Title :

Structure of Hemagglutinin Fusion Peptide and Correlation of the Structure with Fusion Catalysis

Abstract :

Enveloped viruses, like influenza virus are coated with a lipid membrane, and fusion peptides present in the lipid envelope are responsible for the fusion between the viral and the host cell membrane on infection. The fusion peptide is highly conserved such that modest mutation can arrest membrane fusion. Despite the fusion peptide’s critical role in fusion, there is no clear consensus in the literature of the structure and function of the influenza fusion peptide. Research over the last 25 years on the influenza fusion peptide showed very different structures; 20-residue influenza fusion peptide adopts open boomerang structure while the 23-residue adopts a tightly packed closed helical hairpin structure in detergents.1,2 Based on the different interhelical geometries different membrane-binding mechanisms were proposed. The different functional models were based on different structures in detergents, but influenza fusion peptide induces fusion of membranes and not detergents, so the membrane structures are more relevant for function. We recently showed that both the 20- and 23-residue influenza fusion peptide adopts similar structures in membrane.3 In this talk, we will discuss about the determination of the structure of influenza fusion peptide in membranes. Later, how the structural features were correlated to the function of the influenza fusion peptide will be discussed.

References:

1. Han, X.; Bushweller, J. H.; Cafiso, D. S.; Tamm, L. K. Nat. Struct Biol. 2001, 8, 715

2. Lorieau, J. L.; Louis, J. M.; Bax, A. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 11341

3. Ghosh, U.; Xie, L.; Jia, L.; Liang, S.; Weliky, D.P. J Am. Chem. Soc. 2015, 137, 7548

Title :

Watt Webb: Shining Light on Biology

Title :

Activity and crowding, two major players in single probe dynamics

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, aberrant protein citrullination by PADs is associated with multiple autoimmune disorders, including rheumatoid arthritis (RA), multiple sclerosis (MS), ulcerative colitis (UC) and lupus, neurodegenerative diseases and certain forms of cancer. For example, a citrulline-specific probe, Biotin-PG and chemoproteomics platform enabled us to identify various classes of novel citrullinated proteins, including serine protease inhibitors (SERPINs), serine proteases, transport proteins and complement system components along with known citrullinated proteins (e.g., vimentin, enolase, keratin and fibrin) in the serum, synovial fluid and synovial tissue of RA patients. Although the list of citrullinated proteins is ever expanding, the effect of citrullination on the structure and activity of a given protein remains poorly understood mainly due to the lack of a method for site-specific incorporation of citrulline into proteins. We developed a novel technology that enables the site-specific incorporation of citrulline (Cit) into proteins in mammalian cells. This approach exploits an engineered E. coli-derived leucyl tRNA synthetase-tRNA pair that incorporates a photocaged-citrulline (SM60) into proteins in response to a nonsense codon. Subsequently, SM60 is readily converted to Cit with light in vitro and in living cells. To demonstrate the utility of the method, we biochemically characterized the effect of incorporating Cit at two known autocitrullination sites in Protein Arginine Deiminase 4 (PAD4, R372 and R374) and showed that the R372Cit and R374Cit mutants are 181- and 9-fold less active than the wild-type enzyme.

Additionally, I’ll discuss my future plans for research on the covalent modification and degradation 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. Wang, Y. Zheng, S. Sen, A. Chatterjee, P. R. Thompson, Nat. Commun.

2020, Manuscript Accepted.

(Preprint: bioRxiv, https://doi.org/10.1101/2020.06.06.137885)

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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, their metabolites and halogenated nucleosides as well as 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 deiodination 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. We developed nahthyl-based organo-sulphur and/or selenium compounds as functional mimics of DIO3, and showed that deiodination of thyroid hormones and various metabolites by these compounds relies on the synergistic actions of halogen and chalcogen bonding interactions. These nahthyl-based organochalcogen compounds were also used to dehalogenate the halogenated nucleosides that can be incorporated into DNA during DNA replication and cause potential DNA damages in the presence of UV irradiation. Additionally, we discovered that commercial T4, a generic drug prescribed for hypothyroidism, exists in at least two different stable crystalline modifications with different three-dimensional structure, conformation, physical properties and solubility.

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 several PAD inhibitors are known in the literature. To reduce the off-target toxicity, we developed an azobenzene-substituted PAD2 inhibitor that undergoes trans-cis photoisomerism and can be activated at the target cell/tissue with light. Notably, the cis-isomer of this inhibitor is 10-fold more active than its trans-isomer. Furthermore, 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. Detailed studies indicate that the potency and isozyme-selectivity of this inhibitor is due to the formation of a halogen bond between the inhibitor and PAD1 active site. This inhibitor exhibited excellent efficacy for the inhibition of histone H3 citrullination 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, D. Manna, G. Mugesh, Angew. Chem. Int. Ed. 2015, 54, 9298.

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

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

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.

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

ZOOM DETAILS:

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Meeting ID: 490 622 3773
Passcode: 04072020

Join by SIP
This email address is being protected from spambots. You need JavaScript enabled to view it.

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 nature of scientific publishing

Abstract :

The scientific publishing process can often seem like a black box, filled with mystery and misapprehension. In this talk, Bryden Le Bailly, a Senior Editor at Nature, will discuss the publishing process at Nature journals, how best to navigate its pitfalls, and share the answers to some of the most frequently held misconceptions.

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 :

Probing the conformational differences of membrane attached proteins at a single molecule level

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 :

Manipulating Light with Molecular Excitons

Abstract :

There are many applications that demand that the properties of light be controlled by molecular excitons. This includes upconversion applications, where shorter wavelengths are generated from longer wavelengths, and multiple exciton generation and photon multiplication, where a high energy photon is split into smaller energy packets.

Over the past decade, we have applied triplet-triplet annihilation upconversion to photovoltaics. Recently, we achieved photochemical upconversion from beyond the silicon bandgap for the first time.

Singlet fission is a process where a photon-generated singlet state splits into two spin-correlated triplets. In solar cells it is hoped that this will give rise to two excitons per absorbed photon above a certain energy, increasing the efficiency limit to nearly 46%. Here I will discuss the role of the excimer state in singlet fission.

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 :

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).