Allosteric modulation of NF1 GAP: Differential distributions of catalytically competent populations in loss‐of‐function and gain‐of‐function mutants

Protein Science, Год журнала: 2025, Номер 34(2)

Опубликована: Янв. 22, 2025

Abstract Neurofibromin (NF1), a Ras GTPase‐activating protein (GAP), catalyzes Ras‐mediated GTP hydrolysis and thereby negatively regulates the Ras/MAPK pathway. NF1 mutations can cause neurofibromatosis type 1 manifesting tumors, neurodevelopmental disorders. Exactly how missense in GAP‐related domain of (NF1 GRD ) allosterically impact GAP to promote these distinct pathologies is unclear. Especially tantalizing question same‐domain, same‐residue variants exhibit clinical phenotypes. Guided by data, we take up this dilemma. We sampled conformational ensembles complex with GTP‐bound K‐Ras4B performing molecular dynamics simulations. Our results show that retain active conformation but biased propensities catalytically competent populations K‐Ras4B–NF1 complex. In agreement depiction experimental tagging, compared wild type, E1356A E1356V mutants effectively act through loss‐of‐function gain‐of‐function mechanisms, leading developmental disorders, respectively. Allosteric modulation activity biasing different states further demonstrated diminished isoform 2, as powerful predictors function. Taken together, our work identifies hotspot could tune function, suggests targeting oncogenic restoring catalytic activity, offers mechanism for phenotypes determined their propensities.

Язык: Английский

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Mitogen signaling strength and duration can control cell cycle decisions

Science Advances, Год журнала: 2024, Номер 10(27)

Опубликована: Июль 5, 2024

Decades ago, mitogen-promoted signaling duration and strength were observed to be sensed by the cell critical for its decisions: proliferate or differentiate. Landmark publications established importance of mitogen not only in G 1 cycle phase but also through S 2 /M transition. Despite these early milestones, how signal strength, short strong weaker sustained, control fate has been largely unheeded. Here, we center on cardinal signaling-related questions, including (i) fluctuating mitogenic signals are converted into proliferation-differentiation decisions (ii) why extended weak is associated with differentiation, while bursts induce proliferation but, if too long, irreversible senescence. Our innovative broad outlook harnesses biology protein conformational ensembles, helping us define clarify decisions, thus fate.

Язык: Английский

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CDK2 and CDK4: Cell Cycle Functions Evolve Distinct, Catalysis-Competent Conformations, Offering Drug Targets

JACS Au, Год журнала: 2024, Номер 4(5), С. 1911 - 1927

Опубликована: Май 14, 2024

Cyclin-dependent kinases (CDKs), particularly CDK4 and CDK2, are crucial for cell cycle progression from the Gap 1 (G1) to Synthesis (S) phase by phosphorylating targets such as Retinoblastoma Protein (Rb). CDK4, paired with cyclin-D, operates in long G1 phase, while CDK2 cyclin-E, manages brief G1-to-S transition, enabling DNA replication. Aberrant CDK signaling leads uncontrolled proliferation, which is a hallmark of cancer. Exactly how they accomplish their catalytic phosphorylation actions distinct efficiencies poses fundamental, albeit overlooked question. Here we combined available experimental data modeling active complexes establish conformational functional landscapes explain two cyclin/CDK differentially populate catalytically competent states progression. Our premise that could be more important than cyclin-CDK biochemical binding specificity efficiency likely prime determinant We observe dynamic ATP site, regulatory spine, interaction its cyclin partner. The N-terminus cyclin-D acts an allosteric regulator activation loop ATP-binding site CDK4. Integrated suite data, suggest complex less capable remaining conformation, may have lower befitting time scales, point critical residues motifs drive differences. mechanistic landscape apply broadly kinases, propose drug design strategies: (i) Inhibition stabilization targeting regulation (ii) entropy-optimized leverages dynamic, entropic aspects optimize efficacy.

Язык: Английский

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Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function

Journal of Molecular Biology, Год журнала: 2025, Номер unknown, С. 169044 - 169044

Опубликована: Фев. 1, 2025

Язык: Английский

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Distinct allosteric networks in CDK4 and CDK6 in the cell cycle and in drug resistance

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Март 4, 2025

Abstract Cyclin-dependent kinases 4 and 6 (CDK4 CDK6) are key regulators of the G1-S phase transition in cell cycle. In cancer cells, CDK6 overexpression often outcompetes CDK4 driving cycle progression, contributing to resistance against CDK4/6 inhibitors (CDK4/6i). This suggests distinct functional conformational differences between these two kinases, despite their striking structural sequence similarities. Understanding mechanisms that differentiate is crucial, as CDK4/6i—frequently linked overexpression—remains a significant therapeutic challenge. Notably, upregulated CDK4/6i-resistant cancers rapidly proliferating hematopoietic stem underscoring its unique regulatory roles. We hypothesize dynamics explain phosphorylation retinoblastoma protein, Rb, inhibitor efficacy, control. leads us question how dissimilar encode actions . To elucidate differential activities, molecular mechanisms, binding, we combine biochemical assays (MD) simulations. discover have allosteric networks connecting β3-αC loop G-loop. exhibits stronger coupling shorter path lengths regions, resulting higher kinase activity upon cyclin binding impacting specificity. also an unrecognized role unstructured C-terminus, which allosterically connects stabilizes R-spine, facilitating slightly activity. Our findings bridge gap similarity divergence CDK6, advancing understanding regulation biology. Graphical abstract

Язык: Английский

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Distinct allosteric networks in CDK4 and CDK6 in the cell cycle and in drug resistance

Journal of Molecular Biology, Год журнала: 2025, Номер unknown, С. 169121 - 169121

Опубликована: Март 1, 2025

Язык: Английский

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Binding Modalities and Phase-Specific Regulation of Cyclin/Cyclin-Dependent Kinase Complexes in the Cell Cycle

The Journal of Physical Chemistry B, Год журнала: 2024, Номер unknown

Опубликована: Сен. 24, 2024

Cyclin-dependent kinases (CDKs) are activated upon cyclin-binding to enable progression through the cell cycle. Dominant CDKs and cyclins in mammalian cells include CDK1, CDK2, CDK4, CDK6 corresponding A, B, D, E. While only certain, "typical" cyclin/CDK complexes primarily responsible for cycle progression, "atypical" can form sometimes perform same roles as typical complexes. We asked what structural features of favor formation complexes, a vital yet not fully explored question. use computational docking biophysical analyses exhaustively evaluate structure stability all CDK cyclin listed above. find that binding is generally stronger than atypical especially when an active conformation. Typical have denser clusters, indicating they more defined sites Our results help explain three notable function cycle: (i) why CDK4 cyclin-D exceptionally high specificity each other; (ii) both cyclin-A cyclin-B strongly activate whereas CDK2 by cyclin-A; (iii) cyclin-E normally activates but CDK1. Overall, this work reveals modalities how lead preference versus differ between observations suggest targeting catalytic actions destabilizing their native differential interfaces.

Язык: Английский

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CELL CYCLE DYSREGULATION IN CANCER

Pharmacological Reviews, Год журнала: 2024, Номер 77(2), С. 100030 - 100030

Опубликована: Дек. 24, 2024

Cancer is a systemic manifestation of aberrant cell cycle activity and dysregulated growth. Genetic mutations can determine tumor onset by either augmenting division rates or restraining normal controls such as arrest apoptosis. As result, cells not only undergo uncontrolled but also become compromised in their ability to exit the accurately. Regulation progression enabled specific surveillance mechanisms known checkpoints, aberrations these signaling pathways often culminate cancer. For instance, DNA damage which preclude generation augmentation G1, S, G2 phases, are defective cancer cells, allowing spite accumulation genetic errors. Notably, tumors have evolved dependent on checkpoints for survival. example, checkpoint replication stress mitotic rarely remain intact because any could result irreparable catastrophic chromosomal missegregation leading death. In this review, we initially focus control functions involved then proceed examine how provide new therapeutic windows that be exploited therapy. SIGNIFICANCE STATEMENT: Conversely, missegregation, This review focuses an emerging understanding opportunities

Язык: Английский

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Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function

Опубликована: Янв. 1, 2024

Язык: Английский

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