Ramakrishnan Lab

Publications

 

In Review / In Press preprint

  1. Thoduvayil S, Chatterjee A, Weerakkody J, Coleman J, Sathish Ramakrishnan*. Distinct protein ID secretory vesicles controlling biphasic insulin secretion. In Review.
  2. Sathish Ramakrishnan*, Nair A, Pichurin J, Thoduvayil S, Radhakrishnan A, Gowtham S, Chatterji A, Kyrikides T, Gunasekara RW. Programmable Light-Driven Platform for Rapid Isolation and Fractionation of Extracellular, Cell membrane and Biomimetic Lipid Vesicles for Scalable Gene Therapy Applications. In Review at Advanced Materials.
  3. Acharya P, Carr AJ, Hajicek N, Thoduvayil S, Cannon K, KalyanaSundaram V, Zhang Q, Baker R, Sathish Ramakrishnan, Sondek J, Zhang Q. Simultaneous monitoring of PIP2, DAG, and IP3 with a small-molecule reporter for PLC isozymes. In Review at Cell Chemical Biology.

Published peer‑reviewed

  1. Bera M, Kalyana Sundaram V, Thoduvayil S, Coleman J, Pincet F, Sathish Ramakrishnan*. Highly Stable Planar Asymmetric Suspended Membranes for Investigating Protein Dynamics and Membrane Fusion. Nature Protocols 2025.
  2. Mion D, Bunel L, Sathish Ramakrishnan, Heo P, Pincet F. Biomimetic membrane in a microfluidic chip for the electrical and optical monitoring of biological reactions. Nature Protocols 2025.
  3. Weerakkody J, Tseng T, Topper M, Thoduvayil S, Radhakrishnan A, Kyriakides T, Gunasekara R, Sathish Ramakrishnan*. Photosensitive Nanoprobes for Size-Specific Isolation and Enrichment of Synthetic and Extracellular Vesicle Subpopulations. Advanced Functional Materials (Cover) 2024.
  4. Bera M, Kalyana Sundaram V, Thoduvayil S, Coleman J, Pincet F, Sathish Ramakrishnan, Rothman JE, Krishnakumar SS. Synaptophysin Chaperones the Assembly of 12 SNAREpins under each Ready-Release Vesicle. PNAS 2023.
  5. Panda A, Giska F, Duncan A, Welch A, Brown C, McAllister A, Parameswaran H, Coleman J, Sathish Ramakrishnan, Guan L, Krishnakumar S, Sansom M, Rothman JE, Gupta K. Lipid vesicle native mass spectrometry for direct determination of oligomeric organization of integral membrane proteins and lipids from bilayer. Nature Methods (Cover) 2023.
  6. Thoduvayil S, Weerakkody JS, Kalyana Sundaram V, Topper M, Bera M, Coleman J, Li X, Mariappan M, Sathish Ramakrishnan*. Rapid Quantification of First and Second Phase Insulin Secretion Dynamics using an In vitro Platform for Improving Insulin Therapy. Cell Calcium 2023.
  7. Kalyana Sundaram V, Chatterjee A, Bera M, Grushin K, Panda A, Li F, Coleman J, Lee S, Sathish Ramakrishnan, Ernst AM, Gupta K, Rothman JE, Krishnakumar SS. Roles for diacylglycerol in synaptic vesicle priming and release revealed by complete reconstitution of core protein machinery. PNAS 2023.
  8. Kalyana Sundaram V, Bera M, Coleman J, Weerakkody J, Krishnakumar SS, Sathish Ramakrishnan*. Native Planar Asymmetric Suspended Membrane for Single-Molecule Investigations: Plasma Membrane on a Chip. Small (Cover, Highlighted in Advanced Science News) 2022.
  9. Sathish Ramakrishnan*, Weerakkody J. Suspended Lipid Bilayer: A Versatile Platform for Nextgen Drug Discovery and Biomedical Applications. Accounts of Materials Research (Cover, Invited) 2022.
  10. Bera M, Sathish Ramakrishnan, Coleman J, Rothman JE, and Krishnakumar SS. Molecular Determinants of Complexin Clamping and Activation Function. eLife 2022.
  11. Li F, Kalyana Sundaram V, Gatta AT, Coleman J, Sathish Ramakrishnan, Krishnakumar SS, Pincet F, Rothman JE. Vesicle capture by discrete self-assembled clusters of membrane-bound Munc13-1. FEBS Letters 2021.
  12. Sathish Ramakrishnan, Bera M, Coleman J, Rothman JE, and Krishnakumar SS. Synergistic Roles of Synaptotagmin-1 and Complexin in Calcium Regulated Neuronal Exocytosis. eLife 2020.
  13. Sathish Ramakrishnan, Bera M, Coleman J, Krishnakumar SS, Pincet F, and Rothman JE. Synaptotagmin oligomers are necessary and can be sufficient to form a Ca2+-sensitive fusion clamp. FEBS Letters 2019.
  14. Heo P, Sathish Ramakrishnan, Coleman J, Rothman J, Fleury JB, Pincet F. Highly Reproducible Physiological Asymmetric Membrane with Freely Diffusing Embedded Proteins in a 3D-Printed Microfluidic Setup. Small 2019.
  15. Coleman J, Jouannot O,# Sathish Ramakrishnan,# Zanetti N, Wang J, Salpietro V, Houlden H, Rothman J, Krishnakumar S. PRRT2 Regulates Synaptic Fusion by Directly Moderating SNARE Complex Assembly. Cell Reports 2018.
  16. Sathish Ramakrishnan,# Gohlke A,# Li F, Coleman J, Xu W, Rothman J, Pincet F. High throughput single vesicle fusion using free-standing membranes and automated analysis. Langmuir 2018.
  17. Sathish Ramakrishnan, Martin M, Cloitre T, Agarwal V, Cusinier F, Gergely C. Porous silicon microcavities redefine colorimetric ELISA sensitivity for ultrasensitive detection of autoimmune antibodies. Sensors and Actuators B: Chemical 2018.
  18. Papa Z, Sathish Ramakrishnan, Martin M, Cloitre T, Zimayi L, Toth Z, Gergely C, Budai J. Ellipsometric behavior of patterned layers – depolarization and quasi absorption. Applied Surface Science 2017.
  19. Sathish Ramakrishnan*, Zhu J, Gergely C. Organic-Inorganic Interface simulations for new material discoveries. WIREs: Computational Molecular Science (Cover; Highlighted in Advanced Science News) 2017.
  20. Papa Z,# Sathish Ramakrishnan,# Martin M, Marquez J, Zimanyi L, Toth Z, Gergely C. Interactions at the silicon-peptide surfaces – Evidence of peptide multilayer assembly. Langmuir 2016.
  21. Sathish Ramakrishnan, Jebors S, Martin M, Cloitre T, Agarwal V, Mehdi A, Martinez J, Subra G, Gergely C. Engineered adhesion peptides for improved silicon adsorption. Langmuir 2015.
  22. Sathish Ramakrishnan, Martin M, Cloitre T, Firlej L, Gergely C. Design rules for metal binding biomolecules: Understanding of amino acid adsorption on platinum crystallographic facets by density functional theoretical calculations. PCCP 2015.
  23. Sathish Ramakrishnan, Martin M, Cloitre T, Firlej L, Cusinier FJ, Gergely C. Molecular Mechanism of Selective Binding of Peptides to Silicon Surface. J. Chem. Inf. Model. 2014.
  24. Sathish Ramakrishnan, Estephan E, Martin M, Cloitre T & Gergely C. Probing the mechanism of material specific peptides for optical sensors. Proc. SPIE 8765 2013.
  25. Sathish Ramakrishnan, Martin M, Cloitre T, Firlej L, Gergely C. Insights on the facet specific adsorption of amino acids and peptides towards platinum. J. Chem. Inf. Model. 2013.
  26. Salehi H, Middendorp E, Panayotov I, Collart Dutilleul PY, Vegh AG, Sathish Ramakrishnan, Gergely C, Cuisinier F. Confocal Raman data analysis enables identifying apoptosis of MCF-7 cells caused by paclitaxel. Journal of Biomedical Optics 2013.
  27. Salehi H, Middendorp E, Végh AG, Sathish Ramakrishnan, Gergely C, Cuisinier FJG. Detection of apoptosis caused by paclitaxel in MCF-7 cells by confocal Raman microscopy. Proc. SPIE 2013.