TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

April 25, 2018 at 2.30 pm in AG-80

Title :

Metallic Conductivity in Proteins: A New Paradigm for Biological Electron Transfer and Bioelectronics

Abstract :

Electron transfer is central to all life processes. Every living cell must get rid of a large number of electrons left behind in metabolism when nutrients convert into energy. Aerobic organisms use oxygen to dump these electrons. Electron transfer in proteins occurs through either tunneling or hopping a few nanometers via inorganic cofactors. However, the common soil bacteria Geobacter sulfurreducens transfers electrons over hundreds of micrometers, to insoluble electron acceptors1 or syntrophic partner species2. Electron transfer is using hair-like protein filaments called pili1,2 that function as molecular nanowires and this allows bacteria to survive in environments that lack membrane-permeable electron acceptors such as oxygen. The conductivity of pili exhibits temperature dependence similar to that of disordered metallic polymers1,3. However, metallic conductivity is considered improbable in proteins due to the lack of periodicity in protein structure, thermal fluctuations, and low conductivity values.

I will present our recent electrical, optical and structural studies to identify the structural, molecular and physical mechanism of metallic conductivity in pili. To determine the molecular architecture responsible for conductivity, we are using a suite of complementary experimental and computational methods such as molecular dynamics, x-ray diffraction, circular dichroism, fluorescence microscopy and infrared spectroscopy. Our studies suggest that aromatic amino acids in pili are closely packed from each other        (< 4 Å), forming pi stacking, that can cause in intermolecular electron delocalization, conferring metallic conductivity to pili. Notably, we observe large conformational changes that accelerate electron transfer in pili. Furthermore, we show that improved metallic nature in the pili correlates with the improved pi stacking. These studies defy the current biochemical assumption that all proteins are electronic insulators and need inorganic cofactors for electron transfer. Pili thus represent a new class of electronically functional proteins that can transport electrons at rates and distances unprecedented in biology. I will discuss the implications of these studies for biological electron transfer as well as for bioelectronics.

 

[1] Malvankar et al. Nature Nanotechnology, 6, 573-579 (2011)

[2] Summers et al. Science, 330, 1413-1415 (2010)

[3] Malvankar et al. Nature Nanotechnology, 9, 1012-1017 (2014)

 

 

Research website: https://malvankarlab.yale.edu

 

April 23, 2018 at 4.00 pm in AG-69

Title :

Optical Charge Transfer Transitions Associated with Charged Amino Acids: Creating a Spectral Basis Set to Interpret ProCharTS

April 20, 2018 at 2.30 pm in AG-66

Title :

Peptide Ligand G Protein-Coupled Receptors are Dynamic Molecules in Lipid Membrane

Abstract :

G protein-coupled receptors (GPCRs) constitute a large group of membrane proteins, known to undergo a set of well-defined structural transitions upon activation and signaling. In our work, we address the molecular dynamics of peptide ligand GPCRs using solution and solid-state NMR. We work with human class A GPCRs that are activated by peptide hormones, such as neuropeptide Y (NPY) or ghrelin. The GPCRs are expressed in prokaryotic systems or by cell-free synthesis. In the talk, results on three research topics will be discussed. (i) Studies on the equilibrium dynamics of GPCRs using static 15N CP NMR, 15N NMR spectra acquired as a function of the CP contact time, and 13C MAS NMR experiments confirm the high molecular dynamics of three peptide ligand GPCRs. Quantitative determination of 1H-13C order parameters through measurement of the 1H-13C dipolar couplings in separated local field NMR experiments revealed axially symmetric motions of the GPCRs and molecular fluctuations of large amplitude [1, 2]. (ii) Data will be reported that led to the development of structural models of NPY bound to the Y1 and the Y2 receptors. Isotope-labeled NPY was used to determine the secondary structure of the receptor bound ligand. Upon receptor binding, the C-terminal α‑helix of NPY, formed in membrane environment in the absence of receptor, is unwound starting at Thr32 to make optimal contact of the C‑terminal residues within the binding pocket. The NMR signals of several hydrophobic residues in the α-helical region of NPY were broadened upon receptor binding. The ligands are tethered to the second extracellular loop by hydrophobic contacts, with the N-terminal part of its helix facing the solvent. The C‑terminal pentapeptide of NPY inserts deeply into the transmembrane bundle, making optimal contacts to the Y2 receptor including a contact NPY’s amidated C‑terminus with Gln3.32 in a polar cluster within helices 2 and 3 of the receptor [3, 4]. (iii) We will report data on the dynamics and ligand binding of the human GHS receptor, which plays a key role in the development of obesity [5].

 

[1]Schmidt et al. Chemistry 2014, 20, 4986.

[2] Thomas et al. J. Biomol. NMR 2015, 61, 347.

[3] Kaiser et al. Angew. Chem. Int. Ed. 2015, 52, 7446.

[4] Yang et al. Nature 2018, DOI: 10.1038/s41586-018-0046-x, in press.

 

[5] Schrottke et al. Sci. Rep. 2017, 7, 46128.

 

April 16, 2018 at 4.00 pm in AG-69

Title :

New approaches for studying the structure of protein oligomers in lipids and in solutions

Abstract :

Understanding the interaction between membranes and amyloid protein oligomers is a key unsolved challenge in the field of biophysics. Here we describe new tools to address this challenge. We show that single molecule photobleaching with a home-built Total Internal Reflection Fluorescence Microscope can measure the relative membrane affinity of each type of oligomers. Also, an Atomic Force Microscope coupled to a home-built Confocal Fluorescence Microscope can probe the membrane phase dependant binding of these oligomers.  Separately, fiber-optic in-probe modulation of pH  during an NMR experiment can potentially probe the evolving oligomeric structure.

April 12, 2018 at 4.00 pm in AG-66

Title :

Mechanistic Insights into the Inhibition of Fibrillation of Alpha-Synuclein by Triphala and Destabilization of Preformed Fibrils

April 9, 2018 at 4.00 pm in AG-69

Title :

Understanding the Effect of Distant Mutation on the Charge Transfer Band of Azurin Using Ultrafast Spectroscopy

April 2, 2018 at 4.00 pm in AG-69

Title :

Mn(II) Sensor Diaries: Stumbling upon a Hg(II) Sensor

March 26, 2018 at 4.00 pm in AG-69

Title :

Seminal Electrode Materials for Battery and Supercapacitor Applications

March 21, 2018 at 2.30 pm in AG-80

Title :

Variational Random Phase Approximation Method for Accurate Ionization Potentials and Interaction Energies

Abstract :

A critical and outstanding challenge of electronic structure method development is to deliver both accurate total energy differences and quasiparticle spectra. I will address this challenge using a generalized Kohn-Sham (GKS) approach that variationally minimizes the random phase approximation (RPA) ground-state energy as a functional of the one-particle density matrix. The GKS-RPA approach enables highly accurate predictions of all observables from derivatives of a single variationally stable energy functional, and leads to remarkable advancements. Intermolecular binding-energies and quasiparticle spectra from GKS-RPA improve significantly upon those from state-of-the-art post-Kohn-Sham RPA or G0W0 theory. Anions, which are often unstable and poorly described by semi-local density functional approximations, are well described within GKS-RPA. Core ionization energies, which are traditionally hard to compute, can be accurately estimated using GKS-RPA; pilot applications for modeling solvation effects in conjunction with X-ray photoelectron spectroscopy will be discussed. Overall, the GKS scheme alleviates some of the most serious problems with semi-local density functional approximations, and paves the way for a new generation of electronic structure methods.

References:

  1. G. Chen, V. K. Voora, M. Agee, S. Balasubramani, and F. Furche. “Random phase approximation methods”, Annu. Rev. Phys. Chem., 2017, 68, 421. 
  2. V. K. Voora, S. G. Balasubramani, and F. Furche. “Variational Generalized Kohn-Sham Approach Combining Random Phase Approximation and Green’s Function Methods”, https://escholarship.org/uc/item/7gf3h1h9. 

 

March 20, 2018 at 2.30 pm in AG-80

Title :

Nonvalence Correlation-Bound Anionic States: A New Doorway to Electron Transfer 

Abstract :

The mechanistic details and the dynamics of electron transfer to molecules continue to be poorly understood. The key to unraveling this fundamentally important chemical process hinges upon a sound understanding of electron binding states. Here I will discuss the discovery, theoretical characterization and role of nonvalence correlation-bound (NVCB) states as a new low-energy doorway for electron capture and transfer. In the NVCB states of anions, the excess electron occupies a very diffuse orbital while its binding to the molecule or cluster is dominated by long-range dispersion-type correlation forces. Ab initio methods and one-electron model Hamiltonians will be used to characterize the NVCB anionic states. The existence of NVCB states and its implications for gas-  and condensed-phase electron transfer will be illustrated using examples ranging from small molecules to large fullerene systems. 

 

References:

  1. V. K. Voora, A. Kairalapova, T. Sommerfeld, and K. D. Jordan. “Theoretical approaches for treating non-valence correlation-bound anions”, J. Chem. Phys., 2017, 147, 214114.
  2. V. K. Voora, and K. D. Jordan. “Nonvalence correlation-bound anion states of spherical fullerenes”, Nano Lett., 2014, 14, 4602. 
  3. V. K. Voora, L. S. Cederbaum, and K. D. Jordan. “Existence of a correlation bound s-type anion state of C60”, J. Phys. Chem. Lett., 2013, 4, 849. 
  4. J. P. Rogers, C. S. Anstöter, and J. R. R. Verlet. “Ultrafast dynamics of low-energy electron attachment via a non-valence correlation-bound state”, Nat. Chem., 2018, http://dx.doi.org/10.1038/nchem.2912.  

 

March 14, 2018 at 2.30 pm in AG-80

Title :

Proton Coupled Electron Transfer and Charge Transfer Reactions at Solid-Liquid Interfaces and Homogeneous Environment

Abstract :

Proton coupled electron transfer (PCET) reactions are integral part of several catalytic processes that are crucial for energy storage, fuel cell research and several biological processes. On the other hand, excited state charge transfer reactions are at the heart of many photoinduced processes. In this presentation, I will discuss (i) computational study of PCET reaction between ZnO nanocrystal and an organic radical (ii) new theoretical methods to calculate solvent reorganization energies for electron transfer and PCET reactions in electrochemical systems, and (iii) implementation of a novel method to incorporate nuclear quantum effects in charge transfer dynamics. In the first part of the presentation I will show how to estimate rate constant for PCET between photoreduced ZnO nanocrystal and TEMPO. For reactions that involve a substantial redistribution of charge density in a polar environment, it is important to estimate the energy penalty involved in rearranging the solvent dipoles in order to estimate rate constant for the charge transfer process. In the second part of this talk I will describe a new method for calculating this important parameter, solvent reorganization energy, in the context of electrochemical electron transfer and PCET reactions. In the final part of this talk I will introduce my ongoing research on incorporating nuclear quantum effects in charge transfer dynamics within the framework of ring polymer surface hopping algorithm.

March 13, 2018 at 2.30 pm in AG-80

Title :

Homogeneous and Interfacial Proton Coupled Electron Transfer Reactions

Abstract :

Proton coupled electron transfer (PCET) reactions are integral part of several catalytic processes, e.g. reduction of dioxygen to water, oxidation of water to dioxygen, carbon dioxide reduction, reduction of dinitrogen to ammonia, that are crucial for energy storage, fuel cell research and several biological processes. In this presentation, I will discuss (i) computational investigations of role of PCET reaction in the mechanism of oxygen reduction reaction by a Co-salophen complex in the presence of p-hydroquinone as a co-catalyst, (ii) computational study of PCET reaction between ZnO nanocrystal and an organic radical. In the first part of the talk we will see that my calculations along with substantial experimental studies provide ample evidence for reduction of dioxygen to a coordinated hydrogen peroxide intermediate, which is subsequently reduced to water. The role of p-hydroquinone as electron proton transfer mediator is explored in details. In the second part of the presentation I will show how to estimate rate constant for PCET between photoreduced ZnO nanocrystal and TEMPO. We will further explore the role of proton diffusion inside the ZnO nanocrystal coupled to PCET reaction at the surface to explain the experimental studies of reaction dynamics of the PCET reaction mentioned above at longer timescales.

March 12, 2018 at 4.00 pm in AG-69

Title :

High Surface Area Aluminosilicates : Novel synthesis and unraveling the active sites by catalysis and Solid State NMR

March 5, 2018 at 4.00 pm in AG-69

Title :

Xeno-nuclei enable protein-specific modulation of order-disorder transition

Abstract :

The ability to modulate the order to disorder or vice versa transition of a specific protein in a milieu of many proteins can be an important tool for chemical biology and pharmacology. Kinetics and thermodynamics of protein folding are routinely modulated by changing solvent conditions, but such changes are not very protein specific. Specific ligands with the ability to alter the stability of a 

protein are rarely available. Here, we propose a general approach for designing such ligands by mimicking the folding nucleus of a protein. The key idea is to choose a part of the protein itself, which is suspected/known to be the nucleation site for the folding pathway, and then to put it in a pre-formed shape to modulate the folding/unfolding. This xeno-nucleus can in principle, be used to selectively modulate the folding of a particular protein from a mixture of different proteins. 

We show that the ⓵ - ⓶ part (residues 1 to 17) of ubiquitin [1], which is known to fold into a β-hairpin shape and to nucleate the folding of the rest of the protein, can make folding faster when it is introduced as a separate peptide at excess concentrations. No such acceleration is observed when the xeno-nucleus is unfolded to start with. Interestingly, the protein also becomes less stable, as the unfolding rate becomes even faster. We show that this effect is protein-specific, as another protein with no such β-hairpin (e.g. bovine serum albumin) remains unaffected by the peptide. Our results suggest that the folding of almost any protein that possesses a well-defined folding nucleus can be modulated, if a nucleus-mimicking molecule with a stabilized structure can be constructed. 

References: 

1. Atomic-level description of ubiquitin folding. PNAS, 2013, 110 (15), 5915–5920.

 

February 28, 2018 at 2.30 pm in AG-66

Title :

Science Stories: Communicating Science as Career, Hobby, or Habit

Abstract :

Whether it’s a new, better battery material, a company with controversial new drug, or tracking the impacts of climate change, science is an important part of the news. Science journalists translate research from the lab for public audiences—and they rely on working scientists to be a part of that process. Jessica Marshall will speak about the ins and outs of producing chemistry news for C&EN readers, and she’ll discuss her prior work as a freelance science writer. She’ll also talk about ways that working scientists can improve their communication—whether in speaking with other scientists or as sources for the news media. Science communication can be a rewarding career for science graduates—and those who remain at the bench can increase their work’s impact by clear communication. This session will discuss both roles: science communicator and communicating scientist. Come join the conversation.

About the Speaker:

Jessica Marshall is an associate editor at Chemical & Engineering News. Prior to joining C&EN, she spent a decade as a freelance science and environment writer. Her work appeared in Nature, TheAtlantic.com, Discover, Proceedings of the National Academy of Sciences, New Scientist, and other outlets. She contributed to The Science Writers’ Handbook: Everything You Need to Know to Pitch, Publish and Prosper in the Digital Age. She attended the University of California, Santa Cruz Science Communication Program. Prior to that, she earned a Ph.D. in chemical engineering at the University of California, Berkeley, and a B.S.E. in chemical engineering at Princeton University.  She lives in Seattle with her husband and three children.