Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes
Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interac...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Upadhyay, Sanjay K. [verfasserIn] |
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| Format: |
Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2012 |
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| Schlagwörter: |
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| Anmerkung: |
© Springer Science+Business Media B.V. 2012 |
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| Übergeordnetes Werk: |
Enthalten in: Journal of computer aided molecular design - Springer Netherlands, 1987, 26(2012), 7 vom: 26. Mai, Seite 847-864 |
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| Übergeordnetes Werk: |
volume:26 ; year:2012 ; number:7 ; day:26 ; month:05 ; pages:847-864 |
| Links: |
|---|
| DOI / URN: |
10.1007/s10822-012-9579-5 |
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| Katalog-ID: |
OLC2034739051 |
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| 245 | 1 | 0 | |a Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes |
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| 520 | |a Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein–protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins. | ||
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| 650 | 4 | |a ATP | |
| 650 | 4 | |a Galactose | |
| 650 | 4 | |a GAL genes | |
| 700 | 1 | |a Sasidhar, Yellamraju U. |4 aut | |
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10.1007/s10822-012-9579-5 doi (DE-627)OLC2034739051 (DE-He213)s10822-012-9579-5-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Upadhyay, Sanjay K. verfasserin aut Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes 2012 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein–protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins. Gal1p Gal3p Gal80p Docking Molecular dynamics ATP Galactose GAL genes Sasidhar, Yellamraju U. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2012), 7 vom: 26. Mai, Seite 847-864 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2012 number:7 day:26 month:05 pages:847-864 https://doi.org/10.1007/s10822-012-9579-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2012 7 26 05 847-864 |
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10.1007/s10822-012-9579-5 doi (DE-627)OLC2034739051 (DE-He213)s10822-012-9579-5-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Upadhyay, Sanjay K. verfasserin aut Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes 2012 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein–protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins. Gal1p Gal3p Gal80p Docking Molecular dynamics ATP Galactose GAL genes Sasidhar, Yellamraju U. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2012), 7 vom: 26. Mai, Seite 847-864 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2012 number:7 day:26 month:05 pages:847-864 https://doi.org/10.1007/s10822-012-9579-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2012 7 26 05 847-864 |
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10.1007/s10822-012-9579-5 doi (DE-627)OLC2034739051 (DE-He213)s10822-012-9579-5-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Upadhyay, Sanjay K. verfasserin aut Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes 2012 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein–protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins. Gal1p Gal3p Gal80p Docking Molecular dynamics ATP Galactose GAL genes Sasidhar, Yellamraju U. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2012), 7 vom: 26. Mai, Seite 847-864 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2012 number:7 day:26 month:05 pages:847-864 https://doi.org/10.1007/s10822-012-9579-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2012 7 26 05 847-864 |
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10.1007/s10822-012-9579-5 doi (DE-627)OLC2034739051 (DE-He213)s10822-012-9579-5-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Upadhyay, Sanjay K. verfasserin aut Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes 2012 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein–protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins. Gal1p Gal3p Gal80p Docking Molecular dynamics ATP Galactose GAL genes Sasidhar, Yellamraju U. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2012), 7 vom: 26. Mai, Seite 847-864 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2012 number:7 day:26 month:05 pages:847-864 https://doi.org/10.1007/s10822-012-9579-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2012 7 26 05 847-864 |
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10.1007/s10822-012-9579-5 doi (DE-627)OLC2034739051 (DE-He213)s10822-012-9579-5-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Upadhyay, Sanjay K. verfasserin aut Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes 2012 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein–protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins. Gal1p Gal3p Gal80p Docking Molecular dynamics ATP Galactose GAL genes Sasidhar, Yellamraju U. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2012), 7 vom: 26. Mai, Seite 847-864 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2012 number:7 day:26 month:05 pages:847-864 https://doi.org/10.1007/s10822-012-9579-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2012 7 26 05 847-864 |
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Enthalten in Journal of computer aided molecular design 26(2012), 7 vom: 26. Mai, Seite 847-864 volume:26 year:2012 number:7 day:26 month:05 pages:847-864 |
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Upadhyay, Sanjay K. ddc 570 ssgn 12 fid PHARM fid BIODIV misc Gal1p misc Gal3p misc Gal80p misc Docking misc Molecular dynamics misc ATP misc Galactose misc GAL genes Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes |
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570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes Gal1p Gal3p Gal80p Docking Molecular dynamics ATP Galactose GAL genes |
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Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes |
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molecular simulation and docking studies of gal1p and gal3p proteins in the presence and absence of ligands atp and galactose: implication for transcriptional activation of gal genes |
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Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes |
| abstract |
Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein–protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins. © Springer Science+Business Media B.V. 2012 |
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Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein–protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins. © Springer Science+Business Media B.V. 2012 |
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Abstract The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein–protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins. © Springer Science+Business Media B.V. 2012 |
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