ArticlePloS one2009
Molecular dynamics simulation of ligand dissociation from liver fatty acid binding protein.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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.
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.
Who cites it
19 citing papers in PubMed.
- Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors.Molecules (Basel, Switzerland) · 2023Article
- Ceramide-1-phosphate transfer protein promotes sphingolipid reorientation needed for binding during membrane interaction.Journal of lipid research · 2022Article
- Ligand Entry into Fatty Acid Binding Protein via Local Unfolding Instead of Gap Widening.Biophysical journal · 2020Article
- Atomistic Insights into the Functional Instability of the Second Helix of Fatty Acid Binding Protein.Biophysical journal · 2019Article
- The Observation of Ligand-Binding-Relevant Open States of Fatty Acid Binding Protein by Molecular Dynamics Simulations and a Markov State Model.International journal of molecular sciences · 2019Article
- Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport.Nucleic acids research · 2019Article
- Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant.Biophysical journal · 2019Article
- Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins.BMC structural biology · 2018Article
- Human hydroxymethylbilane synthase: Molecular dynamics of the pyrrole chain elongation identifies step-specific residues that cause AIP.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Exploring ligand dissociation pathways from aminopeptidase N using random acceleration molecular dynamics simulation.Journal of molecular modeling · 2016Article
- Liver fatty acid-binding protein as a diagnostic marker for non-alcoholic fatty liver disease.Wiener klinische Wochenschrift · 2016Article
- Substrate tunnels in enzymes: structure-function relationships and computational methodology.Proteins · 2015Review
- Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations.Biochemistry · 2014Article
- Binding site multiplicity with fatty acid ligands: implications for the regulation of PKR kinase autophosphorylation with palmitate.Proteins · 2014Article
- Insights from molecular dynamics: the binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters.Journal of molecular graphics & modelling · 2012Article
- Characterization of 4-HNE modified L-FABP reveals alterations in structural and functional dynamics.PloS one · 2012Article
- Overview of lipid peroxidation products and hepatic protein modification in alcoholic liver disease.Chemico-biological interactions · 2011Review
- The human fatty acid-binding protein family: evolutionary divergences and functions.Human genomics · 2011Review
- Millisecond timescale dynamics of human liver fatty acid binding protein: testing of its relevance to the ligand entry process.Biophysical journal · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The mechanisms of how ligands enter and leave the binding cavity of fatty acid binding proteins (FABPs) have been a puzzling question over decades. Liver fatty acid binding protein (LFABP) is a unique family member which accommodates two molecules of fatty acids in its cavity and exhibits the capability of interacting with a variety of ligands with different chemical structures and properties. Investigating the ligand dissociation processes of LFABP is thus a quite interesting topic, which however is rather difficult for both experimental approaches and ordinary simulation strategies. In the current study, random expulsion molecular dynamics simulation, which accelerates ligand motions for rapid dissociation, was used to explore the potential egress routes of ligands from LFABP. The results showed that the previously hypothesized "portal region" could be readily used for the dissociation of ligands at both the low affinity site and the high affinity site. Besides, one alternative portal was shown to be highly favorable for ligand egress from the high affinity site and be related to the unique structural feature of LFABP. This result lends strong support to the hypothesis from the previous NMR exchange studies, which in turn indicates an important role for this alternative portal. Another less favored potential portal located near the N-terminal end was also identified. Identification of the dissociation pathways will allow further mechanistic understanding of fatty acid uptake and release by computational and/or experimental techniques.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.