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Surface plasmon resonance facility

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Surface plasmon resonance (SPR) is a label-free, real- time technique capable of measuring binding affinities and kinetics for bio-molecular interactions. SPR has become a key bio-sensing technology in the areas of biological research and medical sciences.

Make and Model

GE Healthcare, Biacore T200

Specifications/Features

  • Can study interactions at physiologicaltemperatures. Analysis temperature range 4°C to 45°C.

  • Rapid buffer scouting application for fast assay development.

  • Integrated buffer degasser ensures data quality at elevated temperatures.

  • Designed to support large-scale research applications

Facility in-charge

Contact Email

spr[dot] bios[at] iitb[dot] ac[dot] in

Location

Department of Biosciences and Bioengineering,
I.I.T. Bombay,
Powai, Mumbai - 400076
Phone Number: 022 25764757
Contact Person: Dr. Veenita Shah

Facility Management Member(s)

(w.e.f. )

Prof. Sanjeeva Srivastava
Prof. G Subrahmanyam
Prof. Samir K. Maji
Prof. Kiran Kondabagil
Prof. N S Punekar
Prof. Sarika Mehra
Prof. Ruchi Anand
Dr. M N Gandhi

Registration Link:

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Information-External users

Information File45.12 KB

Registration form-External users

Registration form29.46 KB
Technical Specifications



 

  • Detection technology : Surface Plasmon Resonance (SPR) biosensor
  • Information provided : Kinetic and affinity data (KD , ka, and kd ), specificity, selectivity, concentration, and thermodynamic data
  • Data presentation : Result tables, result plots, and real-time monitoring of sensorgrams
  • Analysis time per cycle : Typically 2 to 15 min
  • Automation : 48 h unattended operation
  • Sample type : LMW drug candidates to high molecular weight proteins (also DNA, RNA, polysaccharides, lipids, cells, and viruses) in various sample environments (e.g., in DMSO-containing buffers,plasma, and serum)
  • Required sample Injection volume : plus 20 - 50 µl volume (application dependent)
  • Injection volume : 2 to 350 µl
  • Flow rate range : From 1 to 100 µl/min
  • Flow cell volume : 0.06 µl
  • Flow cell height : 40µm
  • Sample/reagent capacity : 1 x 96-or 384-well microplate and up to 33 reagent vials
  • Analysis temperature : 4oC to 45oC (maximum 20oC below range ambient temperature)
  • Sample storage : 4oC to 45oC (maximum 15oC below ambient temperature)
  • Sample refractive index range : 1.33 to 1.40
  • Buffer selector : Automatic switching between 4 buffers
  • In-line reference subtraction : Automatic

 

 

 


Designed to support large-scale research applications

  • Supports 96- and 384-well microplates
  • Up to 48 hours unattended operation
  • Temperature control of sample compartment
  • Analyze up to 384 samples per run


Study interactions at physiological temperatures

  • Analysis temperature range 4oC to 45oC
  • Integrated buffer degasser ensures data quality at elevated temperatures


Rapid buffer scouting for fast assay development

  • Built-in buffer selector enables up to four different buffers to be tested at one time


Sample recovery for identification by mass spectrometry

  • Predefined software templates define entire recovery process
  • Analytes recovered in a small volume, with minimal carry-over
  • Deposition in vial containing digestion solution


Software solutions for fast assay development, analysis and evaluation

  • High level of guidance for development and setup of assays
  • Dedicated software support for data evaluation

 

 

Publications:

• Rane, J. S., Kumari, A., and Panda, D. (2019). An acetylation mimicking mutation, K274Q, in tau imparts neurotoxicity by enhancing tau aggregation and inhibiting tubulin polymerization. Biochemical Journal, 476(10), 1401-1417. doi: 10.1042/BCJ20190042

• Sharma K, Mehra S, Singh Sawner A, Markam PS, Panigrahi R, Navalkar A, Chatterjee D, Kumar R, Kadu P, Patel K, Ray S, Kumar A and Maji SK (2020), Effect of disease-associated P123H and V70M mutations on β-synuclein fibrillation. ACS Chem Neuroscience, 16; 11(18):2836-2848. DOI: 10.1021/acschemneuro.0c00405.

• Harish M, Venkatraman P. Evolution of biophysical tools for quantitative protein interactions and drug discovery Emerg Top Life Sci. 2021 May 14;5(1):1-12. doi: 10.1042/ETLS20200258.PMID: 33739398

• Chatterjee1 , R.S. Jacob1 , S. Ray1 , A. Navalkar1 , N. Singh1 , S. Sengupta1,2 , L. Gadhe1 4 , P. Kadu1 , D. Datta1 , A. Paul1 , A. Sakunthala1 , S. Mehra1 , C. Pindi3 , S. Kumar4 , P. S. Singru4 5 , S. Senapati3 and S. K. Maji (2022),Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin 2 functional amyloids 3

• The paper entitled 'Mechanistic physicochemical insights into glycation and drug transport by serum albumin: Implications in diabetic conditions' is not published yet. It is recommended for revision in Biochimie

Conference:

• Nag A., Pittu Sandhya Rani and Mehra, S., “SCO4122 is a redox responsive regulator of Mar R family that regulates the efflux pump SCO4121 in Streptomyces coelicolor", ASM Microbe, June 20- June 24, 2021, Online

Facility Detailed Application

Label-free interaction analysis is of increasing importance for scientists in the fields of academic, pharmaceutical, biotechnology and diagnostic. SPR-based systems generate unique data on the interactions between proteins and other molecules, including small molecule drug candidates. During research, development and manufacture, these data give insights into protein functionality, elucidate disease mechanisms and play a key role in the critical decisions needed for efficient development and production of therapeutics. 

SPR systems are used in areas such as pharmaceutical drug discovery, antibody characterization, proteomics, immunogenicity, biotherapeutic development and manufacture, and many life science research applications. In the food analysis market, such a system and ready-to-use kits provide key manufacturers with the ability to determine quality and safety in areas such as quantification of vitamin content. Some of the major applications utilizing the valuable information derived from SPR include : 

  • Screening for binding partners and ranking of binding ability, for instance in drug discovery and biopharmaceutical development
  • Determination of simultaneous interaction capabilities, for example epitope mapping with monoclonal antibodies
  • Detection of specific molecules such as anti-drug antibodies in immunogenicity studies.
  • Determination of interactant concentration in samples, from measurements under conditions where interaction levels can be related to concentration
  • Measurement of interaction kinetics and affinity, made possible by real-time detection of interaction events

 

References : 

Aubailly, L., Drucbert, A.-S., Danzé, P.-M., Forzy, G., 2011. Comparison of surface plasmon resonance transferrin quantification with a common immunoturbidimetric method. Clinical Biochemistry 44, 731-735.

Berggard, T., Linse, S., James, P., 2007. Methods for the detection and analysis of protein-protein interactions. PROTEOMICS 7, 2833-2842.

Boozer, C., Kim, G., Cong, S., Guan, H., Londergan, T., 2006. Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies. Current Opinion in Biotechnology 17, 400-405.

Christopher, J.A., Brown, J., Doré, A.S., Errey, J.C., Koglin, M., Marshall, F.H., Myszka, D.G., Rich, R.L., Tate, C.G., Tehan, B., Warne, T., Congreve, M., 2013. Biophysical Fragment Screening of the β1-Adrenergic Receptor: Identification of High Affinity Arylpiperazine Leads Using Structure-Based Drug Design. Journal of Medicinal Chemistry 56, 3446-3455.

Hahnefeld, C., Drewianka, S., Herberg, F., 2004. Determination of Kinetic Data Using Surface Plasmon Resonance Biosensors, in: Decler, J., Reischl, U. (Eds.), Molecular Diagnosis of Infectious Diseases. Humana Press, pp. 299-320.

Homola, J., 2003. Present and future of surface plasmon resonance biosensors. Anal Bioanal Chem 377, 528-539.

Ladd, J., Lu, H., Taylor, A.D., Goodell, V., Disis, M.L., Jiang, S., 2009. Direct detection of carcinoembryonic antigen autoantibodies in clinical human serum samples using a surface plasmon resonance sensor. Colloids and Surfaces B: Biointerfaces 70, 1-6.

Pattnaik, P., 2005. Surface plasmon resonance. Appl Biochem Biotechnol 126, 79-92.

Reddy, P., Sadhu, S., Ray, S., Srivastava, S., 2012. Cancer biomarker detection by surface plasmon resonance biosensors. Clinics in laboratory medicine 32, 47-72.

Rich, R., Errey, J., Marshall, F., Myszka, D., 2011. Biacore analysis with stabilized G-protein-coupled receptors. Analytical Biochemistry 409, 267-272.

Rich, R.L., Myszka, D.G., 2000. Advances in surface plasmon resonance biosensor analysis. Current Opinion in Biotechnology 11, 54-61.

Rich, R.L., Myszka, D.G., 2007. Higher-throughput, label-free, real-time molecular interaction analysis. Analytical Biochemistry 361, 1-6.

Rich, R.L., Myszka, D.G., 2011. Survey of the 2009 commercial optical biosensor literature. Journal of Molecular Recognition 24, 892-914.

Situ, C., Mooney, M.H., Elliott, C.T., Buijs, J., 2010. Advances in surface plasmon resonance biosensor technology towards high-throughput, food-safety analysis. TrAC Trends in Analytical Chemistry 29, 1305-1315.

Suenaga, E., Mizuno, H., Penmetcha, K.K.R., 2012. Monitoring influenza hemagglutinin and glycan interactions using surface plasmon resonance. Biosensors and Bioelectronics 32, 195-201.

Vaisocherová, H., Faca, V.M., Taylor, A.D., Hanash, S., Jiang, S., 2009. Comparative study of SPR and ELISA methods based on analysis of CD166/ALCAM levels in cancer and control human sera. Biosensors and Bioelectronics 24, 2143-2148.

Yuk, J., Ha, K., 2005. Proteomic applications of surface plasmon resonance biosensors: analysis of protein arrays. Experimental and Molecular Medicine 37, 1-10.
 

 

 



Surface plasmon resonance (SPR) based instruments use an optical method to measure the changes in refractive index within about 150 nm from the sensor surface. They monitor molecular interactions in real time, using a non-invasive label-free technology that responds to changes in the concentration of molecules at a sensor surface as molecules bind to or dissociate from the surface. The essential components of a Biacore analytical system are sensor chip, optical detector and integrated microfluidic cartridge (IFC) (Figure 1). To study the interaction between two binding partners, one partner is attached to the sensor surface (ligand) and the other is passed over the surface through flow cells in sample solution (analyte). As the analyte binds to the ligand the accumulation of protein on the sensor surface causes an increase in refractive index. A sensorgram is a plot of response against time, showing the progress of the interaction (Figure 2). The SPR response is directly proportional to the change in mass concentration close to the surface.




The system can be used to study interactions involving any kind of molecule, from organic drug candidates to proteins, nucleic acids, glycoproteins and even viruses and whole cells. Since the response is a measure of the change in mass concentration, the response per molar unit of interactant is proportional to the molecular weight (smaller molecules give lower molar responses). The detection principle does not require any of the interactants to be labeled, and measurements can be performed on complex mixtures such as cell culture supernatants or cell extracts as well as purified interactants. The identity of the interactant monitored in a complex sample matrix is determined by the interaction specificity of the partner attached to the surface. The SPR detection principle is non-invasive and works equally well on clear and colored or opaque samples. The system uses a range of sensor surfaces with a controlled flow system (comprising 4 flow cells) for delivery of samples and reagents to the sensor surface. 

 

 

 

Publications using data from this facility

  • 2018:

  • V Dey, S Patankar. Molecular basis for the lack of auto-inhibition of Plasmodium falciparum importin α (2018). Biochemical and Biophysical Research Communications. 2018. 

  • GM Mohite, R Kumar, R Panigrahi, A Navalkar, N Singh, D Datta, S Mehra, S Ray, LG Gadhe, S Das, N Singh, D Chatterjee, A Kumar and SK Maji. Comparison of kinetics, toxicity, oligomers formation and membrane binding capacity of α-synuclein familial mutations at A53 site including newly discovered A53V mutation. Biochemistry, (2018), 57(35):5183-5187.

  • 2019:

  • Rane, J. S., Kumari, A., and Panda, D. (2019). An acetylation mimicking mutation, K274Q, in tau imparts neurotoxicity by enhancing tau aggregation and inhibiting tubulin polymerization. Biochemical Journal, 476(10), 1401-1417. doi: 10.1042/BCJ20190042

  • Rane, J. S., Kumari, A., and Panda, D. (2019). An acetylation mimicking mutation, K274Q, in tau imparts neurotoxicity by enhancing tau aggregation and inhibiting tubulin polymerization. Biochemical Journal, 476(10), 1401-1417. doi: 10.1042/BCJ20190042

  • 2020:

  • Sharma K, Mehra S, Singh Sawner A, Markam PS, Panigrahi R, Navalkar A, Chatterjee D, Kumar R, Kadu P, Patel K, Ray S, Kumar A and Maji SK (2020), Effect of disease-associated P123H and V70M mutations on β-synuclein fibrillation. ACS Chem Neuroscience, 16; 11(18):2836-2848. DOI: 10.1021/acschemneuro.0c00405.

  • Jigme Wangchuk, Dr. Kiran Kondabagil’s lab–Research article submitted (Acceptance awaited).

  • Sharma K, Mehra S, Singh Sawner A, Markam PS, Panigrahi R, Navalkar A, Chatterjee D, Kumar R, Kadu P, Patel K, Ray S, Kumar A and Maji SK (2020), Effect of disease-associated P123H and V70M mutations on β-synuclein fibrillation. ACS Chem Neuroscience, 16; 11(18):2836-2848. DOI: 10.1021/acschemneuro.0c00405.

  • 2021:
  • Harish M, Venkatraman P. Evolution of biophysical tools for quantitative protein interactions and drug discovery Emerg Top Life Sci. 2021 May 14;5(1):1-12. doi: 10.1042/ETLS20200258.PMID: 33739398
  • Wangchuk J, Chatterjee A, Patil S, Madugula SK, Kondabagil K. The coevolution of large and small terminases of bacteriophages is a result of purifying selection leading to phenotypic stabilization. Virology. 2021 Dec;564:13-25.
  • 2022:
  • Chatterjee1 , R.S. Jacob1 , S. Ray1 , A. Navalkar1 , N. Singh1 , S. Sengupta1,2 , L. Gadhe1 4 , P. Kadu1 , D. Datta1 , A. Paul1 , A. Sakunthala1 , S. Mehra1 , C. Pindi3 , S. Kumar4 , P. S. Singru4 5 , S. Senapati3 and S. K. Maji (2022),Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin 2 functional amyloids 3. eLife2022;11:e73835 DOI:10.7544/ELIFE.73835 
  • Kadu, P., Gadhe, L., Navalkar, A., Patel, K., Kumar, R., Sastry, M., & Maji, S. K. (2022). Charge and hydrophobicity of amyloidogenic protein/peptide templates regulate the growth and morphology of gold nanoparticles. Nanoscale, 14(40), 15021-15033.
  • Gaikwad, D. D., Bangar, N. S., Apte, M. M., Gvalani, A., & Tupe, R. S. (2022). Mineralocorticoid interaction with glycated albumin downregulates NRF–2 signaling pathway in renal cells: Insights into diabetic nephropathy. International Journal of Biological Macromolecules, 220, 837-851.
  • Bhambid, M. D., Dey, V., Walunj, S. B., & Patankar, S. (2022). Toxoplasma gondii importin α shows weak auto-inhibition. bioRxiv, 2022-10.
  • Dey, A., Mitra, D., Rachineni, K., Khatri, L. R., Paithankar, H., Vajpai, N., & Kumar, A. (2022). Mapping of Methyl Epitopes of a Peptide‐Drug with Its Receptor by 2D STDDMethyl TROSY NMR Spectroscopy. ChemBioChem, e202200489.
  • Harish M, Venkatraman P. (2021) Evolution of biophysical tools for quantitative protein interactions and drug discovery Emerg Top Life Sci, 5(1):1-12.
  • The paper entitled 'Mechanistic physicochemical insights into glycation and drug transport by serum albumin: Implications in diabetic conditions' is not published yet. Revision in Biochimie.

    2023:

  • Poudyal, M., Patel, K., Sawner, A.S., Gadhe, L., Kadu, P., Datta, D., Mukerjee, S., Ray, S., Navalkar, A., Maiti, S., Chatterjee, D., Bera, R., Gahlot, N., Padinhateeri, R. and Maji, S. K. (2023), Liquid condensate is a common state of proteins and polypeptides at the regime of high intermolecular interactions, Nature Communication under revision.
  • Panigrahi, R., Krishnan, R., Singh, J. S., Padinhateeri, R., & Kumar, A. (2023). SUMO1 hinders α‐Synuclein fibrillation by inducing structural compaction. Protein Science,e4632.

Conference:

 

  • Conference (as a speaker):- Gordon Research Seminar on Computational Aspects of Biomolecular NMR (GRS) held June 08, 2019 - June 09, 2019, at Les Diablerets, Switzerland.

  • Nag A., Pittu Sandhya Rani and Mehra, S., “SCO4122 is a redox responsive regulator of MarR family that regulates the efflux pump SCO4121 in Streptomyces coelicolor", ASM Microbe, June 20- June 24, 2021, Online

Minutes of Facility Management Committee

Surface Plasmon Resonance Trainings and Meetings

(1) Training in GE R&D center, Bangalore: 27.8.13-29.8.13

Objective: To provide the basic understanding and knowledge about the principle of surface Plasmon resonance and its applications in protein-protein interaction studies for selected students (TAs) from IIT MUMBAI sent to GE, Healthcare (Bangalore).

Types of assays demonstrated: Protein-protein interaction: Binding and Kinetics assay

Number of Participants: 8

(2) SPR - Protein-protein interaction training in IITB, Mumbai: 5.9.13-7.9.13

Objective: To provide the basic understanding and knowledge about the principle of SPR and its applications in protein-protein interaction studies for all interested IIT students and staff.

Types of assays demonstrated: Protein-protein interaction: Binding and Kinetics assay

Number of Participants: 33

(3) SPR - Protein-small molecule interaction training in IITB, Mumbai: 25.11.13-29.11.13

Objective: To promote the knowledge on SPR applications with emphasis on Protein-small molecule interaction studies.

Types of assays demonstrated: Protein-small molecule interaction: Binding and Kinetics assay

Number of Participants: 10

(4) SPR committee meeting: 15.1.14

Members Present: Prof. Sanjeeva Srivastava (Convener), Prof. G. Subrahmanyam, Prof. Samir K. Maji, Prof. Kiran Kondabagil, Prof. Sarika Mehra, Prof. Ruchi Anand, Dr. Veenita Shah (Application Scientist)

Minutes: The SPR committee members went over the initial standardization data and discussed some operational modalities of the facility. Suggestions were provided for improving the detection limit of the method for protein-small molecule interactions as well as requirements for the facility.

(5) SPR committee meeting: 11.2.14

Members Present: Prof. Sanjeeva Srivastava (Convener), Prof. N. S. Punekar, Dr. Veenita Shah (Application Scientist)

Minutes: The SPR committee members discussed the operational modalities of the facility. An update was provided to the members on the ongoing efforts for making the facility functional, and suggestions were provided for the same.

(6) SPR committee meeting: 25.2.14

Members Present: Prof. Sanjeeva Srivastava (Convener), Prof. Kiran Kondabagil, Prof. Sarika Mehra, Dr. Mayuri N. Gandhi, Dr. Veenita Shah (Application Scientist)

Minutes: The SPR committee members discussed the operational progress of the facility and results of optimization experiments. An update was provided to the committee on the recent Annual Review meeting (held on 12.2.14) as well as the experimental data obtained with improved sensitivity of detection for small molecule studies.

(7) SPR protein and small molecule training in IITB, Mumbai: 8.4.14-9.4.14

Objective: To refresh the basics of SPR and its applications, and educate students with the necessary advanced knowledge in developing assays, setting up experiments and analyzing the data for protein-protein interaction studies and protein-small molecule screening.

Types of assays demonstrated: Protein-protein binding assay and Protein-small molecule Kinetics assay

Number of Participants: 20

 

SPR-FMC-Minutes-1st July

Instructions for sample preparation/submission
  • User should submit the samples along with the registration form.
  • Experiments should be discussed with PI/TA and the facility in-charge before proceeding.
  • Purity of samples is extremely important for generating good data.
  • Protein concentrations should be measured accurately before starting the experiment.
  • The molecular weight as well as the pI of the proteins should be known before immobilization.
  • All buffers should be filtered through 0.22 μm filters and degassed.
  • Do not degas buffers containing detergent. Add detergent after degassing.
  • For organic solvent containing buffer, filter using organic solvent resistant membrane.
  • Cell extracts and nanoparticles can block integrated micro fluidic cartridges and syringes.
  • Any query regarding your SPR experiment can be emailed on spr [dot] bios [at] iitb [dot] ac [dot] in
  • Appointments will be provided as per que and the user will be informed about the same.
  • Kindly perform some literature review on this kind of work performed on either same or similar samples. Accumulate as much information as possible for better quality results.
Instructions for Registration
  • Only online sample registration through the IRCC webpage will be accepted.
  • The user will be informed first about the meeting date and time, and later about the experiment date via email.
  • If the meeting/experimental appointment is made but the user can't go, kindly send an email immediately to spr [dot] bios [at] iitb [dot] ac [dot] in to cancel the slot.
  • Please come prepared with some literature reference papers describing as much as possible for sample preparation and experimental conditions for similar kind of studies.