Publications by authors named "Arpita Mrigwani"

4 Publications

  • Page 1 of 1

N-Terminal Extensions Appear to Frustrate HU Heterodimer Formation by Strengthening Intersubunit Contacts and Blocking the Formation of a Heterotetrameric Intermediate.

Biochemistry 2021 Jun 21;60(23):1836-1852. Epub 2021 May 21.

Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar, Punjab 140306, India.

HU is a bacterial nucleoid-associated protein. Two homologues, known as HU-A, and HU-B, are found in within which the early, late, and stationary phases of growth are dominated by HU-AA, HU-BB, and HU-AB dimers, respectively. Here, using genetic manipulation, mass spectrometry, spectroscopy, chromatography, and electrophoretic examination of glutaraldehyde-mediated cross-linking of subunits, in combination with experiments involving mixing, co-expression, unfolding, and refolding of HU chains, we show that the spontaneous formation of HU-AB heterodimers that is reported to occur upon mixing of wild-type HU-AA and HU-BB homodimers does not occur if chains possess N-terminal extensions. We show that N-terminal extensions interfere with the conversion of homodimers into heterodimers. We also show that heterodimers are readily formed at anticipated levels by chains possessing N-terminal extensions , when direct chain-chain interactions are facilitated through production of HU-A and HU-B chains from proximal genes located upon the same plasmid. From the data, two explanations emerge regarding the mechanism by which N-terminal extensions happen to adversely affect the conversion of homodimers into heterodimers. (1) The disappearance of the α-amino group at HU's N-terminus impacts the intersubunit stacking of β-sheets at HU's dimeric interface, reducing the ease with which subunits dissociate from each other. Simultaneously, (2) the presence of an N-terminal extension appears to sterically prevent the association of HU-AA and HU-BB homodimers into a critically required, heterotetrameric intermediate (within which homodimers could otherwise exchange subunits without releasing monomers into solution, by remaining physically associated with each other).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.biochem.1c00081DOI Listing
June 2021

An inquiry-based approach in large undergraduate labs: Learning, by doing it the "wrong" way.

Biochem Mol Biol Educ 2020 05 3;48(3):227-235. Epub 2020 Jan 3.

Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sahibzada Ajit Singh Nagar, Punjab, India.

Undergraduate laboratory courses, owing to their larger sizes and shorter time slots, are often conducted in highly structured modes. However, this approach is known to interfere with students' engagement in the experiments. To enhance students' engagement, we propose an alternative mode of running laboratory courses by creating some "disorder" in a previously adopted structure. After performing an experiment in the right way, the students were asked to repeat the experiment but with a variation at certain steps leading to the experiment being done the "wrong" way. Although this approach led to fewer experiments being conducted in a semester, it significantly enhanced the students' involvement. This was also reflected in the students' feedback. The majority of students preferred repeating an experiment with a variant protocol than performing a new experiment. Although we have tested this inquiry-based approach only for an undergraduate laboratory course in molecular biology, we believe such an approach could also be extended to undergraduate laboratory courses of other subjects.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/bmb.21331DOI Listing
May 2020

Structural-Mechanical and Biochemical Functions of Classical Cadherins at Cellular Junctions: A Review and Some Hypotheses.

Adv Exp Med Biol 2018;1112:107-138

Centre for Protein Science, Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab, India.

This article begins with a general review of cell adhesion molecules (CAMs) and narrows the focus down progressively to the cadherins (calcium binding-dependent CAMs), classifications of subfamilies of the cadherins, type I (E- and N-) cadherins, evolutionary relationships amongst cadherins, structural-mechanical and functional consequences of calcium binding to the cadherins, differential molecular interactions involving the extracellular (ecto) and intracellular (cytoplasmic) domains of the cadherins, multiple adherence-related homophilic and heterophilic interactions and associated functions of E- and N-cadherin in organismal development and disease and cadherin trafficking and membrane rafts. It ends by summarizing multiple perspectives and hypotheses concerning different aspects of cadherin structure, stability and function.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-981-13-3065-0_9DOI Listing
July 2019

Sequence complexity of amyloidogenic regions in intrinsically disordered human proteins.

PLoS One 2014 3;9(3):e89781. Epub 2014 Mar 3.

Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India.

An amyloidogenic region (AR) in a protein sequence plays a significant role in protein aggregation and amyloid formation. We have investigated the sequence complexity of AR that is present in intrinsically disordered human proteins. More than 80% human proteins in the disordered protein databases (DisProt+IDEAL) contained one or more ARs. With decrease of protein disorder, AR content in the protein sequence was decreased. A probability density distribution analysis and discrete analysis of AR sequences showed that ∼8% residue in a protein sequence was in AR and the region was in average 8 residues long. The residues in the AR were high in sequence complexity and it seldom overlapped with low complexity regions (LCR), which was largely abundant in disorder proteins. The sequences in the AR showed mixed conformational adaptability towards α-helix, β-sheet/strand and coil conformations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0089781PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3940659PMC
January 2015