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Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains

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Role of Internal Water on Protein Thermal Stability : The Case of Homologous G Domains. / Rahaman, Obaidur; Kalimeri, Maria; Melchionna, Simone; Hénin, Jérôme; Sterpone, Fabio.

In: Journal of Physical Chemistry Part B, Vol. 119, No. 29, 23.07.2015, p. 8939-8949.

Research output: Contribution to journalArticleScientificpeer-review

Harvard

Rahaman, O, Kalimeri, M, Melchionna, S, Hénin, J & Sterpone, F 2015, 'Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains', Journal of Physical Chemistry Part B, vol. 119, no. 29, pp. 8939-8949. https://doi.org/10.1021/jp507571u

APA

Rahaman, O., Kalimeri, M., Melchionna, S., Hénin, J., & Sterpone, F. (2015). Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains. Journal of Physical Chemistry Part B, 119(29), 8939-8949. https://doi.org/10.1021/jp507571u

Vancouver

Rahaman O, Kalimeri M, Melchionna S, Hénin J, Sterpone F. Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains. Journal of Physical Chemistry Part B. 2015 Jul 23;119(29):8939-8949. https://doi.org/10.1021/jp507571u

Author

Rahaman, Obaidur ; Kalimeri, Maria ; Melchionna, Simone ; Hénin, Jérôme ; Sterpone, Fabio. / Role of Internal Water on Protein Thermal Stability : The Case of Homologous G Domains. In: Journal of Physical Chemistry Part B. 2015 ; Vol. 119, No. 29. pp. 8939-8949.

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@article{cf5e33c2d49a43afb0eb0fd6fbed016c,
title = "Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains",
abstract = "In this work, we address the question of whether the enhanced stability of thermophilic proteins has a direct connection with internal hydration. Our model systems are two homologous G domains of different stability: the mesophilic G domain of the elongation factor thermal unstable protein from E. coli and the hyperthermophilic G domain of the EF-1α protein from S. solfataricus. Using molecular dynamics simulation at the microsecond time scale, we show that both proteins host water molecules in internal cavities and that these molecules exchange with the external solution in the nanosecond time scale. The hydration free energy of these sites evaluated via extensive calculations is found to be favorable for both systems, with the hyperthermophilic protein offering a slightly more favorable environment to host water molecules. We estimate that, under ambient conditions, the free energy gain due to internal hydration is about 1.3 kcal/mol in favor of the hyperthermophilic variant. However, we also find that, at the high working temperature of the hyperthermophile, the cavities are rather dehydrated, meaning that under extreme conditions other molecular factors secure the stability of the protein. Interestingly, we detect a clear correlation between the hydration of internal cavities and the protein conformational landscape. The emerging picture is that internal hydration is an effective observable to probe the conformational landscape of proteins. In the specific context of our investigation, the analysis confirms that the hyperthermophilic G domain is characterized by multiple states and it has a more flexible structure than its mesophilic homologue. (Figure Presented).",
author = "Obaidur Rahaman and Maria Kalimeri and Simone Melchionna and J{\'e}r{\^o}me H{\'e}nin and Fabio Sterpone",
year = "2015",
month = "7",
day = "23",
doi = "10.1021/jp507571u",
language = "English",
volume = "119",
pages = "8939--8949",
journal = "Journal of Physical Chemistry Part B",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "29",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Role of Internal Water on Protein Thermal Stability

T2 - The Case of Homologous G Domains

AU - Rahaman, Obaidur

AU - Kalimeri, Maria

AU - Melchionna, Simone

AU - Hénin, Jérôme

AU - Sterpone, Fabio

PY - 2015/7/23

Y1 - 2015/7/23

N2 - In this work, we address the question of whether the enhanced stability of thermophilic proteins has a direct connection with internal hydration. Our model systems are two homologous G domains of different stability: the mesophilic G domain of the elongation factor thermal unstable protein from E. coli and the hyperthermophilic G domain of the EF-1α protein from S. solfataricus. Using molecular dynamics simulation at the microsecond time scale, we show that both proteins host water molecules in internal cavities and that these molecules exchange with the external solution in the nanosecond time scale. The hydration free energy of these sites evaluated via extensive calculations is found to be favorable for both systems, with the hyperthermophilic protein offering a slightly more favorable environment to host water molecules. We estimate that, under ambient conditions, the free energy gain due to internal hydration is about 1.3 kcal/mol in favor of the hyperthermophilic variant. However, we also find that, at the high working temperature of the hyperthermophile, the cavities are rather dehydrated, meaning that under extreme conditions other molecular factors secure the stability of the protein. Interestingly, we detect a clear correlation between the hydration of internal cavities and the protein conformational landscape. The emerging picture is that internal hydration is an effective observable to probe the conformational landscape of proteins. In the specific context of our investigation, the analysis confirms that the hyperthermophilic G domain is characterized by multiple states and it has a more flexible structure than its mesophilic homologue. (Figure Presented).

AB - In this work, we address the question of whether the enhanced stability of thermophilic proteins has a direct connection with internal hydration. Our model systems are two homologous G domains of different stability: the mesophilic G domain of the elongation factor thermal unstable protein from E. coli and the hyperthermophilic G domain of the EF-1α protein from S. solfataricus. Using molecular dynamics simulation at the microsecond time scale, we show that both proteins host water molecules in internal cavities and that these molecules exchange with the external solution in the nanosecond time scale. The hydration free energy of these sites evaluated via extensive calculations is found to be favorable for both systems, with the hyperthermophilic protein offering a slightly more favorable environment to host water molecules. We estimate that, under ambient conditions, the free energy gain due to internal hydration is about 1.3 kcal/mol in favor of the hyperthermophilic variant. However, we also find that, at the high working temperature of the hyperthermophile, the cavities are rather dehydrated, meaning that under extreme conditions other molecular factors secure the stability of the protein. Interestingly, we detect a clear correlation between the hydration of internal cavities and the protein conformational landscape. The emerging picture is that internal hydration is an effective observable to probe the conformational landscape of proteins. In the specific context of our investigation, the analysis confirms that the hyperthermophilic G domain is characterized by multiple states and it has a more flexible structure than its mesophilic homologue. (Figure Presented).

UR - http://www.scopus.com/inward/record.url?scp=84937843946&partnerID=8YFLogxK

U2 - 10.1021/jp507571u

DO - 10.1021/jp507571u

M3 - Article

VL - 119

SP - 8939

EP - 8949

JO - Journal of Physical Chemistry Part B

JF - Journal of Physical Chemistry Part B

SN - 1520-6106

IS - 29

ER -