Ashan Dayananda

Unique CD8 + T Cell Populations Expand during ART and Predict Delayed HIV-1 Rebound

Jie Wang, Gautam Kundu, Philip K. Ehrenberg, Aviva Geretz et autres

Abstract Antiretroviral therapy (ART) suppresses HIV-1 replication but does not eliminate the latent reservoir, resulting in viral rebound with variable kinetics after treatment interruption. How the immune cell states established during ART influences timing of rebound is not fully understood. In this …

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BPS2026 – Revealing the conformational dynamics of Hsp104 using Markov state modeling and machine learning

Sumedhi Jayasekara, Tharushi Rajaguru, Ashan Dayananda, George Stan

BPS2026 – Probing the effect of pore loop mutations on the gateway transitions of caseinolytic peptidase P using machine learning and molecular dynamics

Hayden Dennison, Ashan Dayananda, Tharushi Rajaguru, George Stan

Probing the Gate-Opening Transition in the Bacterial ClpP Peptidase Using Molecular Dynamics Simulations and Machine Learning

Tharushi Rajaguru, Ashan Dayananda, T. S. Hayden Dennison, George Stan

Preserving proteome integrity is crucial for maintaining cell viability across all kingdoms of life. The bacterial caseinolytic protease (ClpP) plays a critical role in maintaining protein homeostasis by degrading misfolded or damaged proteins within the cellular environment. The N-terminal region of each …

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BPS2025 - Using machine learning techniques to characterize the functional states of Hsp104

Tharushi Rajaguru, Sumedhi Jayasekara, Ashan Dayananda, George Stan

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BPS2025 - Probing the allosteric network of the ClpB disaggregase

Zhaocheng Zhang, Ashan Dayananda, Krishan Walpalage, Gilad Haran et autres

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Probing allosteric mechanisms of the Hsp104 disaggregase using machine learning techniques

Tharushi Rajaguru, Sumedhi Jayasekara, Ashan Dayananda, George Stan

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Probing allosteric communication in the ClpB AAA+ disaggregase

Zhaocheng Zhang, Ashan Dayananda, Gilad Haran, George Stan

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Single-molecule FRET probes allosteric effects on protein-translocating pore loops of a AAA+ machine

Marija Iljina, Hisham Mazal, Ashan Dayananda, Zhaocheng Zhang et autres

AAA+ proteins (ATPases associated with various cellular activities) comprise a family of powerful ring-shaped ATP-dependent translocases that carry out numerous vital substrate-remodeling functions. ClpB is a AAA+ protein disaggregation machine that forms a two-tiered hexameric ring, with flexible pore loops protruding into …

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Design, Rationalization, and Automation of a Catalytic Sensing Mechanism for Homogeneous SERS Biosensors

Steven M. Quarin, Amanda C. Macke, Lyndsay N. Kissell, Maria S. Kelly et autres

The current pandemic has shown that we need sensitive and deployable diagnostic technologies. Surface-enhanced Raman scattering (SERS) sensors can be an ideal solution for developing such advanced point-of-need (PON) diagnostic tests. Homogeneous (reagentless) SERS sensors work by directly responding to the target …

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Allosteric communication in the gating mechanism for controlled protein degradation by the bacterial ClpP peptidase

Ashan Dayananda, T. S. Hayden Dennison, Hewafonsekage Yasan Y. Fonseka, Mohammad Sadegh Avestan et autres

Proteolysis is essential for the control of metabolic pathways and the cell cycle. Bacterial caseinolytic proteases (Clp) use peptidase components, such as ClpP, to degrade defective substrate proteins and to regulate cellular levels of stress-response proteins. To ensure selective degradation, access to …

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Allosteric Communication in the Gating Mechanism for Controlled Protein Degradation by the Bacterial ClpP Peptidase

Ashan Dayananda, T. S. Hayden Dennison, Hewafonsekage Yasan Y. Fonseka, Mohammad Sadegh Avestan et autres

Proteolysis is essential for the control of metabolic pathways and cell cycle. Bacterial caseinolytic proteases (Clp) use peptidase components, such as ClpP, to degrade defective substrate proteins and to regulate cellular levels of stress-response proteins. To ensure selective degradation, access to the …

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