Title :

Chemical Biology of Protein Citrullination

Abstract :

In this seminar, I’ll discuss my postdoctoral research on protein citrullination, a post-translational modification associated with multiple autoimmune disorders, and my research proposals.

     Protein citrullination by protein arginine deiminases (PADs – PAD1, 2, 3 and 4) plays pivotal roles in several physiological processes, such as epigenetic regulation of gene expression, neutrophil extracellular trap (NET) formation and DNA-damage induced apoptosis. However, strong links between aberrant protein citrullination and multiple autoimmune disorders as well as certain forms of cancer have established PADs as potential therapeutic targets. As PADs are cysteine hydrolases and contain a cysteine residue in the active site, cysteine-targeted haloacetamidine warheads installed on suitable small molecule scaffolds are generally used to irreversibly inhibit PADs. Since photoactivation of small molecule drugs at the target tissue can significantly reduce their off-target toxicity, we incorporated an azobenzene photoswitch that undergoes trans-cis isomerization in the presence of light in a known PAD inhibitor scaffold, BB-Cl-amidine. This led to the development of a PAD2 inhibitor that exhibits 10-fold higher potency upon irradiation with 350 nm light. This inhibitor can be activated in HEK293TPAD2 cells with light for the inhibition of histone H3 citrullination.

     Citrullination has remarkable effects on the structure and activity of proteins. For example, citrullination of serine protease inhibitors (SERPINs) and nicotinamide N-methyl transferase (NNMT) dramatically abolishes their activity. Interestingly, autocitrullination of PAD4 is proposed to regulate its enzymatic activity. Although numerous proteins are known to be citrullinated at various positions, the downstream implications of citrullination at each of these positions in a given protein remain elusive. To aid this, we developed, for the first time, a photocaged-citrulline for site-specific incorporation into proteins and subsequent conversion into citrulline (Cit) with light. Using amber codon suppression technique and an engineered leucyl-tRNA synthetase (LeuRS)/tRNALeu pair, we incorporated citrulline into enhanced green fluorescent protein (GFP) at 39 position and into PAD4 at two known autocitrullination sites, 372 and 374. Using various enzyme kinetic assays, we have shown that the R372Cit and R374Cit mutants of PAD4 are 292- and 10-fold, respectively, less active than the wild-type enzyme, indicating that citrullination has remarkable effect on the activity of PAD4.

     In addition to the aforementioned topics, I’ll also discuss my future plans for research on the covalent modification of proteins and photochemical control of the bioactivity of small molecules.

References:

1. S. Mondal, P. R. Thompson, Acc. Chem. Res. 2019, 52, 818.

2. S. Mondal, S. S. Parelkar, M. Nagar, P. R. Thompson, ACS Chem. Biol. 2018, 13, 1057.

3. S. Sen, S. Mondal, L. Zheng, A. Salinger, W. Fast, E. Weerapana, P. R. Thompson ACS Chem. Biol., 2019, 14, 613-618.

4. S. Mondal,† S. Wang,† Y. Zheng, A. Chatterjee, P. R. Thompson, Unpublished results

Title :

From Designing Enzyme Mimetics to Probing Protein Citrullination

Abstract :

In this seminar, I’ll discuss my doctoral research on the biomimetic dehalogenation of thyroid hormones (THs), their metabolites and halogenated nucleosides as well as part of my postdoctoral research on the development of small molecule inhibitors and chemical probes of protein arginine deiminases (PADs) that catalyze protein citrullination.

     Thyroid gland produces thyroxine (T4) as a prohormone and regioselective deiodinations by a group of mammalian selenoenzymes, iodothyronine deiodinase type 1 (DIO1), type 2 (DIO2) and type 3 (DIO3) play important roles in the activation and inactivation of T4. Naphthyl-based organo- sulphur and/or selenium compounds are developed as functionally mimics of DIO3. The kinetics and regioselectivity of biomimetic deiodinations of THs and their metabolites are explained on the basis of S/Se∙∙∙I halogen bonding and S/Se∙∙∙S/Se chalcogen bonding. These organochalcogen compounds also mediate the dehalogenation of halogenated nucleosides that are incorporated into DNA during DNA replication and cause potential DNA damages in the presence of UV irradiation. In addition to these, I’ll also discuss the polymorphism of commercial thyroxine, a life-saver of millions of people suffering from hypothyroidism, and its implications on the bioavailability of the drug.

     Citrullination is a post-translational modification of arginine, catalyzed by a group of hydrolases called protein arginine deiminases (PADs – PAD1, 2, 3 and 4). Despite various physiological roles, protein hypercitrullination is associated with various diseases including rheumatoid arthritis (RA), lupus, ulcerative colitis (UC), multiple sclerosis (MS) and certain cancers. These strong disease links have established PADs as potential therapeutic targets and numerous PAD inhibitors are known in the literature. Using a fluoroacetamidine warhead and iodo-substitutions in the molecular scaffold, we developed the first potent PAD1 inhibitor with 74-fold selectivity over other PADs. Structure-activity relationship studies indicate that the potency and isozyme-selectivity of this inhibitor is due to the formation of a halogen bond between the iodine atoms and PAD1 active site. This inhibitor exhibits excellent efficiency for the inhibition of PAD1 in HEK293TPAD1 cells and mouse zygotes. Based on this molecular scaffold, we also developed a PAD1-selective activity-based probe with remarkable cellular efficacy and proteome selectivity.

References:

1. S. Mondal, K. Raja, U. Schweizer, G. Mugesh, Angew. Chem. Int. Ed. 2016, 55, 7606.

2. S. Mondal, G. Mugesh, Chem. Eur. J. 2014, 20, 11120.

3. S. Mondal, D. Manna, G. Mugesh, Angew. Chem. Int. Ed. 2015, 54, 9298.

4. S. Mondal, G. Mugesh, Angew. Chem. Int. Ed. 2015, 54, 10833.

5. S. Mondal, G. Mugesh, Chem. Eur. J., 2019, 25, 1773.

5. S. Mondal, P. R. Thompson, Acc. Chem. Res. 2019, 52, 818.

6. S. Mondal, X. Gong, X. Zhang, A. J. Salinger, L. Zheng, S. Sen, E. Weerapana, X. Zhang,

    P. R. Thompson, Angew. Chem. Int. Ed. 2019, 58, 12476.

Title :

The Low-Temperature Molecular Precursor Approach to Energy Storage Materials

Abstract :

The low-temperature synthesis of inorganic materials and their interfaces at the atomic and molecular level provides numerous opportunities for the design and improvement of inorganic materials in heterogeneous catalysis for sustainable chemical energy conversion or other energy-saving areas. The transformation of molecules to materials is an emergence phenomenon, that is, the process creates novel complex properties of the resulting material entities which are absent in the starting material. Using suitable molecular single-source precursors for functional inorganic nanomaterial synthesis allows for reliable control over uniform particle size distribution, stoichiometry which can help to reach desired chemical and physical properties. In my talk I would like to outline main advantages and challenges of the molecular precursor approach in light of selected recent developments of molecule-to-nanomaterials synthesis for renewable energy applications, relevant for the oxygen evolution reaction (OER), hydrogen evolution reaction (HER) and overall water-splitting. Electrochemical water-splitting into hydrogen (H₂) and oxygen (O₂) is widely regarded as a promising approach to producing environmentally-friendly fuel for future energy supply. In the recent years, inexpensive, earth-abundant and environmentally benign transition metal oxides, hydroxides and other functional materials in conjunction with semiconducting co-catalyst that can independently catalyze OER and HER have been established. Still the major challenge is to provide reliable catalyst systems for HER, OER and overall water-splitting which are highly efficient, robust and long-term stable (at least for several months without loosing activity). The advantage of using the low-temperature molecular precursor approach to derive at unique core-shell structures , e.g. leading to the most efficient HER electrocatalysts reported to date, will also be discussed.

Title :

Mechanistic studies of membrane remodeling in receptor mediated endocytosis

Abstract :

Receptor mediated endocytosis requires the generation of membrane curvature. Followed by external stimulation, various G-protein coupled receptors and epidermal growth factor receptors are internalized and recycled by this crucial membrane trafficking pathway. Bin/Amphiphysin/RVS (BAR) superfamily proteins have emerged as key effectors in membrane reshaping during the endocytic events. In addition to a crescent shaped BAR domain, many of these proteins contain a Src homology 3 (SH3) domain. BAR proteins sense and generate membrane curvature with their membrane binding domain whereas the SH3 domain regulates their interaction with other protein binding partners. Receptors containing proline rich domains (PRD) have been found to interact with different classes of SH3 domain containing proteins. While it has been hypothesized that the SH3 domain-PRD interaction plays an important role in BAR protein mediated receptor internalization, the exact mechanism has thus far remained elusive. We mimic SH3 domain-PRD interactions in artificial lipid bilayers and investigate their effects on the characteristic membrane curvature generation properties of BAR proteins. PRDs covalently linked to the lipid bilayer are designed to recruit the BAR proteins. The associated membrane shape changes are monitored by both optical and electron microscopy techniques. I will discuss our insights into BAR protein mediated membrane remodeling in receptor internalization processes in light of our recent biophysical studies. 

Title :

Design Strategies Towards Stabilization of Organic Radical Ions and their Electroactive Partners

Abstract :

p-conjugated molecules are intriguing building blocks to realize diverse range of closed and open-shell molecular materials.¹ The major challenge facing their applications is the intrinsic reactivity of highly electron-deficient and electron-rich molecules in the neutral and radical ion forms. In this context, the naphthalenediimide (NDI) and the perylenediimide (PDI) p-scaffolds provide an intriguing platform to design new electro-active molecules.²

In this talk, we would discuss how the arylenediimide scaffolds integrated with specific design elements^3a can be utilized to synthesize and isolate new ambient stable radical ions. We have recently extended our efforts in synthetic spin chemistry towards the development of eco-friendly synthetic protocols towards radical ions.^3b Along with this, we recently isolated new planar as well as twisted ambient stable radical anions as well as the strongest electron acceptors with calculated LUMO of -5.2 eV.^4a,b Considering the other end of the electrochemical window, we have been able to isolate highly electron-rich, di-reduced NDI systems, which have an unusual doubly zwitterionic molecular structure and redox switchable aromatic-antiaromatic sites.⁵ In short, we would discuss the possibilities to expand the electrochemical window of the arylenediimides maintaining their ambient stability. We believe their excited states would be of interest for photocatalysis and other relevant opto-electronic applications.

References

1.   Morita, Y.; Suzuki, S.; Sato, K.; Takui, T.Nature Chem. 2011, 3, 197.

2.   A review on electron-poor arylenediimides: Kumar, S.; Shukla, J.; Kumar, Y.; Mukhopadhyay, P. Org. Chem. Front., 2018, 5, 2254.

3.   a) Kumar, S.; Ajayakumar, M. R.; Hundal, G.; Mukhopadhyay, P. J. Am. Chem. Soc. 2014, 136, 12004; b) Kumar, S.; Mukhopadhyay, P. Green. Chem. 2018, 20, 4620.

4.   a) Kumar, Y.; Kumar, S.; Mandal, K.; Mukhopadhyay, P. Angew. Chem. Int. Ed. 2018, 57, 16318; b) Kumar, Y.; Kumar, S.;Bansal, D.; Mukhopadhyay, P. Org. Lett. 2019,21,2185.

5.   Kumar, S.; Shukla, J.; Kumar, Y.;  Mandal, K.; Prakash, R.; Ram, P.; Mukhopadhyay, P. Chem. Sci. 2019, 10, 6482.

Title :

Optoelectronic Properties of Perovskite Materials for Photovoltaic Application

Abstract :

Recently, significant research interest has been devoted on the fundamental understanding of the underlying mechanism in solar cells and innovation of new photovoltaic materials. Aim of this research work and its impact deals with the structure-property-performance correlation of the alternative materials for photovoltaic application. The multication complex perovskites (ABO₃ and A₂B'B"O₆ type) which exhibit attractive optical properties along with the electrical properties have been explored for the low cost and efficient photovoltaic application. In this respect, lead free double perovskite oxide, La₂NiMnO₆, has shown a promising photovoltaic performance under AM1.5G solar spectrum.

Title :

Morphology Optimization and Photophysical Studies of Perovskite Solar Cell

Abstract :

There is an urgent need to shift all existing power systems such as household electricty, transportation, etc. on renewable and clean sources of  energy such as solar and wind energy etc. To harness solar energy lot of new materials have been discovered that caused the generational evolution of solar cells. Recently, organic-inorganic hybrid perovskite solar cells (PSCs), a third generation solar cell, have received significant research interest due to its high efficiency and low cost fabrication. The major research focus of PSCs is on interface modification, compositional engineering and morphology tailoring since these factors plays crucial role in efficiency modulation. We found that perovskite film morphology and photophysics are the crucial factors in fabricating highly efficient and stable solar cells. We optimized the morphology ofCH₃NH₃PbI₃  perovskites film at room temperature using dual solvent elimination method, antisolvent treatment and solvent annealing and found that these methods are very important to grain size engineering.

Title :

Time-Domain Raman Spectroscopy and Its Application to Ultrafast Photochemical/Photobiological Reactions

Abstract :

Since its discovery 90 years ago, Raman spectroscopy has been developing continuously, and it is now one of the most important spectroscopies which is extensively utilized in various fields of science and technology. In traditional Raman spectroscopy, the energetically-shifted inelastic light scattering (Raman scattering) is measured, and the energy shift from the excitation light provides information about the vibrational energy of the molecules. On the other hand, using an ultrashort optical pulse that has a duration shorter than the vibrational period of molecules, we can carry out time-domain Raman spectroscopy in which we induce coherent nuclear motion of the molecule with the impulsive stimulated Raman process and observe Raman-active vibrations directly in the time domain. In principle, the information obtainable with time-domain Raman spectroscopy is equivalent to that obtained by ordinary frequency-domain Raman spectroscopy. However, because time-domain Raman spectroscopy is performed with only femtosecond pulses, we can trace the temporal change of the molecular vibrations with a femtosecond accuracy by combining it with a femtosecond pump pulse that starts chemical reactions [1-3]. In this lecture, I talk about the recent progress of our research about femtosecond time-domain Raman spectroscopy. A newly developed apparatus using 7-fs optical pulses allowed us to investigate the ultrafast dynamics of complex molecular systems such as the chromophore isomerization in photoreceptor proteins and the chemical bond formation process in molecular assemblies [4, 5, 6]. We also showed the possibility of multi-dimensional time-domain Raman spectroscopy that reveals the anharmonicity of reactive excited-state potential energy surfaces of complex molecules [7].

References:

1.       S. Fujiyoshi, S. Takeuchi and T. Tahara, J. Phys. Chem. A, 107, 494 (2003).

2.       G. Cerullo, L. Lüer, C. Manzoni, S. De Silvestri, O. Shoshana and S. Ruhman, J. Phys. Chem. A, 107, 8339 (2003).

3.       S. Takeuchi, S. Ruhman, T. Tsuneda, M. Chiba, T. Taketsugu and T. Tahara, Science 322, 1073 (2008).

4.       T. Fujisawa, H. Kuramochi, H. Hosoi, S. Takeuchi and T. Tahara, J. Am. Chem. Soc. 138, 3942 (2016).

5.       H. Kuramochi, S. Takeuchi, K. Yonezawa, H. Kamikubo, M. Kataoka and T. Tahara, Nat. Chem. 9, 660 (2017).

6.       H. Kuramochi, S. Takeuchi, M. Iwamura, K. Nozaki, T. Tahara, J. Am. Chem. Soc. in press (2019).

7.     H. Kuramochi, S. Takeuchi and T. Tahara, Sci. Adv. 5, eaau4490 (2019).

Title :

Allele-Specific Engineering of Methyllysine Writers and Readers for Controlling Chromatin-Dependent Processes

Abstract :

One of the key players in regulating the gene pattern is the post-translational modifications (PTMs) of histone proteins. Histone modifications regulate the transcriptional potential of genes by interacting with reader/effector protein domains. Post-translational modifications on methyllysine are ubiquitous in biological systems and critical for mammalian development. Specific perturbation of such interactions has remained a challenging endeavor. We hypothesized that incorporation of an unnatural modification with the aid of an engineered writer domain and its recognition by reader domain would regulate the downstream genes (epigenetic editing) leading to modification of the epigenetic landscape. The engineered orthogonal pairs together with catalytically inactive Cas9 would specifically modulate the expression of a gene of interest, thereby providing control on transcription machinery. We employed the allele-specific strategy towards engineering the epigenetic landscape at protein-protein interface orthogonal to the human proteome. We generated a hole-modified methyltransferase (writer) that would install an aryllysine moiety on histones in-cellulo. We established the orthogonality of the engineered system, overcame the permeability issue of SAM analogues, developed an antibody and established the applicability of the system in cells. Our data confirms successful benzylation of histone proteins in mammalian cells at sites known to be regulated by SUV39h2 (writer protein) in cellulo. Further we engineered a chromodomain (reader) with a pocket to accommodate the bulky modifications. We established the biochemical integrity of the engineered interface, provided structural evidence for domain integrity, demonstrated the generality of the approach, and validated its applicability to identify transcriptional regulators. We have shown that the orthogonal reader domain on binding to the unnatural modification remains functionally intact and to regulate the epigenetic landscape similar engineering can be translated to other reader-histone proteins as well. 

Title :

Designing nano-biocatalyst with improved enzymatic activity and stability

Abstract :

In the current scenario, there is a need to develop clean, reliable, biocompatible and benign processes for the industrial manufacturing of chemicals. Notwithstanding all these advantages of enzymes, industrial application of enzymes is often hampered by a lack of long-term operational stability and difficult recovery and re-use of the enzyme. Hence, re-engineering of enzymes with high activities in the given environments is required for enzymatic catalysis in industrial biocatalytic processes. The redesign of enzyme can be achieved by chemical approaches including immobilization and chemical modification which represents a simple but effective route. In most of the conventional immobilization methods, the activity of enzymes is usually lower than its native counterpart which is mainly due to the hindered substrate accessing and/or unfavourable conformational transition of enzyme within the matrix. Hence, it is necessary to develop new method which can amplify catalytic activity along with the improvement in the enzyme properties. Recently, the construction of organic–inorganic hybrid material is a rapidly expanding field of material chemistry for its advanced designs with a specific structure and functionality. Organic–inorganic hybrid platform can be prepared simply by using metal ions as the inorganic component and the organic component at room temperature under aqueous conditions. The main advantages of using hybrid organic-inorganic matrix for enzyme immobilization are: (i). Organic-inorganic platform can help to form strong bonding with enzyme which can prevent the leaching of enzyme in reaction mixture. (ii) The presence of metallic counterpart in hybrid material can exhibit the allosteric effect on enzyme which can ultimately enhance the enzyme activity. (iii) Hybrid material can stabilize the conformational structure in various in-hospitalized conditions and chemical environment.

To enhance robustness, thermal stability, and extended the shelf-life time for industrial applications, in this research work, an organic-inorganic hybrid platform for enzyme immobilization has been developed via rapid single pot technique using biomineralization methodology. The allosteric effect (due to metal ion) and structural configuration of enzyme not only helped to enhance the enzyme activity but also improved the stability (mechanically robustness and thermally stable) due to protective shield. Further, the immobilized enzyme was characterized by powdered X-ray diffraction (XRD), Fourier transform infrared (FT-IR) and confocal scanning laser microscopy. The size and morphology were analysed by scanning electron microscopy (SEM). Also, the kinetic parameters (V_max and K_M) and thermal stability of free and immobilized enzyme were determined in terms of thermal deactivation constant (k_d), half-life(t_1/2) and deactivation energy (E_d). In addition, conformational changes occurring after immobilization were estimated by FT-IR data analysis tools. Lastly, reusability and storage stability of enzymes were studied to check its durability and industrial feasibility. This exploration of immobilization technology is anticipated to inspire further advancement in the novel design and functionality of the support matrix for a wide range of applications.

Title :

Double Similarity Transformed Coupled Cluster Theory: Non-Covalent Interactions and Excited State Energetics

Abstract :

The existing ab-initio theories often require high computational scaling to account for the ground and excited state energetics in a quantitatively correct manner. In this talk, I shall propose an inexpensive dual exponential Ansatz based recursive similarity transformed Coupled Cluster methodology, which accurately captures dynamical correlation of weakly correlated molecular systems in an affordable manner. The superior accuracy of the proposed method in describing non-covalent interactions is ensured by the inclusion of high rank correlation effects and a balanced treatment of screened Coulomb interactions. Further, starting with a correlated description of the ground state, I shall propose a Linear Response formulation to describe electronically excited states of isolated gas phase molecules. I will demonstrate how our method strikes the right balance between computational cost and accuracy. The efficacy of the formulation will be demonstrated with a number of numerical examples.

Title :

Molecular Structure and Weak Interactions Explored by Broadband Microwave Spectroscopy

Abstract :

Microwave spectroscopy allows details of structure to be measured for molecules and complexes which are isolated in the gas phase. One aim is to quantify weak interactions with high selectivity such that intrinsic character can be separated from effects of a solvent or matrix. This theme will be illustrated through recent studies of molecules containing imidazole. It will be shown that two isomers of a complex formed between this molecule and water can be isolated and spectroscopically-characterised in the gas phase. A second aim is to explore the gas phase chemistry prompted by laser vaporisation of solids in the presence of a mixture of chemical precursors, a process known to allow the generation of small molecules that can be found in interstellar and circumstellar environments. Laser vaporisation of platinum in the presence of gaseous hydrocarbons allows very efficient generation of PtC₃, an atypical and exotic platinum carbene which has structural similarities with the oxycarbon species, OC₃. Experiments are performed using a unique broadband rotational spectrometer that allows the simultaneous observation of many rotational transitions across a broad bandwidth.  

Title :

Design and characterization of Ferritin based bio-catalyst

Title :

From atoms and molecules to solids… A glimpse into my research journey so far…

Abstract :

It is a well-known fact that every material in the universe is composed of atoms, which in turn comprise nuclei and electrons. A comprehensive understanding of the interactions among such sub-atomic particles have enabled us to tailor materials for a plethora of applications that heavily govern our day-to-day living. Thanks to advances in computation and theory development, investigating these interactions systematically has been possible. Based on the type of system, different computational methods are used to achieve this. For example, at the atomic scale, quantum chemistry simulations implemented within a localized orbital (or atomic orbital) basis set are performed routinely. On the other hand, for periodic solids, density functional theory (DFT) generally implemented within a plane-wave basis set, is used. Obviously, the list of methods is not restricted to those mentioned above. My talk will attempt to cover my journey so far, where I have been exposed to both perspectives of thinking. I will be providing a glimpse of my current work on time-dependent thermally-assisted-occupation DFT (TDTAO-DFT) which is a low-cost method to study excited states. This method is based on a modified DFT scheme known as TAO-DFT, which explicitly incorporates the non-dynamical correlation effect in ground-state simulations, but retains the low computational complexity of conventional DFT. In line with the title of my presentation, which coincides with the reverse chronology of my research journey, I will present my earlier works on solid state simulations using phosphorene (a quasi–two-dimensional sheet of phosphorus atoms) as an example. Here, I will be demonstrating how the electronic properties are tuned without affecting its excellent transport properties as well mechanical and structural stability.

Title :

Distribution of Isomerized and Racemized Amyloid b Isoforms in the Sporadic Alzheimer’s Disease using Ion-Mobility Mass Spectrometry

Abstract :

Extracellular amyloid plaques and intracellular neurofibrillary tangles are the pathological hallmarks of Alzheimer’s Disease (AD). It takes on average 19 years for amyloid b (Ab) peptides to deposit as insoluble plaques from onset to clinical dementia symptoms in AD. Such long-lived proteins and peptides without degradation and clearance can undergo further post-translational modifications (PTM). Several biochemical and analytical approaches have estimated very high degree of isomerization and racemization of Asp and Ser residues in Ab purified from the insoluble plaques, along with sequential loss of the N-terminal amino acids. In this study we have characterized the most common isomerization and racemization of the Asp-1 and Asp-7 residues of the Ab peptides present in AD brain based on both their chromatographic resolution as well as their collisional cross section (CCS) using high resolution ion mobility (IM) Q-TOF mass spectrometer (Agilent 6560). Using stable isotope labeled peptides we have also quantified the amount of these isomers/racemers in the different fractionated biochemical pools of the temporal cortex grey matter of human AD and control brains. Distribution of these isomerized and racemized peptides change from lower levels in the soluble/peripheral memebraneous to higher levels in the insoluble/aggregated debris in AD brain, also indicating loss in the biochemical exchange of the pool of Ab with the progression of the disease. These findings have implications in Ab neurotoxicity, oligomerization, structures of amyloid fibrils present in the AD brain as well establishing CSF/blood-based biomarkers.