Biology subjects

Paydar, M.

Publications and source records attributed to Paydar, M..

3 recordsLinked to original sources

bioRxiv2026

A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic Architecture

To probe drug mechanism of action (MOA) and interrogate the genetic architecture of human cells, we carried out isogenic genome-wide CRISPR/Cas9 knockout screens against 310 diverse drugs, bioactive compounds, and stress conditions. Stringent statistical correction for gene knockout fitness defects yielded a large-scale matrix of >12,000 high confidence chemical-genetic interactions (CGIs). This dataset revealed many previously unappreciated off-target effects for well-characterized compounds and novel MOAs for uncharacterized compounds. The CGI matrix uncovered dense genetic modules that yielded new biological insights into phospholipidosis, mitotic regulation, metabolism, the DNA damage response, and mTOR signaling. The dataset allowed identification of multi-drug sensitization and resistance mechanisms, inference of gene function, elaboration of cross-process connectivity, evaluation of the cell type specificity of CGIs, prediction of chemical synergism, and extensive annotation of understudied genes. This resource provides a map of the genetic landscape in human cells and a framework to help guide drug discovery.

systems biology↗

bioRxiv2020

Evidence for conformational change-induced hydrolysis of β-tubulin-GTP

Microtubules, protein polymers of /{beta}-tubulin dimers, form the structural framework for many essential cellular processes including cell shape formation, intracellular transport, and segregation of chromosomes during cell division. It is known that tubulin-GTP hydrolysis is closely associated with microtubule polymerization dynamics. However, the precise roles of GTP hydrolysis in tubulin polymerization and microtubule depolymerization, and how it is initiated are still not clearly defined. We report here that tubulin-GTP hydrolysis can be triggered by conformational change induced by the depolymerizing kinesin-13 proteins or by the stabilizing chemical agent paclitaxel. We provide biochemical evidence that conformational change precedes tubulin-GTP hydrolysis, confirming this process is mechanically driven and structurally directional. Furthermore, we quantitatively measure the average size of the presumptive stabilizing "GTP cap" at growing microtubule ends. Together, our findings provide the molecular basis for tubulin-GTP hydrolysis and its role in microtubule polymerization and depolymerization.

biochemistry↗

bioRxiv2020

Structural basis of mechano-chemical coupling by the mitotic kinesin KIF14

KIF14 is a mitotic kinesin protein important for cytokinesis. Its overexpression is associated with a variety of cancers and mutations in KIF14 result in cerebral and renal development defects. Like other kinesins, KIF14 contains a highly conserved catalytic motor domain where the energy from ATP hydrolysis is converted to directed movement along microtubules. Although much is known regarding the molecular mechanism of kinesin motility, there is a lack of structural information of kinesin-microtubule interactions at sufficient resolution to unambiguously assess how conformational changes related to ATP hydrolysis, microtubule binding and translocation are coupled. Here we determined the near-atomic resolution cryo-electron microscopy structures of five different KIF14 constructs bound to microtubules in the presence of different nucleotide analogues mimicking distinct steps of the ATPase cycle. Eighteen independent structures together with supporting functional assays provide a comprehensive view of the kinesin conformational changes occurring with microtubule and nucleotide binding. Our data shows that: 1) microtubule binding induces opening of the KIF14 nucleotide binding pocket; 2) AMP-PNP and ADP-AlFx induce closure of the nucleotide binding pocket in microtubule bound KIF14 and this conformational change is allosterically controlled by the neck-linker domain; 3) the neck-linker domain when undocked prevents the nucleotide-binding-pocket to fully close and dampens ATP hydrolysis; 4) fifteen neck-linker residues are required to assume the docked conformation; 5) the nucleotide analogue ADP-AlFx adopts a distinct configuration in an open nucleotide-binding-pocket; 6) the neck-linker position controls the hydrolysis step rather than nucleotide binding in the KIF14 ATPase cycle; 7) the two motor domains of a KIF14 dimer adopt distinct conformations when simultaneously bound to the microtubule. These observations provide the structural basis for a coordinated chemo-mechanical kinesin plus end translocation model.

cell biology↗