Evidence map›Paper›PMID 26453217›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2016

Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels.

Hyunbum Jang, Fernando Teran Arce, Joon Lee, Alan L Gillman, Srinivasan Ramachandran, Bruce L Kagan, Ratnesh Lal, Ruth Nussinov

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.5field-weighted citation impact, top 32% 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

4 citing papers in PubMed, 7 citations in OpenAlex.

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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

8 authors at 4 institutions in 2 countries.

Hyunbum JangCancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA. jangh2@mail.nih.gov.
Fernando Teran ArceDepartment of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA.
Joon LeeDepartment of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA.
Alan L GillmanDepartment of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA.
Srinivasan RamachandranDepartment of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA.
Bruce L KaganDepartment of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90024, USA.
Ratnesh LalDepartment of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA.
Ruth NussinovCancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA. nussinor@helix.nih.gov.
University of California, San Diego · USFrederick National Laboratory for Cancer Research · USTel Aviv University · ILUniversity of California, Los Angeles · US

Funding

Protein Structure, Stability, and Amyloid FormationZIABC010440 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI NUSSINOV, RUTH · 2009 to 2025
$11.8M
Biomolecular Recognition and Binding MechanismsZIABC010441 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI NUSSINOV, RUTH · 2009 to 2025
$9.4M
Amyloid ion channels to design therapeutics for neurodegenerative diseasesR01AG028709 · NIA · UNIVERSITY OF CHICAGO · PI LAL, RATNESHWAR · 2006 to 2018
$3.6M
Protein Structure, Stability, and Amyloid FormationZ01BC010440 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI NUSSINOV, RUTH · 2002 to 2008
$1.4M
CCR NIH HHS HHSN261200800001CIntramural NIH HHS Z01 BC010440NCI NIH HHS HHSN261200800001ENIA NIH HHS R01 AG028709
6 · The paper itself

Abstract

Aggregation can be studied by a range of methods, experimental and computational. Aggregates form in solution, across solid surfaces, and on and in the membrane, where they may assemble into unregulated leaking ion channels. Experimental probes of ion channel conformations and dynamics are challenging. Atomistic molecular dynamics (MD) simulations are capable of providing insight into structural details of amyloid ion channels in the membrane at a resolution not achievable experimentally. Since data suggest that late stage Alzheimer's disease involves formation of toxic ion channels, MD simulations have been used aiming to gain insight into the channel shapes, morphologies, pore dimensions, conformational heterogeneity, and activity. These can be exploited for drug discovery. Here we describe computational methods to model amyloid ion channels containing the β-sheet motif at atomic scale and to calculate toxic pore activity in the membrane.

Indexed as

Alzheimer DiseaseAmyloid beta-PeptidesComputational BiologyHumansIon ChannelsMolecular Dynamics SimulationPeptide FragmentsProtein Structure, SecondaryAmyloid beta-PeptidesIon ChannelsPeptide FragmentsAmyloid channelCHARMMLipid bilayerMolecular dynamics simulationsNAMDβ-Sheet channel

Identifiers

PMID26453217
PMCPMC7511997
OpenAlexW2417745771

What OpenQuestion holds

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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.