Reprogramming Living Cells With An Engineering Language
The molecular connectivity between genes and proteins inside a cell shows a good degree of resemblance with complex electrical circuits. This inspires the possibility of engineering a cell similar to an engineering device. Synthetic biology is an emerging field of bioengineering, where scientist use electrical and computer engineering principle to re-program cellular function for creating new cellular function with a potential to solve next generation challenges in medicine, energy, and space travel. In this talk, we discuss our synthetic biology efforts to build a technology platform for cellular robotics and systems biology effort to understand the effect of zero gravity on human and bacterial cells during space travel.
Msh4-Msh5 Induced DNA Conformational Changes Provide Insights into its Role in Meiotic Recombination
MutSg plays a role in meiotic recombination facilitating crossover formation between homologous chromosomes. Failure to form crossovers leads to improper segregation of chromosomes and aneuploidy, which in humans results in infertility and birth defects. To improve current understanding of MutSg function, we investigated the binding affinities and structures of MutSg in complex with DNA substrates that model homologous recombination intermediates. Our findings demonstrate that Sc Msh4-Msh5 binds Holliday Junction-like substrates, 3' overhangs, single stranded (ss) forks and the D-loop with nanomolar affinity. Energy transfer experiments further demonstrate that DNA structure is modulated by the binding interaction with the largest changes associated with substrates containing a ss end. For junction-like intermediates, Msh4-Msh5 binding either stabilizes the existing stacked structure or induces formation of the stacked X conformation. Significantly, we find that upon binding Msh4-Msh5 stacks an open junction construct to the same extent as the standard junction. These results suggest that MutSg stabilizes the stacked X junction conformation, which is refractory to branch migration, possibly until resolution by MutLg. We developed and refined structural models of Msh4-Msh5 interacting with HJ and duplex DNA using homology modelling and molecular dynamics simulations. Importantly, these modelled structures reveal a putative DNA-binding region (DBR), in which the protein makes asymmetric contacts with the junction. We further identified DNA bases and protein residues that are potentially important for binding and recognition. Mutation of these residues or deletion of the DBR results in reduced affinity for HJ and dsDNA. Furthermore, DNA bases predicted to interact with the protein exhibit changes in dynamic motion upon binding that are reduced with mutated protein. Taken together, these results provide significant insight into MutSg binding interactions and the structure-function relationships of these complexes.
A conserved and buried edge-to-face aromatic interaction in SUMO: Implications for SUMO pathway and viral replication
Often multiple aromatic amino acids buried at a protein’s core are involved in mutual paired interactions. Although ab initio energy calculations have highlighted the importance of orientations between aromatic rings for stable aromatic interaction, studies in the context of a protein’s fold and function are elusive. Small Ubiquitin-Like Modifier (SUMO) is a common post-translational modifier that affects diverse cellular processes. Here, we report that a highly conserved aromatic triad is a unique signature of SUMO that is absent in other Ubiquitin Like homologous folds. The specific edge-to-face conformation between a pair of interacting aromatics in the triad is vital to the fold and stability of SUMO. NMR structural studies showed perturbation of the conformation of the aromatics disrupts several long-range tertiary contacts in SUMO, leading to a heterogeneous and dynamic protein with attenuated SUMOylation in both in-vitro and in cellular conditions. Our results highlight that absolute co-conservation of specific aromatic pairs inside a protein core is indispensable for its stability and function. The Human CytoMegaloVirus (HCMV) is a member of the gamma herpes virus family, whose life-cycle is significantly dependent on the host SUMOylation machinery. IE2 is an immediate early expressed HCMV proteins, which regulate the viral replicative cycle. I will present results that uncover an unprecedented mechanism used by the viral transactivator IE2 to exploit a cross-talk of two post-translational modifications Phosphorylation and SUMOylation, to ensure an effective viral replication.
Investigations on Functional Materials for Hybrid Sulfur Cycle for Thermochemical Hydrogen Production
Thermochemical water splitting cycles has shown great potential towards efficient production of hydrogen on an industrial scale. Hybrid Sulfur cycle (Hy-S) is one of the most preferably studied thermochemical cycle due to several advantages. Hy-S cycle involves two steps, i.e. sulfuric acid decomposition reaction and aqueous SO2electrolysis. Development of functional materials such as catalysts, electrocatalysts, membrane electrode assemblies etc., was undertaken with an objective to improve the reaction kinetics and efficiency of the Hy-S cycle.
Iron oxide based catalyst was chosen and efforts were made to overcome the sintering issues encountered during its prolonged uses. For the purpose, dispersed iron oxide (15 wt.%) on various supports (SiO2, TiO2, CeO2and ZrO2) were synthesized and evaluated their activity for sulfuric acid decomposition reaction. The catalytic activity for the acid decomposition at 750°C followed the order: Fe2O3/SiO2> Fe2TiO5/TiO2> Fe2O3/ZrO2> Fe2O3/CeO2. Various preparation methods like polyol, wet-impregnation, hydrothermal and equilibrium adsorption were also employed to maximize the catalyst performance of Fe2O3/SiO2catalyst for acid decomposition reaction. The Fe2O3 (15wt.%)/SiO2samples prepared by polyol method exhibited highest activity for the sulfuric acid decomposition reaction and the activity trend at 800 °C was found to be as follows: polyol > equilibrium-adsorption> wet-impregnation ~ hydrothermal. Further stability of Fe2O3(15wt.%)/SiO2 catalyst during prolonged uses (100 h) for sulfuric acid decomposition reaction at 800 °C was evaluated.
The catalytic properties of the dispersed iron oxide samples were correlated to nature of support, structure, morphology and the redox properties of iron oxide phase. Detailed investigations on both fresh and used catalyst were studied to elucidate the mechanistic aspects of the acid decomposition process. The most probable mechanism of sulfuric acid decomposition over dispersed iron oxide catalyst which involved formation and decomposition of surface sulfate species was proposed.
Solar thermal sulfuric acid decomposition employing concentrated solar heat from a 1.8 m diameter dish and in-house developed quartz receiver-reactor was also successfully demonstrated. A maximum SO2yield of 38 % was achieved with Fe2O3/(15wt. %)/SiO2catalyst at weight hourly space velocity (WHSV) of ~ 28 g acid/gcat/h, at 750-850 °C.
A series of Pt/C electrocatalysts with varying platinum content (10-40 wt.%) were successfully prepared and electrochemical properties were tested for hydrogen evolution reaction(HER) and aqueous SO2oxidation reaction. Amongst these, catalyst containing 20 wt. % Pt was found to be the most effective. Further, a single cell PEM based aqueous SO2electrolyzer (4cm2 active area) was designed, fabricated and tested with the membrane electrode assembly comprising of the most active Pt/C electrocatalyst. A current density of ~75 mAcm2 was achieved at a cell voltage of 1 V. As a non-noble metal based electrocatalyst, molybdenum carbide electrocatalysts dispersed on carbon with varying Mo content (10-40 wt.%) were synthesized and evaluated for HER. Through these studies 20 wt% Mo content was found to be the optimum loading to attain maximum electroactivity for HER.
Non-Linear Optical Organic Micro-Resonators
Bottom-up molecular self-assembly technique has emerged as one of the powerful methods to produce miniaturized organic photonic structures, such as optical waveguides, lasers, resonators, filters, circuits and modulators. Optical waveguides and modulators are used to control the light propagation down to microscale and modulate the light propagation speed, respectively. In optical resonators their mirror-like geometry allows them to tightly trap the photons by repeated total internal reflection at the air-matter interface and act as optical gain media exhibiting high-quality factor (Q) with the low optical loss. We have been performing single-particle micro-PL spectroscopy studies to exploit the geometrical features of diverse self-assembled organic structures for photonic applications. In my talk, I will discuss some original results achieved in our group in linear and non-linear optical organic optical waveguide and microresonators useful for signal enhancement, sensing and lasing applications. I will also discuss our attempts towards creation and study of photonic molecules.
Adv. Mater. 2017, 29, 1605260.
Adv. Mater. 2013, 25, 2963.
 Angew. Chem. Int. Ed. 2012, 51, 3556.
Adv. Funct. Mater. 2013, 23, 5875.
Adv. Funct. Mater. 2011, 21, 667.
Adv. Opt. Mater. 2018, in the press [progress Report].
Adv. Opt. Mater. 2017, 5, 1600613.
Adv. Opt. Mater. 2016, 4, 112-119.
Adv. Opt. Mater. 2015, 3, 1035.
Adv. Opt. Mater. 2013, 1, 305.
 ACS Appl. Mater. Interfaces, 2018, 10, 16723.
 J. Mater. Chem. C 2018, DOI: 10.1039/C8TC02638F.
 J. Mater. Chem. C 2017, 5, 7262.
 J. Mater. Chem. C 2017, 2, 1404.
 Chem.Nano.Mat. 2018, 4, 764.
Exploring the Challenges in Computational Enzyme Design
Enzymes are nature’s most efficient catalysts and are also harnessed in synthetic chemistry for the sustainable production of several non-natural products. However, the design of new enzymes presents a major practical and fundamental challenge. Despite an interesting progress, the main advances are achieved through directed evolution and not by computational design.1 Moreover, several designed systems adopt the less efficient route of ground state destabilization instead of transition state stabilization. In the talk, I will discuss the design of two enzymes; Kemp eliminases and haloalkane dehalogenase. Kemp eliminases are computationally designed enzymes that catalyze the conversion of 5-nitrobenzisoxazole to cyanophenol product. Haloalkane dehalogenase; DhlA is an important enzyme that helps in breaking down the toxic haloalkanes (1,2-dichloroethane) to alcohol via a series of steps. EVB (Empirical valence bond) approach is used to calculate the activation energies for the wild type and mutants. For Kemp eliminases, the origin of catalysis in different systems is rationalized on the basis of solvation free energies.2 The different trends observed in the directed evolution of different systems is investigated to understand the effect of multiple mutations. For halolalkane dehalogenase, after successfully reproducing the activation barriers of known mutants, new mutations are proposed on the basis of structural data.3 We mutated residues that are known to contribute to catalysis and then attempted to restore the activity by mutating residues in the first and second solvation shells. Various factors responsible for certain anomalies and the challenges encountered during computational enzyme design will be discussed.
 Frushicheva, M. P.; Cao, J.; Chu, Z. T.; Warshel, A. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 16869.
 (a) Jindal, G.; Ramachandran, B.; Bora, R. B.; Warshel, A. ACS Catal. 2017, 7, 3301. (b) Jindal, G.; Mondal, D.; Warshel, A. J. Phys. Chem. B 2017, 121, 6831.
 Jindal, G.; Slánská, K.; Kolev, V.; Damborsky, J.; Prokop, Z.; Warshel, A. Proc. Natl. Acad. Sci. U. S. A. 2018 (Under Revision).
Computational Studies on Mechanism and Stereoinduction in Asymmetric Catalysis
One of the leading goals in contemporary catalysis is to render improved efficiency to existing catalytic protocols.1 While different forms of catalysis have witnessed tremendous success in the synthesis of complex molecules, there is minimal clarity at the mechanistic front. Further developments in the new form of catalysis/catalysts require a thorough knowledge of the reaction pathways. In asymmetric catalysis, the rationalization of selectivity is of prime importance as it paves the way for rational catalyst design. In the current talk, I will discuss the use of use of computational tools in providing a mechanistic understanding and insights into the factors controlling the stereoselectivity in a few landmark asymmetric reactions catalyzed by axially chiral catalysts/ligands. In particular, all calculations have been carried out with hybrid density functional theory (DFT) methods (B3LYP, M06, M06-2X and B3LYP-D3). The talk will focus on three forms of catalysis; 1) organocatalysis, 2) metal catalysis and, 3) cooperative catalysis. The first part encompasses the role of a newly developed class of chiral imidodiphosphoric acids in inducing selectivity in an asymmetric sulfoxidation reaction.2 The second part will focus on the fine tuning of noncovalent interactions to design new phosphoramidite ligands for an asymmetric diamination reaction.3 In the last part, the role of chiral Brønsted acids when used in conjunction with Pd metal and the importance of ligand exchange in the formation of spirocyclic ring formation will be elucidated.4
 Houk, K. N.; Cheong, P. H.-Y. Nature 2008, 455, 309.
 Jindal, G.; Sunoj, R. B. Angew. Chem. Int. Ed. 2014, 53, 4432.
 (a) Jindal, G.; Sunoj, R. B. Chem. Eur. J. 2012, 18, 7045. (b) Jindal, G.; Sunoj, R. B. Org. Biomol. Chem. 2014, 12, 2745.
 (a) Jindal, G.; Sunoj, R. B. J. Am. Chem. Soc. 2014, 136, 15998. (b) Jindal, G.; Sunoj, R. B. Org. Lett. 2015, 17, 2874.
Carbonyl-carbonyl interactions in small molecules and proteins
The carbonyl group is ubiquitous in both chemistry and biology. Apart from being involved in numerous chemical transformations, it can also participate in various distinct weak noncovalent interactions including hydrogen bonding (C=O•••H), carbonyl-chalcogen interactions (C=O•••X; X = S, Se, Te) and nucleophile-carbonyl interactions. In recent years, carbonyl-carbonyl (CO•••CO) interaction has emerged as an important noncovalent interaction that was observed in various small molecules, polyesters, peptoids, protein secondary structures and collagen-like peptides. It is believed that this interaction is n→π* in nature where the lone pair of oxygen of the donor carbonyl group is delocalized over the antibonding π orbital of C=O bond of another nearby acceptor carbonyl group. In this talk, I will discuss our current understanding of CO•••CO interactions with a focus on the “reciprocal” variant of n→π* interaction that we recently discovered. I will also discuss about the various structural motifs of CO•••CO interactions and put forward a hypothesis based on CO•••CO interactions that could explain the stabilization of polyproline II and collagen triple helices.
GroEL Chaperonin Assisted Protein Folding: studied by PETFCS and SmFRET
Many newly synthesized unfolded polypeptides require assistance by molecular chaperones in order to reach their active folded states. The GroEL/GroES chaperonin system is one of the most important bacterial chaperonin systems, which fulfills an essential function in assisting the folding of cytosolic proteins. GroEL is a homo-tetradecameric double-ring assembly of 60 kDa subunits with two opposing central cavities stacked back to back. Upon binding of ATP and the co chaperone GroES, GroEL transiently encapsulates newly synthesized or misfolded substrate proteins, which then can fold to the native state while being shielded from the crowded cytosolic environment. The mechanism of GroEL remains controversial whether GroEL acts as a passive cage, merely providing an aggregation preventing micro compartment, or whether GroEL actively accelerates the refolding of a subset of substrate proteins by modulation of the folding energy landscape.
We resorted to a variety of single molecule fluorescence techniques to address this controversy. A novel and sensitive dual color fluorescence cross-correlation spectroscopy assay shows the absence of transient aggregates at single molecular concentration. Using a single molecule FRET (SmFRET) based assay, we show that the acceleration of substrate protein folding by GroEL is preserved under single molecule conditions, where aggregation is excluded. We apply photoinduced electron transfer fluorescence quenching correlation spectroscopy (PETFCS) to demonstrate that the acceleration of substrate protein folding is achieved by encapsulation of a dynamic folding intermediate inside the GroEL cavity. Furthermore, we provide evidence that modulation of the folding energy landscape is a result not only of steric confinement during encapsulation, but also of the net negative charge of the GroEL cage wall. Taken together, these results represent a substantial advance in our understanding of the mechanism of the prokaryotic chaperonin system and our findings suggest that GroEL, by an active chaperonin mechanism, promotes substrate protein folding by entropic destabilization of folding intermediates.
Direct observation of the Mechanical Foldase Activity of Trigger Factor Chaperone by Magnetic tweezers
Proteins fold under mechanical forces in a number of biological processes, ranging from muscle contraction to co-translational folding at the mouth of the ribosome. As force hinders the folding reaction, chaperones must play a crucial role in this scenario. Nevertheless, to date, it has not been possible to monitor the direct influence of a chaperone on a protein folding under force. Here, we introduce single molecule magnetic tweezers to study the folding dynamics of protein L in presence of the prototypical molecular chaperone Trigger Factor (TF) over the range of physiological forces (4 to 10 pN). Our results show that TF modulates the folding of protein L by prominently increasing the probability of folding against the force and accelerating the refolding kinetics. Moreover, we find that the ability of TF to catalyze the folding reaction depends on the pulling force; as the force increases, higher concentrations of TF are needed for rescue folding, although no effect is observed above 12 pN even with saturating amounts of TF. Here, we propose for the first time that chaperones such as TF can work as foldases under force, playing a relevant role in many biological processes such as protein translation.
Design of Catalysts and Nano-Heaters by Decorating Ultrasmall Nanoparticles and Pseudo-Single Atoms of Metal on DFNS: Tuning their Plasmonic Response by Hot Spot Engineering
Charge Transport and Catalysis Reactions at the Electrified Interfaces
Possibility of studying the properties of molecules or nanostructures at single enity level offers huge opportunities to tune structure property relationships at nanoscale. The problem with current state-of-the-art nanomaterials and energy research involving charge or electron transport at electrode|molecule interface as a key process is centered in the fact that no single experimental technique can independently provide complete information on nanoscale structure-property relationships. The development of fast, cost effective and structure sensitive characterization methods at single entity level is the target of much current nanotechnology research.
During this presentation, I will try to show the experimental framework (experimental technique and methodologies development) that I am planning to implement/develop in my future laboratory to address the key issue of nanoscale structure-property relationships under in-operando conditions.1-4
1. Kaliginedi et al., Nanoscale. 2015, 7 (42), 17685-17692.
2. Rudnev, A., Kaliginedi et al., Science Advances. 2017, 3, e1602297.
3. Seth, C., Kaliginedi et al., Chemical Science. 2017, 8, 1576-1591.
4. Atesci, H., Kaliginedi et al., Nature Nanotechnology. 2018, 13, 117.
Charge transport at Electrode|Molecule interface: From Molecular Electronics to Energy Research Applications
The idea of building electronic devices using single molecule as an active component was first proposed by Aviram and Ratner in the early seventies.1 Indeed, molecules are of great interest for application in electronic devices because of their small size, recognition properties, ability of self-organization, possibility of chemical modification and customisation. Thus, the ability to measure and control charge transport across metal|molecule|metal junction is of considerable fundamental interest and represents a key step towards the development of molecular electronic and spintronics devices.2-6
In addition to the applications in molecular electronics and spintronics research, studying charge or electron transport properties at metal|molecule interfaces under the influence of external stimuli like light, temperature, electrochemical potential or magnetic field will have a variety of applications in other research fields like (i) energy research (for example, solar cells, where the charge or electron transfer at metal|molecule interfaces plays a crucial role in determining the efficiency of the solar cell); (ii) photocatalysis and electrocatalysis (activity of a catalyst depends on the effective charge transport at electrode|catalyst interface); (iii) Sensors (sensitivity and selectivity of a sensor may depend on the effective charge transport at electrode|sensor moiety interface) and etc.5,7
In the first part of my presentation, I will introduce working principle of measurement techniques (i.e STM break junctions (STM-BJ), mechanically controllable break junction (MCBJ) and conducting probe AFM (CP-AFM) techniques) and data analysis procedures used to extract conductance properties of molecular junctions.2 Using the results from several case studies, I will try to demonstrate a frame work for building structure-property correlations of metal|molecule|metal junctions at single and multi-molecular level.2-6 In the later part of my presentation, I will discuss the molecular conductance measurement results which will have direct consequences in electrocatalysis and energy researh.3,5,7
1. Aviram, A.,Ratner, M., Chem. Phys. Lett. 1974, 29, 277.
2. Kaliginedi et al., Journal of American chemical society. 2012, 134, 5262–5275.
3. Rudnev, A., Kaliginedi et al., Science Advances. 2017, 3, e1602297.
4. Seth, C., Kaliginedi et al., Chemical Science. 2017, 8, 1576-1591.
5. Atesci, H., Kaliginedi et al., Nature Nanotechnology. 2018, 13, 117.
6. Kaliginedi et al., PCCP. 2015, 16, 23529.
7. Kaliginedi et al., Nanoscale. 2015, 7, 17685.
Circular permutations in azurin: Creating new termini for pulling along different directions
Plant Viruses for the Delivery of Platinum Anticancer Therapeutics
Platinum-based anticancer drugs such as cisplatin, carboplatin, and oxaliplatin are used in the treatment of nearly half of the population of the cancer patients undergoing chemotherapy. These drugs, however, lack selectivity and have dose-limiting toxicities, low bio-availability, rapid clearance from the body, and may encounter drug resistance mechanisms, leading to the recurrence of the cancer. Therefore, efficient loading of drugs in novel delivery agents has the potential to substantially improve therapy by directly targeting the diseased tissue and avoiding unwanted side effects. Given that the development of new drugs is expensive, reducing toxicity caused by existing drugs by packaging them into delivery vehicles is attractive and can be achieved by controlled and targeted methodologies. Although presently available nano-sized delivery agents impart safety, their limited efficacy and inability to penetrate tissue adequately are some of the limitations. Consequently, development of new drug delivery methods has been a subject of recent burgeoning interest.
Viruses are very simple in structure and composition, and they can be considered as biology-derived nanocarriers, naturally evolved to carry and delivery cargos to target cells. Moreover, they can transfect host cells with a very high efficiency. However, their immunogenic nature hinders their development as drug carriers. In this regard, plant viruses form an emerging platform technology as they offer several advantages over mammalian vectors.
In this talk, I will highlight the use of tobacco mosaic virus (TMV) for the delivery of platinum anticancer therapeutics. It has been shown previously by our research group that the highly potent analogues of cisplatin, phenanthriplatin (1) and its aqua-form (2), are differentially taken up in the TMV channel. Whereas ~1000 molecules of 1 are loaded in TMV, 2 is taken up in higher quantities (~2000 molecules per TMV particle). Studies on delineating the mechanism of their differential uptake and their stabilization in the TMV channel will be discussed in detail. Furthermore, I will also discuss on the heat-transition of TMV nanorods to nanospheres (SNPs) in the presence of 1, which leads to significant uptake of 1 in the bulk of SNPs, and their mechanism of formation. These SNPs are stable in the fetal bovine serum (FBS) medium and they do not release 1 at pH 7.4 and pH 5, which may further prevent the toxicity arising due to off-target release of drugs. To an added advantage, the release of 1 is only triggered by proteolytic enzyme like trypsin which is a constituent of endosome. SNP delivery system presents a comparable to better anticancer efficacy in the panel of cancer cell lines. These investigations inform the design of future drug analogues that can be efficiently encapsulated, stabilized in different morphologies of TMV, and delivered to the tumor site.
1.A. E. Czapar, Y. Zheng, I. A. Riddel, S. Shukla, S. G. Awuah, S. J. Lippard, N. F. Steinmetz, ACS Nano, 2016, 10, 4119-4126.
2.A. A. Vernekar, G. Berger, A. E. Czapar, F. A. Veliz, D. Wang, N. F. Steinmetz, S. J. Lippard, J. Am. Chem. Soc., 2018, 140, 4279-4287.
3.A. A. Vernekar, F. A. Veliz, N. F. Steinmetz, S. J. Lippard, (SNP work will be submitted soon).