About me

Asghar Razavi, Ph.D.

Weill Cornell Medicine
1300 York Ave, New York, NY, 10065

This website illustrates my academic research during my postdoctoral work with Harel Weinstein at Weill Cornell Medical College and PhD work with Vincent Voelz at Temple university.

My postdoctoral academic research was focused on understanding function of membrane proteins that clear neurotransmitters from synaptic cleft. These family of proteins are called neurotransmitter:sodium symporters (NSS) since their function depends on electrochemical gradient of sodium ions across membrane. Important members of NSS family include dopamine transporter (DAT), serotonin transporter (SERT), and norepinephrine transporter (NTE) that remove dopamine, serotonin, and norepinephrine from synaptic cleft. Proper control of the amount of neurotransmitter in the synapse is important for many brain functions and imbalances are linked to brain related diseases like depression, bipolar disorders, ADHD, Schizophrenia, and Parkinson’s. In my research, I combine MD simulations with kinetic models based on Markov State Models (MSMs) to understand function of NSS family of proteins.

curriculum-vitae (PDF)

Dopamine Transporter

The dopamine transporter (DAT) is a membrane protein belonging to the Neurotransmitter:Sodium Symporter (NSS) family, which also includes the closely related serotonin and norepinephrine transporters. NSS are responsible for clearance of released neurotransmitters (e.g. dopamine, by DAT) from the synaptic cleft. Function of NSS transporters in neuronal signaling implicate them in the mechanisms of action of abused psychostimulants, such as cocaine and amphetamine, and in various psychiatric and neurological disorders including drug addiction, schizophrenia, and Parkinson’s disease.

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Na+/K+-ATPase (NKA) is a membrane protein that transports Na+ ions out of the cell and brings K+ ions into the cell against their concentration gradient. To function, NKA harnesses the chemical energy stored in an ATP molecule to cycle between two major conformational states during active pumping: a high affinity state for Na+, and a high affinity state for K+. The recent availability of the crystal structures [1] for these states, now makes it possible to computationally determine the factors that control selectivity for Na+ versus K+ ions.  High selectivity of NKA for Na+ or K+ may be a result of thermodynamic (different affinities for binding sites) as well as kinetic (barriers along binding pathways) factors.

  • Journal article: Molecular simulations and free-energy calculations suggest conformation-dependent anion binding to a cytoplasmic site as a mechanism for Na+/K+-ATPase ion selectivity, Asghar M Razavi, Lucie Delemotte, Joshua R Berlin, Vincenzo Carnevale, and Vincent A Voelz, Journal of Biological Chemistry 292: 12412-12423, 2017 [PDF]
  • Conference talk: Razavi, A. M., Carnevale, V., Delemotte, L., & Voelz, V.A. (2015, February 9). Understanding selectivity of the Na+/K+ -ATPase using a computational approach. Platform presentation conducted at the meeting of the Biophysical Society, Baltimore, MD
  • Poster: Razavi, A. M., Delemotte, L., Carnevale, V., & Voelz, V.A. (2015, June). Understanding selectivity of Na+/K+-ATPase by computational approach. Poster presented at the Gordon Research Conference, Lewiston, ME. [PDF]
  • Poster: Razavi, A. M., Delemotte, L., Carnevale, V., &  Voelz, V.A. (2015, May). Understanding selectivity of Na+/K+ -ATPase by computational approach. Poster presented at the Protein Folding Consortium Workshop, Berkeley, CA. [PDF]
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GPCR Opsin

Several class-A G protein-coupled receptor (GPCR) proteins act as constitutive phospholipid scramblases.  Here we combined extensive molecular dynamics simulations with tICA and Markov State Models to unravel how a G Protein-Coupled Receptor flips lipids.

  • Journal article: Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin, Giulia Morra, Asghar M. Razavi, Kalpana Pandey, Harel Weinstein, Anant K. Menon, George Khelashvili, Structure 26: 356–367, 2018
  • Poster: Morra G., Razavi A., Pandey K., Weinstein H., & Menon A., Khelashvili G. (2018, February).The GPCR Opsin Translocates Lipids via a Dynamic Mechanism Specified by Markov State Model Analysis of Molecular Dynamics Trajectories. Poster presentation conducted at the meeting of the Biophysical Society, San Francisco, CA.

GB1 Hairpin

Experimental research has shown that the stability of the C-terminal hairpin of Protein G (GB1) increases with the number of tryptophan (Trp) residues. However, the increase in Trp residues also increase the folding time. To understand the roots of this behavior we performed extensive explicit water molecular dynamic (MD) simulations (~10 milliseconds total) on the GB1 hairpin and its Trp zipper mutants.

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Surprisal Adaptive Sampling

Markov state models (MSMs), which model conforma
tional dynamics as a network of transitions between metastable states, have 
been increasingly used to model the thermodynamics and kinetics of
biomolecules. In considering perturbations to molecular dynamics induced
 by sequence mutations, chemical modifications, or changes in external
 conditions, it is important to assess how transition rates change, 
independent of changes in metastable state definitions.

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The ability of biofilms to attach surfaces is crucial for their life cycle. LapA is a protein that is responsible for this strong adhesion. Another protein called LapG can cleave N-terminal of LapA, hence freeing bacteria from surface. Normally, LapG is in interaction with LapD protein and therefore it is not free to cleave LapA. In this computational/experimental project, our goal is to design small peptidomemtics that can interrupt LapD-LapG interactions, therefore LapG will be free to cleave LapA. Initially, we designed peptidomimetics with 7 and 9 residues (7-mers and 9-mers), however, after fast computational screening using replica exchange implicit solvent MD, 9-mer designs seen to be more potent.

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