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Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species

Overview of attention for article published in BMC Structural Biology, October 2014
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • One of the highest-scoring outputs from this source (#7 of 174)
  • High Attention Score compared to outputs of the same age (85th percentile)

Mentioned by

blogs
1 blog
twitter
3 tweeters
facebook
1 Facebook page

Citations

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6 Dimensions

Readers on

mendeley
24 Mendeley
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1 CiteULike
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Title
Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species
Published in
BMC Structural Biology, October 2014
DOI 10.1186/s12900-014-0023-z
Pubmed ID
Authors

Kirill E. Medvedev, Nikolay A. Alemasov, Yuri N. Vorobjev, Elena V. Boldyreva, Nikolay A. Kolchanov, Dmitry A. Afonnikov

Abstract

BackgroundThe identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures.ResultsThe current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified.ConclusionsThe results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.

Twitter Demographics

The data shown below were collected from the profiles of 3 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 24 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 24 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 8 33%
Researcher 4 17%
Professor 2 8%
Student > Master 2 8%
Student > Bachelor 1 4%
Other 5 21%
Unknown 2 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 8 33%
Chemistry 3 13%
Biochemistry, Genetics and Molecular Biology 2 8%
Mathematics 1 4%
Environmental Science 1 4%
Other 4 17%
Unknown 5 21%

Attention Score in Context

This research output has an Altmetric Attention Score of 9. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 17 October 2015.
All research outputs
#1,670,254
of 12,378,406 outputs
Outputs from BMC Structural Biology
#7
of 174 outputs
Outputs of similar age
#32,412
of 222,158 outputs
Outputs of similar age from BMC Structural Biology
#1
of 4 outputs
Altmetric has tracked 12,378,406 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 174 research outputs from this source. They receive a mean Attention Score of 2.9. This one has done particularly well, scoring higher than 95% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 222,158 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 85% of its contemporaries.
We're also able to compare this research output to 4 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them