Faculty Details - Lady Brabourne College

Personal Profile

Name	Dr. Soma Samaddar
Designation	Associate Professor
Department	Chemistry
Email Id	somas2k@yahoo.com
Year of Joining present service	2006
Date of Joining WBES	17-02-2006

Educational Qualifications

Passout Year	Examination	Passout From	Division
2009	Ph.D.	Jadavpur University	NA
1999	CSIR-NET	NA	NA
1999	Master of Science (M.Sc.)	Jadavpur University	First
1997	Bachelor of Science (B.Sc.)	Jadavpur University	First class Second
1994	Higher Secondary (H.S.)	Krishnagar Government Girls High School	WB Rank 34
1992	Secondary	Holy Family Girls High School Krishnagar	First

College Served

College Name	Served From	Served Till
Lady Brabourne College	Feb, 2006	Aug, 2021

Teaching Experience

UG Experience	PG Experience
19 Years 2 Months	8 Years 10 Months

UG or PG	College Name	From Date	To Date	Duration
PG	Lady Brabourne College	Jul, 2016	May, 2025	8 Years 10 Month
UG	Lady Brabourne College	Feb, 2006	May, 2025	19 Years 3 Month

Area of Research and Interest

Details
Physical Chemistry
Biophysics: Structure function studies of Aminoacyl tRNA synthetases. Substrate Binding, Hydration and Denaturation of Aminoacyl- tRNA Synthetase Protein denaturation profile studies using spectrophotometry. • Osmolyte effect on denaturation of proteins: Folding of polypeptide chain into a precise three dimensional structure has been a subject of intense study over past several decades. Much attention is now devoted to protein folding in vivo, where the cellular environment profoundly influences folding. Presence of osmolytes is one of the key differences in vitro and in vivo environments. Osmolytes are small molecules that accumulate inside the cell at relatively high concentrations and protect the intracellular proteins against environmental stress. Thus they play a crucial role in the protein stabilization. This study reports the effect of osmolytes on partially denatured states of proteins. Many different types of osmolytes have been used for our study e.g. glycine-betaine, L-glutamate, D-sorbitol, glycerol, Trimethyl amine oxide, Triethylene glycol. In this chapter detailed study has been done using Glutaminyl-tRNA synthetase as a model system. Among all the osmolytes L-glutamate effects are large on GlnRS. Also glycine-betaine has strong counteraction ability against urea. The effect of osmolytes on three other different proteins Carbonic Anhydrase, SN228 -repressor and Tubulin were studied. All these study showed that osmolyte effect on protein is osmolyte-protein pair specific. It has been shown by NMR studies that urea binds to protein and the binding stoichiometry reduces dramatically in presence of osmolyte. To study the binding interaction between protein and osmolyte, diffusion constants of osmolytes are measured in presence of different concentrations of proteins. The osmolyte binding to protein is small or near zero. It is found that osmolytes do not bind to proteins. However, it has been pointed out that the effect of an osmolyte may vary from protein to protein. So it is concluded that although the osmophobic force is likely to be of great importance, specific effects of different osmolytes may exist. •Characterization of a urea induced Premolten globule state of Glutanimyl-tRNA synthetase from E.coli The urea induced equilibrium unfolding behavior of Glutaminyl-tRNA synthetase (GlnRS) in 0.25 M potassium L-glutamate, a naturally occurring osmolyte in E.coli, is characterized by at least three distinct transitions. The first major transition is characterized by dramatic decrease in fluorescence intensity and significant increase in ANS binding. This transition leads to formation of the previously reported molten globule state. Large emission maximum shift of tryptophan fluorescence spectra and decline of ANS binding without significant loss of secondary structure characterizes the second transition to another compact denatured state. This compact denatured state has all the characteristics of a pre-molten globule state. The final transition at highest urea concentration to the fully unfolded state is accompanied by almost total loss of far UV CD signal and ANS binding, as also reported before. The nature of the compact denatured states and the fully unfolded state has been studied using solvation dynamics and time-resolved anisotropy decay using a covalently attached probe, acrylodan. Both measurements suggest that the pre-molten globule intermediate is more flexible than the molten globule although the secondary structure is largely similar. Dynamic light scattering studies reveal that this state is even more aggregation-prone than the molten globule state. We hypothesize that flexibility is an important criterion for the aggregation process. • Contribution of Electrostatics in RNA-Protein binding Proteins interact with nucleic acids to control gene regulation and expression. In order to understand these control processes in atomic detail, the structural and energetic basis for the specificity and stability of binding must be elucidated. Various protein-DNA complexes were studied in detail previously. Protein-tRNA interactions are also very specific but have not been studied computationally. This chapter reports detailed study of electrostatic interactions between tRNAgln and GlnRS. At physiological pH, tRNA has regular (-) ve charges along their chains, which would produce electric field around them. Salt effect on tRNA binding to Aminoacyl tRNA synthetase has been computationally studied extensively with Poission Boltzmann equation. Values of various components of free energy term contributing to the total salt dependent electrostatic free energy are calculated e.g., coulombic energy, reaction field energy, ionic contribution, osmotic pressure term and rho-phi term. Finally total electrostatic energy is calculated at different salt concentrations. The log-log plot of association constants versus KCl concentration shows monotonic decrease in affinity with increasing KCl concentration. The slope of the straight line corresponds to a cation release stoichiometry of 1.7 for this complex. It is found here that tRNA has weaker electric field around it and the decrease in the association constant with increasing monovalent ion concentration is relatively small for cognate tRNA binding when compared to known DNA-protein interactions. Amount of ion-release is low. The electroneutral nature of tRNA binding domain may be responsible for this low ion release stoichiometry. • Heavy metal (mercury) contamination of Biotic component: A gradual case study. • Biomedical waste management-an infrastructural study in Kolkata based hospitals .

Details

Physical Chemistry

Biophysics: Structure function studies of Aminoacyl tRNA synthetases. Substrate Binding, Hydration and Denaturation of Aminoacyl- tRNA Synthetase Protein denaturation profile studies using spectrophotometry. • Osmolyte effect on denaturation of proteins: Folding of polypeptide chain into a precise three dimensional structure has been a subject of intense study over past several decades. Much attention is now devoted to protein folding in vivo, where the cellular environment profoundly influences folding. Presence of osmolytes is one of the key differences in vitro and in vivo environments. Osmolytes are small molecules that accumulate inside the cell at relatively high concentrations and protect the intracellular proteins against environmental stress. Thus they play a crucial role in the protein stabilization. This study reports the effect of osmolytes on partially denatured states of proteins. Many different types of osmolytes have been used for our study e.g. glycine-betaine, L-glutamate, D-sorbitol, glycerol, Trimethyl amine oxide, Triethylene glycol. In this chapter detailed study has been done using Glutaminyl-tRNA synthetase as a model system. Among all the osmolytes L-glutamate effects are large on GlnRS. Also glycine-betaine has strong counteraction ability against urea. The effect of osmolytes on three other different proteins Carbonic Anhydrase, SN228 -repressor and Tubulin were studied. All these study showed that osmolyte effect on protein is osmolyte-protein pair specific. It has been shown by NMR studies that urea binds to protein and the binding stoichiometry reduces dramatically in presence of osmolyte. To study the binding interaction between protein and osmolyte, diffusion constants of osmolytes are measured in presence of different concentrations of proteins. The osmolyte binding to protein is small or near zero. It is found that osmolytes do not bind to proteins. However, it has been pointed out that the effect of an osmolyte may vary from protein to protein. So it is concluded that although the osmophobic force is likely to be of great importance, specific effects of different osmolytes may exist. •Characterization of a urea induced Premolten globule state of Glutanimyl-tRNA synthetase from E.coli The urea induced equilibrium unfolding behavior of Glutaminyl-tRNA synthetase (GlnRS) in 0.25 M potassium L-glutamate, a naturally occurring osmolyte in E.coli, is characterized by at least three distinct transitions. The first major transition is characterized by dramatic decrease in fluorescence intensity and significant increase in ANS binding. This transition leads to formation of the previously reported molten globule state. Large emission maximum shift of tryptophan fluorescence spectra and decline of ANS binding without significant loss of secondary structure characterizes the second transition to another compact denatured state. This compact denatured state has all the characteristics of a pre-molten globule state. The final transition at highest urea concentration to the fully unfolded state is accompanied by almost total loss of far UV CD signal and ANS binding, as also reported before. The nature of the compact denatured states and the fully unfolded state has been studied using solvation dynamics and time-resolved anisotropy decay using a covalently attached probe, acrylodan. Both measurements suggest that the pre-molten globule intermediate is more flexible than the molten globule although the secondary structure is largely similar. Dynamic light scattering studies reveal that this state is even more aggregation-prone than the molten globule state. We hypothesize that flexibility is an important criterion for the aggregation process. • Contribution of Electrostatics in RNA-Protein binding Proteins interact with nucleic acids to control gene regulation and expression. In order to understand these control processes in atomic detail, the structural and energetic basis for the specificity and stability of binding must be elucidated. Various protein-DNA complexes were studied in detail previously. Protein-tRNA interactions are also very specific but have not been studied computationally. This chapter reports detailed study of electrostatic interactions between tRNAgln and GlnRS. At physiological pH, tRNA has regular (-) ve charges along their chains, which would produce electric field around them. Salt effect on tRNA binding to Aminoacyl tRNA synthetase has been computationally studied extensively with Poission Boltzmann equation. Values of various components of free energy term contributing to the total salt dependent electrostatic free energy are calculated e.g., coulombic energy, reaction field energy, ionic contribution, osmotic pressure term and rho-phi term. Finally total electrostatic energy is calculated at different salt concentrations. The log-log plot of association constants versus KCl concentration shows monotonic decrease in affinity with increasing KCl concentration. The slope of the straight line corresponds to a cation release stoichiometry of 1.7 for this complex. It is found here that tRNA has weaker electric field around it and the decrease in the association constant with increasing monovalent ion concentration is relatively small for cognate tRNA binding when compared to known DNA-protein interactions. Amount of ion-release is low. The electroneutral nature of tRNA binding domain may be responsible for this low ion release stoichiometry. • Heavy metal (mercury) contamination of Biotic component: A gradual case study. • Biomedical waste management-an infrastructural study in Kolkata based hospitals .

Project details

Sl No.	Project Name	Year From	Year To	Funding Agency	Sanction No	Amount Sanction	Type
1	Heavy metal (mercury) contamination of Biotic component: A gradual case study.	10-10-2017	09-09-2019	UGC	UGC No. F. PSW-085/15-16(ERO)	330000	Minor
2	Biomedical waste management-an infrastructural study in Kolkata based hospitals	03-08-2011	02-08-2013	UGC	UGC No. F. PSW-039/11-12	158000	Minor

Publication: Research Papers in Journals

Sl No.	Year/Month	Title	Name of Journal	Volume / Page No.
1	May, 2020	Heavy Metal Contamination in Biotic Component: A gradual case study in West Bengal	International Journal of Chemical and Environmental Sciences( IJCAES)	Vol 1 Issue 3, 2020
2	Jul, 2017	Fluorescence Spectroscopy: A Powerful Tool for Biological Systems	International Journal of Engineering Technology, Management and Applied Sciences-IJETMAS	July 2017, Volume 5, Issue 7,
3	Mar, 2017	Biomedical Waste Management: An Infrastructural case study of Kolkata based Hospitals	International Journal of Engineering Technology, Management and Applied Sciences-IJETMAS	March 2017, Volume 5 Issue 3,
4	Mar, 2017	Biomedical Waste Management: An Emergent Issue in Eastern India	International Journal of Research in Pharmacy and Chemistry	IJRPC 2017, 7(4), 482-500
5	Mar, 2016	Osmolyte Effect on Denaturation of Proteins	International Journal of Current Microbiology and Applied Sciences	ISSN: 2319-7706 Volume 5 Number 6 (2016) pp. 790-797
6	Oct, 2015	Contribution of Electrostatics in RNA-Protein binding	International Journal of Engineering Technology, Management and Applied Sciences	October 2015, Volume 3, Issue 10
7	Mar, 2015	The difficult journey of women in the field of science	Newsletter ,Women’s Study Centre, Lady Brabourne College	Volume 6 March 2015 Pg: 90-95
8	Mar, 2012	Automobile Emission: An overview:	Science Journal Lady Brabourne College	Vol – 3, pp.08,(2012)
9	Aug, 2006	Solvation Dynamics of a Protein in the Pre Molten Globule State	J. Phys. Chem. B	2006, 110, 21210-21215
10	Sep, 2003	Glutamate counteracts the Denaturing Effect of Urea through Its Effect on the Denatured State	The Journal of Biological Chemistry@2003 by The American Society for Biochemistry and Molecular Biology	Vol 278 No 38 Issue of September 19 PP36077-36084 printed in USA
11	Aug, 2003	Solvation change and ion release during aminoacylation by aminoacyl-tRNA synthetases	Nucleic Acids Research, 2003	Vol. 31, No. 20 6035±6042 DOI: 10.1093/nar/gkg779
12	May, 2002	Effect of Phosphorylation on the structure and fold of Transactivation Domain of p53	The journal of Biological Chemistry@2002 by the American Society for Biochemistry and Molecular Biology	Vol 277 No 18 Issue of May 3, PP 15579-15585,2002

Publication: Books

Sl No.	Year/Month	Book Title	Editor/Author	ISBN No.
1	Dec, 2009	Ghaspharinger Danay Jal, A collection of Bengali Poems	Published by: Kamalini Prakashani Marketed by Deys Publishers	978-81-295-1001-3
2	Jan, 2013	Parking Lot-e Tarara Eka	Published by Signet Press( Ananda Bazar Publishers)	978-93-5040-242-9
3	Jan, 2020	Saljhuriar Britantto- A novel by Soma Samaddar	Saptarshi Prakashan	978-93-8983-9128

Publication: Popular Articles

Sl No.	Articles Details
1	Sakkhi Patanga, Rabibasariyo Prabandha , 5th June 2011 Publishers: Anandabazar Patrika
2	Canvase- Short Story won 3rd position in Banglalive Galpo Pratijogita ,2010 Publisher: Banglalive

Talk/Lectures

Sl No.	Date	Title	Organised By
1	11-01-2016	Extension of Basic Chemical Techniques to the field of Biological Sciences	DBT Sponsored workshop by Department of Chemistry Lady Brabourne College
2	11-01-2016	Career Options in Biology for Chemistry Graduates	Department of Chemistry, Lady Brabourne College
3	12-12-2013	Building Strong Academic Chemistry: Developing undergraduate Research and Inquiry and extending the knowledge of basic chemical techniques to the fields of biological Sciences	DBT Sponsored workshop by Department of Chemistry Lady Brabourne College

Scholarship/Award/Felicitations

Sl No.	Year/Month	Details of Awards
1	Sep, 2010	Awarded 3rd prize for short story published in Banglalive Golpo Protijogita 2010
2	Jan, 2000	Junior Research Fellowship and Senior research Fellowship awarded by Bose Institute Calcutta year 2000
3	Dec, 1999	National Scholarship was conferred by Jadavpur University for securing First class Second position in B.SC, Chemistry
4	Dec, 1999	Junior Research Fellowship and Eligibility for Lecturership (NET Fellowship) awarded by Council of Scientific and Industrial Research( CSIR)
5	Jun, 1999	Junior Research Fellowship awarded by Saha Institute of Nuclear Physics in the year of 1999
6	Jul, 1997	National Scholarship and rank certificate for Rank 34 in the Year of 1994-95 Higher Secondary Examination awarded by West Bengal Council of Higher Secondary Education
7	Nov, 1997	Shailabala Biswas Memorial Scholarship awarded by Executive Council, Jadavpur University for results in B.Sc Chemistry (1997)for two consecutive years( 1997-99) .
8	Nov, 1992	Certificate of Merit under National Scholarship Scheme awarded by Director of Public Instruction, West Bengal for result in Madhyamik Examination of year 1992

Any other Information

Other Information

	Philosophy of Dodaden: Self sustaining model of animal care management. There will be several verticals of DODADENS working towards the betterment of lives of Indian dogs. The dogs on the Indian streets who are suffering from malnutrition, victims of extreme abuse and cruelty, accident and left to die on streets, dogs that once lived in a house as a pet but abandoned by the owners and has been thrown on the road for age, illness or high maintenance, dogs who are abandoned by unregistered breeders when they fail to reproduce and just left to die after will have a happy and fulfilling place to stay at Dodaden. They are getting full veterinary care. Now I do vaccinations like anti-rabies, DHPPIL, give medicines for skin diseases, treat them periodically by paravets but mainly on the roads. From time to time we have to send them to NGO s for sterilization to control their population. Till date we are managing it from our own funds. We have just acquired a land for our shelter for these poor voiceless souls. Regularly we feed around sixty furry babies. We have built up a strong network of dedicated volunteers. As caregivers we rescue, treat, take care of animals and take care of adoptions.
Future plan: Residential Administrator will take care of the full unit. Social Media Manager will use social platform to generate awareness about animal care management so that like-minded people from India and world can connect to form a network and an organization. Legal Department will see formal adoptions and handle cruelty to animal cases. We need Trainer for aggressive dogs, Veterinary Doctors, cooks and cleaners and housekeeping staffs. In that sense in PROJECT DODADEN we will generate jobs.
	Creating of following aggregator database and canine database I need detailed knowledge for creating a database which will network all the caregivers, rescuers, feeders of country who are working locally on their individual capacities. Joining them through database and social media platforms will ultimately help these native dogs to get better life.This is my dream project and I have already started working on this since last year. Because I don’t get the drive for just running my sanctuary on the mercy of borrowed funds. I see Dodaden as the leading sanctuary of dogs in India and abroad working towards betterment of these voiceless animals.

Dr. Soma Samaddar