Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation
UR Shrestha, P Juneja, Q Zhang… - Proceedings of the …, 2019 - National Acad Sciences
Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major
role in cell signaling, and are associated with human diseases. To understand IDP function it …
role in cell signaling, and are associated with human diseases. To understand IDP function it …
Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile
UR Shrestha, D Bhowmik… - Proceedings of the …, 2015 - National Acad Sciences
Inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens is a large oligomeric
protein derived from a hyperthermophilic microorganism that is found near hydrothermal …
protein derived from a hyperthermophilic microorganism that is found near hydrothermal …
[HTML][HTML] Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry
…, S Lotz, D McGee, S Shechter, UR Shrestha… - Nature …, 2022 - nature.com
Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading
proteins implicated in diseases. A key step in this process is the formation of a ternary …
proteins implicated in diseases. A key step in this process is the formation of a ternary …
[HTML][HTML] Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations
UR Shrestha, JC Smith, L Petridis - Communications biology, 2021 - nature.com
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged
experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from …
experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from …
Comparison of clinical outcome and radiologic parameters in open TLIF versus MIS-TLIF in single-or double-level lumbar surgeries
HN Modi, U Shrestha - International Journal of Spine Surgery, 2021 - ijssurgery.com
Purpose: The objective of this study was to compare clinical and radiologic parameters between
minimally invasive surgery–transforaminal lumbar interbody fusion (MIS-TLIF) and open …
minimally invasive surgery–transforaminal lumbar interbody fusion (MIS-TLIF) and open …
Arabinose substitution effect on xylan rigidity and self-aggregation
Substituted xylans play an important role in the structure and mechanics of the primary cell
wall of plants. Arabinoxylans (AX) consist of a xylose backbone substituted with arabinose, …
wall of plants. Arabinoxylans (AX) consist of a xylose backbone substituted with arabinose, …
Influence of molecular shape on self-diffusion under severe confinement: A molecular dynamics study
We have investigated the effect of molecular shape and charge asymmetry on the translation
dynamics of confined hydrocarbon molecules having different shapes but similar kinetic …
dynamics of confined hydrocarbon molecules having different shapes but similar kinetic …
[HTML][HTML] Using small-angle scattering data and parametric machine learning to optimize force field parameters for intrinsically disordered proteins
O Demerdash, UR Shrestha, L Petridis… - Frontiers in molecular …, 2019 - frontiersin.org
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs)
play important roles in many aspects of normal cell physiology, such as signal …
play important roles in many aspects of normal cell physiology, such as signal …
Atomic-resolution prediction of degrader-mediated ternary complex structures by combining molecular simulations with hydrogen deuterium exchange
…, S Lotz, D McGee, S Shechter, UR Shrestha… - Biorxiv, 2021 - biorxiv.org
Targeted protein degradation (TPD) has emerged as a powerful approach in drug discovery
for removing (rather than inhibiting) proteins implicated in diseases. A key step in this …
for removing (rather than inhibiting) proteins implicated in diseases. A key step in this …
Quasi-elastic neutron scattering reveals ligand-induced protein dynamics of a G-protein-coupled receptor
UR Shrestha, SMDC Perera, D Bhowmik… - The journal of …, 2016 - ACS Publications
Light activation of the visual G-protein-coupled receptor (GPCR) rhodopsin leads to
significant structural fluctuations of the protein embedded within the membrane yielding the …
significant structural fluctuations of the protein embedded within the membrane yielding the …
