Protein Structure, Stability, and Amyloid Formation

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

Ras and cancer: GTP-dependent K-Ras dimers, the role of calmodulin in KRAS-driven adenocarcinomas, the critical role of oncogenic KRAS in the initiation of cancer through deregulation of the G1 cell cycle, and a new view of Ras isoforms in cancers. We discovered the two major interfaces of GTP-dependent K-Ras dimers (GTP-Dependent K-Ras Dimerization. Muratcioglu S, et al. Structure 23(7): 1325-35, 2015). The first, highly populated beta-sheet dimer interface is at the Switch I and effector binding regions, overlapping Raf's, PI3K's, RalGDS' and additional effectors' binding surfaces. This interface has to be inhibitory to such effectors. The second, helical interface also overlaps some effectors' binding sites. This interface may promote Raf's activation. Our data reveal how Ras self-association can regulate effector binding and activity, and suggest that disruption of the helical dimer interface by drugs may abate Raf's signaling in cancer. We pointed out the overlooked critical role of calmodulin in KRAS-driven adenocarcinomas (The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas. Muratcioglu S, et al. Mol Cancer Res. 13(9): 1265-73, 2015). Calmodulin (CaM) selectively binds to GTP-bound K-Ras4B; but not to its isoforms. Cell proliferation and growth require the MAPK (Ras/Raf/MEK/ERK) and PI3Kalpha/Akt pathways. We proposed that Ca2+/CaM promote PI3K/Akt signaling, and suggest how. Ca2+/CaM involvement may explain puzzling observations like the elevated calcium levels in adenocarcinomas. We hypothesized that CaM recruits and helps activate PI3K at the membrane, and that this is the likely reason for Ca2+/CaM-dependence in adenocarcinomas. CaM can contribute to initiation/progression of ductal (pancreatic, colorectal, lung) cancers via both PI3Kalpha/Akt and Raf/MEK/ERK pathways. Blocking the K-Ras/MAPK pathway and CaM/PI3Kalpha binding in a K-Ras4B/CaM/PI3Kalpha trimer could be a promising adenocarcinoma-specific therapeutic strategy. We further illustrated the critical role of oncogenic KRAS in the initiation of cancer through deregulation of the G1 cell cycle (Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation. Nussinov R, et al. Expert Rev Proteomics 50(6): 669-82, 2015). We also proposed a new view of Ras isoforms in cancers (A New View of Ras Isoforms in Cancers. Nussinov R, et al. Cancer Res. 2016 Jan 1;76(1):18-23). We proposed that small GTPase K-Ras4A have a single state or two states, one resembling K-Ras4B and the other N-Ras. A recent study of K-Ras4A made the remarkable observation that even in the absence of the palmitoyl K-Ras4A can be active at the plasma membrane. Importantly, this suggests that K-Ras4A may exist in two distinct signaling states. In state 1 K-Ras4A is only farnesylated, like K-Ras4B; in state 2 farnesylated and palmitoylated, like N-Ras. The K-Ras4A hypervariable region (HVR) sequence is positively charged, in-between K-Ras4B and N-Ras. Taken together, this raises the possibility that the farnesylated but nonpalmitoylated state 1, like K-Ras4B, binds calmodulin and is associated with colorectal and other adenocarcinomas like lung cancer and PDAC (pancreatic ductal adenocarcinoma). On the other hand, state 2 may be associated with melanoma and other cancers where N-Ras is a major contributor, such as acute myeloid leukemia (AML). Importantly, H-Ras has two - single and double - palmitoylated states that may also serve distinct functional roles. The multiple signaling states of palmitoylated Ras isoforms question the completeness of small GTPase Ras isoform statistics in different cancer types and call for reevaluation of concepts and protocols. They may also call for reconsideration of oncogenic Ras therapeutics. Additionally, we addressed the interaction of Ras with the membrane which is required for its activation and how oncogenic mutations on KRas would affect its behavior (e.g. GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase KRAS4B, Exposing the Effector Binding Site, Lu S, et al. J Biol Chem. 290(48): 28887-900, 2015) and Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region. Jang H, et al. J Biol Chem. 2015) and more. Our work benefits from our collaborations with experimental groups, including structural groups, NMR and crystallography. We are fortunate to have these outstanding collaborations. We have further extended this work to work out the role of the cysteine-rich domain (CRD) of Raf in Raf-Ras interaction, and have been exploring signaling specificity of oncogenic Ras isoforms at the membrane, and the mechanism of activation of PI3K lipid kinase, which despite its important role in cancer, to date has still been a mystery. PI3K lipid kinases phosphorylate PIP2 to PIP3 in the PI3K/Akt/mTOR pathway to regulate cellular processes. They are frequently mutated in cancer. We determined the PI3Kalpha activation mechanism at the atomic level. Unlike protein kinases where the substrate abuts the ATP, crystal structures indicate that in PI3Kalpha, the distance between the gamma phosphate of the ATP and the PIP2 lipid substrate is over 6 Angstrom, much too far for the phosphoryl transfer, raising the question of how catalysis is executed. PI3Kalpha has two subunits, the catalytic p110alpha and the regulatory p85alpha. Our simulations show that release of the autoinhibition exerted by the nSH2 domain of the p85alpha triggers significant conformational change in p110alpha, leading to the exposure of the kinase domain for membrane interaction. Structural rearrangement in the C-lobe of the kinase domain reduces the distance between the ATP gamma-phosphate and the substrate, offering an explanation as to how phosphoryl transfer is executed. An alternative mechanism may involve ATP relocation. This mechanism not only explains how oncogenic mutations promote PI3Kalpha activation by facilitating nSH2 release, or nSH2-release-induced, allosteric motions; it also offers an innovative, PI3K isoform-specific drug discovery principle. Rather than competing with nanomolar range ATP in the ATP-binding pocket and contending with ATP pocket conservation and massive binding targets, this mechanism suggests blocking the PI3Kalpha sequence-specific cavity between the ATP-binding pocket and the substrate binding site. Targeting isoform-specific residues in the cavity may prevent PIP2 phosphorylation. Currently, in collaboration with intramural and extramural investigators, we also aim to uncover Raf's autoinhibition, PI3K double mutations and PTEN activation in the wild type and driver mutations, at the membrane.