasmic binding protein MacRaild, Christopher A. Hernández Daranas, Antonio Bronowska, Agnieszka Homans, Steve W. Global Changes in Local Protein Dynamics Reduce the Entropic Cost of Carbohydrate Binding in the Arabinose-binding Protein |
| description |
Protein dynamics make important but poorly understood contributions to molecular recognition phenomena. To address this, we measure changes in fast protein dynamics that accompany the interaction of the arabinose-binding protein (ABP) with its ligand, d-galactose, using NMR relaxation and molecular dynamics simulation. These two approaches present an entirely consistent view of the dynamic changes that occur in the protein backbone upon ligand binding. Increases in the amplitude of motions are observed throughout the protein, with the exception of a few residues in the binding site, which show restriction of dynamics. These counter-intuitive results imply that a localised binding event causes a global increase in the extent of protein dynamics on the pico- to nanosecond timescale. This global dynamic change constitutes a substantial favourable entropic contribution to the free energy of ligand binding. These results suggest that the structure and dynamics of ABP may be adapted to exploit dynamic changes to reduce the entropic costs of binding. |
| format |
artículo |
| topic_facet |
Ligand binding Thermodynamics NMR relaxation Molecular dynamics Periplasmic binding protein |
| author |
MacRaild, Christopher A. Hernández Daranas, Antonio Bronowska, Agnieszka Homans, Steve W. |
| author_facet |
MacRaild, Christopher A. Hernández Daranas, Antonio Bronowska, Agnieszka Homans, Steve W. |
| author_sort |
MacRaild, Christopher A. |
| title |
Global Changes in Local Protein Dynamics Reduce the Entropic Cost of Carbohydrate Binding in the Arabinose-binding Protein |
| title_short |
Global Changes in Local Protein Dynamics Reduce the Entropic Cost of Carbohydrate Binding in the Arabinose-binding Protein |
| title_full |
Global Changes in Local Protein Dynamics Reduce the Entropic Cost of Carbohydrate Binding in the Arabinose-binding Protein |
| title_fullStr |
Global Changes in Local Protein Dynamics Reduce the Entropic Cost of Carbohydrate Binding in the Arabinose-binding Protein |
| title_full_unstemmed |
Global Changes in Local Protein Dynamics Reduce the Entropic Cost of Carbohydrate Binding in the Arabinose-binding Protein |
| title_sort |
global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein |
| publisher |
Elsevier |
| publishDate |
2007-05-04 |
| url |
http://hdl.handle.net/10261/213361 |
| work_keys_str_mv |
AT macraildchristophera globalchangesinlocalproteindynamicsreducetheentropiccostofcarbohydratebindinginthearabinosebindingprotein AT hernandezdaranasantonio globalchangesinlocalproteindynamicsreducetheentropiccostofcarbohydratebindinginthearabinosebindingprotein AT bronowskaagnieszka globalchangesinlocalproteindynamicsreducetheentropiccostofcarbohydratebindinginthearabinosebindingprotein AT homansstevew globalchangesinlocalproteindynamicsreducetheentropiccostofcarbohydratebindinginthearabinosebindingprotein |
| _version_ |
1777669860084416512 |