Salt-Bridge Energetics in Halophilic Proteins

Nayek, Arnab; Gupta, Parth Sarthi Sen; Banerjee, Sumanta; Mondal, Buddhadev; Bandyopadhyay, Amal Kumar

doi:10.1371/journal.pone.0093862

Cited by 39 publications

(54 citation statements)

References 51 publications

(141 reference statements)

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“…However, unlike earlier study, in eukarya and eubacteria, not all buried salt‐bridge in our dataset are stable. In archaea, all buried‐networked salt‐bridges are stable as earlier, whereas only 36% and 72% of these salt‐bridges are stable in eubacteria and eukarya, respectively (Supporting Information Table S4). In Figure , we see that the desolvation energy of salt‐bridge in protein core is much higher than other types of salt‐bridge.…”

Section: Resultsmentioning

confidence: 70%

“…While the PBE and its solver method is reliable for the computation of direct and indirect component energy terms and hence the net energetics of ion‐pairs, it is an approximate method. Computation either at low pH (<1.0) or without mobile ion concentration may produce erroneous results due to high charge density situations within protein molecules .…”

Section: Discussionmentioning

confidence: 99%

“…So, ion‐pair or salt‐bridge is one of the major contributors to the stability of protein structure and function . It is much more visible when the proteins are adapted in the extremes of physical and chemical environments such as high salt and high temperature . It has been demonstrated that by inserting a single salt‐bridge by mutation in the protein surface increases protein stabilization in the tertiary structure .…”

Section: Introductionmentioning

confidence: 99%

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Comparative studies on ion‐pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya

2020

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Salt‐bridges play a unique role in the structural and functional stability of proteins, especially under harsh environments. How these salt‐bridges contribute to the overall thermodynamic stability of protein structure and function across different domains of life is elusive still date. To address the issue, statistical analyses on the energies of salt‐bridges, involved in proteins' structure and function, are performed across three domains of life, that is, archaea, eubacteria, and eukarya. Results show that although the majority of salt‐bridges are stable and conserved, yet the stability of archaeal proteins (∆∆Gnet = −5.06 ± 3.8) is much more than that of eubacteria (∆∆Gnet = −3.7 ± 2.9) and eukarya (∆∆Gnet = −3.54 ± 3.1). Unlike earlier study with archaea, in eukarya and eubacteria, not all buried salt‐bridge in our dataset are stable. Buried salt‐bridges play surprising role in protein stability, whose variations are clearly observed among these domains. Greater desolvation penalty of buried salt‐bridges is compensated by stable network of salt‐bridges apart from equal contribution of bridge and background energy terms. On the basis proteins' secondary structure, topology, and evolution, our observation shows that salt‐bridges when present closer to each other in sequence tend to form a greater number. Overall, our comparative study provides insight into the role of specific electrostatic interactions in proteins from different domains of life, which we hope, would be useful for protein engineering and bioinformatics study.

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Section: Resultsmentioning

confidence: 70%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative studies on ion‐pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya

2020

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“…The mechanism of the stabilization caused by this breakage of the electrostatic interaction is unclear. However, it has been reported that the formation of a salt bridge is not necessary to stabilize protein structure[48,49]. One of the possible mechanisms for the destabilization induced by the formation of a salt bridge is the case of a buried salt bridge in the molecule[50,51].…”

Section: Discussionmentioning

confidence: 99%

Effect of Glu12-His89 Interaction on Dynamic Structures in HIV-1 p17 Matrix Protein Elucidated by NMR

et al. 2016

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To test the existence of the salt bridge and stability of the HIV-1 p17 matrix protein, an E12A (mutated at helix 1) was established to abolish possible electrostatic interactions. The chemical shift perturbation from the comparison between wild type and E12A suggested the existence of an electrostatic interaction in wild type between E12 and H89 (located in helix 4). Unexpectedly, the studies using urea denaturation indicated that the E12A substitution slightly stabilized the protein. The dynamic structure of E12A was examined under physiological conditions by both amide proton exchange and relaxation studies. The quick exchange method of amide protons revealed that the residues with faster exchange were located at the mutated region, around A12, compared to those of the wild-type protein. In addition, some residues at the region of helix 4, including H89, exhibited faster exchange in the mutant. In contrast, the average values of the kinetic rate constants for amide proton exchange for residues located in all loop regions were slightly lower in E12A than in wild type. Furthermore, the analyses of the order parameter revealed that less flexible structures existed at each loop region in E12A. Interestingly, the structures of the regions including the alpha1-2 loop and helix 5 of E12A exhibited more significant conformational exchanges with the NMR time-scale than those of wild type. Under lower pH conditions, for further destabilization, the helix 1 and alpha2-3 loop in E12A became more fluctuating than at physiological pH. Because the E12A mutant lacks the activities for trimer formation on the basis of the analytical ultra-centrifuge studies on the sedimentation distribution of p17 (Fledderman et al. Biochemistry 49, 9551–9562, 2010), it is possible that the changes in the dynamic structures induced by the absence of the E12-H89 interaction in the p17 matrix protein contributes to a loss of virus assembly.

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“…The concentrations of chlorophyll a (Ch a) and chlorophyll b (Chb) carotenoids (Cx+c) in the extracts were calculated by using the formulae 1-3 [13]: Cha -chlorophyll a concentration (mkg / ml); Chb − chlorophyll b concentration (mkg / ml); Cx+ccarotenoids concentration (mkg / ml).…”

Section: Determination Of Pigments In C Sorokiniana Biomassmentioning

confidence: 99%

Directed cultivation of Chlorella sorokiniana for the increase in carotenoids’ synthesis

et al. 2020

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The metabolism of Chlorella sorokiniana is subjected to changes caused by various cultivation conditions. If dosed ultraviolet radiation is used, there is a possibility of a compensatory increase in the synthesis of carotenoids which prevent oxidative stress. Strain 211-8k was cultured under various lighting conditions: control sample was subjected to fluorescent light; sample 1 was subjected to dosed periodic ultraviolet irradiation for 15 minutes every day and fluorescent lighting; sample 2 was subjected to ultraviolet irradiation for 30 minutes in the stabilization phase. Periodic UV exposure negatively affects the population growth of C. sorokiniana which was possible to detect only on the ninth day and the biomass yield significantly decreased. A single UV exposure for 30 minutes lead to a slight decrease in the yield of air-dry biomass which with a further population growth may be compensated. Periodic exposure to UV radiation stimulates carotenoids synthesis, the yield in terms of dry biomass exceeded the control sample on average by 30%. A single ultraviolet irradiation for 30 minutes in the stabilization phase lead to a decrease in the biomass content of both chlorophyll and carotenoids. Microscopy of microalgae showed that ultraviolet radiation leads to the formation of cells with signs of apoptosis.

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Salt-Bridge Energetics in Halophilic Proteins

Cited by 39 publications

References 51 publications

Comparative studies on ion‐pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya

Comparative studies on ion‐pair energetic, distribution among three domains of life: Archaea, eubacteria, and eukarya

Effect of Glu12-His89 Interaction on Dynamic Structures in HIV-1 p17 Matrix Protein Elucidated by NMR

Directed cultivation of Chlorella sorokiniana for the increase in carotenoids’ synthesis

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