Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase
Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recog...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Kandeel, Mahmoud [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2013 |
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| Schlagwörter: |
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| Anmerkung: |
© Akadémiai Kiadó, Budapest, Hungary 2013 |
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| Übergeordnetes Werk: |
Enthalten in: Journal of thermal analysis and calorimetry - Dordrecht [u.a.] : Springer Science + Business Media B.V., 1969, 115(2013), 3 vom: 28. Juli, Seite 2089-2097 |
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| Übergeordnetes Werk: |
volume:115 ; year:2013 ; number:3 ; day:28 ; month:07 ; pages:2089-2097 |
| Links: |
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| DOI / URN: |
10.1007/s10973-013-3319-5 |
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| Katalog-ID: |
SPR015487326 |
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| 100 | 1 | |a Kandeel, Mahmoud |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase |
| 264 | 1 | |c 2013 | |
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| 337 | |a Computermedien |b c |2 rdamedia | ||
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| 500 | |a © Akadémiai Kiadó, Budapest, Hungary 2013 | ||
| 520 | |a Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. These changes indicate unfavorable conditions for proper binding and lower conformational changes, and suboptimal structural reordering during dGMP binding. | ||
| 650 | 4 | |a Thymidylate kinase |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Isothermal titration calorimetry |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Thermodynamics |7 (dpeaa)DE-He213 | |
| 700 | 1 | |a Noguchi, Yoshihiro |4 aut | |
| 700 | 1 | |a Oh-Hashi, Kentaro |4 aut | |
| 700 | 1 | |a Kim, Hye-Sook |4 aut | |
| 700 | 1 | |a Kitade, Yukio |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of thermal analysis and calorimetry |d Dordrecht [u.a.] : Springer Science + Business Media B.V., 1969 |g 115(2013), 3 vom: 28. Juli, Seite 2089-2097 |w (DE-627)315295422 |w (DE-600)2017304-0 |x 1572-8943 |7 nnns |
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| 912 | |a GBV_ILN_63 | ||
| 912 | |a GBV_ILN_69 | ||
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| 912 | |a GBV_ILN_74 | ||
| 912 | |a GBV_ILN_90 | ||
| 912 | |a GBV_ILN_95 | ||
| 912 | |a GBV_ILN_100 | ||
| 912 | |a GBV_ILN_105 | ||
| 912 | |a GBV_ILN_110 | ||
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| 912 | |a GBV_ILN_170 | ||
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| 912 | |a GBV_ILN_187 | ||
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| 912 | |a GBV_ILN_213 | ||
| 912 | |a GBV_ILN_224 | ||
| 912 | |a GBV_ILN_230 | ||
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| 912 | |a GBV_ILN_293 | ||
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| 912 | |a GBV_ILN_602 | ||
| 912 | |a GBV_ILN_636 | ||
| 912 | |a GBV_ILN_702 | ||
| 912 | |a GBV_ILN_2001 | ||
| 912 | |a GBV_ILN_2003 | ||
| 912 | |a GBV_ILN_2004 | ||
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| 912 | |a GBV_ILN_2007 | ||
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| 912 | |a GBV_ILN_2010 | ||
| 912 | |a GBV_ILN_2011 | ||
| 912 | |a GBV_ILN_2014 | ||
| 912 | |a GBV_ILN_2015 | ||
| 912 | |a GBV_ILN_2020 | ||
| 912 | |a GBV_ILN_2021 | ||
| 912 | |a GBV_ILN_2025 | ||
| 912 | |a GBV_ILN_2026 | ||
| 912 | |a GBV_ILN_2027 | ||
| 912 | |a GBV_ILN_2031 | ||
| 912 | |a GBV_ILN_2034 | ||
| 912 | |a GBV_ILN_2037 | ||
| 912 | |a GBV_ILN_2038 | ||
| 912 | |a GBV_ILN_2039 | ||
| 912 | |a GBV_ILN_2044 | ||
| 912 | |a GBV_ILN_2048 | ||
| 912 | |a GBV_ILN_2049 | ||
| 912 | |a GBV_ILN_2050 | ||
| 912 | |a GBV_ILN_2055 | ||
| 912 | |a GBV_ILN_2056 | ||
| 912 | |a GBV_ILN_2057 | ||
| 912 | |a GBV_ILN_2059 | ||
| 912 | |a GBV_ILN_2061 | ||
| 912 | |a GBV_ILN_2064 | ||
| 912 | |a GBV_ILN_2065 | ||
| 912 | |a GBV_ILN_2068 | ||
| 912 | |a GBV_ILN_2070 | ||
| 912 | |a GBV_ILN_2086 | ||
| 912 | |a GBV_ILN_2088 | ||
| 912 | |a GBV_ILN_2093 | ||
| 912 | |a GBV_ILN_2106 | ||
| 912 | |a GBV_ILN_2107 | ||
| 912 | |a GBV_ILN_2108 | ||
| 912 | |a GBV_ILN_2110 | ||
| 912 | |a GBV_ILN_2111 | ||
| 912 | |a GBV_ILN_2112 | ||
| 912 | |a GBV_ILN_2113 | ||
| 912 | |a GBV_ILN_2116 | ||
| 912 | |a GBV_ILN_2118 | ||
| 912 | |a GBV_ILN_2119 | ||
| 912 | |a GBV_ILN_2122 | ||
| 912 | |a GBV_ILN_2129 | ||
| 912 | |a GBV_ILN_2143 | ||
| 912 | |a GBV_ILN_2144 | ||
| 912 | |a GBV_ILN_2147 | ||
| 912 | |a GBV_ILN_2148 | ||
| 912 | |a GBV_ILN_2152 | ||
| 912 | |a GBV_ILN_2153 | ||
| 912 | |a GBV_ILN_2188 | ||
| 912 | |a GBV_ILN_2190 | ||
| 912 | |a GBV_ILN_2232 | ||
| 912 | |a GBV_ILN_2336 | ||
| 912 | |a GBV_ILN_2446 | ||
| 912 | |a GBV_ILN_2470 | ||
| 912 | |a GBV_ILN_2472 | ||
| 912 | |a GBV_ILN_2507 | ||
| 912 | |a GBV_ILN_2522 | ||
| 912 | |a GBV_ILN_2548 | ||
| 912 | |a GBV_ILN_4012 | ||
| 912 | |a GBV_ILN_4035 | ||
| 912 | |a GBV_ILN_4037 | ||
| 912 | |a GBV_ILN_4046 | ||
| 912 | |a GBV_ILN_4112 | ||
| 912 | |a GBV_ILN_4125 | ||
| 912 | |a GBV_ILN_4126 | ||
| 912 | |a GBV_ILN_4242 | ||
| 912 | |a GBV_ILN_4246 | ||
| 912 | |a GBV_ILN_4249 | ||
| 912 | |a GBV_ILN_4251 | ||
| 912 | |a GBV_ILN_4305 | ||
| 912 | |a GBV_ILN_4306 | ||
| 912 | |a GBV_ILN_4307 | ||
| 912 | |a GBV_ILN_4313 | ||
| 912 | |a GBV_ILN_4322 | ||
| 912 | |a GBV_ILN_4323 | ||
| 912 | |a GBV_ILN_4324 | ||
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| 912 | |a GBV_ILN_4338 | ||
| 912 | |a GBV_ILN_4393 | ||
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| 951 | |a AR | ||
| 952 | |d 115 |j 2013 |e 3 |b 28 |c 07 |h 2089-2097 | ||
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2013 |
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2013 |
| allfields |
10.1007/s10973-013-3319-5 doi (DE-627)SPR015487326 (SPR)s10973-013-3319-5-e DE-627 ger DE-627 rakwb eng Kandeel, Mahmoud verfasserin aut Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Akadémiai Kiadó, Budapest, Hungary 2013 Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. These changes indicate unfavorable conditions for proper binding and lower conformational changes, and suboptimal structural reordering during dGMP binding. Thymidylate kinase (dpeaa)DE-He213 Isothermal titration calorimetry (dpeaa)DE-He213 Thermodynamics (dpeaa)DE-He213 Noguchi, Yoshihiro aut Oh-Hashi, Kentaro aut Kim, Hye-Sook aut Kitade, Yukio aut Enthalten in Journal of thermal analysis and calorimetry Dordrecht [u.a.] : Springer Science + Business Media B.V., 1969 115(2013), 3 vom: 28. Juli, Seite 2089-2097 (DE-627)315295422 (DE-600)2017304-0 1572-8943 nnns volume:115 year:2013 number:3 day:28 month:07 pages:2089-2097 https://dx.doi.org/10.1007/s10973-013-3319-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 115 2013 3 28 07 2089-2097 |
| spelling |
10.1007/s10973-013-3319-5 doi (DE-627)SPR015487326 (SPR)s10973-013-3319-5-e DE-627 ger DE-627 rakwb eng Kandeel, Mahmoud verfasserin aut Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Akadémiai Kiadó, Budapest, Hungary 2013 Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. These changes indicate unfavorable conditions for proper binding and lower conformational changes, and suboptimal structural reordering during dGMP binding. Thymidylate kinase (dpeaa)DE-He213 Isothermal titration calorimetry (dpeaa)DE-He213 Thermodynamics (dpeaa)DE-He213 Noguchi, Yoshihiro aut Oh-Hashi, Kentaro aut Kim, Hye-Sook aut Kitade, Yukio aut Enthalten in Journal of thermal analysis and calorimetry Dordrecht [u.a.] : Springer Science + Business Media B.V., 1969 115(2013), 3 vom: 28. Juli, Seite 2089-2097 (DE-627)315295422 (DE-600)2017304-0 1572-8943 nnns volume:115 year:2013 number:3 day:28 month:07 pages:2089-2097 https://dx.doi.org/10.1007/s10973-013-3319-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 115 2013 3 28 07 2089-2097 |
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10.1007/s10973-013-3319-5 doi (DE-627)SPR015487326 (SPR)s10973-013-3319-5-e DE-627 ger DE-627 rakwb eng Kandeel, Mahmoud verfasserin aut Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Akadémiai Kiadó, Budapest, Hungary 2013 Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. These changes indicate unfavorable conditions for proper binding and lower conformational changes, and suboptimal structural reordering during dGMP binding. Thymidylate kinase (dpeaa)DE-He213 Isothermal titration calorimetry (dpeaa)DE-He213 Thermodynamics (dpeaa)DE-He213 Noguchi, Yoshihiro aut Oh-Hashi, Kentaro aut Kim, Hye-Sook aut Kitade, Yukio aut Enthalten in Journal of thermal analysis and calorimetry Dordrecht [u.a.] : Springer Science + Business Media B.V., 1969 115(2013), 3 vom: 28. Juli, Seite 2089-2097 (DE-627)315295422 (DE-600)2017304-0 1572-8943 nnns volume:115 year:2013 number:3 day:28 month:07 pages:2089-2097 https://dx.doi.org/10.1007/s10973-013-3319-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 115 2013 3 28 07 2089-2097 |
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10.1007/s10973-013-3319-5 doi (DE-627)SPR015487326 (SPR)s10973-013-3319-5-e DE-627 ger DE-627 rakwb eng Kandeel, Mahmoud verfasserin aut Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Akadémiai Kiadó, Budapest, Hungary 2013 Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. These changes indicate unfavorable conditions for proper binding and lower conformational changes, and suboptimal structural reordering during dGMP binding. Thymidylate kinase (dpeaa)DE-He213 Isothermal titration calorimetry (dpeaa)DE-He213 Thermodynamics (dpeaa)DE-He213 Noguchi, Yoshihiro aut Oh-Hashi, Kentaro aut Kim, Hye-Sook aut Kitade, Yukio aut Enthalten in Journal of thermal analysis and calorimetry Dordrecht [u.a.] : Springer Science + Business Media B.V., 1969 115(2013), 3 vom: 28. Juli, Seite 2089-2097 (DE-627)315295422 (DE-600)2017304-0 1572-8943 nnns volume:115 year:2013 number:3 day:28 month:07 pages:2089-2097 https://dx.doi.org/10.1007/s10973-013-3319-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 115 2013 3 28 07 2089-2097 |
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10.1007/s10973-013-3319-5 doi (DE-627)SPR015487326 (SPR)s10973-013-3319-5-e DE-627 ger DE-627 rakwb eng Kandeel, Mahmoud verfasserin aut Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Akadémiai Kiadó, Budapest, Hungary 2013 Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. These changes indicate unfavorable conditions for proper binding and lower conformational changes, and suboptimal structural reordering during dGMP binding. Thymidylate kinase (dpeaa)DE-He213 Isothermal titration calorimetry (dpeaa)DE-He213 Thermodynamics (dpeaa)DE-He213 Noguchi, Yoshihiro aut Oh-Hashi, Kentaro aut Kim, Hye-Sook aut Kitade, Yukio aut Enthalten in Journal of thermal analysis and calorimetry Dordrecht [u.a.] : Springer Science + Business Media B.V., 1969 115(2013), 3 vom: 28. Juli, Seite 2089-2097 (DE-627)315295422 (DE-600)2017304-0 1572-8943 nnns volume:115 year:2013 number:3 day:28 month:07 pages:2089-2097 https://dx.doi.org/10.1007/s10973-013-3319-5 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 115 2013 3 28 07 2089-2097 |
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Kandeel, Mahmoud @@aut@@ Noguchi, Yoshihiro @@aut@@ Oh-Hashi, Kentaro @@aut@@ Kim, Hye-Sook @@aut@@ Kitade, Yukio @@aut@@ |
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We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. 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Kandeel, Mahmoud |
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Kandeel, Mahmoud misc Thymidylate kinase misc Isothermal titration calorimetry misc Thermodynamics Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase |
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Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase Thymidylate kinase (dpeaa)DE-He213 Isothermal titration calorimetry (dpeaa)DE-He213 Thermodynamics (dpeaa)DE-He213 |
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Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase |
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molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase |
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Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase |
| abstract |
Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. These changes indicate unfavorable conditions for proper binding and lower conformational changes, and suboptimal structural reordering during dGMP binding. © Akadémiai Kiadó, Budapest, Hungary 2013 |
| abstractGer |
Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. These changes indicate unfavorable conditions for proper binding and lower conformational changes, and suboptimal structural reordering during dGMP binding. © Akadémiai Kiadó, Budapest, Hungary 2013 |
| abstract_unstemmed |
Abstract Plasmodium deoxyguanylate pathways are an attractive area of investigation for future metabolic and drug discovery studies due to their unusual substrate specificities. We investigated the energetic contribution to thymidylate kinase substrate binding, and the forces underlying ligand recognition. The binding constant varied from 8 × $ 10^{4} $ $ M^{−1} $ at 290 K to 6 × $ 10^{4} $ $ M^{−1} $ at 310 K for dGMP, and from 16 × $ 10^{4} $ $ M^{−1} $ at 290 K to 4 × $ 10^{4} $ $ M^{−1} $ at 310 K for TMP. ΔCp was estimated as −1.75 kJ $ mol^{−1} $ $ K^{−1} $ for TMP and +2 kJ $ mol^{−1} $ $ K^{−1} $ for dGMP. In comparison with TMP, the binding of dGMP to PfTMK produced less favorable enthalpy change, positive or favorable entropic contribution at lower temperature, positive heat capacity change, negative %$ \Updelta S_{\text{HE}}^{^\circ } %$, positive ΔSother, higher total solvent-exposed surface area and more or less rigid body binding. These changes indicate unfavorable conditions for proper binding and lower conformational changes, and suboptimal structural reordering during dGMP binding. © Akadémiai Kiadó, Budapest, Hungary 2013 |
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| title_short |
Molecular dynamics and energetic perceptions of substrate recognition by thymidylate kinase |
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https://dx.doi.org/10.1007/s10973-013-3319-5 |
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Noguchi, Yoshihiro Oh-Hashi, Kentaro Kim, Hye-Sook Kitade, Yukio |
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10.1007/s10973-013-3319-5 |
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2024-07-03T16:34:41.929Z |
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| score |
7.402237 |