Cell membranes play a pivotal role in separating cells from their environments, maintaining cells in an off-equilibrium steady-state, detecting and relaying outside signals into the cells by responding to their environments in specific manners. There has been a strong interest in the scientific community because membrane systems, including both membrane proteins and lipids, serve as therapeutic targets for human diseases. Membrane proteins generally include both integral membrane proteins that are integrated in the membrane and traverse both leaflets of the bilayer and the peripheral membrane proteins that are associated with bilayer membranes or integral membrane proteins. Around 20% – 30% of total proteins of any genome are predicted integral membrane proteins and > 60% of the drugs are believed to act on the membrane proteins. Although knowledge of the number of integral membrane proteins is increasing over time, determination of the structural basis for their functions still lags. It remains difficult to study quantitatively the effects of membrane lipids on the structure and function of membrane proteins. Our objectives are to study the structural basis for the effect of lipids environment on the ion channels such as the potassium ion channels and the ion channels in the regulated secretion. Another objective is the structural basis of the oligomeric assembly of ion channels (potassium ion channels) in the ER and their consequences in the different diseases.
A deeper Understanding
Ion channels in Regulated secretion
Granin family proteins are by default granule proteins that chaperone other secretory molecules through regulated secretion. They have both intracellular and extracellular functions. Chromogranins (CHGs) are believed to function in all three steps of the regulated secretory pathway. It was proposed that CHGs interact with cargos and serve as a low-affinity, high-capacity Ca2+ reserve. Their extracellular functions are executed by CHG-derived peptides that are associated with various human diseases. However, the molecular mechanisms for all CHGs’ intracellular functions remain to be elucidated. We have investigated the functional properties of CHGB proteins in different membrane systems and demonstrated that CHGB inserts into membrane and by itself suffices to form an unconventional chloride channel. We have investigated that CHGB has dual functional states: as a soluble protein, it is processed into small bioactive peptide and when reconstituted in the membrane it functions as a chloride channel. We want to study this channel in detail such as channel regulation, kinetics, whether other granin family proteins have such functions and role of these channels in calcium homeostasis. We will also investigate the affiliation of the granin family proteins to the different neuronal diseases for example Alzheimer’s disease (AD), Parkinson’s disease (PD), ALS and Schizophrenia.
(a). Yadav GP, Current Dilemma on Granin Proteins: Proteins involved in various cellular functions without known mechanisms. Cell Cellular Life Science J (2017), 2(2):000115.
(b). Gaya P. Yadav, Hui Zheng, Qing Yang, Lauren G Douma, Linda B Bloom and Qiu-Xing Jiang; Secretory granule protein chromogranin B (CHGB) forms an anion channel in membrane. Life Science Alliance, Sept 2018, 1(5) e201800139; DOI:10.26508/lsa.201800139.
(c) Gaya P. Yadav & Qiu-Xing Jiang; Reconstituted Membrane Systems for Assaying Membrane Proteins in Controlled Lipid Environments. New Techniques for Studying Biomembranes (2020), 93-121(Book Chapter).
(d) Gaya P. Yadav, Haiyuan Wang, Joke Ouwendijk, Mani Annamalai, Stephen Cross, Qiaochu Wang, D. Walker Hagan, Clayton Mathews, Edward A. Phelps, Paul Verkade, Michael X. Zhu, and Qiu-Xing Jiang; Membrane insertion of chromogranin B for granule maturation in regulated secretion (under review).
Oligomeric assembly of protein in the ER
The membrane proteins are synthesized on the endoplasmic reticulum. Before being functionally active, the newly generated membrane proteins undergo multiples steps: membrane insertion during the translocation via the translocon complex or other systems and the proper assembly of the proteins into a quaternary structure, if required. It has been known that after inserted into the membrane, proteins undergo different structural arrangements in the monomeric form and finally assembled to the functional oligomeric form. Potassium ion channels form a functional channel by assembling four subunits but how they assemble to form tetrameric form is not known. We want to study the structural basis for this phenomenon in detail and unravel the exact mechanism of tetramerization of these channels in the ER.
(a) We have determined the structure of small potassium ion channel (100 kDa tetramer) in Lipid environment by reconstituting them in the nanodisc through Single particle reconstruction (3.57Å resolution).
Possible collaboration and consultancy projects:
- The Cryo-EM Center is open to collaborate with scientists with structural biology projects that involve Cryo-EM or other EM studies. We have already determined multiple structures and are adept in the process and the analysis.
- The Cryo-EM Center is also open for the consultancy projects of a proprietary nature or where results may be too preliminary to share.
- Mohammed E. Sayed, Ao Cheng, Gaya P. Yadav, Andrew T. Ludlow, Jerry W. Shay, Woodring E. Wright, and Qiu-Xing Jiang; Catalysis-dependent inactivation of human telomerase and its reactivation by intracellular telomerase-activating factors (iTAFs). J. Biol. Chem. June 11, 2019.
- Gaya P. Yadav, Hui Zheng, Qing Yang, Lauren G Douma, Linda B Bloom, and Qiu-Xing Jiang; Secretory granule protein chromogranin B (CHGB) forms an anion channel in a membrane. Life Science Alliance, Sept 2018, 1(5) e201800139; DOI:10.26508/lsa.201800139.
- Yadav GP, Current Dilemma on Granin Proteins: Proteins involved in various cellular functions without known mechanisms. Cell Cellular Life Science J (2017), 2(2):000115.
- Liu H, Liang C, Kollipara RK, Matsui M, Ke X, Jeong BC, Wang Z, Yoo KS, Yadav GP, Kinch LN, Grishin NV, Nam Y, Corey DR, Kittler R, Liu Q. HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing. Mol Cell. (2016) 4; 63(3):420-32. DOI: 10.1016/j.molcel.2016.06.014. Epub 2016 Jul 14.
- Yadav GP, Shree S, Maurya R, Rai N, Singh DK, et al. Characterization of tuberculosisSerB2, an Essential HAD-Family Phosphatase, Reveals Novel Properties. (2014) PLoS ONE 9(12): e115409.
- Singh P*, Yadav GP*, Gupta S, Tripathi AK, Ramachandran R, Tripathi RK. A novel dimer-tetramer transition captured by the crystal structure of the HIV-1 Nef. PLoS One. 2011; 6(11): e26629. (*Equal author).
- Vijay Singh, Samiran Hutait, Gaya P. Yadav, Prakas R. Maulik and Sanjay Batra* Unusual retention of isoxazole ring under the influence of 3-(substituted nitrophenyl)-2-isoxazoline during catalytic-hydrogenation of isoxazoline substituted isoxazole systems. Journal of Heterocyclic Chemistry, 2009, 46,762-769.
- Uma Sharan Singh, Ravishankar Nainavat, Gaya P. Yadav, Geetika Kharkwal, Anila Dwivedi, Govind Keshri, M.M Singh, P. R Maulik, and K. Hajela. Synthesis and structure-guided evaluation of estrogen agonist and antagonist activities of some new tetrazolyl indole derivatives, J. Med. Chem., 2008, 43, 2149-2158.
- K. Singh, Mridul Mishra, Nisha Saxena, G.P. Yadav, P.R. Maulik, M.K. Sahoo, R.L. Gaur, P.K. Murthy, R.P. Tripathi. Synthesis of 2-sulfanyl-6-methyl-1, 4-dihydropyrimidines as a new class of antifilarial agents, Eur. J. Med. Chem., 2008,43,2717-2723.
- Virender Singh, Gaya P. Yadav, Prakas R. Maulik, Sanjay Batra, Synthesis of substituted 3-methylene-2-pyridones from Baylis–Hillman derivatives and its application for the generation of 2-pyridone substituted spiroisoxazolines. Tetrahedron,2008, 64, 13, 2979-2991.
- Sudharshan Madapa, Divya Sridhar, Gaya P. Yadav, Prakas R. Maulik and Sanjay Batra. A General Approach to the Synthesis of Substituted Isoxazolo[4,3-c] quinolines via Chalcones. European J. Org. Chem. 2007, 26, 4343–4351.
- Nag, S. Yadav, G.P. Maulik, P.R. Batra, S. Sodium Hydride Mediated Cascade Reaction towards the Synthesis of 1, 5-Disubstituted Uracil from Cyanamides Derived from Baylis-Hillman Adducts. Synthesis; 2007, 06, 911-917.
- Singh, G.P. Yadav, P.R. Maulik, S. Batra, Studies toward the construction of substituted piperidine-2-ones and pyridine-2-ones from Baylis–Hillman adducts: discovery of a facile synthesis of 5-methyl-4-oxo-6-aryl-3-aza-bicyclo[3.1.0]hexane-1-carboxylates, Tetrahedron, 2006, 62, 37, 8731-8739.
- Singh, S. Madapa, G.P. Yadav, P.R. Maulik, S. Batra. Interesting Results of catalytic hydrogenation of 3-(2-Nitrophenyl) isoxazoles and 3-(Nitrophenyl) 4,5-dihydroisoxazoles; Synthesis 2006,12,1995-2004.
- Roy, Amrendra K.; Pathak, Richa; Yadav, Gaya P.; Maulik, Prakas R., Batra, Sanjay, Neighboring-Group Effect: DBU-Promoted Ring Transformation of Substituted Isoxazoles to Substituted Pyrroles, Synthesis 06, 2006, 1021-1027.