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Dr. Ivet Bahar
Distinguished Professor & JK Vries Chair
Computational & Systems Biology Dept
School of Medicine, University of Pittsburgh
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"Bridging Structure & Function, via Dynamics"

In the News...

What do we do?

The dynamics of living systems at the molecular level define cell survival and regulation mechanisms, which in turn, define our physiological responses. Biomolecules work together in the cell in a seamless way: they communicate (intra- and intermolecular signaling), interact with each other (chemical reactions, binding, complex formation, assembly), produce and consume energy (mitochondrial functions, metabolic events), carry cargos (ion or substrate transport). They not only sustain and regulate cell life (transcription, translation, repair), but also orderly terminate it (apoptosis). How do biomolecules achieve so many functions? Because they have flexible structures that can adapt to changes and act in specific ways (intrinsic dynamics) driven by internal or external effects, controlled by principles of physical sciences and engineering, much like synthetic materials or machines. Chemical and physical rules that apply at the microscopic scale are not any different from those of the macroscopic world. Our goal is to help improve our understanding of the basic principles of biomolecular actions with the help of computing technology, visualize/simulate their time evolution, and discover rational intervention methods to counter their dysfunction.

 
Student Spotlight Heading Recent Publications image Research Progress Heading

Cihan received the Best DCSB Student Award for 2016 for his work on developing multi-scale models and simulations for dopaminergic signaling. He aims at understanding the effect of spatial complexity and heterogeneity in the efficiency of dopamine (DA) reuptake. Below is a snapshot from his simulations, displaying the release of DA (red dots) from active zones on DA neurons (green).

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John received the best poster award in the DCSB retreat in June 2016 for his work on the ENM analysis of chromosome contact maps determined by Hi-C experiment.

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Hongchun received the Best DCSB Postdoc Award for 2016 for developing the iGNM database and oGNM server, published in Nucleic Acids Research. The upgraded iGNM database provides an user-friendly interfaces for retrieving information on the dynamics of 95% of PDB structures as well as their biological assemblies. It helps assess which structural elements undergo large correlated fluctuations, and enable conformational changes that may be relevant to function.

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Publications 2016

The work of Mary Cheng and collaborators shed light into the modulation of dopaminergic signaling by targeting human dopamine transporter (hDAT). The comparison of the effects of binding dopamine (DA), amphetamine (AMPH), orphenadrine (ORPH) (repurposable drug) and cocaine to (DAT) showed that DA or AMPH drive a structural transition towards a functional form predisposed to translocate the ligand. In contrast, ORPH inhibits DAT function by arresting it in the outward-facing open conformation. Further assays show that that ORPH, like cocaine, alters DAT uptake and endocytosis.

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Most recent study of Dr Gur. published in Biophys J is highlighted in Ricardo Baron's News & Notable, "Fast sampling of A-to-B Protein Global Conformational Transitions: From Galileo Galilei to Monte Carlo Anisotropic Network Modeling The new methodology, coMD, introduced by Gur et al is stated to "surely prompt new exciting routes to rapidly connect A to B, and vice versa."

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Structural dynamics, including allosteric switches, are evolutionarily maintained to accomplish biological activities, consistent with the paradigm sequence -> structure -> dynamics -> function where 'dynamics' bridges structure and function.

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"Adaptability of protein structures to enable functional interactions and evolutionary implications " Turkan Haliloglu and Ivet BaharCurrent Opinion in Structural BIology (2015) 3517-23.

"Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies" Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar ISci Rep (2014) 4:6245. PMID: 25175563

Controlling ionizing radiation (IR)-induced cell death mitigates radiation damage. Examining tumor suppressor protein p53 network dynamics in response to IR damage found that the strength of p53 transcriptional activity and its coupling (or timing with respect) to mitochondrial pore opening are major determinants of cell fate.

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"Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis" LaRusch J et al.PLoS Genetics (2014) 10:e1004376. PMID: 2503378

Bahar research featured in winter 2014/2015 issue of Pitt Med.

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