Biology subjects

Velez-Vega, C.

Publications and source records attributed to Velez-Vega, C..

3 recordsLinked to original sources

bioRxiv2025

Mapping the free energy landscape of K-Ras4B dimerization

KRAS-4B regulates cellular proliferation and differentiation via its GTPase activity, and it is often mutated in human tumors. Deregulation of the MAPK/ERK pathway as a result of K-Ras4B mutations leads to uncontrolled proliferation, with the dimer/multimerization of K-Ras4B on the plasma membrane believed to be the initiating event for subsequent MAPK/ERK signaling. While K-Ras4B proteins are known to cluster on the plasma membrane, whether they associate through well-defined dimerization interfaces remains an open question. Here, we present the dimerization landscape of active, GTP-bound wild-type and G12D mutant K-Ras4B using coarse-grained unbiased and enhanced sampling molecular dynamics simulations. We recover the experimentally-reported K-Ras4B interfaces, and additionally unveil rugged free energy landscapes with many-yet uncharacterized-minima that feature c-Raf-mediated dimerization interfaces. We further explore whether wild-type or G12D K-Ras4B present different dimerization states, revealing that the G12D mutant is more likely to form diverse dimers compared to WT K-Ras4B. Our work presents evidence that K-Ras4B proteins likely interact through multifaceted interfaces that may enable controlled dimerization in different conformations from a single system, efficiently promoting nanoclustering. Although many weak, non-specific interfaces are forming, the most dominant interfaces occur with nanomolar affinity, offering a structural basis for the design of ligands able to modulate K-Ras4B dimers.

biophysics↗

bioRxiv2022

Evaluation of K-Ras4B dimer interfaces and the role of Raf effectors

K-Ras4B is one the most frequently mutated proteins in cancer, yet mechanistic details of its activation such as its homodimerization on the membrane remain elusive. The structural determinants of K-Ras4B homodimerization have been debated with different conformations being proposed in the literature. Here, we perform microsecond all-atom Molecular Dynamics (MD) simulations on the K-Ras4B monomer in solution, the K-Ras4B monomer on the membrane, and two experimentally-based K-Ras4B dimer models of the 4-5 interface to investigate the stability of these structures bound to GTP on a model cell membrane. We then evaluate the complexes for their propensity to form stable dimers on the plasma membrane in the presence and absence of Raf[RBD-CRD] effectors. We find that Raf[RBD-CRD] effectors enhance dimer stability, suggesting that the presence of effectors is necessary for K-Ras4B dimers stabilization on the cell membrane. Moreover, we observe, for the first time, a dynamic water channel at the K-Ras4B dimer interface, and identify putative allosteric connections in the K-Ras4B dimer interface. To discover novel K-Ras4B interfaces, we perform coarse-grained MD simulations in two dissociated K-Ras4B monomers on the membrane, which reveal that the dominant dimer interface is the 4-5 interface. Finally, a druggability analysis is performed in the different K-Ras4B structures in the monomeric states. Strikingly, all known binding pockets of K-Ras4B are identified only in the structure that is membrane-bound, but not in the solution structure. Based on these results, we propose that modulating the protein-membrane interactions can be an alternative strategy for inhibiting K-Ras4B signaling.

molecular biology↗

bioRxiv2020

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of Mpro, a cysteine protease, have been determined, facilitating structure-based drug design. Mpro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41-Cys145, Mpro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nu-cleophile Cys145 have been debated in previous studies of SARS-CoV Mpro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 Mpro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of Mpro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an -ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N{delta} (HD) and N{epsilon} (HE) protonation of His41 and His164, respectively, the -ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 Mpro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.

biophysics↗