title: GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site.
abstract: K-Ras4B, a frequently mutated oncogene in cancer, plays an essential role in cell growth, differentiation, and survival. Its C-terminal membrane-associated hypervariable region (HVR) is required for full biological activity. In the active GTP-bound state, the HVR interacts with acidic plasma membrane (PM) headgroups, whereas the farnesyl anchors in the membrane; in the inactive GDP-bound state, the HVR may interact with both the PM and the catalytic domain at the effector binding region, obstructing signaling and nucleotide exchange. Here, using molecular dynamics simulations and NMR, we aim to figure out the effects of nucleotides (GTP and GDP) and frequent (G12C, G12D, G12V, G13D, and Q61H) and infrequent (E37K and R164Q) oncogenic mutations on full-length K-Ras4B. The mutations are away from or directly at the HVR switch I/effector binding site. Our results suggest that full-length wild-type GDP-bound K-Ras4B (K-Ras4B(WT)-GDP) is in an intrinsically autoinhibited state via tight HVR-catalytic domain interactions. The looser association in K-Ras4B(WT)-GTP may release the HVR. Some of the oncogenic mutations weaken the HVR-catalytic domain association in the K-Ras4B-GDP/-GTP bound states, which may facilitate the HVR disassociation in a nucleotide-independent manner, thereby up-regulating oncogenic Ras signaling. Thus, our results suggest that mutations can exert their effects in more than one way, abolishing GTP hydrolysis and facilitating effector binding.
authors.affiliation: From the Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China, Cancer and Inflammation Program, Leidos Biomedical Research, Inc., NCI-Frederick, Frederick, Maryland 21702.
authors.forename: Shaoyong
authors.initials: S
authors.lastname: Lu
authors.affiliation: Departments of Chemistry and.
authors.forename: Avik
authors.initials: A
authors.lastname: Banerjee
authors.affiliation: Cancer and Inflammation Program, Leidos Biomedical Research, Inc., NCI-Frederick, Frederick, Maryland 21702.
authors.forename: Hyunbum
authors.identifier: http://orcid.org/0000-0001-9402-4051
authors.initials: H
authors.lastname: Jang
authors.affiliation: From the Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China, jian.zhang@sjtu.edu.cn.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, and vadimg@uic.edu.
authors.forename: Vadim
authors.initials: V
authors.lastname: Gaponenko
authors.affiliation: Cancer and Inflammation Program, Leidos Biomedical Research, Inc., NCI-Frederick, Frederick, Maryland 21702, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel NussinoR@helix.nih.gov.
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D019943:Amino Acid Substitution; D006153:Guanosine Diphosphate / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D009154:Mutation; D017434:Protein Structure, Tertiary; D016283:Proto-Oncogene Proteins p21(ras) / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: C117307:KRAS protein, human; D006153:Guanosine Diphosphate; D006160:Guanosine Triphosphate; D016283:Proto-Oncogene Proteins p21(ras)
keywords: Ras protein; biophysics; computational biology; nuclear magnetic resonance (NMR); protein conformation; protein dynamic