People

Let's Channel our free energies together!

Personnel: Lab Members

Principal Investigator

Personnel: CV

Tapan Kumar Nayak, PhD

Kusuma School of Biological Sciences,

Contact: +11-26597973

IIT Delhi, Hauz Khas,

Email: tapannayak@iitd.ac.in

New Delhi, 110016, India.

EDUCATION

Indian Institute of Science, Bangalore, India

Ph.D. Molecular Biophysics 2010

Thesis: Biophysical studies on the plastic and cooperative properties of single voltage-gated Na+ and leak K+ ion channels.

Adviser: Sujit K. Sikdar, PhD

Jawaharlal Nehru University, New Delhi, India

M.Sc. Life Sciences 2004

Thesis: Prediction of transcription factor binding sites on rRNA gene of E. histolytica.

Adviser: Alok Bhattacharya, PhD

Berhampur University, Odisha, India

B.Sc. Botany (Hons.), Zoology, Chemistry 2002

RESEARCH EXPERIENCE

Research Assistant Professor, SUNY at UB, New York, US 2016-2018

Department of Physiology and Biophysics

Adviser: Anthony Auerbach, PhD

Studied the mechanism of ligand binding and allosteric activation of acetylcholine receptors (AChRs) using single channel patch-clamp and computational modeling.
Explored the structural basis of Nicotine binding to AChRs and its role in addiction and cardiovascular diseases.
Initiated collaboration with Dr. Kinga Szigeti, MD to explore the role of neuronal a7 AChRs in Alzheimer’s and Schizophrenia.

This work resulted in 2, 1st-authored publications (Nature Communications and PNAS) and 1 NIH ROI grant as co-investigator.

Postdoctoral Research Associate, SUNY at UB, New York, US 2010- 2015

Department of Physiology and Biophysics

Advisor: Anthony Auerbach, PhD

Examined the role of fetal neuromuscular AChRs in developmental disorders, such as Escobar and multiple pterygium syndromes.
Developed high-throughput assays to study agonist binding to ligand-gated ion channels from only 1-concentration measurements.
Studied the structure-function of the hydrophobic ‘gate’ that regulates ion conduction in AChRs.

This work resulted in 3, 1st-authored publications (including 2 PNAS), a postdoctoral grant application (AHA, 18%) and 1 NIH RO1 lab grant.

Graduate student, Indian Institute of Science, Bangalore, India 2004-2010

Molecular Biophysics Unit

Advisor: Sujit K. Sikdar, PhD

Demonstrated in voltage-gated Na+ and leak-K+ channels an activity-dependent molecular ‘memory’ that might have neuroprotective role.
Elucidated the mechanism of local anaesthetic lidocaine action on human TREK1.
Collaborated with K. Somasundaram, PhD and S. Raha, PhD to study the modulation of hTREK1 channels by kinases and small molecules.

This work resulted in 3, 1st-authored publications (including 1 Mol. Pharma.) and was funded by Research Fellowship, CSIR, India.

RESEARCH GRANTS AND FELLOWSHIPS

Contributions to Funded research in Auerbach lab

Engineering of Acetylcholine Receptor Function (NS064969) 2016-present

National Institute of Neurological Disorders and Stroke (NINDS), NIH, USA.

Amount: $453,000

Principal Investigator: Anthony Auerbach, PhD

Role: Co-Investigator. My structure-function work on the difference between fetal and adult AChR binding sites and engineering of agonist affinity by altering the ‘outer zone’ residues, formed the bases of this grant. I provided the preliminary data, helped formulate the aims and wrote the research strategy.

Contributions to Past Funded research

Acetylcholine receptor: Binding and gating (R37-NS23513) 2010-2016

National Institute of Neurological Disorders and Stroke (NINDS), NIH, USA.

Amount: $ 469,000

Principal Investigator: Anthony Auerbach, PhD

Role: Co-Author. My research on the unliganded gating of AChRs, ‘interactome’ network at the ‘gate’ in the pore and meticulous measurements of free-energy changes at the agonist binding site to elucidate agonist binding mechanism, provided strong preliminary data for the grant. I also helped fine tune the aims by regular discussions.

Fellowship for Graduate Research

Research Fellowship, Council of Scientific and Industrial Research, India 2004-2009

Amount: $ 15,100 (INR 755,000)

Role: Investigated the biophysical properties of single voltage-gated Na+ and leak-K+ channels by electrophysiological methods. I wrote manuscripts, presented data at conferences and contributed to PI grant applications.

PUBLICATIONS

Tapan K Nayak, Shandilya J, Viz R, Bruhova I, Auerbach A (2018). Efficiency measures the conversion of agonist binding energy into receptor conformational change. J. Gen. Physiol. In Press.
Tapan K Nayak, Auerbach A. (2017). Cyclic activation of endplate acetylcholine receptors. Proc. Natl. Acad. Sci. U.S.A., 114(45):11914-11919.
Tapan K Nayak, Chakrabarty S, Zheng W, Auerbach A. (2016). Structural correlates of affinity in fetal versus adult endplate nicotinic receptors. Nature Communications 7:11352; DOI: 10.1038/ncomms11352.
*Shandilya J, *Gao Y, Tapan K Nayak, Roberts S, Medler K. (2016). AP1 transcription factors are required to maintain the peripheral taste system. Cell Death and Disease. 7(10):e2433. DOI: 10.1038/cddis.2016.343.
Tapan K Nayak, Bruhova I, Chakrabarty S, Gupta S, Zheng W, Auerbach A (2014). Functional differences between neurotransmitter binding sites of muscle acetylcholine receptors. Proc. Natl. Acad. Sci. U.S.A., 111(49): 17660-05.
Iacobucci G, Rahman NA, Valtuena AA, Tapan K Nayak, Gunawardena S (2014). Spatial and temporal characteristics of normal and perturbed axonal transport in vivo. PLos One, 9(5):e97237.
Tapan K Nayak, Auerbach A (2013). Asymmetric transmitter binding sites of fetal muscle acetylcholine receptors shape their synaptic response. Proc. Natl. Acad. Sci. U.S.A., 110(33): 13654-59.
Tapan K Nayak, Purohit PG, Auerbach A (2012). The intrinsic energy of the gating isomerization of a neuromuscular acetylcholine receptor channel. J. Gen. Physiol., 139(5):349-58.
Tapan K Nayak, Dana S, Raha S, Sikdar SK (2011). Activator-induced dynamic disorder and molecular memory in human two-pore domain hTREK1 K+ channel. J. Chem. Biol. 4(2):69-84.
Tapan K Nayak, Harinath S, Nama S, Somasundaram K, Sikdar SK (2009). Inhibition of human two-pore domain K+ channel TREK1 by local anesthetic lidocaine: negative cooperativity and half-of-sites saturation kinetics. Molecular Pharmacology. 76(4): 903-17
Tapan K Nayak, Sikdar SK (2007). Time-dependent molecular memory in single voltage-gated sodium channel. J. Memb. Biol. 219(1-3): 19-36.

PUBLISHED ABSTRACTS IN CONFERENCE PROCEEDINGS AND POSTERS

1.Tapan K Nayak, Auerbach A (2016) Interactome network maps of the acetylcholine receptor ‘gate’ region. Biophys J. 110(3):604a; Biophysical Society

2.Tapan K Nayak, Auerbach A (2016) Fundamental constants for activation of human endplate receptors. Biophys J. 110(3):604a; Biophysical Society

3.Tapan K Nayak, Auerbach A (2015) Differences in agonist energy at the neurotransmitter Binding Sites in the neuromuscular acetylcholine receptors. Biophys J. 108(2):429a; Biophysical Society

4.Chakraborty S, Tapan K Nayak, Bruhova I, Zheng W, Auerbach A (2015) Molecular simulations of muscle AChR agonist binding sites. Biophys J. 108(2):429a; Biophysical Society

5.Tapan K Nayak, Auerbach A (2013). Intrinsic gating energies of fetal-type neuromuscular acetylcholine receptor. Biophys J. 104(2):634a; Biophysical Society.

6.Tapan K Nayak, Purohit PG, Auerbach A (2012). New Estimates for the ‘Allosteric’ constant of neuromuscular acetylcholine receptor-channels. Biophys J. 102(3): 119a; Biophysical Society.

7.Tapan K Nayak, Auerbach A (2011). Energy changes at the acetylcholine gate region. Biophys J. 100(3): 276a-276a; Biophysical Society.

8.Tapan K Nayak, Sikdar SK (2009). Ligand concentration dependent molecular memory in human TREK1 channel. J. Physiol Sci. 59 (S1):259; International Union of Physiological Sciences (IUPS).

POSTERS PRESENTED IN CONFERENCES

1.Tapan K Nayak, Sikdar SK (2008). Activity dependent plasticity in voltage-gated Na+ channels. CMC cardiology winter symposium, CMC, Vellore, India.

HONORS AND AWARDS

AHA Postdoctoral fellowship, American Heart Association, 18 % score. 2014
Young investigator award, International Union of Physiological Sciences. 2009
Research scholar travel grant for international symposium, CSIR-UGC, India. 2009
Best poster award, CMC Cardiology winter symposium, Vellore, India. 2008
Senior Research Fellowship, CSIR-UGC, India. 2007-2009
Junior research fellowship, CSIR-UGC, (top 5 %) India. 2004-2007
Graduate Aptitude Test (GATE), Life Sciences, 98.47 % score (75 rank)
University 1st rank, Botany (Honors), B.Sc., Berhampur University, India. 2002

REVIEWER ACTIVITY

Reviewer for British Journal of Pharmacology. 2016-present
Reviewer for Journal of Physiology. 2014-2015
Reviewer for Journal of Neuroscience. 2013-2016

PROFESSIONAL MEMBERSHIP

Biophysical Society 2010-Present
Society for Neuroscience 2017-Present
International union of Physiological Society 2009-2010

MENTORING EXPERIENCE

Graduate student

Riddhima Vij, Physiology and Biophysics, SUNY at Buffalo. 2015

Currently: Postdoc, Indiana University, Indianapolis, Indiana

Undergraduate students

Asutosh Vihani, Physiology and Biophysics, SUNY at Buffalo. 2013-2014

Currently: PhD, Duke University, Durham, NC

Alexandra Opiel, Physiology and Biophysics, SUNY at Buffalo. 2013

Currently: Works at University at Buffalo, NY

Shravan Sharma, Biotechnology, IIT Kanpur, India. 2008

Currently: Blackstone group, Hong Kong

TEACHING EXPERIENCE

Adjunct faculty, Biomedical Engineering, SUNY at Buffalo, NY, USA 2012-2013

Course: Transport processes in biomedical engineering.

Designed syllabus, conducted course and performed regular assessment for a class of 35 senior undergraduate students. The course involved 32 hrs of lectures to elucidate the transport processes in cells mediated by ion channels, transporters and cargo proteins.
Provided individual counselling, support, held recitations for students and supervised a Teaching Assistant.

Guest Lecture, National Institute of Advanced Studies, IISc, Bangalore, India 2008

Lecture: Deciphering action potential waveform through Hodgkin-Huxley formalism.

People

Principal Investigator

Tapan Kumar Nayak, PhD

Kusuma School of Biological Sciences,

Contact: +11-26597973

IIT Delhi, Hauz Khas,

Email: tapannayak@iitd.ac.in

New Delhi, 110016, India.

EDUCATION

Indian Institute of Science, Bangalore, India

Ph.D. Molecular Biophysics 2010

Thesis: Biophysical studies on the plastic and cooperative properties of single voltage-gated Na+ and leak K+ ion channels.

Adviser: Sujit K. Sikdar, PhD

Jawaharlal Nehru University, New Delhi, India

M.Sc. Life Sciences 2004

Thesis: Prediction of transcription factor binding sites on rRNA gene of E. histolytica.

Adviser: Alok Bhattacharya, PhD

Berhampur University, Odisha, India

B.Sc. Botany (Hons.), Zoology, Chemistry 2002

RESEARCH EXPERIENCE

Research Assistant Professor, SUNY at UB, New York, US 2016-2018

Department of Physiology and Biophysics

Adviser: Anthony Auerbach, PhD

Studied the mechanism of ligand binding and allosteric activation of acetylcholine receptors (AChRs) using single channel patch-clamp and computational modeling.

Explored the structural basis of Nicotine binding to AChRs and its role in addiction and cardiovascular diseases.

Initiated collaboration with Dr. Kinga Szigeti, MD to explore the role of neuronal a7 AChRs in Alzheimer’s and Schizophrenia.

This work resulted in 2, 1st-authored publications (Nature Communications and PNAS) and 1 NIH ROI grant as co-investigator.

Postdoctoral Research Associate, SUNY at UB, New York, US 2010- 2015

Department of Physiology and Biophysics

Advisor: Anthony Auerbach, PhD

Examined the role of fetal neuromuscular AChRs in developmental disorders, such as Escobar and multiple pterygium syndromes.

Developed high-throughput assays to study agonist binding to ligand-gated ion channels from only 1-concentration measurements.

Studied the structure-function of the hydrophobic ‘gate’ that regulates ion conduction in AChRs.

This work resulted in 3, 1st-authored publications (including 2 PNAS), a postdoctoral grant application (AHA, 18%) and 1 NIH RO1 lab grant.

Graduate student, Indian Institute of Science, Bangalore, India 2004-2010

Molecular Biophysics Unit

Advisor: Sujit K. Sikdar, PhD

Demonstrated in voltage-gated Na+ and leak-K+ channels an activity-dependent molecular ‘memory’ that might have neuroprotective role.

Elucidated the mechanism of local anaesthetic lidocaine action on human TREK1.

Collaborated with K. Somasundaram, PhD and S. Raha, PhD to study the modulation of hTREK1 channels by kinases and small molecules.

This work resulted in 3, 1st-authored publications (including 1 Mol. Pharma.) and was funded by Research Fellowship, CSIR, India.

RESEARCH GRANTS AND FELLOWSHIPS

Contributions to Funded research in Auerbach lab

Engineering of Acetylcholine Receptor Function (NS064969) 2016-present

National Institute of Neurological Disorders and Stroke (NINDS), NIH, USA.

Amount: $453,000

Principal Investigator: Anthony Auerbach, PhD

Contributions to Past Funded research

Acetylcholine receptor: Binding and gating (R37-NS23513) 2010-2016

National Institute of Neurological Disorders and Stroke (NINDS), NIH, USA.

Amount: $ 469,000

Principal Investigator: Anthony Auerbach, PhD

Fellowship for Graduate Research

Research Fellowship, Council of Scientific and Industrial Research, India 2004-2009

Amount: $ 15,100 (INR 755,000)

Role: Investigated the biophysical properties of single voltage-gated Na+ and leak-K+ channels by electrophysiological methods. I wrote manuscripts, presented data at conferences and contributed to PI grant applications.

PUBLICATIONS

Tapan K Nayak, Shandilya J, Viz R, Bruhova I, Auerbach A (2018). Efficiency measures the conversion of agonist binding energy into receptor conformational change. J. Gen. Physiol. In Press.

Tapan K Nayak, Auerbach A. (2017). Cyclic activation of endplate acetylcholine receptors. Proc. Natl. Acad. Sci. U.S.A., 114(45):11914-11919.

Tapan K Nayak, Chakrabarty S, Zheng W, Auerbach A. (2016). Structural correlates of affinity in fetal versus adult endplate nicotinic receptors. Nature Communications 7:11352; DOI: 10.1038/ncomms11352.

*Shandilya J, *Gao Y, Tapan K Nayak, Roberts S, Medler K. (2016). AP1 transcription factors are required to maintain the peripheral taste system. Cell Death and Disease. 7(10):e2433. DOI: 10.1038/cddis.2016.343.

Tapan K Nayak, Bruhova I, Chakrabarty S, Gupta S, Zheng W, Auerbach A (2014). Functional differences between neurotransmitter binding sites of muscle acetylcholine receptors. Proc. Natl. Acad. Sci. U.S.A., 111(49): 17660-05.

Iacobucci G, Rahman NA, Valtuena AA, Tapan K Nayak, Gunawardena S (2014). Spatial and temporal characteristics of normal and perturbed axonal transport in vivo. PLos One, 9(5):e97237.

Tapan K Nayak, Auerbach A (2013). Asymmetric transmitter binding sites of fetal muscle acetylcholine receptors shape their synaptic response. Proc. Natl. Acad. Sci. U.S.A., 110(33): 13654-59.

Tapan K Nayak, Purohit PG, Auerbach A (2012). The intrinsic energy of the gating isomerization of a neuromuscular acetylcholine receptor channel. J. Gen. Physiol., 139(5):349-58.

Tapan K Nayak, Dana S, Raha S, Sikdar SK (2011). Activator-induced dynamic disorder and molecular memory in human two-pore domain hTREK1 K+ channel. J. Chem. Biol. 4(2):69-84.

Tapan K Nayak, Harinath S, Nama S, Somasundaram K, Sikdar SK (2009). Inhibition of human two-pore domain K+ channel TREK1 by local anesthetic lidocaine: negative cooperativity and half-of-sites saturation kinetics. Molecular Pharmacology. 76(4): 903-17

Tapan K Nayak, Sikdar SK (2007). Time-dependent molecular memory in single voltage-gated sodium channel. J. Memb. Biol. 219(1-3): 19-36.

PUBLISHED ABSTRACTS IN CONFERENCE PROCEEDINGS AND POSTERS

1.Tapan K Nayak, Auerbach A (2016) Interactome network maps of the acetylcholine receptor ‘gate’ region. Biophys J. 110(3):604a; Biophysical Society

2.Tapan K Nayak, Auerbach A (2016) Fundamental constants for activation of human endplate receptors. Biophys J. 110(3):604a; Biophysical Society

3.Tapan K Nayak, Auerbach A (2015) Differences in agonist energy at the neurotransmitter Binding Sites in the neuromuscular acetylcholine receptors. Biophys J. 108(2):429a; Biophysical Society

4.Chakraborty S, Tapan K Nayak, Bruhova I, Zheng W, Auerbach A (2015) Molecular simulations of muscle AChR agonist binding sites. Biophys J. 108(2):429a; Biophysical Society

5.Tapan K Nayak, Auerbach A (2013). Intrinsic gating energies of fetal-type neuromuscular acetylcholine receptor. Biophys J. 104(2):634a; Biophysical Society.

6.Tapan K Nayak, Purohit PG, Auerbach A (2012). New Estimates for the ‘Allosteric’ constant of neuromuscular acetylcholine receptor-channels. Biophys J. 102(3): 119a; Biophysical Society.

7.Tapan K Nayak, Auerbach A (2011). Energy changes at the acetylcholine gate region. Biophys J. 100(3): 276a-276a; Biophysical Society.

8.Tapan K Nayak, Sikdar SK (2009). Ligand concentration dependent molecular memory in human TREK1 channel. J. Physiol Sci. 59 (S1):259; International Union of Physiological Sciences (IUPS).

POSTERS PRESENTED IN CONFERENCES

1.Tapan K Nayak, Sikdar SK (2008). Activity dependent plasticity in voltage-gated Na+ channels. CMC cardiology winter symposium, CMC, Vellore, India.

HONORS AND AWARDS

Shandilya J, Gao Y, Tapan K Nayak, Roberts S, Medler K. (2016). AP1 transcription factors are required to maintain the peripheral taste system. Cell Death and Disease. 7(10):e2433. DOI: 10.1038/cddis.2016.343.