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KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs.
Structure of a low-population binding intermediate in protein-RNA recognition
- Aditi N. Borkar, Michael F. Bardaro, C. Camilloni, F. A. Aprile, G. Varani, M. Vendruscolo
- Biology, ChemistryProceedings of the National Academy of Sciences
- 10 June 2016
A high-resolution structure of an intermediate state in protein-RNA recognition is determined by using NMR measurements as ensemble-averaged structural restraints in metadynamics simulations, and validated by performing a structure-based design of two mutants with rationally modified binding rates.
Visualization of Early Events in Acetic Acid Denaturation of HIV-1 Protease: A Molecular Dynamics Study
It is illustrated that the α-helix and the β-sheet at the C-terminus of a native and functional PR dimer should maintain both the stability and the function of the enzyme and thus present newer targets for blocking PR function.
Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach
- Aditi N. Borkar, I. Ghosh, D. Bhattacharyya
- ChemistryJournal of biomolecular structure & dynamics
- 1 April 2010
Analyses of base pairing and stacking possibility reveal structural changes accompanying these transitions as well as the flexibility of different base steps towards variations in different torsion angles.
Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.
- Aditi N. Borkar, P. Vallurupalli, C. Camilloni, L. Kay, M. Vendruscolo
- ChemistryPhysical chemistry chemical physics : PCCP
- 25 January 2017
This study uses NMR residual dipolar couplings (RDCs) as structural restraints in replica-averaged metadynamics (RAM) simulations and applies this approach to a 14-mer RNA hairpin containing the prototypical UUCG tetraloop motif, showing that it is possible to construct the free energy landscape of this RNA molecule.
AUTOBA: Automation of backbone assignment from HN(C)N suite of experiments
An efficient algorithm named as AUTOBA (Automatic Backbone Assignment) designed to automate the assignment protocol based on HN(C)N suite of experiments, demonstrated with experimental spectra recorded on two small globular proteins and simulated spectra of 27 other proteins using assignment data from the BMRB.
A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings.
- Aditi N. Borkar, A. De Simone, R. Montalvão, M. Vendruscolo
- ChemistryThe Journal of chemical physics
- 7 June 2013
Initial evidence is provided that with this approach it is possible to determine accurately structural ensembles representing the conformational fluctuations of RNA by applying the reference ensemble test to the trans-activation response element of the human immunodeficiency virus type 1.
Denaturation of HIV-1 Protease (PR) Monomer by Acetic Acid: Mechanistic and Trajectory Insights from Molecular Dynamics Simulations and NMR
- Aditi N. Borkar, M. Rout, R. Hosur
- Chemistry, BiologyJournal of biomolecular structure & dynamics
- 1 April 2012
All-atom MD simulations in explicit solvent and NMR relaxation studies were performed on HIV-1 Protease in 9 M acetic acid, revealing that the α-helix and the surrounding β-strands represent the sensitive regions of the PR that respond maximally to the change in the solvent environment around the PR and are prone to disruption by acetic Acid.
Facile backbone (1H, 15N, 13Ca, and 13C′) assignment of 13C/15N‐labeled proteins using orthogonal projection planes of HNN and HN(C)N experiments and its automation
Two improvements are presented to enhance the utility of the proposed high‐throughput AUTOmatic Backbone Assignment protocol, including use of 2D‐hNnH spectrum and its variants that display additional 1H–15N correlations and thus help to resolve ambiguities arising because of amide 1H shift degeneracy.
Structural basis for assembly and function of the 7SK snRNP complex
The recent structure of human LARP7 and its binding site on 7SK RNA by Feigon and co-workers reveals molecular details into how this protein-RNA interaction contributes to7SK RNA recognition and provides insights into the assembly of the 7SK small nuclear ribonucleoprotein (snRNP) complex for correct transcriptional control.