Zobrazeno 1 - 10
of 17
pro vyhledávání: '"Cahit Dalgicdir"'
Publikováno v:
PLoS Computational Biology, Vol 11, Iss 8, p e1004328 (2015)
Secondary amphiphilicity is inherent to the secondary structural elements of proteins. By forming energetically favorable contacts with each other these amphiphilic building blocks give rise to the formation of a tertiary structure. Small proteins an
Externí odkaz:
https://doaj.org/article/42a295abaf1e4fc8b9b60e02c3a037cb
Publikováno v:
Communications Chemistry, Vol 3, Iss 1, Pp 1-7 (2020)
Amphiphilic cosolvents can cause both swelling and collapse of stimuli responsive polymers, but the mechanisms governing this behavior remain unclear. Here the authors use molecular dynamics simulations to explain interfacial solvation thermodynamics
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doajarticles::786e78549d273f017d3d43d8a03dbe8b
http://link.springer.com/article/10.1038/s42004-020-00405-x
http://link.springer.com/article/10.1038/s42004-020-00405-x
Publikováno v:
The Journal of Physical Chemistry B. 123:3875-3883
We test the OPLS/AA force field for a single PNIPAM 40-mer in aqueous solution using replica exchange molecular dynamics simulations and find that the force field fails to reproduce the experimental temperature behavior. To resolve this issue, we app
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ac0dac69af37ccdfa8bcba914cbaac66
https://doi.org/10.1021/acs.jpcb.9b01644
https://doi.org/10.1021/acs.jpcb.9b01644
Publikováno v:
The Journal of chemical physics. 154(13)
Cosolvent effects on the coil–globule transitions in aqueous polymer solutions are not well understood, especially in the case of amphiphilic cosolvents that preferentially adsorb on the polymer and lead to both polymer swelling and collapse. Altho
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::db30e4257e0d5fb828be71b731687b8d
https://pubmed.ncbi.nlm.nih.gov/33832270
https://pubmed.ncbi.nlm.nih.gov/33832270
Publikováno v:
The Journal of Physical Chemistry B. 123:2463-2465
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bc99356a54ac2fb114b358043df04c88
https://doi.org/10.1021/acs.jpcb.9b01566
https://doi.org/10.1021/acs.jpcb.9b01566
Autor:
Mehmet Sayar, Cahit Dalgicdir
Publikováno v:
The Journal of Physical Chemistry B. 119:15164-15175
Historically, the protein folding problem has mainly been associated with understanding the relationship between amino acid sequence and structure. However, it is known that both the conformation of individual molecules and their aggregation strongly
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9fdb55c2e3d0ea33fb7f51ff756c94af
https://doi.org/10.1021/acs.jpcb.5b08871
https://doi.org/10.1021/acs.jpcb.5b08871
Publikováno v:
The journal of physical chemistry. B. 121(32)
We revisit the mechanism for cononsolvency of PNIPAM in water/methanol mixtures. Using extensive molecular dynamics simulations, we calculate the calorimetric enthalpy of the PNIPAM collapse transition and observe a unique fingerprint of PNIPAM conon
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::46297da9d88c140882e63425a6ed30bb
https://pubmed.ncbi.nlm.nih.gov/30653320
https://pubmed.ncbi.nlm.nih.gov/30653320
Publikováno v:
The Journal of Physical Chemistry B. 123:955-955
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eddae4d03e665c57ab3d9111b2321bcc
https://doi.org/10.1021/acs.jpcb.9b00306
https://doi.org/10.1021/acs.jpcb.9b00306
Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a0f5b43a5f1a99ce5924e1d46039d010
Publikováno v:
Journal of Chemical Physics
Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conform
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::da7bcdda3c439e92dba987f3f52b6724
https://doi.org/10.1063/1.5001087
https://doi.org/10.1063/1.5001087