Eleonora Gianti

Interfacial water in the PRDX1–sulfiredoxin repair intermediate: an all- atom molecular dynamics study

Manal Nael, Laxman Mahadev Alakonda, Eleonora Gianti, Khaled M. Elokely

Abstract Peroxiredoxins protect cells from oxidative damage, and sulfiredoxin (Srx) restores their activity by repairing the overoxidized catalytic cysteine; how the two proteins recognize one another is central to redox signaling and to oxidative-stress-associated disease. We characterize the human peroxiredoxin-1 (PRDX1)–Srx repair …

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Preorganized RdRp-Thumb Dynamics Drives SARS-CoV-2 Polymerase Function

Hannah Gibbs, Artiom Butuc, Preston B. Moore, Eleonora Gianti

ABSTRACT The SARS-CoV-2 RNA-dependent RNA polymerase drives viral genome replication and is a major antiviral target. How intrinsic conformational dynamics organize functional states of the polymerase, however, remains incompletely understood. Here, molecular dynamics (MD) simulations combined with free-energy landscape analysis reveal that …

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Chasing allosteric inhibition of the SARS-CoV-2 PLpro via molecular dynamics simulations with flooding fragments (MDFFr)

Jason G. Pattis, Khaled M. Elokely, Eleonora Gianti

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Chasing allosteric inhibition of the SARS-CoV-2 PLpro via Molecular Dynamics Simulations with Flooding Fragments (MDFFr)

Jason G. Pattis, Khaled M. Elokely, Eleonora Gianti

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Computational investigations of SARS-CoV-2 proofreading exoribonuclease (ExoN) suggest strategies for antiviral design

Eleonora Gianti

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Complex Helical Self‐Organizations and Functions on All Length Scales. From Art, Architecture, Early Machines and Natural Phenomena to Biological and Synthetic Assemblies and Macromolecules

Virgil Percec, Jasper Adamson, Eleonora Gianti

Helical self-organizations are, most probably, the broadest class of complex systems encountered for billions of years in natural phenomena, for several thousands of years in art and architecture, for few thousand years in early examples of machines, and since about only 1950 …

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Computational and functional studies of the PI(4,5)P2 binding site of the TRPM3 ion channel reveal interactions with other regulators

Siyuan Zhao, Vincenzo Carnevale, Matthew Gabrielle, Eleonora Gianti et autres

Transient receptor potential melastatin 3 (TRPM3) is a heat-activated ion channel expressed in peripheral sensory neurons and the central nervous system. TRPM3 activity depends on the membrane phospholipid phosphatidylinositol 4,5-bisphosphate (PI(4,5)P 2 ), but the molecular mechanism of activation by PI(4,5)P 2 …

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Allosteric inhibitors of the main protease of SARS-CoV-2

Subodh Kumar Samrat, Jimin Xu, Xuping Xie, Eleonora Gianti et autres

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Computational and functional characterization of the PI(4,5)P 2 binding site of the TRPM3 ion channel

Siyuan Zhao, Vincenzo Carnevale, Eleonora Gianti, Tibor Rohács

ABSTRACT Transient Receptor Potential Melastatin 3 (TRPM3) is a heat-activated ion channel expressed in peripheral sensory neurons and the central nervous system. TRPM3 activity depends on the membrane phospholipid phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ], but the molecular mechanism of activation by PI(4,5)P …

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Machine Learning at the Interface of Polymer Science and Biology: How Far Can We Go?

Eleonora Gianti, Simona Percec

This Perspective outlines recent progress and future directions for using machine learning (ML), a data-driven method, to address critical questions in the design, synthesis, processing, and characterization of biomacromolecules . The achievement of these tasks requires the navigation of vast and complex …

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Dual Effects of Phosphatidylinositol on TRPV1 Regulation Involve Functionally Distinct Binding Sites

Aysenur Torun Yazici, Eleonora Gianti, Marina A. Kasimova, Vincenzo Carnevale et autres

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Dual regulation of TRPV1 channels by phosphatidylinositol via functionally distinct binding sites

Aysenur Torun Yazici, Eleonora Gianti, Marina A. Kasimova, Bo Hyun Lee et autres

Regulation of the heat- and capsaicin-activated transient receptor potential vanilloid 1 (TRPV1) channel by phosphoinositides is complex and controversial. In the most recent TRPV1 cryo-EM structure, endogenous phosphatidylinositol (PtdIns) was detected in the vanilloid binding site, and phosphoinositides were proposed to act …

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