Biology subjects

Dasetty, S.

Publications and source records attributed to Dasetty, S..

3 recordsLinked to original sources

bioRxiv2025

Prediction of αIIbβ3 integrin structures along its minimum free energy activation pathway

The adhesion protein integrin is a transmembrane heterodimer that plays a pivotal role in cellular processes such as cell signaling and cell migration. To execute its function, integrin undergoes extensive conformational changes from a bent-closed to an extended-open state. Resolving the structures across these changes remains a challenge with both experimental and computational methods, but is crucial for understanding the activation mechanism of integrin. We address this challenge for the platelet integrin IIb {beta}3 by employing finite temperature string method with structures of the images along the initial guess path generated by a multiscale data-driven framework. The full-length all-atom structures along the resulting minimum free energy path between the inactive bent-closed and active extended-open states of IIb {beta}3 integrin are consistent with a variety of experimentally resolved structures. Changes in these predicted structures along the path show that the extension and separation of the and {beta} subunits from the bent-closed to the extended-open state require correlated movements between the subdomain pairs in IIb {beta}3. These results provide new insights into integrin activation mechanism and the predicted structures have potential applications in guiding the design of integrin targeting therapeutics. SIGNIFICANCEIntegrins are receptor proteins that mediate a number of critical cellular processes, but it remains challenging to resolve the molecular details of integrin activation by both experiments and simulations. We address this challenge by employing a computational method to study rare events and resolve the all-atom transient structures of a platelet integrin, IIb {beta}3. The resulting structures are in good agreement with experimentally resolved partial structures and additionally reveal correlated movements between the IIb {beta}3 integrin subdomain pairs during its transition from the inactive to the active conformational state. The structures predicted in this work have applications as therapeutic targets to address diseases linked to IIb {beta}3 integrin dysfunction, such as bleeding and thrombotic disorders.

biophysics↗

bioRxiv2024

Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5-triphosphate) to GDP (guanosine-5-diphosphate) within the {beta}-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the "equation-free" multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments x 8 heterodimers) comprising [~]21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 s unbiased all-atom simulation, we interleave coarse projective "equation-free" jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 s. Our 5.875 s of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether {beta}-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. The approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution. SIGNIFICANCEThe dynamic instability of microtubules (MTs) is essential for a plethora of biological functions, from cell division to intracellular transport. Despite their importance, current computational models often struggle to handle the large-scale, long-term dynamics of all-atom simulations. This computational study employs the "equation-free" method to accelerate relaxation of the all-atom structures of MT tips in both GDP and GTP states which nearly halves the computational demands of simulating very large biomolecular systems. Our findings expose subtle but crucial structural differences between GDP-bound and GTP-bound MTs, particularly in the number of protofilament clusters, and is consistent with a relatively stronger lateral interactions in GTP-bound MT tips.

biophysics↗

bioRxiv2021

Rational engineering of low temperature activity in thermoalkalophilic Geobacillus thermocatenulatus lipase

While thermophilic enzymes have thermostability desired for broad industrial applications, they can lose activity at ambient temperatures far from their optimal. Engineering cold activity into thermophilic enzymes has the potential to broaden the range of temperatures resulting in significant activity (i.e., decreasing the temperature dependence of kcat). Even though it has been widely suggested that cold temperature enzyme activity results from active flexibility that is at odds with the rigidity necessary for thermostable enzymes; however, directed evolution experiments have shown us these properties are not mutually exclusive. In this study, rational protein engineering was used to introduce flexibility inducing mutations around the active sites of Geobacillus thermocatenulatus lipase (GTL). Two mutants were found to have enhanced specific activity compared to wild-type at temperatures between 283 K to 363 K with p-nitrophenol butyrate but not with larger substrates. Kinetics assay revealed both mutations resulted in psychrophilic traits, such as lower activation enthalpy and more negative entropy values compared to wild type in all substrates. Furthermore, the mutants had significantly improved thermostability compared to wild type enzyme, which proves that it is feasible to improve the cold activity without trade-off. Our study provides insight into the enzyme cold adaptation mechanism and design principles for engineering cold activity into thermostable enzymes.

biochemistry↗