Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2-containing membranes: Modeling of DAT N-Terminus/PIP2 Interactions

Journal Article · · Proteins
DOI:https://doi.org/10.1002/prot.24792· OSTI ID:1565270
 [1];  [2];  [1];  [3];  [4];  [4]
  1. Cornell Univ., Ithaca, NY (United States). Weill Medical College, Dept. of Physiology and Biophysics
  2. Cornell Univ., Ithaca, NY (United States). Weill Medical College, Dept. of Physiology and Biophysics; Cornell Univ., Ithaca, NY (United States). Tri-Institutional Training Program in Computational Biology and Medicine
  3. Univ. of Basel (Switzerland). Biozentrum, Center for Molecular Sciences
  4. Cornell Univ., Ithaca, NY (United States). Weill Medical College, Dept. of Physiology and Biophysics, Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Inst. of Computational Biomedicine
+ Show Author Affiliations
The dopamine transporter (DAT) is a transmembrane protein belonging to the family of neurotransmitter:sodium symporters (NSS). Members of the NSS are responsible for the clearance of neurotransmitters from the synaptic cleft, and for their translocation back into the presynaptic nerve terminal. The DAT contains long intracellular N- and C-terminal domains that are strongly implicated in the transporter function. The N-terminus (N-term), in particular, regulates the reverse transport (efflux) of the substrate through DAT. Currently, the molecular mechanisms of the efflux remain elusive in large part due to lack of structural information on the N-terminal segment. Here we report a computational model of the N-term of the human DAT (hDAT), obtained through an ab initio structure prediction, in combination with extensive atomistic molecular dynamics (MD) simulations in the context of a lipid membrane. Our analysis reveals that whereas the N-term is a highly dynamic domain, it contains secondary structure elements that remain stable in the long MD trajectories of interactions with the bilayer (totaling >2.2 μs). Combining MD simulations with continuum mean-field modeling we found that the N-term engages with lipid membranes through electrostatic interactions with the charged lipids PIP2 (phosphatidylinositol 4,5-Biphosphate) or PS (phosphatidylserine) that are present in these bilayers. We identify specific motifs along the N-term implicated in such interactions and show that differential modes of N-term/membrane association result in differential positioning of the structured segments on the membrane surface. These results will inform future structure-based studies that will elucidate the mechanistic role of the N-term in DAT function.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1565270
Journal Information:
Proteins, Journal Name: Proteins Journal Issue: 5 Vol. 83; ISSN 0887-3585
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English

References (73)

Solvation in simulated annealing and high-temperature molecular dynamics of proteins: A restrained water droplet model journal January 2000
Scalable molecular dynamics with NAMD journal January 2005
MATCH: An atom-typing toolset for molecular mechanics force fields journal November 2011
Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods journal June 2009
FAST: A novel protein structure alignment algorithm journal December 2004
Differential effects of amphetamine transport vs. dopamine reverse transport on particulate PKC activity in striatal synaptoneurosomes journal May 2003
Simple transporter trafficking model for amphetamine-induced dopamine efflux journal January 2007
Regulation of the Dopamine Transporter by Phosphorylation book January 2006
Synaptic uptake and beyond: the sodium- and chloride-dependent neurotransmitter transporter family SLC6 journal February 2004
A Closer Look at Amphetamine-Induced Reverse Transport and Trafficking of the Dopamine and Norepinephrine Transporters journal February 2009
Protein kinase C and dopamine transport—2. Effects of amphetamine in vitro journal December 1992
VMD: Visual molecular dynamics journal February 1996
Monoamine Transporter as a Target Molecule for Psychostimulants book January 2009
Dopamine transporters are dephosphorylated in striatal homogenates and in vitro by protein phosphatase 1 journal January 2003
CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes journal July 2009
Modeling Membrane Deformations and Lipid Demixing upon Protein-Membrane Interaction: The BAR Dimer Adsorption journal September 2009
A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP2 journal January 2010
Ion-Controlled Conformational Dynamics in the Outward-Open Transition from an Occluded State of LeuT journal September 2012
The cost of living in the membrane: A case study of hydrophobic mismatch for the multi-segment protein LeuT journal April 2013
Calmodulin Kinase II Interacts with the Dopamine Transporter C Terminus to Regulate Amphetamine-Induced Reverse Transport journal August 2006
Mechanisms of neurotransmitter release by amphetamines: A review journal April 2005
Lipid composition of PC12 pheochromocytoma cells: characterization of globoside as a major neutral glycolipid journal January 1988
Phosphatidylinositol 4,5-Biphosphate (PIP 2 ) Lipids Regulate the Phosphorylation of Syntaxin N-Terminus by Modulating Both Its Position and Local Structure journal September 2012
Structure and Regulatory Interactions of the Cytoplasmic Terminal Domains of Serotonin Transporter journal August 2014
Sodium-Coupled Neurotransmitter Transporters journal May 2008
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K a Predictions journal December 2010
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles journal August 2012
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types journal June 2010
Structural Intermediates in a Model of the Substrate Translocation Path of the Bacterial Glutamate Transporter Homologue GltPh journal April 2012
Microsecond Molecular Dynamics Simulations of Lipid Mixing journal September 2014
Insights into transport mechanism from LeuT engineered to transport tryptophan: Insights into transport mechanism journal September 2011
Substrate binds in the S1 site of the F253A mutant of LeuT, a neurotransmitter sodium symporter homologue journal July 2012
De novo mutation in the dopamine transporter gene associates dopamine dysfunction with autism spectrum disorder journal August 2013
Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters journal July 2005
Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus journal October 2005
Antidepressant binding site in a bacterial homologue of neurotransmitter transporters journal August 2007
Neurotransmitter/sodium symporter orthologue LeuT has a single high-affinity substrate site journal December 2010
X-ray structures of LeuT in substrate-free outward-open and apo inward-open states journal January 2012
X-ray structure of dopamine transporter elucidates antidepressant mechanism journal September 2013
PIP2 regulates psychostimulant behaviors through its interaction with a membrane protein journal June 2014
The binding sites for cocaine and dopamine in the dopamine transporter overlap journal June 2008
Flotillin-1 is essential for PKC-triggered endocytosis and membrane microdomain localization of DAT journal March 2011
Structures of LeuT in bicelles define conformation and substrate binding in a membrane-like context journal January 2012
A smooth particle mesh Ewald method journal November 1995
Amphetamine induces dopamine efflux through a dopamine transporter channel journal February 2005
Amphetamine actions at the serotonin transporter rely on the availability of phosphatidylinositol-4,5-bisphosphate journal June 2013
Chloride binding site of neurotransmitter sodium symporters journal May 2013
Electrostatics of nanosystems: Application to microtubules and the ribosome journal August 2001
The N Terminus of Monoamine Transporters Is a Lever Required for the Action of Amphetamines journal January 2010
Dopamine Transporter Phosphorylation Site Threonine 53 Regulates Substrate Reuptake and Amphetamine-stimulated Efflux journal June 2012
Phosphorylation of Dopamine Transporter Serine 7 Modulates Cocaine Analog Binding journal November 2012
Dopamine Transporters Are Phosphorylated on N-terminal Serines in Rat Striatum journal May 2002
Amphetamine Regulation of Dopamine Transport: COMBINED MEASUREMENTS OF TRANSPORTER CURRENTS AND TRANSPORTER IMAGING SUPPORT THE ENDOCYTOSIS OF AN ACTIVE CARRIER journal December 2003
An Intracellular Interaction Network Regulates Conformational Transitions in the Dopamine Transporter journal April 2008
OpenStructure: a flexible software framework for computational structural biology journal August 2010
Dopamine transporter deficiency syndrome: phenotypic spectrum from infancy to adulthood journal March 2014
NCBI BLAST: a better web interface journal May 2008
OpenStructure : an integrated software framework for computational structural biology journal April 2013
The solute carrier 6 family of transporters: The Solute Carrier Family 6 journal August 2012
A Comprehensive Structure-Based Alignment of Prokaryotic and Eukaryotic Neurotransmitter/Na + Symporters (NSS) Aids in the Use of the LeuT Structure to Probe NSS Structure and Function journal July 2006
Syntaxin 1A Interaction with the Dopamine Transporter Promotes Amphetamine-Induced Dopamine Efflux journal July 2008
A Juxtamembrane Mutation in the N Terminus of the Dopamine Transporter Induces Preference for an Inward-Facing Conformation journal December 2008
A Competitive Inhibitor Traps LeuT in an Open-to-Out Conformation journal December 2008
Electrostatic Interactions in Macromolecules: Theory and Applications journal June 1990
Macromolecular Modeling with Rosetta journal June 2008
Missense dopamine transporter mutations associate with adult parkinsonism and ADHD journal June 2014
N-Terminal Phosphorylation of the Dopamine Transporter Is Required for Amphetamine-Induced Efflux journal March 2004
Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model journal February 2013
The Substrate-Driven Transition to an Inward-Facing Conformation in the Functional Mechanism of the Dopamine Transporter journal January 2011
Anomalous Dopamine Release Associated with a Human Dopamine Transporter Coding Variant journal July 2008
Dysregulation of Dopamine Transporters via Dopamine D2 Autoreceptors Triggers Anomalous Dopamine Efflux Associated with Attention-Deficit Hyperactivity Disorder journal April 2010
Attention Deficit/Hyperactivity Disorder-Derived Coding Variation in the Dopamine Transporter Disrupts Microdomain Targeting and Trafficking Regulation journal April 2012
Protein Diffusion on Charged Membranes: A Dynamic Mean-Field Model Describes Time Evolution and Lipid Reorganization journal April 2008

Similar Records

Spontaneous Inward Opening of the Dopamine Transporter Is Triggered by PIP 2 -Regulated Dynamics of the N-Terminus
Journal Article · Mon Aug 17 00:00:00 EDT 2015 · ACS Chemical Neuroscience · OSTI ID:1565451
A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter
Journal Article · Thu Jan 05 19:00:00 EST 2017 · Scientific Reports · OSTI ID:1490988

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
amphetamine
biochemistry & molecular biology
biophysics
efflux
electrostatics
molecular dynamics
neurotransmitter transporter
phosphorylation
signaling
sodium symporter