Abstract：
:A coarse-grained Brownian dynamics model was used to simulate two proteins of similar sizes inside model membrane pores of varying size and hydrophobicity. The two proteins, which have radii of gyration of approximately 9.5 Å in their native states, are a 36-residue hydrophilic villin head piece (HP-36) and a 40-residue hydrophobic amyloid beta (Aβ-40). From calculations of the separation factor, it is found that the two proteins are best separated using a pore radius of 15 Å and that hydrophobic pores select Aβ-40 while the hydrophilic pores preferentially pass through HP-36. In addition, it is found that a simple model based on the net hydropathy of a protein is capable of estimating the separation factor trends of other protein pairs. Together, the coarse-grained Brownian dynamics model and the simple model are fast methodologies to guide experimental membrane design and to provide insights on protein structure variations. Graphical Abstract Simulation setup and snapshots of protein in various pore sizes.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Zhang Y,Zhang Y,McCready MJ,Maginn EJdoi
10.1007/s00894-019-3985-8subject
Has Abstractpub_date
2019-04-25 00:00:00pages
132issue
5eissn
1610-2940issn
0948-5023pii
10.1007/s00894-019-3985-8journal_volume
25pub_type
杂志文章abstract：:The performances of quantum chemistry methods (i.e., DFT and ab initio) in calculating the structural and vibrational properties of phosphates and phosphorylated compounds have been evaluated. Diethyl-phosphate, phosphonic acid, dihydrogen phosphate anion, phosphoric acid dimer and protonated glycylphosphotyrosine dip...
journal_title：Journal of molecular modeling
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journal_title：Journal of molecular modeling
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更新日期：2012-07-01 00:00:00
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journal_title：Journal of molecular modeling
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更新日期：2020-05-11 00:00:00
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journal_title：Journal of molecular modeling
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更新日期：2008-11-01 00:00:00
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journal_title：Journal of molecular modeling
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journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-003-0151-z
更新日期：2003-10-01 00:00:00
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journal_title：Journal of molecular modeling
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更新日期：2016-04-01 00:00:00
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更新日期：2015-11-01 00:00:00
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journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-002-0099-4
更新日期：2002-10-01 00:00:00
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journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1551-8
更新日期：2013-01-01 00:00:00
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journal_title：Journal of molecular modeling
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doi：10.1007/s00894-007-0191-x
更新日期：2007-07-01 00:00:00
