PI: Dr. Ivet Bahar

Druggability Simulations (Dr. Indira Shrivastava)


Druggability simulations is essentially Molecular Dynamics simulations in which target proteins are embedded in water and organic probes.   This method incorporates target flexibility for more accurate modeling of flexibile binding sites and identification of allosteric sites.   Details of this method can be found here: http://prody.csb.pitt.edu/drugui/

Dynamics of Neurotransmitter Transporters and Modulation of their Function (Dr. Mary Hongying Cheng)

Neurotransmitter:sodium symporters (NSSs) play a central role in neurotransmission. The function of NSSs is modulated by regulatory proteins, addictive drugs (e.g. cocaine and amphetamine) and lipids.  Our current research focuses on understanding the molecular mechanisms of i) transporter function, i.e. the transport cycle (See Cheng and Bahar 2015; Cheng and Bahar 2014); ii) modulation of the transporter function by addictive drugs (i.e. amphetamine and cocaine; Cheng et al 2015), and regulatory proteins (i.e. G-protein, and CaMKII), and iii) transporter interactions with neuronal lipids (i.e., cholesterol and PIP2). We are particularly interested in developing and implementing multi-scale computing technology for investigating biological systems at both molecular-to-cellular levels and simulating spatio-temporal events relevant to biological function and dysfunction.

Conformational states visited during LeuT transport cycle and corresponding hydration patterns and changes in interactions at intracelluar and extracelluar gates. Six states, labeled, are distinguished, including three newly determined ones by our advanced MD simulations: holo-occluded, inward-facing substrate-bound open (IFo*), and apo-occluded. The putative two intracelluar gating pairs R5-D369 and W8-Y268-Y265 are detected. Hydrated regions are indicated by blue shaded areas. (Cheng and Bahar, 2014, PLos Comp. Biol.)

Network Modeling of Cellular Processes (Dr. Bing Liu)

Drug abuse and related diseases influence the regulation of cellular processes such as cell survival/death and immune response. We are using systems biology approaches to understand the dynamics of the protein-protein interaction and metabolic networks and that underlies these cellular processes, and to predict (poly)pharmacological strategies for improving treatments. We have constructed kinetic models for a variety of cellular processes, including apoptosis (Liu et al, 2014), ferroptosis (Kagan et al, under review), innate immune response (Liu et al, 2016), autophagy, and dopamine transporter trafficking and efflux. We are currently using these models to study the methamphetamine-induced autophagy-apoptosis cell decision, the amphetamine-induced regulation of dopamine transporter, and the type-2 inflammation in asthma induced autophagic cell survival and ferroptotic cell death. (Liu et al ,2014)

Receptor Simulations (Dr. Ji Young Lee)

amparnmdarUnderstanding protein structure is very important in drug discovery. The main challenge is modeling protein flexibility which is a critical factor in ligand binding. This is a difficult problem because of the complexity and specificity of interactions, the multiplicity of conformations, and insufficient data on the structure and energetics of protein-ligand interactions. We are tackling this problem using normal mode analysis and molecular dynamics simulations to provide insights into the activation/inactivation mechanism of target proteins. As one of our studies, we have been studying ionotropic glutamate receptors (iGluRs) which are ion channels mediating excitatory neurotransmission. Using Anisotropic Network Model (ANM) calculations, we have found that two prominent subfamily members of iGluRs, AMPA receptor (AMPAR) and NMDA receptor (NMDAR), share robust movements as shown in the movie (see Dutta et al, 2015; see more movies of global dynamics of AMPAR and NMDAR).


Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter

(Mary Hongying Cheng and Ivet Bahar  Structure (2015))

Dopamine transporter (DAT) controls neurotransmitter dopamine (DA) homeostasis by reuptake of excess DA from the synapse into the presynaptic neuron, assisted by the co-transport of two sodium ions. Malfunction of human DAT (hDAT) has been implicated in many neurological disorders. The first DAT structure (dDAT, from Drosophila melanogaster) has been recently resolved, which permit us to conduct a structure-based computational study of the time-resolved mechanism of DA reuptake by hDAT at full atomic scale. Using homology modeling and full-atomic microseconds accelerated simulation, we investigated the complete DA translocation including uptake from the EC region to its intracellular release and highlighted the key interactions that mediate DA translocation through hDAT. Our major observations are: spontaneous closure of extracellular gates prompted by DA binding; stabilization of a holo-occluded intermediate distinguished by close association of TM1b and TM6a with TM10 and resulting cluster of hydrophobic residues that prevents the hydration of the binding site; subsequent exposure to intracellular water triggered by Na2 dislocation, accompanied by a redistribution of salt bridges at the cytosolic surface; concerted tilting of TM5 and TM7, critical to opening the exit pore for substrate/ion channeling, enabled by the stretching of the G258-G263 loop, disruption of N82-N353 hydrogen bond, which drives the release of a Na+ ion and the Cl- ion; and DA release induced only after protonation of D79. Following Figure illustrates the transport mechanism, deduced from our over 13 sets micro-seconds MD simulations.










Dopamine extracellular binding, translocation, and intracellular release, captured by MD simulations.

In the movie, purple balls represent dopamine molecule; yellow and cyan spheres the co-transported sodium and chloride. The residues forming the extracellular gate R85-D476 and intracellular gate R60-D436 are shown in cyan (basic) and red (acidic) sticks, respectively.

Cheng MH, Bahar I (2015) Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter Structure 23: 2171-81PMID: 26481814; PMC4635030

Cheng MH, Bahar I (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle PLoS Comput Biol 10: e1003879; PMID: 25299050; PMC4191883