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All Outputs (9)

Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution (2024)
Journal Article
Ward, S., Childs, A., Staley, C., Waugh, C., Watts, J. A., Kotowska, A. M., …Borkar, A. N. (2024). Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution. Nature Communications, 15(1), Article 4367. https://doi.org/10.1038/s41467-024-48694-3

The 3D architecture of RNAs governs their molecular interactions, chemical reactions, and biological functions. However, a large number of RNAs and their protein complexes remain poorly understood due to the limitations of conventional structural bio... Read More about Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution.

The auxin efflux carrier PIN1a regulates vascular patterning in cereal roots (2024)
Journal Article
Fusi, R., Milner, S. G., Rosignoli, S., Bovina, R., De Jesus Vieira Teixeira, C., Lou, H., …Bhosale, R. (2024). The auxin efflux carrier PIN1a regulates vascular patterning in cereal roots. New Phytologist, https://doi.org/10.1111/nph.19777

Barley (Hordeum vulgare) is an important global cereal crop and a model in genetic studies. Despite advances in characterising barley genomic resources, few mutant studies have identified genes controlling root architecture and anatomy, which plays a... Read More about The auxin efflux carrier PIN1a regulates vascular patterning in cereal roots.

Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 (ZmCIPK15) (2021)
Journal Article
Schneider, H. M., Lor, V. S. N., Hanlon, M. T., Perkins, A., Kaeppler, S. M., Borkar, A. N., …Lynch, J. P. (2022). Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 (ZmCIPK15). Plant, Cell and Environment, 45(3), 837-853. https://doi.org/10.1111/pce.14135

Crops with reduced nutrient and water requirements are urgently needed in global agriculture. Root growth angle plays an important role in nutrient and water acquisition. A maize diversity panel of 481 genotypes was screened for variation in root ang... Read More about Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 (ZmCIPK15).

KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs (2020)
Journal Article
Bacon, C. W., Challa, A., Hyder, U., Shukla, A., Borkar, A. N., Bayo, J., …D’Orso, I. (2020). KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs. Molecular Cell, 78(6), 1133-1151.e14. https://doi.org/10.1016/j.molcel.2020.04.024

Precise control of the RNA polymerase II (RNA Pol II) cycle, including pausing and pause release, maintains transcriptional homeostasis and organismal functions. Despite previous work to understand individual transcription steps, we reveal a mechanis... Read More about KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs.

Crystal structure of the C-terminal domain of DENR (2020)
Journal Article
Lomakin, I. B., De, S., Wang, J., Borkar, A. N., & Steitz, T. A. (2020). Crystal structure of the C-terminal domain of DENR. Computational and Structural Biotechnology Journal, 18, 696-704. https://doi.org/10.1016/j.csbj.2020.03.009

© 2020 The Authors The density regulated protein (DENR) forms a stable heterodimer with malignant T-cell-amplified sequence 1 (MCT-1). DENR-MCT-1 heterodimer then participates in regulation of non-canonical translation initiation and ribosomal recycl... Read More about Crystal structure of the C-terminal domain of DENR.

Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop (2016)
Journal Article
Borkar, A. N., Vallurupalli, P., Camilloni, C., Kay, L. E., & Vendruscolo, M. (2017). Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop. Physical Chemistry Chemical Physics, 19(4), 2797-2804. https://doi.org/10.1039/c6cp08313g

© the Owner Societies 2017. RNA molecules in solution tend to undergo structural fluctuations of relatively large amplitude and to populate a range of different conformations some of which with low populations. It is still very challenging, however,... Read More about Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.

Structure of a low-population binding intermediate in protein-RNA recognition (2016)
Journal Article
Borkar, A. N., Bardaro, M. F., Camilloni, C., Aprile, F. A., Varani, G., & Vendruscolo, M. (2016). Structure of a low-population binding intermediate in protein-RNA recognition. Proceedings of the National Academy of Sciences, 113(26), 7171-7176. https://doi.org/10.1073/pnas.1521349113

All biochemical reactions in living organisms require molecular recognition events. In particular, the interactions between protein and RNA molecules are crucial in the regulation of gene expression. However, the transient nature of the conformations... Read More about Structure of a low-population binding intermediate in protein-RNA recognition.

A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings (2013)
Journal Article
Borkar, A. N., De Simone, A., Montalvao, R. W., & Vendruscolo, M. (2013). A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings. Journal of Chemical Physics, 138(21), Article 215103. https://doi.org/10.1063/1.4804301

We describe a method of determining the conformational fluctuations of RNA based on the incorporation of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) as replica-averaged structural restraints in molecular dynamics simulations. I... Read More about A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings.