Ion pairs and the thermotolerance of proteins from hyperthermophiles: a ‘traffic rule’ for hot roads

Karshikoff, Andrey; Ladenstein, Rudolf

doi:10.1016/s0968-0004(01)01918-1

Cited by 281 publications

(243 citation statements)

References 34 publications

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“…For the same set of water molecules we evaluated the hydration free energy at T = 360 K. The calculations were performed starting from the same protein configurations used at T = 300 K, thus we assumed that the temperature excitation does not distort these representative conformations of the folded state. At high temperature, water binding free energy decreases substantially for most sites, in both proteins; water transfer into some of the protein sites is even unfavorable (6). As a result, there is no significant difference in overall free energy of internal hydration, yielding no clear contribution to the stability gap.…”

Section: Stability At High Temperaturementioning

confidence: 98%

“…The local binding free energy of a water molecule in a given site was calculated by adding all the components: (6) In our implementation, the free energy ΔG inter is given by two terms. The first one measures the coupling between the water molecule and the environment in the presence of the harmonic restraint and is calculated using the FEP method as implemented in NAMD, while the second one removes the contribution from the harmonic restraint in the interacting system (see below).…”

Section: Free Energy Calculationsmentioning

confidence: 99%

“…Several molecular factors ensure this extreme stability and their combination results in different thermodynamic strategies for thermal adaptation [1][2][3][4] . With respect to their mesophilic homologues, (hyper)thermophiles are generally enriched in charged amino-acids and cross-linked by a larger number of hydrogen bonds (HB) and salt-bridges that contribute to stabilize the protein fold [5][6][7] . They have shorter loops that protect the fold from thermal excitation by reducing the extension of weak spots at the protein surface [2][3][4]8,9 .…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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In this work we address the question whether the enhanced stability of thermophilic proteins has a direct connection with internal hydration. Our model systems are two homologues 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-α 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 favourable for both systems, with the hyperthermophilic protein offering a slightly more favourable 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 at 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.

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Section: Stability At High Temperaturementioning

confidence: 98%

Section: Free Energy Calculationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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“…The role played by ionic interactions was for a long time, and still is, controversial [9], assuming that they are generally destabilizing. However, recent research on proteins from hyperthermophiles has led to a considerable change of this picture, demonstrating that these proteins often are characterized by an increased number of surface charges and ionic networks which play dominant roles in enhancing extreme thermostability [2,13,14,31] to take into account the effects of temperature on the hydration of ionic bonds has been of special importance in this context. It was shown that at elevated temperatures the desolvation penalty paid on the formation of a salt bridge decreases, thus leading to a favorable stabilizing contribution [7].…”

Section: Introductionmentioning

confidence: 99%

Heat Capacity, Configurational Entropy, and the Role of Ionic Interactions in Protein Thermostability

Ladenstein¹

2008

Biotechnology & Biotechnological Equipment

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“…Some general "rules" have been established that explain the differences in stability between structurally related high-stability and low-stability proteins (17,18). It has been shown that the flexibility of loop structures plays an important role in determining the stability of the protein (19).…”

mentioning

confidence: 99%

Chicken Avidin-related Protein 4/5 Shows Superior Thermal Stability when Compared with Avidin while Retaining High Affinity to Biotin

Hytönen

Nyholm

Pentikäinen

et al. 2004

Journal of Biological Chemistry

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The protein chicken avidin is a commonly used tool in various applications. The avidin gene belongs to a gene family that also includes seven other members known as the avidin-related genes (AVR). We report here on the extremely high thermal stability and functional characteristics of avidin-related protein AVR4/5, a member of the avidin protein family. The thermal stability characteristics of AVR4/5 were examined using a differential scanning calorimeter, microparticle analysis, and a microplate assay. Its biotin-binding properties were studied using an isothermal calorimeter and IAsys optical biosensor. According to these analyses, in the absence of biotin AVR4/5 is clearly more stable (T m ‫؍‬ 107.4 ؎ 0.3°C) than avidin (T m ‫؍‬ 83.5 ؎ 0.1°C) or bacterial streptavidin (T m ‫؍‬ 75.5°C). AVR4/5 also exhibits a high affinity for biotin (K d Ϸ 3.6 ؋ 10 ؊14 M) comparable to that of avidin and streptavidin (K d Ϸ 10 ؊15 M). Molecular modeling and site-directed mutagenesis were used to study the molecular details behind the observed high thermostability. The results indicate that AVR4/5 and its mutants have high potential as new improved tools for applications where exceptionally high stability and tight biotin binding are needed.

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Ion pairs and the thermotolerance of proteins from hyperthermophiles: a ‘traffic rule’ for hot roads

Cited by 281 publications

References 34 publications

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

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

Heat Capacity, Configurational Entropy, and the Role of Ionic Interactions in Protein Thermostability

Chicken Avidin-related Protein 4/5 Shows Superior Thermal Stability when Compared with Avidin while Retaining High Affinity to Biotin

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