STUDY OF THE THERMAL STABILITY OF BARNASE PROTEIN MUTANTS WITH MOLKERN SOFTWARE
A thermal stability study of several barnase mutants has been carried out by the λ dynamics method. The method has been implemented in the MOLKERN software package. Mutations of amino acids with non-zero charge are chosen for the study, because in this case λ dynamics gives results differing dramati...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2014-12-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/57 |
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| _version_ | 1832575404088492032 |
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| author | E. S. Fomin N. A. Alemasov |
| author_facet | E. S. Fomin N. A. Alemasov |
| author_sort | E. S. Fomin |
| collection | DOAJ |
| description | A thermal stability study of several barnase mutants has been carried out by the λ dynamics method. The method has been implemented in the MOLKERN software package. Mutations of amino acids with non-zero charge are chosen for the study, because in this case λ dynamics gives results differing dramatically (> 10 kJ/mol) from experimental data in nearly one-fourth of cases. A new modification of λ potentials is proposed, which takes into account charge changes, as well as the Net-Q method, in order to obtain reliable charge distributions for charged amino acids. The results obtained for the R72G mutation show a better agreement with experimental values than the results of other authors. |
| format | Article |
| id | doaj-art-dfbb8348b6b8476fadc60ab008d4e502 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2014-12-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-dfbb8348b6b8476fadc60ab008d4e5022025-02-01T09:57:58ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592014-12-0116241542641STUDY OF THE THERMAL STABILITY OF BARNASE PROTEIN MUTANTS WITH MOLKERN SOFTWAREE. S. Fomin0N. A. Alemasov1Institute of Cytology and Genetics, SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics, SB RAS, Novosibirsk, RussiaA thermal stability study of several barnase mutants has been carried out by the λ dynamics method. The method has been implemented in the MOLKERN software package. Mutations of amino acids with non-zero charge are chosen for the study, because in this case λ dynamics gives results differing dramatically (> 10 kJ/mol) from experimental data in nearly one-fourth of cases. A new modification of λ potentials is proposed, which takes into account charge changes, as well as the Net-Q method, in order to obtain reliable charge distributions for charged amino acids. The results obtained for the R72G mutation show a better agreement with experimental values than the results of other authors.https://vavilov.elpub.ru/jour/article/view/57barnasemolecular dynamicsλ dynamicsfree energy differenceprotein thermal stability |
| spellingShingle | E. S. Fomin N. A. Alemasov STUDY OF THE THERMAL STABILITY OF BARNASE PROTEIN MUTANTS WITH MOLKERN SOFTWARE Вавиловский журнал генетики и селекции barnase molecular dynamics λ dynamics free energy difference protein thermal stability |
| title | STUDY OF THE THERMAL STABILITY OF BARNASE PROTEIN MUTANTS WITH MOLKERN SOFTWARE |
| title_full | STUDY OF THE THERMAL STABILITY OF BARNASE PROTEIN MUTANTS WITH MOLKERN SOFTWARE |
| title_fullStr | STUDY OF THE THERMAL STABILITY OF BARNASE PROTEIN MUTANTS WITH MOLKERN SOFTWARE |
| title_full_unstemmed | STUDY OF THE THERMAL STABILITY OF BARNASE PROTEIN MUTANTS WITH MOLKERN SOFTWARE |
| title_short | STUDY OF THE THERMAL STABILITY OF BARNASE PROTEIN MUTANTS WITH MOLKERN SOFTWARE |
| title_sort | study of the thermal stability of barnase protein mutants with molkern software |
| topic | barnase molecular dynamics λ dynamics free energy difference protein thermal stability |
| url | https://vavilov.elpub.ru/jour/article/view/57 |
| work_keys_str_mv | AT esfomin studyofthethermalstabilityofbarnaseproteinmutantswithmolkernsoftware AT naalemasov studyofthethermalstabilityofbarnaseproteinmutantswithmolkernsoftware |