Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamicsPresented in part at the Sixth International Conference on AIDS, San Francisco, CA, June 20-24, 1990.
The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 expl...
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E-Artikel |
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| Sprache: |
Englisch |
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1993 |
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5 Ill. 11 |
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Wiley InterScience Backfile Collection 1832-2000 |
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in: Proteins: Structure, Function, and Genetics - New York, NY : Wiley-Liss, 15(1993) vom: Apr., Seite 374-384 |
| Übergeordnetes Werk: |
volume:15 ; year:1993 ; month:04 ; pages:374-384 ; extent:11 |
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| 520 | |a The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N- and C-0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N-terminus displayed the greatest fluctuational disorder whereas the C-terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy-atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV-1 protease monomer than the subunit conformation seen in the X-ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley-Liss, Inc. | ||
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(DE-627)NLEJ159931843 DE-627 ger DE-627 rakwb eng Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamicsPresented in part at the Sixth International Conference on AIDS, San Francisco, CA, June 20-24, 1990. 1993 5 Ill. 11 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N- and C-0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N-terminus displayed the greatest fluctuational disorder whereas the C-terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy-atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV-1 protease monomer than the subunit conformation seen in the X-ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley-Liss, Inc. Wiley InterScience Backfile Collection 1832-2000 Venable, Richard M. oth Carson, Frederick W. oth Brooks, Bernard R. oth in Proteins: Structure, Function, and Genetics New York, NY : Wiley-Liss 15(1993) vom: Apr., Seite 374-384 (DE-627)NLEJ159070740 (DE-600)1475032-6 0887-3585 nnns volume:15 year:1993 month:04 pages:374-384 extent:11 http://dx.doi.org/10.1002/prot.340150405 text/html Deutschlandweit zugänglich GBV_USEFLAG_U ZDB-1-WIS GBV_NL_ARTICLE AR 15 1993 4 374-384 11 |
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(DE-627)NLEJ159931843 DE-627 ger DE-627 rakwb eng Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamicsPresented in part at the Sixth International Conference on AIDS, San Francisco, CA, June 20-24, 1990. 1993 5 Ill. 11 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N- and C-0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N-terminus displayed the greatest fluctuational disorder whereas the C-terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy-atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV-1 protease monomer than the subunit conformation seen in the X-ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley-Liss, Inc. Wiley InterScience Backfile Collection 1832-2000 Venable, Richard M. oth Carson, Frederick W. oth Brooks, Bernard R. oth in Proteins: Structure, Function, and Genetics New York, NY : Wiley-Liss 15(1993) vom: Apr., Seite 374-384 (DE-627)NLEJ159070740 (DE-600)1475032-6 0887-3585 nnns volume:15 year:1993 month:04 pages:374-384 extent:11 http://dx.doi.org/10.1002/prot.340150405 text/html Deutschlandweit zugänglich GBV_USEFLAG_U ZDB-1-WIS GBV_NL_ARTICLE AR 15 1993 4 374-384 11 |
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(DE-627)NLEJ159931843 DE-627 ger DE-627 rakwb eng Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamicsPresented in part at the Sixth International Conference on AIDS, San Francisco, CA, June 20-24, 1990. 1993 5 Ill. 11 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N- and C-0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N-terminus displayed the greatest fluctuational disorder whereas the C-terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy-atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV-1 protease monomer than the subunit conformation seen in the X-ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley-Liss, Inc. Wiley InterScience Backfile Collection 1832-2000 Venable, Richard M. oth Carson, Frederick W. oth Brooks, Bernard R. oth in Proteins: Structure, Function, and Genetics New York, NY : Wiley-Liss 15(1993) vom: Apr., Seite 374-384 (DE-627)NLEJ159070740 (DE-600)1475032-6 0887-3585 nnns volume:15 year:1993 month:04 pages:374-384 extent:11 http://dx.doi.org/10.1002/prot.340150405 text/html Deutschlandweit zugänglich GBV_USEFLAG_U ZDB-1-WIS GBV_NL_ARTICLE AR 15 1993 4 374-384 11 |
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(DE-627)NLEJ159931843 DE-627 ger DE-627 rakwb eng Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamicsPresented in part at the Sixth International Conference on AIDS, San Francisco, CA, June 20-24, 1990. 1993 5 Ill. 11 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N- and C-0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N-terminus displayed the greatest fluctuational disorder whereas the C-terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy-atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV-1 protease monomer than the subunit conformation seen in the X-ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley-Liss, Inc. Wiley InterScience Backfile Collection 1832-2000 Venable, Richard M. oth Carson, Frederick W. oth Brooks, Bernard R. oth in Proteins: Structure, Function, and Genetics New York, NY : Wiley-Liss 15(1993) vom: Apr., Seite 374-384 (DE-627)NLEJ159070740 (DE-600)1475032-6 0887-3585 nnns volume:15 year:1993 month:04 pages:374-384 extent:11 http://dx.doi.org/10.1002/prot.340150405 text/html Deutschlandweit zugänglich GBV_USEFLAG_U ZDB-1-WIS GBV_NL_ARTICLE AR 15 1993 4 374-384 11 |
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(DE-627)NLEJ159931843 DE-627 ger DE-627 rakwb eng Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamicsPresented in part at the Sixth International Conference on AIDS, San Francisco, CA, June 20-24, 1990. 1993 5 Ill. 11 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N- and C-0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N-terminus displayed the greatest fluctuational disorder whereas the C-terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy-atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV-1 protease monomer than the subunit conformation seen in the X-ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley-Liss, Inc. Wiley InterScience Backfile Collection 1832-2000 Venable, Richard M. oth Carson, Frederick W. oth Brooks, Bernard R. oth in Proteins: Structure, Function, and Genetics New York, NY : Wiley-Liss 15(1993) vom: Apr., Seite 374-384 (DE-627)NLEJ159070740 (DE-600)1475032-6 0887-3585 nnns volume:15 year:1993 month:04 pages:374-384 extent:11 http://dx.doi.org/10.1002/prot.340150405 text/html Deutschlandweit zugänglich GBV_USEFLAG_U ZDB-1-WIS GBV_NL_ARTICLE AR 15 1993 4 374-384 11 |
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theoretical studies of relaxation of a monomeric subunit of hiv-1 protease in water using molecular dynamicspresented in part at the sixth international conference on aids, san francisco, ca, june 20-24, 1990 |
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Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamicsPresented in part at the Sixth International Conference on AIDS, San Francisco, CA, June 20-24, 1990. |
| abstract |
The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N- and C-0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N-terminus displayed the greatest fluctuational disorder whereas the C-terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy-atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV-1 protease monomer than the subunit conformation seen in the X-ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley-Liss, Inc. |
| abstractGer |
The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N- and C-0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N-terminus displayed the greatest fluctuational disorder whereas the C-terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy-atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV-1 protease monomer than the subunit conformation seen in the X-ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley-Liss, Inc. |
| abstract_unstemmed |
The dynamic behavior of one 99-residue subunit of the dimeric aspartyl protease of HIV-1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N- and C-0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N-terminus displayed the greatest fluctuational disorder whereas the C-terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy-atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that the relaxed structure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV-1 protease monomer than the subunit conformation seen in the X-ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. © 1993 Wiley-Liss, Inc. |
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Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamicsPresented in part at the Sixth International Conference on AIDS, San Francisco, CA, June 20-24, 1990. |
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