Evidence map›Paper›PMID 31025120›Full record

ArticleJournal of molecular modeling2019

Prediction of membrane separation efficiency for hydrophobic and hydrophilic proteins : A coarse-grained Brownian dynamics simulation study.

Yushan Zhang, Yong Zhang, Mark J McCready, Edward J Maginn

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In one paragraph

Article in Journal of molecular modeling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact, top 97% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 1 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors at 1 institution in 1 country.

Yushan ZhangDepartment of Chemical and Biomolecular Engineering, University of Notre Dame, 182 Fitzpatrick Hall, Notre Dame, IN, 46556, USA.
Yong ZhangDepartment of Chemical and Biomolecular Engineering, University of Notre Dame, 182 Fitzpatrick Hall, Notre Dame, IN, 46556, USA.
Mark J McCreadyDepartment of Chemical and Biomolecular Engineering, University of Notre Dame, 182 Fitzpatrick Hall, Notre Dame, IN, 46556, USA.
Edward J MaginnDepartment of Chemical and Biomolecular Engineering, University of Notre Dame, 182 Fitzpatrick Hall, Notre Dame, IN, 46556, USA. ed@nd.edu.ORCID http://orcid.org/0000-0002-6309-1347
University of Notre Dame · US

Funding

National Science Foundation 1511862
6 · The paper itself

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.

Indexed as

Models, MolecularMolecular Dynamics SimulationAmyloid beta-PeptidesHumansHydrophobic and Hydrophilic InteractionsNeurofilament ProteinsPeptide FragmentsProtein ConformationProtein FoldingAmyloid beta-PeptidesNeurofilament ProteinsPeptide Fragmentsvillin headpiece subdomain peptideBrownian dynamics simulationHydrophobicityProtein separationsSeparation efficiency

Identifiers

PMID31025120
OpenAlexW2941355976

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.