Evidence map›Paper›PMID 31055154›Full record

ArticleJournal of molecular graphics & modelling2019

Cryo-EM density map fitting driven in-silico structure of human soluble guanylate cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding.

Rana Rehan Khalid, Arooma Maryam, Vasiliki E Fadouloglou, Abdul Rauf Siddiqi, Yang Zhang

Open access · greenAbstract read
In one paragraph

Article in Journal of molecular graphics & modelling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
1.0field-weighted citation impact, top 23% 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

3 citing papers in PubMed, 8 citations in OpenAlex.

  1. Review
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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

5 authors at 5 institutions in 4 countries.

Rana Rehan KhalidDepartment of Biosciences, COMSATS University, Islamabad, 45550, Pakistan; Department of Biostatistics and Medical Informatics, Acibadem Universitesi, Istanbul, 34752, Turkey; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA. Electronic address: ray.binm@gmail.com.
Arooma MaryamDepartment of Biosciences, COMSATS University, Islamabad, 45550, Pakistan; Department of Pharmaceutical Chemistry, Biruni Universitesi, Istanbul, 34010, Turkey. Electronic address: aroomabinm@yahoo.com.
Vasiliki E FadouloglouDepartment of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece. Electronic address: fadoulog@imbb.forth.gr.
Abdul Rauf SiddiqiDepartment of Biosciences, COMSATS University, Islamabad, 45550, Pakistan. Electronic address: araufsiddiqi@comsats.edu.pk.
Yang ZhangDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA. Electronic address: zhng@umich.edu.
Acıbadem University · TRBiruni University · TRCOMSATS University Islamabad · PKDemocritus University of Thrace · GRUniversity of Michigan–Ann Arbor · US

Funding

Structure-based functional annotation of microbial genomesR01AI134678 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Lydia Petra Freddolino, SCOTT J. HULTGREN · 2018 to 2026
$6.5M
I-TASSER based atomic-level protein structure predictionR01GM083107 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ZHANG, YANG · 2008 to 2019
$3.5M
Template-based docking refinement approach to protein-protein structure modelingR01GM116960 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ZHANG, YANG · 2016 to 2019
$1.4M
Advanced approaches to protein structure predictionR35GM136422 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ZHANG, YANG · 2020 to 2021
$946k
High-Performance Computing Cluster for Biomedical ResearchS10OD026825 · OD · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ATHEY, BRIAN DAVID · 2020 to 2020
$600k
NIAID NIH HHS R01 AI134678NIGMS NIH HHS R01 GM083107NIGMS NIH HHS R01 GM116960NIGMS NIH HHS R35 GM136422NIH HHS S10 OD026825
6 · The paper itself

Abstract

The human soluble Guanylate Cyclase (hsGC) is a heterodimeric heme-containing enzyme which regulates many important physiological processes. In eukaryotes, hsGC is the only known receptor for nitric oxide (NO) signaling. Improper NO signaling results in various disease conditions such as neurodegeneration, hypertension, stroke and erectile dysfunction. To understand the mechanisms of these diseases, structure determination of the hsGC dimer complex is crucial. However, so far all the attempts for the experimental structure determination of the protein were unsuccessful. The current study explores the possibility to model the quaternary structure of hsGC using a hybrid approach that combines state-of-the-art protein structure prediction tools with cryo-EM experimental data. The resultant 3D model shows close consistency with structural and functional insights extracted from biochemistry experiment data. Overall, the atomic-level complex structure determination of hsGC helps to unveil the inter-domain communication upon NO binding, which should be of important usefulness for elucidating the biological function of this important enzyme and for developing new treatments against the hsGC associated human diseases.

Indexed as

Amino Acid SequenceComputer SimulationCryoelectron MicroscopyHemeHumansNitric OxideSequence AlignmentSignal TransductionSoluble Guanylyl CyclaseHemeNitric OxideSoluble Guanylyl CyclaseCryo-EM density map fittingHomology modellingMulti-domain assemblyProtein-protein dockingSingle/multiple-chain threading

Identifiers

PMID31055154
PMCPMC7956049
OpenAlexW2941080262

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.