Research Project: Ras Proteinlerinin Homodimer ve Heterodimer Kompleksleri ve Etkileşimlerinin Hesaplamalı ve Deneysel Yöntemlerle İncelenmesi
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Contributors
Funders
ID
TB.00205
Authors
Keskin, Özlem
Faculty Member
Publications
K-Ras4B/calmodulin/PI3Kα: a promising new adenocarcinoma-specific drug target?
(Taylor and Francis Ltd, 2016) Gürsoy, Attila; Keskin, Özlem; Muratçıoğlu, Serena; Nussinov, Ruth; Tsai, Chung-Jung; Jang, Hyunbum; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
Introduction: Decades of efforts have yet to yield a safe and effective drug to target KRAS-driven pancreatic, colorectal and lung cancers; particularly those driven by the highly oncogenic splice variant KRAS4B. K-Ras4B's fairly smooth surface, cancer tissue/cell heterogeneity, tolerated lipid post-translational modification exchange, as well as drug-elicited toxicity present a daunting challenge. Areas covered: Within this framework, hee we focus on a new adenocarcinoma-specific drug concept. Calmodulin (CaM) binds to K-Ras4B but not to the H-Ras or N-Ras isoforms. Physiologically, in calcium- and calmodulin-rich environments such as ductal tissues, calmodulin can sequester K-Ras4B from the membrane; in cancer, CaM/Ca2+ can replace the missing receptor tyrosine kinase (RTK) signal, acting to fully activate PI3K alpha. Expert opinion: An oncogenic GTP-bound K-Ras4B/CaM/PI3K alpha complex is supported by available experimental and clinical data; therefore, targeting it may address a pressing therapeutic need. High resolution electron microscopy (EM) or crystal structure of the tripartite complex would allow orthosteric or allosteric drug discovery to disrupt the CaM/PI3K alpha interface and thus Akt/mTOR signaling. However, since drug resistance is expected to develop, combining it with compensatory pathways, particularly those involved in cell-cycle control, appears a reasonable strategy.
Arl2-mediated allosteric release of farnesylated kras4b from shuttling factor pde delta
(2018) Gürsoy, Attila; Keskin, Özlem; Özdemir, E. Sıla; Jang, Hyunbum; Nussinov, Ruth; Department of Computer Engineering; Department of Chemical and Biological Engineering; KUTTAM (Koç University Research Center for Translational Medicine); Yes; College of Engineering; Research Center
Proper localization of Ras proteins at the plasma membrane (PM) is crucial for their functions. To get to the PM, KRas4B and some other Ras family proteins bind to the PDE delta shuttling protein through their farnesylated hypervariable regions (HVRs). The docking of their famesyl (and to a lesser extent geranylgeranyl) in the hydrophobic pocket of PDE delta's stabilizes the interaction. At the PM, guanosine 5'-triphosphate (GTP)-bound Arf-like protein 2 (Arl2) assists in the release of Ras from the PDE delta. However, exactly how is still unclear. Using all-atom molecular dynamics simulations, we unraveled the detailed mechanism of Arl2-mediated release of KRas4B, the most abundant oncogenic Ras isoform, from PDE delta. We simulated ternary Arl2 PDE delta KRas4B HVR complexes and observed that Arl2 binding weakens the PDE delta farnesylated HVR interaction. Our detailed analysis showed that allosteric changes (involving beta 6 of PDE delta and additional PDE delta residues) compress the hydrophobic PDE delta pocket and push the HVR out. Mutating PDE delta residues that mediate allosteric changes in PDE delta terminates the release process. Mutant Ras proteins are enriched in human cancers, with currently no drugs in the clinics. This mechanistic account may inspire efforts to develop drugs suppressing oncogenic KRas4B release.
PDEδ binding to ras isoforms provides a route to proper membrane localization
(American Chemical Society, 2017) Gürsoy, Attila; Keskin, Özlem; Muratçıoğlu, Serena; Jang, Hyunbum; Nussinov, Ruth; Department of Computer Engineering; Department of Chemical and Biological Engineering; Yes; College of Engineering
To signal, Ras isoforms must be enriched at the plasma membrane (PM). It was suggested that phosphodies-terase-delta (PDE delta) can bind and shuttle some farnesylated Ras isoforms to the PM, but not all. Among these, interest focused on K-Ras4B, the most abundant oncogenic Ras isoform. To study PDE delta/Ras interactions, we modeled and simulated the PDE delta/K-Ras4B complex. We obtained structures, which were similar to two subsequently determined crystal structures. We next modeled and simulated complexes of PDE delta with the farnesylated hypervariable regions K-Ras4A and N-Ras. Earlier data suggested that PDE delta extracts K-Ras4B and N-Ras from the PM, but surprisingly not K-kas4A. Earlier analysis of the crystal structures advanced that the presence of large/charged residues adjacent to the farnesylated site precludes the PDE delta interaction. Here, we show that PDE delta can bind to farnesylated K-Ras4A and N-Ras like K-Ras4B, albeit not as strongly. This weaker binding, coupled with the stronger anchoring of K-Ras4A in the membrane (but not of electrostatically neutral N-Ras), can explain the observation why PDE delta is unable to effectively extract K-Ras4A. We thus propose that farnesylated Ras isoforms can bind PDE delta to fulfill the required PM enrichment, and argue that the different environments, PM versus solution, can resolve apparently puzzling Ras observations. These are novel insights that would not be expected based on the crystal structures alone, which provide an elegant rationale for previously puzzling observations of the differential effects of PDE delta on farnesylated Ras family proteins.
Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2
(American Society for Biochemistry and Molecular Biology (ASBMB), 2018) Gürsoy, Attila; Keskin, Özlem; Özdemir, E. Sıla; Jang, Hyunbum; Li, Zhigang; Sacks, David B.; Nussinov, Ruth; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Yes; College of Engineering; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
IQ motif-containing GTPase-activating proteins (IQGAPs) are scaffolding proteins playing central roles in cell-cell adhesion, polarity, and motility. The Rho GTPases Cdc42 and Rac1, in their GTP-bound active forms, interact with all three human IQGAPs. The IQGAP-Cdc42 interaction promotes metastasis by enhancing actin polymerization. However, despite their high sequence identity, Cdc42 and Rac1 differ in their interactions with IQGAP. Two Cdc42 molecules can bind to the Ex-domain and the RasGAP site of the GTPase-activating protein (GAP)related domain (GRD) of IQGAP and promote IQGAP dimerization. Only one Rac1 molecule might bind to the RasGAP site of GRD and may not facilitate the dimerization, and the exact mechanism of Cdc42 and Rac1 binding to IQGAP is unclear. Using all-atom molecular dynamics simulations, site-directed mutagenesis, and Western blotting, we unraveled the detailed mechanisms of Cdc42 and Rac1 interactions with IQGAP2. We observed that Cdc42 binding to the Ex-domain of GRD of IQGAP2 (GRD2) releases the Ex-domain at the C-terminal region of GRD2, facilitating IQGAP2 dimerization. Cdc42 binding to the Ex-domain promoted allosteric changes in the RasGAP site, providing a binding site for the second Cdc42 in the RasGAP site. Of note, the Cdc42 "insert loop" was important for the interaction of the first Cdc42 with the Ex-domain. By contrast, differences in Rac1 insert-loop sequence and structure precluded its interaction with the Ex-domain. Rac1 could bind only to the RasGAP site of apo-GRD2 and could not facilitate IQGAP2 dimerization. Our detailed mechanistic insights help decipher how Cdc42 can stimulate actin polymerization in metastasis.
Predicting protein-protein interactions from the molecular to the proteome level
(American Chemical Society, 2016) Gürsoy, Attila; Keskin, Özlem; Tunçbağ, Nurcan; Department of Computer Engineering; Department of Chemical and Biological Engineering; CCBB (The Center for Computational Biology and Bioinformatics); Yes; College of Engineering; Research Center
Identification of protein protein interactions (PPIs) is at the center of molecular biology considering the unquestionable role of proteins in cells. Combinatorial interactions result in a repertoire of multiple functions; hence, knowledge of PPI and binding regions naturally serve to functional proteomics and drug discovery. Given experimental limitations to find all interactions in a proteome, computational prediction/modeling of protein interactions is a prerequisite to proceed on the way to complete interactions at the proteome level. This review aims to provide a background on PPIs and their types. Computational methods for PPI predictions can use a variety of biological data including sequence-, evolution-, expression-, and structure-based data. Physical and statistical modeling are commonly used to integrate these data and infer PPI predictions. We review and list the state-of-the-art methods, servers, databases, and tools for protein-protein interaction prediction.
