Search Results - "Shrestha, Utsab"

Water molecule ordering on the surface of an intrinsically disordered protein by Vural, Derya, Shrestha, Utsab R., Petridis, Loukas, Smith, Jeremy C.

“…The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the…”
Get full text

Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation by Shrestha, Utsab R., Juneja, Puneet, Zhang, Qiu, Gurumoorthy, Viswanathan, Borreguero, Jose M., Urban, Volker, Cheng, Xiaolin, Pingali, Sai Venkatesh, Smith, Jeremy C., O’Neill, Hugh M., Petridis, Loukas

“…Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To…”
Get full text

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations by Shrestha, Utsab R., Smith, Jeremy C., Petridis, Loukas

“…Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often…”
Get full text

Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry by Dixon, Tom, MacPherson, Derek, Mostofian, Barmak, Dauzhenka, Taras, Lotz, Samuel, McGee, Dwight, Shechter, Sharon, Shrestha, Utsab R., Wiewiora, Rafal, McDargh, Zachary A., Pei, Fen, Pal, Rajat, Ribeiro, João V., Wilkerson, Tanner, Sachdeva, Vipin, Gao, Ning, Jain, Shourya, Sparks, Samuel, Li, Yunxing, Vinitsky, Alexander, Zhang, Xin, Razavi, Asghar M., Kolossváry, István, Imbriglio, Jason, Evdokimov, Artem, Bergeron, Louise, Zhou, Wenchang, Adhikari, Jagat, Ruprecht, Benjamin, Dickson, Alex, Xu, Huafeng, Sherman, Woody, Izaguirre, Jesus A.

“…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…”
Get full text

Disordered Domain Shifts the Conformational Ensemble of the Folded Regulatory Domain of the Multidomain Oncoprotein c‑Src by Gurumoorthy, Viswanathan, Shrestha, Utsab R., Zhang, Qiu, Pingali, Sai Venkatesh, Boder, Eric T., Urban, Volker S., Smith, Jeremy C., Petridis, Loukas, O’Neill, Hugh

“…c-Src kinase is a multidomain non-receptor tyrosine kinase that aberrantly phosphorylates several signaling proteins in cancers. Although the structural…”
Get full text

Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study by Agarwal, Rupesh, Shrestha, Utsab R., Chu, Xiang-Qiang, Petridis, Loukas, Smith, Jeremy C.

“…The mesophilic inorganic pyrophosphatase from Escherichia coli (EcPPase) retains function at 353 K, the physiological temperature of hyperthermophilic…”
Get full text

Arabinose substitution effect on xylan rigidity and self-aggregation by Shrestha, Utsab R., Smith, Sydney, Pingali, Sai Venkatesh, Yang, Hui, Zahran, Mai, Breunig, Lloyd, Wilson, Liza A., Kowali, Margaret, Kubicki, James D., Cosgrove, Daniel J., O’Neill, Hugh M., Petridis, Loukas

“…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…”
Get full text

Effect of molecular shape on rotation under severe confinement by Dhiman, I., Bhowmik, D., Shrestha, Utsab R., Cole, D.R., Gautam, S.

“…[Display omitted] •Orientational structure and dynamics of four molecules in ZSM5 is studied separately.•The selected molecules have similar kinetic diameters…”
Get full text

Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile by Shrestha, Utsab R., Bhowmik, Debsindhu, Copley, John R. D., Tyagi, Madhusudan, Leão, Juscelino B., Chu, Xiang-qiang, 储祥蔷

“…Inorganic pyrophosphatase (IPPase) fromThermococcus thioreducensis a large oligomeric protein derived from a hyperthermophilic microorganism that is found near…”
Get full text

Small-Angle Neutron Scattering Reveals Energy Landscape for Rhodopsin Photoactivation by Perera, Suchithranga M. D. C, Chawla, Udeep, Shrestha, Utsab R, Bhowmik, Debsindhu, Struts, Andrey V, Qian, Shuo, Chu, Xiang-Qiang, Brown, Michael F

“…Knowledge of the activation principles for G-protein-coupled receptors (GPCRs) is critical to development of new pharmaceuticals. Rhodopsin is the archetype…”
Get full text

Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins by Demerdash, Omar, Shrestha, Utsab R, Petridis, Loukas, Smith, Jeremy C, Mitchell, Julie C, Ramanathan, Arvind

“…Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) play important roles in many aspects of normal cell…”
Get full text

Experimental mapping of short-wavelength phonons in proteins by Shrestha, Utsab R., Mamontov, Eugene, O'Neill, Hugh M., Zhang, Qiu, Kolesnikov, Alexander I., Chu, Xiangqiang

“…Phonons are quasi-particles, observed as lattice vibrations in periodic materials, that often dampen in the presence of structural perturbations. Nevertheless,…”
Get full text

Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G‑Protein-Coupled Receptor by Shrestha, Utsab R, Perera, Suchithranga M. D. C, Bhowmik, Debsindhu, Chawla, Udeep, Mamontov, Eugene, Brown, Michael F, Chu, Xiang-Qiang

“…Light activation of the visual G-protein-coupled receptor (GPCR) rhodopsin leads to significant structural fluctuations of the protein embedded within the…”
Get full text

Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity by Shrestha, Utsab R, Bhowmik, Debsindhu, Van Delinder, Kurt W, Mamontov, Eugene, O’Neill, Hugh, Zhang, Qiu, Alatas, Ahmet, Chu, Xiang-Qiang

“…In this article, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations…”
Get full text

Symptomatic epidural cement leakage after percutaneous vertebroplasty: A case report of successful management by surgical excision with literature review by Hitesh N Modi, Utsab Shrestha, Nagesh Bhandari, Udit D Patel

“…The purpose of this case report was to present successfully treated case of symptomatic cement leakage after percutaneous vertebroplasty procedure (PVP) with…”
Get full text

idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments by Borreguero, Jose, Islam, Fahima, Shrestha, Utsab, Petridis, Loukas

“…It is estimated that about 30% of the eucariotic proteome consists of intrinsically dis-ordered proteins (IDP’s), yet their presence in public structural…”
Get full text

Water molecule ordering on the surface of an intrinsically disordered protein by Vural, Derya, Shrestha, Utsab R., Petridis, Loukas, Smith, Jeremy C.

“…The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the…”
Get full text

Correlation of lumbar disc degeneration and spinal-pelvic sagittal balance by Liu, Hui, Shrivastava, Shilabant Rajesh, Zheng, Zhao-min, Wang, Jian-ru, Yang, Hao, Li, Ze-min, Wang, Tai-ping, Wang, Hua, Utsab, Shrestha

“…To elucidate the relationship between spino-pelvic sagittal balance parameters and lumbar intervertebral disc degeneration of each segment through…”
Get more information

Comparison of Clinical Outcome and Radiologic Parameters in Open TLIF Versus MIS-TLIF in Single- or Double-Level Lumbar Surgeries by Modi, Hitesh N, Shrestha, Utsab

“…The objective of this study was to compare clinical and radiologic parameters between minimally invasive surgery-transforaminal lumbar interbody fusion…”
Get full text

Domain camoflouge of c-Src: segmental labeling highlights oncoprotein domains for neutron scattering by Gurumoorthy, Viswanathan, Shrestha, Utsab, Venkatesh Pingali, Sai, Smith, Jeremy C., Urban, Volker, Petridis, Loukas, O'Neill, Hugh M.

Get full text