1
|
Nussinov R, Liu Y, Zhang W, Jang H. Protein conformational ensembles in function: roles and mechanisms. RSC Chem Biol 2023; 4:850-864. [PMID: 37920394 PMCID: PMC10619138 DOI: 10.1039/d3cb00114h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/02/2023] [Indexed: 11/04/2023] Open
Abstract
The sequence-structure-function paradigm has dominated twentieth century molecular biology. The paradigm tacitly stipulated that for each sequence there exists a single, well-organized protein structure. Yet, to sustain cell life, function requires (i) that there be more than a single structure, (ii) that there be switching between the structures, and (iii) that the structures be incompletely organized. These fundamental tenets called for an updated sequence-conformational ensemble-function paradigm. The powerful energy landscape idea, which is the foundation of modernized molecular biology, imported the conformational ensemble framework from physics and chemistry. This framework embraces the recognition that proteins are dynamic and are always interconverting between conformational states with varying energies. The more stable the conformation the more populated it is. The changes in the populations of the states are required for cell life. As an example, in vivo, under physiological conditions, wild type kinases commonly populate their more stable "closed", inactive, conformations. However, there are minor populations of the "open", ligand-free states. Upon their stabilization, e.g., by high affinity interactions or mutations, their ensembles shift to occupy the active states. Here we discuss the role of conformational propensities in function. We provide multiple examples of diverse systems, including protein kinases, lipid kinases, and Ras GTPases, discuss diverse conformational mechanisms, and provide a broad outlook on protein ensembles in the cell. We propose that the number of molecules in the active state (inactive for repressors), determine protein function, and that the dynamic, relative conformational propensities, rather than the rigid structures, are the hallmark of cell life.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University Tel Aviv 69978 Israel
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
| | - Wengang Zhang
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
| |
Collapse
|
2
|
Reed R, Park K, Waddell B, Timbers TA, Li C, Baxi K, Giacomin RM, Leroux MR, Carvalho CE. The Caenorhabditis elegans Shugoshin regulates TAC-1 in cilia. Sci Rep 2023; 13:9410. [PMID: 37296204 PMCID: PMC10256747 DOI: 10.1038/s41598-023-36430-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/03/2023] [Indexed: 06/12/2023] Open
Abstract
The conserved Shugoshin (SGO) protein family is essential for mediating proper chromosome segregation from yeast to humans but has also been implicated in diverse roles outside of the nucleus. SGO's roles include inhibiting incorrect spindle attachment in the kinetochore, regulating the spindle assembly checkpoint (SAC), and ensuring centriole cohesion in the centrosome, all functions that involve different microtubule scaffolding structures in the cell. In Caenorhabditis elegans, a species with holocentric chromosomes, SGO-1 is not required for cohesin protection or spindle attachment but appears important for licensing meiotic recombination. Here we provide the first functional evidence that in C. elegans, Shugoshin functions in another extranuclear, microtubule-based structure, the primary cilium. We identify the centrosomal and microtubule-regulating transforming acidic coiled-coil protein, TACC/TAC-1, which also localizes to the basal body, as an SGO-1 binding protein. Genetic analyses indicate that TAC-1 activity must be maintained below a threshold at the ciliary base for correct cilia function, and that SGO-1 likely participates in constraining TAC-1 to the basal body by influencing the function of the transition zone 'ciliary gate'. This research expands our understanding of cellular functions of Shugoshin proteins and contributes to the growing examples of overlap between kinetochore, centrosome and cilia proteomes.
Collapse
Affiliation(s)
- R Reed
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - K Park
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - B Waddell
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - T A Timbers
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - C Li
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - K Baxi
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - R M Giacomin
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - M R Leroux
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
| | - C E Carvalho
- Department of Biology, University of Saskatchewan, Saskatoon, Canada.
| |
Collapse
|
3
|
Manoharan GB, Laurini C, Bottone S, Ben Fredj N, Abankwa DK. K-Ras Binds Calmodulin-Related Centrin1 with Potential Implications for K-Ras Driven Cancer Cell Stemness. Cancers (Basel) 2023; 15:3087. [PMID: 37370697 DOI: 10.3390/cancers15123087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Recent data suggest that K-Ras4B (hereafter K-Ras) can drive cancer cell stemness via calmodulin (CaM)-dependent, non-canonical Wnt-signalling. Here we examined whether another Ca2+-binding protein, the CaM-related centrin1, binds to K-Ras and could mediate some K-Ras functions that were previously ascribed to CaM. While CaM and centrin1 appear to distinguish between peptides that were derived from their classical targets, they both bind to K-Ras in cells. Cellular BRET- and immunoprecipitation data suggest that CaM engages more with K-Ras than centrin1 and that the interaction with the C-terminal membrane anchor of K-Ras is sufficient for this. Surprisingly, binding of neither K-Ras nor its membrane anchor alone to CaM or centrin1 is sensitive to inhibition of prenylation. In support of an involvement of the G-domain of K-Ras in cellular complexes with these Ca2+-binding proteins, we find that oncogenic K-RasG12V displays increased engagement with both CaM and centrin1. This is abrogated by addition of the D38A effector-site mutation, suggesting that K-RasG12V is held together with CaM or centrin1 in complexes with effectors. When treated with CaM inhibitors, the BRET-interaction of K-RasG12V with centrin1 was also disrupted in the low micromolar range, comparable to that with CaM. While CaM predominates in regulating functional membrane anchorage of K-Ras, it has a very similar co-distribution with centrin1 on mitotic organelles. Given these results, a significant overlap of the CaM- and centrin1-dependent functions of K-Ras is suggested.
Collapse
Affiliation(s)
- Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Christina Laurini
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Sara Bottone
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Nesrine Ben Fredj
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Daniel Kwaku Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| |
Collapse
|
4
|
Hauvermale AL, Cárdenas JJ, Bednarek SY, Steber CM. GA signaling expands: The plant UBX domain-containing protein 1 is a binding partner for the GA receptor. PLANT PHYSIOLOGY 2022; 190:2651-2670. [PMID: 36149293 PMCID: PMC9706445 DOI: 10.1093/plphys/kiac406] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/19/2022] [Indexed: 06/07/2023]
Abstract
The plant Ubiquitin Regulatory X (UBX) domain-containing protein 1 (PUX1) functions as a negative regulator of gibberellin (GA) signaling. GAs are plant hormones that stimulate seed germination, the transition to flowering, and cell elongation and division. Loss of Arabidopsis (Arabidopsis thaliana) PUX1 resulted in a "GA-overdose" phenotype including early flowering, increased stem and root elongation, and partial resistance to the GA-biosynthesis inhibitor paclobutrazol during seed germination and root elongation. Furthermore, GA application failed to stimulate further stem elongation or flowering onset suggesting that elongation and flowering response to GA had reached its maximum. GA hormone partially repressed PUX1 protein accumulation, and PUX1 showed a GA-independent interaction with the GA receptor GA-INSENSITIVE DWARF-1 (GID1). This suggests that PUX1 is GA regulated and/or regulates elements of the GA signaling pathway. Consistent with PUX1 function as a negative regulator of GA signaling, the pux1 mutant caused increased GID1 expression and decreased accumulation of the DELLA REPRESSOR OF GA1-3, RGA. PUX1 is a negative regulator of the hexameric AAA+ ATPase CDC48, a protein that functions in diverse cellular processes including unfolding proteins in preparation for proteasomal degradation, cell division, and expansion. PUX1 binding to GID1 required the UBX domain, a binding motif necessary for CDC48 interaction. Moreover, PUX1 overexpression in cell culture not only stimulated the disassembly of CDC48 hexamer but also resulted in co-fractionation of GID1, PUX1, and CDC48 subunits in velocity sedimentation assays. Based on our results, we propose that PUX1 and CDC48 are additional factors that need to be incorporated into our understanding of GA signaling.
Collapse
Affiliation(s)
- Amber L Hauvermale
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
- Molecular Plant Sciences, Washington State University, Pullman, Washington, USA
| | - Jessica J Cárdenas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | | |
Collapse
|
5
|
Nguyen K, López CA, Neale C, Van QN, Carpenter TS, Di Natale F, Travers T, Tran TH, Chan AH, Bhatia H, Frank PH, Tonelli M, Zhang X, Gulten G, Reddy T, Burns V, Oppelstrup T, Hengartner N, Simanshu DK, Bremer PT, Chen D, Glosli JN, Shrestha R, Turbyville T, Streitz FH, Nissley DV, Ingólfsson HI, Stephen AG, Lightstone FC, Gnanakaran S. Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophys J 2022; 121:3630-3650. [PMID: 35778842 PMCID: PMC9617161 DOI: 10.1016/j.bpj.2022.06.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Abstract
During the activation of mitogen-activated protein kinase (MAPK) signaling, the RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF bind to active RAS at the plasma membrane. The orientation of RAS at the membrane may be critical for formation of the RAS-RBDCRD complex and subsequent signaling. To explore how RAS membrane orientation relates to the protein dynamics within the RAS-RBDCRD complex, we perform multiscale coarse-grained and all-atom molecular dynamics (MD) simulations of KRAS4b bound to the RBD and CRD domains of RAF-1, both in solution and anchored to a model plasma membrane. Solution MD simulations describe dynamic KRAS4b-CRD conformations, suggesting that the CRD has sufficient flexibility in this environment to substantially change its binding interface with KRAS4b. In contrast, when the ternary complex is anchored to the membrane, the mobility of the CRD relative to KRAS4b is restricted, resulting in fewer distinct KRAS4b-CRD conformations. These simulations implicate membrane orientations of the ternary complex that are consistent with NMR measurements. While a crystal structure-like conformation is observed in both solution and membrane simulations, a particular intermolecular rearrangement of the ternary complex is observed only when it is anchored to the membrane. This configuration emerges when the CRD hydrophobic loops are inserted into the membrane and helices α3-5 of KRAS4b are solvent exposed. This membrane-specific configuration is stabilized by KRAS4b-CRD contacts that are not observed in the crystal structure. These results suggest modulatory interplay between the CRD and plasma membrane that correlate with RAS/RAF complex structure and dynamics, and potentially influence subsequent steps in the activation of MAPK signaling.
Collapse
Affiliation(s)
- Kien Nguyen
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Francesco Di Natale
- Applications, Simulations, and Quality, Lawrence Livermore National Laboratory, Livermore, California
| | | | - Timothy H Tran
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Albert H Chan
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Harsh Bhatia
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - Peter H Frank
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Gulcin Gulten
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Tyler Reddy
- CCS-7, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Violetta Burns
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Tomas Oppelstrup
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Nick Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Dhirendra K Simanshu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Peer-Timo Bremer
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - De Chen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - James N Glosli
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Rebika Shrestha
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Thomas Turbyville
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Dwight V Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
| |
Collapse
|
6
|
Huynh MV, Hobbs GA, Schaefer A, Pierobon M, Carey LM, Diehl JN, DeLiberty JM, Thurman RD, Cooke AR, Goodwin CM, Cook JH, Lin L, Waters AM, Rashid NU, Petricoin EF, Campbell SL, Haigis KM, Simeone DM, Lyssiotis CA, Cox AD, Der CJ. Functional and biological heterogeneity of KRAS Q61 mutations. Sci Signal 2022; 15:eabn2694. [PMID: 35944066 PMCID: PMC9534304 DOI: 10.1126/scisignal.abn2694] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Missense mutations at the three hotspots in the guanosine triphosphatase (GTPase) RAS-Gly12, Gly13, and Gln61 (commonly known as G12, G13, and Q61, respectively)-occur differentially among the three RAS isoforms. Q61 mutations in KRAS are infrequent and differ markedly in occurrence. Q61H is the predominant mutant (at 57%), followed by Q61R/L/K (collectively 40%), and Q61P and Q61E are the rarest (2 and 1%, respectively). Probability analysis suggested that mutational susceptibility to different DNA base changes cannot account for this distribution. Therefore, we investigated whether these frequencies might be explained by differences in the biochemical, structural, and biological properties of KRASQ61 mutants. Expression of KRASQ61 mutants in NIH 3T3 fibroblasts and RIE-1 epithelial cells caused various alterations in morphology, growth transformation, effector signaling, and metabolism. The relatively rare KRASQ61E mutant stimulated actin stress fiber formation, a phenotype distinct from that of KRASQ61H/R/L/P, which disrupted actin cytoskeletal organization. The crystal structure of KRASQ61E was unexpectedly similar to that of wild-type KRAS, a potential basis for its weak oncogenicity. KRASQ61H/L/R-mutant pancreatic ductal adenocarcinoma (PDAC) cell lines exhibited KRAS-dependent growth and, as observed with KRASG12-mutant PDAC, were susceptible to concurrent inhibition of ERK-MAPK signaling and of autophagy. Our results uncover phenotypic heterogeneity among KRASQ61 mutants and support the potential utility of therapeutic strategies that target KRASQ61 mutant-specific signaling and cellular output.
Collapse
Affiliation(s)
- Minh V. Huynh
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - G. Aaron Hobbs
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Leiah M. Carey
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan M. DeLiberty
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D. Thurman
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adelaide R. Cooke
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua H. Cook
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical
School, Boston, MA 02115, USA
| | - Lin Lin
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Andrew M. Waters
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Naim U. Rashid
- Department of Biostatistics, University of North Carolina
at Chapel Hill, NC 27955, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Sharon L. Campbell
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin M. Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
- Harvard Digestive Disease Center, Harvard Medical School,
Boston, MA 02115, USA
| | - Diane M. Simeone
- Perlmutter Cancer Center, New York University, New York,
NY10016, USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of
Gastroenterology, University of Michigan, Ann Arbor, MI 48198, USA
- University of Michigan Comprehensive Cancer Center, Ann
Arbor, MI 48109, USA
| | - Adrienne D. Cox
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North
Carolina at Chapel Hill, Chapel Hill, NC 2799, USA
| | - Channing J. Der
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
7
|
Huynh MV, Parsonage D, Forshaw TE, Chirasani VR, Hobbs GA, Wu H, Lee J, Furdui CM, Poole LB, Campbell SL. Oncogenic KRAS G12C: Kinetic and redox characterization of covalent inhibition. J Biol Chem 2022; 298:102186. [PMID: 35753348 PMCID: PMC9352912 DOI: 10.1016/j.jbc.2022.102186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 12/02/2022] Open
Abstract
The recent development of mutant-selective inhibitors for the oncogenic KRASG12C allele has generated considerable excitement. These inhibitors covalently engage the mutant C12 thiol located within the phosphoryl binding loop of RAS, locking the KRASG12C protein in an inactive state. While clinical trials of these inhibitors have been promising, mechanistic questions regarding the reactivity of this thiol remain. Here, we show by NMR and an independent biochemical assay that the pKa of the C12 thiol is depressed (pKa ∼7.6), consistent with susceptibility to chemical ligation. Using a validated fluorescent KRASY137W variant amenable to stopped-flow spectroscopy, we characterized the kinetics of KRASG12C fluorescence changes upon addition of ARS-853 or AMG 510, noting that at low temperatures, ARS-853 addition elicited both a rapid first phase of fluorescence change (attributed to binding, Kd = 36.0 ± 0.7 μM) and a second, slower pH-dependent phase, taken to represent covalent ligation. Consistent with the lower pKa of the C12 thiol, we found that reversible and irreversible oxidation of KRASG12C occurred readily both in vitro and in the cellular environment, preventing the covalent binding of ARS-853. Moreover, we found that oxidation of the KRASG12C Cys12 to a sulfinate altered RAS conformation and dynamics to be more similar to KRASG12D in comparison to the unmodified protein, as assessed by molecular dynamics simulations. Taken together, these findings provide insight for future KRASG12C drug discovery efforts, and identify the occurrence of G12C oxidation with currently unknown biological ramifications.
Collapse
Affiliation(s)
- Minh V Huynh
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tom E Forshaw
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Venkat R Chirasani
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - G Aaron Hobbs
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hanzhi Wu
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jingyun Lee
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
| | - Sharon L Campbell
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| |
Collapse
|
8
|
Duncan ED, Han KJ, Trout MA, Prekeris R. Ubiquitylation by Rab40b/Cul5 regulates Rap2 localization and activity during cell migration. J Cell Biol 2022; 221:213068. [PMID: 35293963 PMCID: PMC8931537 DOI: 10.1083/jcb.202107114] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/08/2021] [Accepted: 02/01/2022] [Indexed: 02/07/2023] Open
Abstract
Cell migration is a complex process that involves coordinated changes in membrane transport and actin cytoskeleton dynamics. Ras-like small monomeric GTPases, such as Rap2, play a key role in regulating actin cytoskeleton dynamics and cell adhesions. However, how Rap2 function, localization, and activation are regulated during cell migration is not fully understood. We previously identified the small GTPase Rab40b as a regulator of breast cancer cell migration. Rab40b contains a suppressor of cytokine signaling (SOCS) box, which facilitates binding to Cullin5, a known E3 ubiquitin ligase component responsible for protein ubiquitylation. In this study, we show that the Rab40b/Cullin5 complex ubiquitylates Rap2. Importantly, we demonstrate that ubiquitylation regulates Rap2 activation as well as recycling of Rap2 from the endolysosomal compartment to the lamellipodia of migrating breast cancer cells. Based on these data, we propose that Rab40b/Cullin5 ubiquitylates and regulates Rap2-dependent actin dynamics at the leading edge, a process that is required for breast cancer cell migration and invasion.
Collapse
Affiliation(s)
- Emily D Duncan
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ke-Jun Han
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Margaret A Trout
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
9
|
Cluet D, Vergier B, Levy NP, Dehau L, Thurman A, Amri I, Spichty M. Titration of apparent in-cellula affinities of protein-protein interactions. Chembiochem 2021; 23:e202100640. [PMID: 34932835 DOI: 10.1002/cbic.202100640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/21/2021] [Indexed: 11/07/2022]
Abstract
A genetic assay permits simultaneous quantification of two interacting proteins and their bound fraction at the single-cell level using flow cytometry. Apparent in-cellula affinities of protein-protein interactions can be extracted from the acquired data through a titration-like analysis. The applicability of this approach is demonstrated on a diverse set of interactions with proteins from different families and organisms and with in-vitro dissociation constants ranging from picomolar to micromolar.
Collapse
Affiliation(s)
- David Cluet
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Blandine Vergier
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Nicolas-Pierre Levy
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Lucie Dehau
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Alexandre Thurman
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Ikram Amri
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Martin Spichty
- Laboratoire d'Innovation Moléculaire et Applications, Université de Strasbourg -, Centre National de la Recherche Scientifique, Université de Haute-Alsace, 3 bis rue Alfred Werner, 68057, Mulhouse Cedex, France
| |
Collapse
|
10
|
Cui Y, Ma L, Schacke S, Yin JC, Hsueh YP, Jin H, Morrison H. Merlin cooperates with neurofibromin and Spred1 to suppress the Ras-Erk pathway. Hum Mol Genet 2020; 29:3793-3806. [PMID: 33331896 DOI: 10.1093/hmg/ddaa263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022] Open
Abstract
The Ras-Erk pathway is frequently overactivated in human tumors. Neurofibromatosis types 1 and 2 (NF1, NF2) are characterized by multiple tumors of Schwann cell origin. The NF1 tumor suppressor neurofibromin is a principal Ras-GAP accelerating Ras inactivation, whereas the NF2 tumor suppressor merlin is a scaffold protein coordinating multiple signaling pathways. We have previously reported that merlin interacts with Ras and p120RasGAP. Here, we show that merlin can also interact with the neurofibromin/Spred1 complex via merlin-binding sites present on both proteins. Further, merlin can directly bind to the Ras-binding domain (RBD) and the kinase domain (KiD) of Raf1. As the third component of the neurofibromin/Spred1 complex, merlin cannot increase the Ras-GAP activity; rather, it blocks Ras binding to Raf1 by functioning as a 'selective Ras barrier'. Merlin-deficient Schwann cells require the Ras-Erk pathway activity for proliferation. Accordingly, suppression of the Ras-Erk pathway likely contributes to merlin's tumor suppressor activity. Taken together, our results, and studies by others, support targeting or co-targeting of this pathway as a therapy for NF2 inactivation-related tumors.
Collapse
Affiliation(s)
- Yan Cui
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Lin Ma
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.,College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Stephan Schacke
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Jiani C Yin
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Laboratory of Biotherapy, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou 310016, China
| | - Helen Morrison
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Germany
| |
Collapse
|
11
|
Travers T, López CA, Agamasu C, Hettige JJ, Messing S, García AE, Stephen AG, Gnanakaran S. Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD. Biophys J 2020; 119:525-538. [PMID: 32649863 PMCID: PMC7399501 DOI: 10.1016/j.bpj.2020.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 11/25/2022] Open
Abstract
CRAF activation requires binding to membrane-anchored and active GTP-bound RAS. Whereas its RAS-binding domain (RBD) contains the main binding interface to the RAS G domain, its cysteine-rich domain (CRD) is responsible for association to anionic lipid-rich membranes. Both RAF domains are connected by a short linker, and it remains unclear if the two domains act independently or if one domain can impact the function of the other. Here, we used a combination of coarse-grained and all-atom molecular dynamics simulations of a CRAF RBD-CRD construct to investigate the dynamics of the RBD when it is tethered to CRD that is anchored to a POPC:POPS model membrane. First, we show that the RBD positioning is very dynamic with a preferential localization near the membrane surface. Next, we show that membrane-localized RBD has its RAS-binding interface mostly inaccessible because of its proximity to the membrane. Several positively charged residues in this interface were identified from simulations as important for driving RBD association to the membrane. Surface plasmon resonance (SPR) measurements confirmed that mutations of these RBD residues reduced the liposome partitioning of RBD-CRD. Last, simulations indicated that the presence of RBD near the membrane led to a local enrichment of anionic lipids that could potentially enhance the membrane affinity of the entire RBD-CRD construct. This was supported by SPR measurements that showed stronger liposome partitioning of RBD-CRD relative to CRD alone. These findings thus suggest that the RBD and CRD have synergistic effects on their membrane dynamics, with CRD bringing RBD closer to the membrane that impacts its accessibility to RAS and with RBD causing local anionic lipid enrichment that enhances the overall affinity between the membrane and RBD-CRD. These mechanisms have potential implications on the order of events of the interactions between RAS and CRAF at the membrane.
Collapse
Affiliation(s)
- Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico
| | - Constance Agamasu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | | | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico.
| |
Collapse
|
12
|
Lowegard AU, Frenkel MS, Holt GT, Jou JD, Ojewole AA, Donald BR. Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface. PLoS Comput Biol 2020; 16:e1007447. [PMID: 32511232 PMCID: PMC7329130 DOI: 10.1371/journal.pcbi.1007447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 07/01/2020] [Accepted: 05/13/2020] [Indexed: 11/25/2022] Open
Abstract
The K* algorithm provably approximates partition functions for a set of states (e.g., protein, ligand, and protein-ligand complex) to a user-specified accuracy ε. Often, reaching an ε-approximation for a particular set of partition functions takes a prohibitive amount of time and space. To alleviate some of this cost, we introduce two new algorithms into the osprey suite for protein design: fries, a Fast Removal of Inadequately Energied Sequences, and EWAK*, an Energy Window Approximation to K*. fries pre-processes the sequence space to limit a design to only the most stable, energetically favorable sequence possibilities. EWAK* then takes this pruned sequence space as input and, using a user-specified energy window, calculates K* scores using the lowest energy conformations. We expect fries/EWAK* to be most useful in cases where there are many unstable sequences in the design sequence space and when users are satisfied with enumerating the low-energy ensemble of conformations. In combination, these algorithms provably retain calculational accuracy while limiting the input sequence space and the conformations included in each partition function calculation to only the most energetically favorable, effectively reducing runtime while still enriching for desirable sequences. This combined approach led to significant speed-ups compared to the previous state-of-the-art multi-sequence algorithm, BBK*, while maintaining its efficiency and accuracy, which we show across 40 different protein systems and a total of 2,826 protein design problems. Additionally, as a proof of concept, we used these new algorithms to redesign the protein-protein interface (PPI) of the c-Raf-RBD:KRas complex. The Ras-binding domain of the protein kinase c-Raf (c-Raf-RBD) is the tightest known binder of KRas, a protein implicated in difficult-to-treat cancers. fries/EWAK* accurately retrospectively predicted the effect of 41 different sets of mutations in the PPI of the c-Raf-RBD:KRas complex. Notably, these mutations include mutations whose effect had previously been incorrectly predicted using other computational methods. Next, we used fries/EWAK* for prospective design and discovered a novel point mutation that improves binding of c-Raf-RBD to KRas in its active, GTP-bound state (KRasGTP). We combined this new mutation with two previously reported mutations (which were highly-ranked by osprey) to create a new variant of c-Raf-RBD, c-Raf-RBD(RKY). fries/EWAK* in osprey computationally predicted that this new variant binds even more tightly than the previous best-binding variant, c-Raf-RBD(RK). We measured the binding affinity of c-Raf-RBD(RKY) using a bio-layer interferometry (BLI) assay, and found that this new variant exhibits single-digit nanomolar affinity for KRasGTP, confirming the computational predictions made with fries/EWAK*. This new variant binds roughly five times more tightly than the previous best known binder and roughly 36 times more tightly than the design starting point (wild-type c-Raf-RBD). This study steps through the advancement and development of computational protein design by presenting theory, new algorithms, accurate retrospective designs, new prospective designs, and biochemical validation. Computational structure-based protein design is an innovative tool for redesigning proteins to introduce a particular or novel function. One such function is improving the binding of one protein to another, which can increase our understanding of important protein systems. Herein we introduce two novel, provable algorithms, fries and EWAK*, for more efficient computational structure-based protein design as well as their application to the redesign of the c-Raf-RBD:KRas protein-protein interface. These new algorithms speed-up computational structure-based protein design while maintaining accurate calculations, allowing for larger, previously infeasible protein designs. Additionally, using fries and EWAK* within the osprey suite, we designed the tightest known binder of KRas, a heavily studied cancer target that interacts with a number of different proteins. This previously undiscovered variant of a KRas-binding domain, c-Raf-RBD, has potential to serve as a tool to further probe the protein-protein interface of KRas with its effectors and its discovery alone emphasizes the potential for more successful applications of computational structure-based protein design.
Collapse
Affiliation(s)
- Anna U. Lowegard
- Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Marcel S. Frenkel
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Graham T. Holt
- Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Jonathan D. Jou
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Adegoke A. Ojewole
- Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
| | - Bruce R. Donald
- Department of Computer Science, Duke University, Durham, North Carolina, United States of America
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
13
|
Nussinov R, Jang H, Zhang M, Tsai CJ, Sablina AA. The Mystery of Rap1 Suppression of Oncogenic Ras. Trends Cancer 2020; 6:369-379. [PMID: 32249186 PMCID: PMC7211489 DOI: 10.1016/j.trecan.2020.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 12/11/2022]
Abstract
Decades ago, Rap1, a small GTPase very similar to Ras, was observed to suppress oncogenic Ras phenotype, reverting its transformation. The proposed reason, persisting since, has been competition between Ras and Rap1 for a common target. Yet, none was found. There was also Rap1's puzzling suppression of Raf-1 versus activation of BRAF. Reemerging interest in Rap1 envisages capturing its Ras suppression action by inhibitors. Here, we review the literature and resolve the enigma. In vivo oncogenic Ras exists in isoform-distinct nanoclusters. The presence of Rap1 within the nanoclusters reduces the number of the clustered oncogenic Ras molecules, thus suppressing Raf-1 activation and mitogen-activated protein kinase (MAPK) signaling. Nanoclustering suggests that Rap1 suppression is Ras isoform dependent. Altogether, a potent Rap1-like inhibitor appears unlikely.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Anna A Sablina
- VIB Center for the Biology of Disease and KU Leuven Department of Oncology, Leuven Cancer Institute, Leuven, Belgium
| |
Collapse
|
14
|
Kopra K, Vuorinen E, Abreu-Blanco M, Wang Q, Eskonen V, Gillette W, Pulliainen AT, Holderfield M, Härmä H. Homogeneous Dual-Parametric-Coupled Assay for Simultaneous Nucleotide Exchange and KRAS/RAF-RBD Interaction Monitoring. Anal Chem 2020; 92:4971-4979. [PMID: 32106676 PMCID: PMC7143314 DOI: 10.1021/acs.analchem.9b05126] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/28/2020] [Indexed: 02/07/2023]
Abstract
We have developed a rapid and sensitive single-well dual-parametric method introduced in linked RAS nucleotide exchange and RAS/RAF-RBD interaction assays. RAS mutations are frequent drivers of multiple different human cancers, but the development of therapeutic strategies has been challenging. Traditionally, efforts to disrupt the RAS function have focused on nucleotide exchange inhibitors, GTP-RAS interaction inhibitors, and activators increasing GTPase activity of mutant RAS proteins. As the amount of biological knowledge grows, targeted biochemical assays enabling high-throughput screening have become increasingly interesting. We have previously introduced a homogeneous quenching resonance energy transfer (QRET) assay for nucleotide binding studies with RAS and heterotrimeric G proteins. Here, we introduce a novel homogeneous signaling technique called QTR-FRET, which combine QRET technology and time-resolved Förster resonance energy transfer (TR-FRET). The dual-parametric QTR-FRET technique enables the linking of guanine nucleotide exchange factor-induced Eu3+-GTP association to RAS, monitored at 615 nm, and subsequent Eu3+-GTP-loaded RAS interaction with RAF-RBD-Alexa680 monitored at 730 nm. Both reactions were monitored in a single-well assay applicable for inhibitor screening and real-time reaction monitoring. This homogeneous assay enables separable detection of both nucleotide exchange and RAS/RAF interaction inhibitors using low nanomolar protein concentrations. To demonstrate a wider applicability as a screening and real-time reaction monitoring method, the QTR-FRET technique was also applied for G(i)α GTP-loading and pertussis toxin-catalyzed ADP-ribosylation of G(i)α, for which we synthesized a novel γ-GTP-Eu3+ molecule. The study indicates that the QTR-FRET detection technique presented here can be readily applied to dual-parametric assays for various targets.
Collapse
Affiliation(s)
- Kari Kopra
- Materials
Chemistry and Chemical Analysis, University
of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Emmiliisa Vuorinen
- Materials
Chemistry and Chemical Analysis, University
of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Maria Abreu-Blanco
- Leidos
Biomedical Research, Inc., Frederick National
Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Qi Wang
- Institute
of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Ville Eskonen
- Materials
Chemistry and Chemical Analysis, University
of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - William Gillette
- Leidos
Biomedical Research, Inc., Frederick National
Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Arto T. Pulliainen
- Institute
of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Matthew Holderfield
- Leidos
Biomedical Research, Inc., Frederick National
Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Harri Härmä
- Materials
Chemistry and Chemical Analysis, University
of Turku, Vatselankatu 2, 20500 Turku, Finland
| |
Collapse
|
15
|
Cluet D, Amri I, Vergier B, Léault J, Audibert A, Grosjean C, Calabrési D, Spichty M. A Quantitative Tri-fluorescent Yeast Two-hybrid System: From Flow Cytometry to In cellula Affinities. Mol Cell Proteomics 2020; 19:701-715. [PMID: 32015065 PMCID: PMC7124468 DOI: 10.1074/mcp.tir119.001692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/31/2020] [Indexed: 12/14/2022] Open
Abstract
We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pm to 17 μm After only two hours of reaction, expression of the reporter can be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflect the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.
Collapse
Affiliation(s)
- David Cluet
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Ikram Amri
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Blandine Vergier
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Jérémie Léault
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Astrid Audibert
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Clémence Grosjean
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Dylan Calabrési
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Martin Spichty
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France.
| |
Collapse
|
16
|
Muratcioglu S, Aydin C, Odabasi E, Ozdemir ES, Firat-Karalar EN, Jang H, Tsai CJ, Nussinov R, Kavakli IH, Gursoy A, Keskin O. Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling. J Mol Biol 2020; 432:1199-1215. [PMID: 31931009 PMCID: PMC8533050 DOI: 10.1016/j.jmb.2020.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 12/31/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023]
Abstract
Ras recruits and activates effectors that transmit receptor-initiated signals. Monomeric Ras can bind Raf; however, Raf's activation requires dimerization, which can be facilitated by Ras dimerization. Previously, we showed that active K-Ras4B dimerizes in silico and in vitro through two major interfaces: (i) β-interface, mapped to Switch I and effector-binding regions, (ii) α-interface at the allosteric lobe. Here, we chose constitutively active K-Ras4B as our control and two double mutants (K101D and R102E; and R41E and K42D) in the α- and β-interfaces. Two of the mutations are from The Cancer Genome Atlas (TCGA) and the Catalogue Of Somatic Mutations In Cancer (COSMIC) data sets. R41 and R102 are found in several adenocarcinomas in Ras isoforms. We performed site-directed mutagenesis, cellular localization experiments, and molecular dynamics (MD) simulations to assess the impact of the mutations on K-Ras4B dimerization and function. α-interface K101D/R102E double mutations reduced dimerization but only slightly reduced downstream phosphorylated extracellular signal-regulated kinase (ERK) (pERK) levels. While β-interface R41E/K42D double mutations did not interfere with dimerization, they almost completely blocked K-Ras4B-mediated ERK phosphorylation. Both double mutations increased downstream phosphorylated Akt (pAkt) levels in cells. Changes in pERK and pAkt levels altered ERK- and Akt-regulated gene expressions, such as EGR1, JUN, and BCL2L11. These results underscore the role of the α-interface in K-Ras4B homodimerization and the β-surface in effector binding. MD simulations highlight that the membrane and hypervariable region (HVR) interact with both α- and β-interfaces of K-Ras4B mutants, respectively, inhibiting homodimerization and probably effector binding. Mutations at both interfaces interfered with mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase signaling but in different forms and extents. We conclude that dimerization is not necessary but enhances downstream MAPK signaling.
Collapse
Affiliation(s)
- Serena Muratcioglu
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey
| | - Cihan Aydin
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey
| | - Ezgi Odabasi
- Departments of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - E Sila Ozdemir
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey
| | | | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ibrahim Halil Kavakli
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey; Departments of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Attila Gursoy
- Departments of Computer Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey.
| | - Ozlem Keskin
- Departments of Chemical and Biological Engineering, Research Center for Translational Medicine, Koc University, Istanbul 34450, Turkey.
| |
Collapse
|
17
|
Serebriiskii IG, Elmekawy M, Golemis EA. Identification of the KRIT1 Protein by LexA-Based Yeast Two-Hybrid System. Methods Mol Biol 2020; 2152:269-289. [PMID: 32524559 DOI: 10.1007/978-1-0716-0640-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cerebral cavernous malformation (CCM) is a vascular malformation of the central nervous system that is associated with leaky capillaries, and a predisposition to serious clinical conditions including intracerebral hemorrhage and seizures. Germline or sporadic mutations in the CCM1/KRIT1 gene are responsible for the majority of cases of CCM. In this article, we describe the original characterization of the CCM1/KRIT1 gene. This cloning was done through the use of a variant of the yeast two-hybrid screen known as the interaction trap, using the RAS-family GTPase KREV1/RAP1A as a bait. The partial clone of KRIT1 (Krev1 Interaction Trapped) initially identified was extended through 5'RACE and computational analysis to obtain a full-length cDNA, then used in a sequential screen to define the integrin-associated ICAP1 protein as a KRIT1 partner protein. We discuss how these interactions are relevant to the current understanding of KRIT1/CCM1 biology, and provide a protocol for library screening with the Interaction Trap.
Collapse
Affiliation(s)
- Ilya G Serebriiskii
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia.
| | - Mohamed Elmekawy
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Moscow Institute of Physics and Technology, Moscow Region, Russia
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
| |
Collapse
|
18
|
Nussinov R, Tsai CJ, Jang H. Does Ras Activate Raf and PI3K Allosterically? Front Oncol 2019; 9:1231. [PMID: 31799192 PMCID: PMC6874141 DOI: 10.3389/fonc.2019.01231] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
The mechanism through which oncogenic Ras activates its effectors is vastly important to resolve. If allostery is at play, then targeting allosteric pathways could help in quelling activation of MAPK (Raf/MEK/ERK) and PI3K (PI3K/Akt/mTOR) cell proliferation pathways. On the face of it, allosteric activation is reasonable: Ras binding perturbs the conformational ensembles of its effectors. Here, however, we suggest that at least for Raf, PI3K, and NORE1A (RASSF5), that is unlikely. Raf's long disordered linker dampens effective allosteric activation. Instead, we suggest that the high-affinity Ras–Raf binding relieves Raf's autoinhibition, shifting Raf's ensemble from the inactive to the nanocluster-mediated dimerized active state, as Ras also does for NORE1A. PI3K is recruited and allosterically activated by RTK (e.g., EGFR) at the membrane. Ras restrains PI3K's distribution and active site orientation. It stabilizes and facilitates PIP2 binding at the active site and increases the PI3K residence time at the membrane. Thus, RTKs allosterically activate PI3Kα; however, merging their action with Ras accomplishes full activation. Here we review their activation mechanisms in this light and draw attention to implications for their pharmacology.
Collapse
Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
| |
Collapse
|
19
|
Feng G, Qin L, Liao Z, Xiao X, Li B, Cui W, Liang L, Mo Y, Huang G, Li P, Zhou X, Zhang Z, Xiao X. Knockdown Rab11-FIP2 inhibits migration and invasion of nasopharyngeal carcinoma via suppressing Rho GTPase signaling. J Cell Biochem 2019; 121:1072-1086. [PMID: 31452257 DOI: 10.1002/jcb.29344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
Abstract
Rab11 family interacting protein 2 (Rab11-FIP2) is a conserved protein and effector molecule for the small GTPase Rab11. By interacting with Rab11 and MYO5B, Rab11-FIP2 regulates endosome trafficking of plasma membrane proteins, promoting cellular motility. The endosomal trafficking system in nasopharyngeal carcinoma (NPC) remains unclear. Here, an outlier analysis using the Oncomine database suggested that Rab11-FIP2 but not Rab11 and MYO5B was overexpressed in NPC. We confirmed that the transcription of Rab11-FIP2 was upregulated in NPC cell lines and primary tumor tissues as compared with a normal nasopharyngeal epithelial cell line and normal nasopharynx tissues. We further confirmed the elevated protein expression level of Rab11-FIP2 in NPC biopsies. Instead of regulating the epithelial-mesenchymal transition or Akt signaling pathway, knockdown of Rab11-FIP2 inhibited the migration and invasion ability of NPC cell lines by decreasing the expression of Rac and Cdc42. In summary, Rab11-FIP2 could be an oncogene in NPC, mainly contributing to metastatic capacity by activating Rho GTPase signaling.
Collapse
Affiliation(s)
- Guofei Feng
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Liting Qin
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhipeng Liao
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiling Xiao
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Bo Li
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wanmeng Cui
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Libin Liang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yingxi Mo
- Department of Research, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Guangwu Huang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ping Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoying Zhou
- Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Zhe Zhang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xue Xiao
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| |
Collapse
|
20
|
Goody RS, Müller MP, Rauh D. Mutant-Specific Targeting of Ras G12C Activity by Covalently Reacting Small Molecules. Cell Chem Biol 2019; 26:1338-1348. [PMID: 31378709 DOI: 10.1016/j.chembiol.2019.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/08/2019] [Accepted: 07/07/2019] [Indexed: 11/17/2022]
Abstract
In this review we discuss and compare recently introduced molecules that are able to react covalently with an oncogenic mutant of KRas, KRas G12C. Two different classes of compounds in question have been developed, both leading to the mutant being locked in the inactive (guanosine diphosphate [GDP]-bound) state. The first are compounds that interact reversibly with the switch-II pocket (S-IIP) before covalent interaction. The second class interact in a competitive manner with the GDP/guanosine triphosphate (GTP) binding site. The fundamental physico-chemical principles of the two inhibitor classes are evaluated. For GDP/GTP-competing molecules, we show that special attention must be paid to the influence of guanine nucleotide exchange factors (GEFs) and their elevated activity in cells harboring abnormally activated Ras mutants. A new approach is suggested involving compounds that interact with the guanine binding site of the GTPase, but in a manner that is independent of the interaction of the GTPase with its cognate GEF.
Collapse
Affiliation(s)
- Roger S Goody
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Matthias P Müller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany; Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany; Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| |
Collapse
|
21
|
Eijkelenboom A, van Schaik FMA, van Es RM, Ten Broek RW, Rinne T, van der Vleuten C, Flucke U, Ligtenberg MJL, Rehmann H. Functional characterisation of a novel class of in-frame insertion variants of KRAS and HRAS. Sci Rep 2019; 9:8239. [PMID: 31160609 PMCID: PMC6547725 DOI: 10.1038/s41598-019-44584-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022] Open
Abstract
Mutations in the RAS genes are identified in a variety of clinical settings, ranging from somatic mutations in oncology to germline mutations in developmental disorders, also known as 'RASopathies', and vascular malformations/overgrowth syndromes. Generally single amino acid substitutions are identified, that result in an increase of the GTP bound fraction of the RAS proteins causing constitutive signalling. Here, a series of 7 in-frame insertions and duplications in HRAS (n = 5) and KRAS (n = 2) is presented, resulting in the insertion of 7-10 amino acids residues in the switch II region. These variants were identified in routine diagnostic screening of 299 samples for somatic mutations in vascular malformations/overgrowth syndromes (n = 6) and in germline analyses for RASopathies (n = 1). Biophysical characterization shows the inability of Guanine Nucleotide Exchange Factors to induce GTP loading and reduced intrinsic and GAP-stimulated GTP hydrolysis. As a consequence of these opposing effects, increased RAS signalling is detected in a cellular model system. Therefore these in-frame insertions represent a new class of weakly activating clinically relevant RAS variants.
Collapse
Affiliation(s)
- Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Frederik M A van Schaik
- Department of Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Robert M van Es
- Department of Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands
| | - Roel W Ten Broek
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Carine van der Vleuten
- Department of Dermatology, Radboudumc Center of Expertise Hecovan, Radboud university medical center, Nijmegen, The Netherlands
| | - Uta Flucke
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Holger Rehmann
- Department of Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht, 3584 CX, The Netherlands. .,Expertise Centre for Structural Biology, University Medical Center Utrecht, Utrecht University, Utrecht, 3584 CX, The Netherlands.
| |
Collapse
|
22
|
Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput Biol 2019; 15:e1006658. [PMID: 30921324 PMCID: PMC6438456 DOI: 10.1371/journal.pcbi.1006658] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
At the root of the so-called precision medicine or precision oncology, which is our focus here, is the hypothesis that cancer treatment would be considerably better if therapies were guided by a tumor’s genomic alterations. This hypothesis has sparked major initiatives focusing on whole-genome and/or exome sequencing, creation of large databases, and developing tools for their statistical analyses—all aspiring to identify actionable alterations, and thus molecular targets, in a patient. At the center of the massive amount of collected sequence data is their interpretations that largely rest on statistical analysis and phenotypic observations. Statistics is vital, because it guides identification of cancer-driving alterations. However, statistics of mutations do not identify a change in protein conformation; therefore, it may not define sufficiently accurate actionable mutations, neglecting those that are rare. Among the many thematic overviews of precision oncology, this review innovates by further comprehensively including precision pharmacology, and within this framework, articulating its protein structural landscape and consequences to cellular signaling pathways. It provides the underlying physicochemical basis, thereby also opening the door to a broader community.
Collapse
|
23
|
M-Ras/Shoc2 signaling modulates E-cadherin turnover and cell-cell adhesion during collective cell migration. Proc Natl Acad Sci U S A 2019; 116:3536-3545. [PMID: 30808747 PMCID: PMC6397545 DOI: 10.1073/pnas.1805919116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Collective cell migration is required for normal embryonic development and contributes to various biological processes, including wound healing and cancer cell invasion. The M-Ras GTPase and its effector, the Shoc2 scaffold, are proteins mutated in the developmental RASopathy Noonan syndrome, and, here, we report that activated M-Ras recruits Shoc2 to cell surface junctions where M-Ras/Shoc2 signaling contributes to the dynamic regulation of cell-cell junction turnover required for collective cell migration. MCF10A cells expressing the dominant-inhibitory M-RasS27N variant or those lacking Shoc2 exhibited reduced junction turnover and were unable to migrate effectively as a group. Through further depletion/reconstitution studies, we found that M-Ras/Shoc2 signaling contributes to junction turnover by modulating the E-cadherin/p120-catenin interaction and, in turn, the junctional expression of E-cadherin. The regulatory effect of the M-Ras/Shoc2 complex was mediated at least in part through the phosphoregulation of p120-catenin and required downstream ERK cascade activation. Strikingly, cells rescued with the Noonan-associated, myristoylated-Shoc2 mutant (Myr-Shoc2) displayed a gain-of-function (GOF) phenotype, with the cells exhibiting increased junction turnover and reduced E-cadherin/p120-catenin binding and migrating as a faster but less cohesive group. Consistent with these results, Noonan-associated C-Raf mutants that bypass the need for M-Ras/Shoc2 signaling exhibited a similar GOF phenotype when expressed in Shoc2-depleted MCF10A cells. Finally, expression of the Noonan-associated Myr-Shoc2 or C-Raf mutants, but not their WT counterparts, induced gastrulation defects indicative of aberrant cell migration in zebrafish embryos, further demonstrating the function of the M-Ras/Shoc2/ERK cascade signaling axis in the dynamic control of coordinated cell movement.
Collapse
|
24
|
Oncogenic KRas mobility in the membrane and signaling response. Semin Cancer Biol 2019; 54:109-113. [DOI: 10.1016/j.semcancer.2018.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 12/12/2022]
|
25
|
Autoinhibition in Ras effectors Raf, PI3Kα, and RASSF5: a comprehensive review underscoring the challenges in pharmacological intervention. Biophys Rev 2018; 10:1263-1282. [PMID: 30269291 PMCID: PMC6233353 DOI: 10.1007/s12551-018-0461-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 02/06/2023] Open
Abstract
Autoinhibition is an effective mechanism that guards proteins against spurious activation. Despite its ubiquity, the distinct organizations of the autoinhibited states and their release mechanisms differ. Signaling is most responsive to the cell environment only if a small shift in the equilibrium is required to switch the system from an inactive (occluded) to an active (exposed) state. Ras signaling follows this paradigm. This underscores the challenge in pharmacological intervention to exploit and enhance autoinhibited states. Here, we review autoinhibition and release mechanisms at the membrane focusing on three representative Ras effectors, Raf protein kinase, PI3Kα lipid kinase, and NORE1A (RASSF5) tumor suppressor, and point to the ramifications to drug discovery. We further touch on Ras upstream and downstream signaling, Ras activation, and the Ras superfamily in this light, altogether providing a broad outlook of the principles and complexities of autoinhibition.
Collapse
|
26
|
Phosphorylation promotes binding affinity of Rap-Raf complex by allosteric modulation of switch loop dynamics. Sci Rep 2018; 8:12976. [PMID: 30154518 PMCID: PMC6113251 DOI: 10.1038/s41598-018-31234-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/13/2018] [Indexed: 12/14/2022] Open
Abstract
The effects of phosphorylation of a serine residue on the structural and dynamic properties of Ras-like protein, Rap, and its interactions with effector protein Ras binding domain (RBD) of Raf kinase, in the presence of GTP, are investigated via molecular dynamics simulations. The simulations show that phosphorylation significantly effects the dynamics of functional loops of Rap which participate in the stability of the complex with effector proteins. The effects of phosphorylation on Rap are significant and detailed conformational analysis suggest that the Rap protein, when phosphorylated and with GTP ligand, samples different conformational space as compared to non-phosphorylated protein. In addition, phosphorylation of SER11 opens up a new cavity in the Rap protein which can be further explored for possible drug interactions. Residue network analysis shows that the phosphorylation of Rap results in a community spanning both Rap and RBD and strongly suggests transmission of allosteric effects of local alterations in Rap to distal regions of RBD, potentially affecting the downstream signalling. Binding free energy calculations suggest that phosphorylation of SER11 residue increases the binding between Rap and Raf corroborating the network analysis results. The increased binding of the Rap-Raf complex can have cascading effects along the signalling pathways where availability of Raf can influence the oncogenic effects of Ras proteins. These simulations underscore the importance of post translational modifications like phosphorylation on the functional dynamics in proteins and can be an alternative to drug-targeting, especially in notoriously undruggable oncoproteins belonging to Ras-like GTPase family.
Collapse
|
27
|
Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment. Nat Commun 2018; 9:3169. [PMID: 30093669 PMCID: PMC6085350 DOI: 10.1038/s41467-018-05707-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022] Open
Abstract
Targeting specific protein–protein interactions (PPIs) is an attractive concept for drug development, but hard to implement since intracellular antibodies do not penetrate cells and most small-molecule drugs are considered unsuitable for PPI inhibition. A potential solution to these problems is to select intracellular antibody fragments to block PPIs, use these antibody fragments for target validation in disease models and finally derive small molecules overlapping the antibody-binding site. Here, we explore this strategy using an anti-mutant RAS antibody fragment as a competitor in a small-molecule library screen for identifying RAS-binding compounds. The initial hits are optimized by structure-based design, resulting in potent RAS-binding compounds that interact with RAS inside the cells, prevent RAS-effector interactions and inhibit endogenous RAS-dependent signalling. Our results may aid RAS-dependent cancer drug development and demonstrate a general concept for developing small compounds to replace intracellular antibody fragments, enabling rational drug development to target validated PPIs. Intracellular antibodies can inhibit disease-relevant protein interactions, but inefficient cellular uptake limits their utility. Using a RAS-targeting intracellular antibody as a screening tool, the authors here identify small molecules that inhibit RAS-effector interactions and readily penetrate cells.
Collapse
|
28
|
Bery N, Cruz-Migoni A, Bataille CJ, Quevedo CE, Tulmin H, Miller A, Russell A, Phillips SE, Carr SB, Rabbitts TH. BRET-based RAS biosensors that show a novel small molecule is an inhibitor of RAS-effector protein-protein interactions. eLife 2018; 7:37122. [PMID: 29989546 PMCID: PMC6039175 DOI: 10.7554/elife.37122] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/16/2018] [Indexed: 12/13/2022] Open
Abstract
The RAS family of proteins is amongst the most highly mutated in human cancers and has so far eluded drug therapy. Currently, much effort is being made to discover mutant RAS inhibitors and in vitro screening for RAS-binding drugs must be followed by cell-based assays. Here, we have developed a robust set of bioluminescence resonance energy transfer (BRET)-based RAS biosensors that enable monitoring of RAS-effector interaction inhibition in living cells. These include KRAS, HRAS and NRAS and a variety of different mutations that mirror those found in human cancers with the major RAS effectors such as CRAF, PI3K and RALGDS. We highlighted the utility of these RAS biosensors by showing a RAS-binding compound is a potent pan-RAS-effector interactions inhibitor in cells. The RAS biosensors represent a useful tool to investigate and characterize the potency of anti-RAS inhibitors in cells and more generally any RAS protein-protein interaction (PPI) in cells. A group of proteins known as the RAS family plays a critical role in controlling animal cell growth and division. RAS proteins are normally active only some of the time, but genetic mutations can create permanently active forms of the proteins. These constantly interact with other proteins called effectors. In response, cells multiply uncontrollably and give rise to cancers. In an attempt to find new cancer treatments, researchers across the globe are trying to develop inhibitor drugs that prevent RAS and effector proteins from interacting. New drugs are often tested in laboratory experiments that directly apply the drugs to the proteins that they are designed to work on. But in some cases a drug may work wellin the laboratory but fail to work when used in cells. Unfortunately, there are few ways to judge how well inhibitor drugs work inside living cells. Bery et al. have now developed RAS biosensors – a collection of proteins that bind to RAS and produce light more brightly when RAS interacts with effector proteins in living cells. Tests on cells treated with an antibody that works inside cells and is known to prevent interactions between RAS and effector proteins confirmed that the RAS biosensors work well. Bery et al. then used the RAS biosensors to show that a new RAS inhibitor works in human cancer cells. The RAS biosensors are available upon request to researchers across the globe. They should form an important tool for testing potential treatments for cancers that contain mutated RAS proteins.
Collapse
Affiliation(s)
- Nicolas Bery
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Abimael Cruz-Migoni
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, United Kingdom
| | | | - Camilo E Quevedo
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Hanna Tulmin
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ami Miller
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Simon Ev Phillips
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Stephen B Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, United Kingdom.,Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Terence H Rabbitts
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
29
|
Travers T, López CA, Van QN, Neale C, Tonelli M, Stephen AG, Gnanakaran S. Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain. Sci Rep 2018; 8:8461. [PMID: 29855542 PMCID: PMC5981303 DOI: 10.1038/s41598-018-26832-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/18/2018] [Indexed: 01/14/2023] Open
Abstract
Activation of RAF kinase involves the association of its RAS-binding domain (RBD) and cysteine-rich domain (CRD) with membrane-anchored RAS. However, the overall architecture of the RAS/RBD/CRD ternary complex and the orientations of its constituent domains at the membrane remain unclear. Here, we have combined all-atom and coarse-grained molecular dynamics (MD) simulations with experimental data to construct and validate a model of membrane-anchored CRD, and used this as a basis to explore models of membrane-anchored RAS/RBD/CRD complex. First, simulations of the CRD revealed that it anchors to the membrane via insertion of its two hydrophobic loops, which is consistent with our NMR measurements of CRD bound to nanodiscs. Simulations of the CRD in the context of membrane-anchored RAS/RBD then show how CRD association with either RAS or RBD could play an unexpected role in guiding the membrane orientations of RAS/RBD. This finding has implications for the formation of RAS-RAS dimers, as different membrane orientations of RAS expose distinct putative dimerization interfaces.
Collapse
Affiliation(s)
- Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, United States
| | - Chris Neale
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Marco Tonelli
- National Magnetic Resource Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, United States
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.
| |
Collapse
|
30
|
Schöpel M, Shkura O, Seidel J, Kock K, Zhong X, Löffek S, Helfrich I, Bachmann HS, Scherkenbeck J, Herrmann C, Stoll R. Allosteric Activation of GDP-Bound Ras Isoforms by Bisphenol Derivative Plasticisers. Int J Mol Sci 2018; 19:ijms19041133. [PMID: 29642594 PMCID: PMC5979466 DOI: 10.3390/ijms19041133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 01/13/2023] Open
Abstract
The protein family of small GTPases controls cellular processes by acting as a binary switch between an active and an inactive state. The most prominent family members are H-Ras, N-Ras, and K-Ras isoforms, which are highly related and frequently mutated in cancer. Bisphenols are widespread in modern life because of their industrial application as plasticisers. Bisphenol A (BPA) is the best-known member and has gained significant scientific as well as public attention as an endocrine disrupting chemical, a fact that eventually led to its replacement. However, compounds used to replace BPA still contain the molecular scaffold of bisphenols. BPA, BPAF, BPB, BPE, BPF, and an amine-substituted BPAF-derivate all interact with all GDP-bound Ras-Isoforms through binding to a common site on these proteins. NMR-, SOScat-, and GDI- assay-based data revealed a new bisphenol-induced, allosterically activated GDP-bound Ras conformation that define these plasticisers as Ras allosteric agonists.
Collapse
Affiliation(s)
- Miriam Schöpel
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Oleksandr Shkura
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Jana Seidel
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Klaus Kock
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Xueyin Zhong
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Stefanie Löffek
- Skin Cancer Unit of the Dermatology Department, West German Cancer Center, University Hospital Essen, University Duisburg-Essen and the German Cancer Consortium (DKTK), D-45147 Essen, Germany.
| | - Iris Helfrich
- Skin Cancer Unit of the Dermatology Department, West German Cancer Center, University Hospital Essen, University Duisburg-Essen and the German Cancer Consortium (DKTK), D-45147 Essen, Germany.
| | - Hagen S Bachmann
- Institute of Pharmacology and Toxicology, Witten/Herdecke University, Stockumer Str. 10, D-58453 Witten, Germany.
| | - Jürgen Scherkenbeck
- Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, D-42119 Wuppertal, Germany.
| | - Christian Herrmann
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Raphael Stoll
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| |
Collapse
|
31
|
Thurman R, Siraliev-Perez E, Campbell SL. RAS ubiquitylation modulates effector interactions. Small GTPases 2017; 11:180-185. [PMID: 29185849 DOI: 10.1080/21541248.2017.1371267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RAS proteins function as molecular switches that regulate cellular growth by cycling between active GTP- and inactive GDP bound states. While RAS activity is modulated by factors (guanine nucleotide exchange and GTPase activating proteins) that control levels of active Ras-GTP, RAS proteins also undergo a number of post-translational modifications that regulate their function. One such modification is ubiquitylation. Monoubiquitylation of KRAS at lysine 147 (mUbRAS) enhances Ras activation and promotes signaling through the RAF and Phosphoinositide 3-Kinase (PI3K) signaling pathways. We have previously shown that mUbRAS leads to activation of RAS through a defect in GTPase activating protein (GAP) mediated downregulation, similar to the action of most oncogenic mutations. Consistent with these findings, we now show that mUbRASimpairsRAS binding to the p120 GAP catalytic domain. Mutations in activated G12V RAS that prevent ubiquitylaton at 147 show a decrease in tumorigenesis, suggesting that in addition to activating KRAS, monoubiquitylation at this site may promote downstream signaling and transformation. To investigate whether mUbRAS alters RAS effector interactions, we chemically ubiquitylated KRAS at residue 147 and characterized binding of mUbRAS to RAS binding domains (RBDs) from three distinct downstream effectors that play key roles in RAS-mediated transformation. Results from these studies show a decrease in binding of mUbRAS (7-10-fold) relative to the CRAF RAS Binding Domain (RBD), the catalytic subunit of Phosphoinositide 3-Kinase catalytic gamma (PI3Kcγ) and RALGDS RBD. Intriguingly, we find that mUbRAS shows greatly enhanced (> 40-fold) binding to the CRAF RBD when bound to GDP. These findings, taken together, suggest that mUbRASmay promoteactivation of RAS through a GAP defect, and facilitate RAF association and MAPK signaling in a nucleotide independent manner.
Collapse
Affiliation(s)
- Ryan Thurman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Edhriz Siraliev-Perez
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Sharon L Campbell
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
32
|
Zhu Y, Mei F, Luo P, Cheng X. A cell-based, quantitative and isoform-specific assay for exchange proteins directly activated by cAMP. Sci Rep 2017; 7:6200. [PMID: 28740152 PMCID: PMC5524698 DOI: 10.1038/s41598-017-06432-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/13/2017] [Indexed: 12/17/2022] Open
Abstract
Extensive functional studies of the exchange protein directly activated by cAMP (EPAC) family of signaling molecules have demonstrated that EPAC proteins play a fundamental role in several physiological and pathophysiological responses, therefore are attractive drug targets. In this report, the development of a cell-based, medium to high throughput screening assay that is capable of monitoring EPAC-mediated activation of cellular Rap1 in an isoform-specific manner is described. This assay adapts a conventional ELISA format with immobilized RalGDS-RBD as a bait to selectively capture GTP-bound active Rap1. As a result, it fills an urgent need for a cell-based EPAC assay that can be conveniently performed using microtiter plates for the discovery and/or validation of isoform-specific EPAC agonists and antagonists.
Collapse
Affiliation(s)
- Yingmin Zhu
- Department of Integrative Biology and Pharmacology, Texas Therapeutics Institute, University of Health Science Center, Houston, Texas, USA
| | - Fang Mei
- Department of Integrative Biology and Pharmacology, Texas Therapeutics Institute, University of Health Science Center, Houston, Texas, USA
| | - Pei Luo
- Department of Integrative Biology and Pharmacology, Texas Therapeutics Institute, University of Health Science Center, Houston, Texas, USA
| | - Xiaodong Cheng
- Department of Integrative Biology and Pharmacology, Texas Therapeutics Institute, University of Health Science Center, Houston, Texas, USA.
| |
Collapse
|
33
|
Zhang SY, Sperlich B, Li FY, Al-Ayoubi S, Chen HX, Zhao YF, Li YM, Weise K, Winter R, Chen YX. Phosphorylation Weakens but Does Not Inhibit Membrane Binding and Clustering of K-Ras4B. ACS Chem Biol 2017; 12:1703-1710. [PMID: 28448716 DOI: 10.1021/acschembio.7b00165] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
K-Ras4B is one of the most frequently mutated Ras isoforms in cancer. The signaling activity of K-Ras4B depends on its localization to the plasma membrane (PM), which is mainly mediated by its polybasic farnesylated C-terminus. On top of the constitutive cycles that maintain the PM enrichment of K-Ras4B, conditional phosphorylation at Ser181 located within this motif has been found to be involved in regulating K-Ras4B's cell distribution and signaling activity. However, discordant observations have undermined our understanding of the role this phosphorylation plays. Here, we report an efficient strategy for producing K-Ras4B simultaneously bearing phosphate, farnesyl, and methyl modifications on a preparative scale, a very useful in vitro system when used in concert with model biomembranes. By using this system, we determined that phosphorylation at Ser181 does not fully inhibit membrane binding and clustering of K-Ras4B but reduces its membrane binding affinity, depending on membrane fluidity. In addition, phosphorylated K-Ras4B maintains tight association with its cytosolic shuttle protein PDEδ. After delivering K-Ras4B containing nonhydrolyzable phosphoserine mimetic into cells, the protein displayed a decreasing PM distribution compared with nonphosphorylable K-Ras4B, implying that phosphorylation might facilitate the dissociation of K-Ras4B from the PM. In addition, phosphorylation does not alter the localization of K-Ras4B in the liquid-disordered lipid subdomains of the membrane but slightly alters the thermotropic properties of K-Ras4B-incorporated membranes probably due to minor differences in membrane partitioning and dynamics. These results provide novel mechanistic insights into the role that phosphorylation at Ser181 plays in regulating K-Ras4B's distribution and activity.
Collapse
Affiliation(s)
- Si-Yu Zhang
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Benjamin Sperlich
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
| | - Fang-Yi Li
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Samy Al-Ayoubi
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
| | - Hong-Xue Chen
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu-Fen Zhao
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yan-Mei Li
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Katrin Weise
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
| | - Roland Winter
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
| | - Yong-Xiang Chen
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
34
|
Koturenkiene A, Makbul C, Herrmann C, Constantinescu-Aruxandei D. Kinetic characterization of apoptotic Ras signaling through Nore1-MST1 complex formation. Biol Chem 2017; 398:701-707. [PMID: 28141542 DOI: 10.1515/hsz-2016-0291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/24/2017] [Indexed: 01/13/2023]
Abstract
Ras-mediated apoptotic signaling is expected to be mediated via Rassf-MST complexes, but the system has been poorly characterized in vitro until now. Here we demonstrate that active H-Ras, Nore1A and MST1 form a stable ternary complex in vitro without other external factors, Nore1A interacting simultaneously with H-Ras and MST1 via its RBD and SARAH domain, respectively. Moreover, our data show for the first time that the SARAH domain of Nore1A plays a role in the Nore1A binding to H-Ras. Finally, we analyze the relation between the electrostatic and hydrophobic forces and kinetic constants of the Nore1A - H-Ras complex.
Collapse
Affiliation(s)
- Agne Koturenkiene
- Department of Physical Chemistry I, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum
| | - Cihan Makbul
- Department of Physical Chemistry I, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum
| | - Christian Herrmann
- Department of Physical Chemistry I, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum
| | | |
Collapse
|
35
|
Rassf Proteins as Modulators of Mst1 Kinase Activity. Sci Rep 2017; 7:45020. [PMID: 28327630 PMCID: PMC5361201 DOI: 10.1038/srep45020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022] Open
Abstract
Rassf1A/5 tumor suppressors serve as adaptor proteins possessing a modular architecture with the C-terminal consisting of a coiled-coil SARAH (Salvador-Rassf-Hippo) domain and the central portion being composed of Ras associated (RA) domain. Here, we investigate the effect of Rassf effectors on Mst1 function by mapping the interaction of various domains of Rassf1A/5 and Mst1 kinase using surface plasmon resonance (SPR). The results revealed that apart from the C-terminal SARAH domain of Mst1 which interacts to form heterodimers with Rassf1A/5, the N-terminal kinase domain of Mst1 plays a crucial role in the stabilization of this complex. In addition, SPR experiments show that the RA domains play an important role in fine-tuning the Mst1-Rassf interaction, with Rassf5 being a preferred partner over a similar Rassf1A construct. It was also demonstrated that the activity profile of Mst1 in presence of Rassf adaptors completely switches. A Rassf-Mst1 complexed version of the kinase becomes apoptotic by positively regulating Mst1-H2B mediated serine 14 histone H2B phosphorylation, a hallmark of chromatin condensation. In contrast, the heterodimerization of Mst1 with Rassf1A/5 suppresses the phosphorylation of FoxO, thereby inhibiting the downstream Mst1-FoxO signalling pathway.
Collapse
|
36
|
SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras. Nat Cell Biol 2017; 19:292-305. [PMID: 28263956 PMCID: PMC5386136 DOI: 10.1038/ncb3487] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 02/06/2017] [Indexed: 12/17/2022]
Abstract
SHANK3, a synaptic scaffold protein and actin regulator, is widely
expressed outside of the central nervous system with predominantly unknown
function. Solving the structure of the SHANK3 N-terminal region revealed that
the SPN-domain is an unexpected Ras-association domain with high affinity for
GTP-bound Ras and Rap G-proteins. The role of Rap1 in integrin activation is
well established but the mechanisms to antagonize it remain largely unknown.
Here, we show that SHANK1 and SHANK3 act as integrin activation inhibitors by
sequestering active Rap1 and R-Ras via the SPN-domain and thus limiting their
bioavailability at the plasma membrane. Consistently, SHANK3
silencing triggers increased plasma membrane Rap1 activity, cell spreading,
migration and invasion. Autism-related mutations within the SHANK3 SPN-domain
(R12C and L68P) disrupt G-protein interaction and fail to counteract integrin
activation along the Rap1/RIAM/talin axis in cancer cells and neurons.
Altogether, we establish SHANKs as critical regulators of G-protein signalling
and integrin-dependent processes.
Collapse
|
37
|
Yin G, Kistler S, George SD, Kuhlmann N, Garvey L, Huynh M, Bagni RK, Lammers M, Der CJ, Campbell SL. A KRAS GTPase K104Q Mutant Retains Downstream Signaling by Offsetting Defects in Regulation. J Biol Chem 2017; 292:4446-4456. [PMID: 28154176 DOI: 10.1074/jbc.m116.762435] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/27/2017] [Indexed: 11/06/2022] Open
Abstract
The KRAS GTPase plays a critical role in the control of cellular growth. The activity of KRAS is regulated by guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs), and also post-translational modification. Lysine 104 in KRAS can be modified by ubiquitylation and acetylation, but the role of this residue in intrinsic KRAS function has not been well characterized. We find that lysine 104 is important for GEF recognition, because mutations at this position impaired GEF-mediated nucleotide exchange. Because the KRAS K104Q mutant has recently been employed as an acetylation mimetic, we conducted a series of studies to evaluate its in vitro and cell-based properties. Herein, we found that KRAS K104Q exhibited defects in both GEF-mediated exchange and GAP-mediated GTP hydrolysis, consistent with NMR-detected structural perturbations in localized regions of KRAS important for recognition of these regulatory proteins. Despite the partial defect in both GEF and GAP regulation, KRAS K104Q did not alter steady-state GTP-bound levels or the ability of the oncogenic KRAS G12V mutant to cause morphologic transformation of NIH 3T3 mouse fibroblasts and of WT KRAS to rescue the growth defect of mouse embryonic fibroblasts deficient in all Ras genes. We conclude that the KRAS K104Q mutant retains both WT and mutant KRAS function, probably due to offsetting defects in recognition of factors that up-regulate (GEF) and down-regulate (GAP) RAS activity.
Collapse
Affiliation(s)
- Guowei Yin
- From the Department of Biochemistry and Biophysics
| | - Samantha Kistler
- From the Department of Biochemistry and Biophysics.,Department of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy
| | - Samuel D George
- Department of Pharmacology, and.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27699
| | - Nora Kuhlmann
- the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne, Germany, and
| | - Leslie Garvey
- the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Minh Huynh
- From the Department of Biochemistry and Biophysics.,Department of Pharmacology, and.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27699
| | - Rachel K Bagni
- the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Michael Lammers
- the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne, Germany, and
| | - Channing J Der
- Department of Pharmacology, and.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27699
| | - Sharon L Campbell
- From the Department of Biochemistry and Biophysics, .,Department of Pharmacology, and.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27699
| |
Collapse
|
38
|
Asati V, Mahapatra DK, Bharti SK. K-Ras and its inhibitors towards personalized cancer treatment: Pharmacological and structural perspectives. Eur J Med Chem 2017; 125:299-314. [DOI: 10.1016/j.ejmech.2016.09.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 02/07/2023]
|
39
|
Nakhaeizadeh H, Amin E, Nakhaei-Rad S, Dvorsky R, Ahmadian MR. The RAS-Effector Interface: Isoform-Specific Differences in the Effector Binding Regions. PLoS One 2016; 11:e0167145. [PMID: 27936046 PMCID: PMC5147862 DOI: 10.1371/journal.pone.0167145] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/09/2016] [Indexed: 12/31/2022] Open
Abstract
RAS effectors specifically interact with the GTP-bound form of RAS in response to extracellular signals and link them to downstream signaling pathways. The molecular nature of effector interaction by RAS is well-studied but yet still incompletely understood in a comprehensive and systematic way. Here, structure-function relationships in the interaction between different RAS proteins and various effectors were investigated in detail by combining our in vitro data with in silico data. Equilibrium dissociation constants were determined for the binding of HRAS, KRAS, NRAS, RRAS1 and RRAS2 to both the RAS binding (RB) domain of CRAF and PI3Kα, and the RAS association (RA) domain of RASSF5, RALGDS and PLCε, respectively, using fluorescence polarization. An interaction matrix, constructed on the basis of available crystal structures, allowed identification of hotspots as critical determinants for RAS-effector interaction. New insights provided by this study are the dissection of the identified hotspots in five distinct regions (R1 to R5) in spite of high sequence variability not only between, but also within, RB/RA domain-containing effectors proteins. Finally, we propose that intermolecular β-sheet interaction in R1 is a central recognition region while R3 may determine specific contacts of RAS versus RRAS isoforms with effectors.
Collapse
Affiliation(s)
- Hossein Nakhaeizadeh
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Ehsan Amin
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Saeideh Nakhaei-Rad
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
- * E-mail:
| |
Collapse
|
40
|
Harrison RA, Lu J, Carrasco M, Hunter J, Manandhar A, Gondi S, Westover KD, Engen JR. Structural Dynamics in Ras and Related Proteins upon Nucleotide Switching. J Mol Biol 2016; 428:4723-4735. [PMID: 27751724 DOI: 10.1016/j.jmb.2016.10.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/17/2016] [Accepted: 10/10/2016] [Indexed: 12/31/2022]
Abstract
Structural dynamics of Ras proteins contributes to their activity in signal transduction cascades. Directly targeting Ras proteins with small molecules may rely on the movement of a conserved structural motif, switch II. To understand Ras signaling and advance Ras-targeting strategies, experimental methods to measure Ras dynamics are required. Here, we demonstrate the utility of hydrogen-deuterium exchange (HDX) mass spectrometry (MS) to measure Ras dynamics by studying representatives from two branches of the Ras superfamily, Ras and Rho. A comparison of differential deuterium exchange between active (GMPPNP-bound) and inactive (GDP-bound) proteins revealed differences between the families, with the most notable differences occurring in the phosphate-binding loop and switch II. The P-loop exchange signature correlated with switch II dynamics observed in molecular dynamics simulations focused on measuring main-chain movement. HDX provides a means of evaluating Ras protein dynamics, which may be useful for understanding the mechanisms of Ras signaling, including activated signaling of pathologic mutants, and for targeting strategies that rely on protein dynamics.
Collapse
Affiliation(s)
- Rane A Harrison
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jia Lu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Martin Carrasco
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John Hunter
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anuj Manandhar
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| |
Collapse
|
41
|
Gera N, Swanson KD, Jin T. β-Arrestin 1-dependent regulation of Rap2 is required for fMLP-stimulated chemotaxis in neutrophil-like HL-60 cells. J Leukoc Biol 2016; 101:239-251. [PMID: 27493245 DOI: 10.1189/jlb.2a1215-572r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 06/13/2016] [Accepted: 07/15/2016] [Indexed: 01/14/2023] Open
Abstract
β-Arrestins have emerged as key regulators of cytoskeletal rearrangement that are required for directed cell migration. Whereas it is known that β-arrestins are required for formyl-Met-Leu-Phe receptor (FPR) recycling, less is known about their role in regulating FPR-mediated neutrophil chemotaxis. Here, we show that β-arrestin 1 (ArrB1) coaccumulated with F-actin within the leading edge of neutrophil-like HL-60 cells during chemotaxis, and its knockdown resulted in markedly reduced migration within fMLP gradients. The small GTPase Ras-related protein 2 (Rap2) was found to bind ArrB1 under resting conditions but dissociated upon fMLP stimulation. The FPR-dependent activation of Rap2 required ArrB1 but was independent of Gαi activity. Significantly, depletion of either ArrB1 or Rap2 resulted in reduced chemotaxis and defects in cellular repolarization within fMLP gradients. These data strongly suggest a model in which FPR is able to direct ArrB1 and other bound proteins that are required for lamellipodial extension to the leading edge in migrating neutrophils, thereby orientating and directing cell migration.
Collapse
Affiliation(s)
- Nidhi Gera
- Chemotaxis Signal Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA; and
| | - Kenneth D Swanson
- Department of Neurology, Division of Neuro-Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Tian Jin
- Chemotaxis Signal Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA; and
| |
Collapse
|
42
|
Coyle SM. Reverse engineering GTPase programming languages with reconstituted signaling networks. Small GTPases 2016; 7:168-72. [PMID: 27128855 PMCID: PMC5003541 DOI: 10.1080/21541248.2016.1178367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/08/2016] [Accepted: 04/11/2016] [Indexed: 10/21/2022] Open
Abstract
The Ras superfamily GTPases represent one of the most prolific signaling currencies used in Eukaryotes. With these remarkable molecules, evolution has built GTPase networks that control diverse cellular processes such as growth, morphology, motility and trafficking. (1-4) Our knowledge of the individual players that underlie the function of these networks is deep; decades of biochemical and structural data has provided a mechanistic understanding of the molecules that turn GTPases ON and OFF, as well as how those GTPase states signal by controlling the assembly of downstream effectors. However, we know less about how these different activities work together as a system to specify complex dynamic signaling outcomes. Decoding this molecular "programming language" would help us understand how different species and cell types have used the same GTPase machinery in different ways to accomplish different tasks, and would also provide new insights as to how mutations to these networks can cause disease. We recently developed a bead-based microscopy assay to watch reconstituted H-Ras signaling systems at work under arbitrary configurations of regulators and effectors. (5) Here we highlight key observations and insights from this study and propose extensions to our method to further study this and other GTPase signaling systems.
Collapse
Affiliation(s)
- Scott M. Coyle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| |
Collapse
|
43
|
Yip KT, Zhong XY, Seibel N, Pütz S, Autzen J, Gasper R, Hofmann E, Scherkenbeck J, Stoll R. Small Molecules Antagonise the MIA-Fibronectin Interaction in Malignant Melanoma. Sci Rep 2016; 6:25119. [PMID: 27151361 PMCID: PMC4858652 DOI: 10.1038/srep25119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/11/2016] [Indexed: 02/01/2023] Open
Abstract
Melanoma inhibitory activity (MIA), an extracellular protein highly expressed by malignant melanoma cells, plays an important functional role in melanoma development, progression, and metastasis. After its secretion, MIA directly interacts with extracellular matrix proteins, such as fibronectin (FN). By this mechanism, MIA actively facilitates focal cell detachment from surrounding structures and strongly promotes tumour cell invasion and migration. Hence, the molecular understanding of MIA's function provides a promising target for the development of new strategies in malignant melanoma therapy. Here, we describe for the first time the discovery of small molecules that are able to disrupt the MIA-FN complex by selectively binding to a new druggable pocket, which we could identify on MIA by structural analysis and fragment-based screening. Our findings may inspire novel drug discovery efforts aiming at a therapeutically effective treatment of melanoma by targeting MIA.
Collapse
Affiliation(s)
- King Tuo Yip
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| | - Xue Yin Zhong
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| | - Nadia Seibel
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| | - Stefanie Pütz
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| | - Jasmin Autzen
- University of Wuppertal, Faculty of Chemistry, Wuppertal, 42119, Germany
| | - Raphael Gasper
- Ruhr University of Bochum, Faculty of Biology and Biotechnology, Bochum, 44801, Germany
| | - Eckhard Hofmann
- Ruhr University of Bochum, Faculty of Biology and Biotechnology, Bochum, 44801, Germany
| | | | - Raphael Stoll
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| |
Collapse
|
44
|
Coyle SM, Lim WA. Mapping the functional versatility and fragility of Ras GTPase signaling circuits through in vitro network reconstitution. eLife 2016; 5. [PMID: 26765565 PMCID: PMC4775219 DOI: 10.7554/elife.12435] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/13/2016] [Indexed: 01/06/2023] Open
Abstract
The Ras-superfamily GTPases are central controllers of cell proliferation and morphology. Ras signaling is mediated by a system of interacting molecules: upstream enzymes (GEF/GAP) regulate Ras's ability to recruit multiple competing downstream effectors. We developed a multiplexed, multi-turnover assay for measuring the dynamic signaling behavior of in vitro reconstituted H-Ras signaling systems. By including both upstream regulators and downstream effectors, we can systematically map how different network configurations shape the dynamic system response. The concentration and identity of both upstream and downstream signaling components strongly impacted the timing, duration, shape, and amplitude of effector outputs. The distorted output of oncogenic alleles of Ras was highly dependent on the balance of positive (GAP) and negative (GEF) regulators in the system. We found that different effectors interpreted the same inputs with distinct output dynamics, enabling a Ras system to encode multiple unique temporal outputs in response to a single input. We also found that different Ras-to-GEF positive feedback mechanisms could reshape output dynamics in distinct ways, such as signal amplification or overshoot minimization. Mapping of the space of output behaviors accessible to Ras provides a design manual for programming Ras circuits, and reveals how these systems are readily adapted to produce an array of dynamic signaling behaviors. Nonetheless, this versatility comes with a trade-off of fragility, as there exist numerous paths to altered signaling behaviors that could cause disease.
Collapse
Affiliation(s)
- Scott M Coyle
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Program in Biological Sciences, University of California, San Francisco, San Francisco, United States.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, United States
| | - Wendell A Lim
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Program in Biological Sciences, University of California, San Francisco, San Francisco, United States.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
45
|
Plak K, Pots H, Van Haastert PJM, Kortholt A. Direct Interaction between TalinB and Rap1 is necessary for adhesion of Dictyostelium cells. BMC Cell Biol 2016; 17:1. [PMID: 26744136 PMCID: PMC4861126 DOI: 10.1186/s12860-015-0078-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 12/22/2015] [Indexed: 11/10/2022] Open
Abstract
Background The small G-protein Rap1 is an important regulator of cellular adhesion in Dictyostelium, however so far the downstream signalling pathways for cell adhesion are not completely characterized. In mammalian cells talin is crucial for adhesion and Rap1 was shown to be a key regulator of talin signalling. Results In a proteomic screen we identified TalinB as a potential Rap1 effector in Dictyostelium. In subsequent pull-down experiments we demonstrate that the Ras association (RA) domain of TalinB interacts specifically with active Rap1. Studies with a mutated RA domain revealed that the RA domain is essential for TalinB-Rap1 interaction, and that this interaction contributes to cell-substrate adhesion during single-celled growth and is crucial for cell-cell adhesion during multicellular development. Conclusions Dictyostelium Rap1 directly binds to TalinB via the conserved RA domain. This interaction is critical for adhesion, which becomes essential for high adhesive force demanding processes, like morphogenesis during multicellular development of Dictyostelium. In mammalian cells the established Rap1-talin interaction is indirect and acts through the scaffold protein - RIAM. Interestingly, direct binding of mouse Rap1 to the RA domain of Talin1 has recently been demonstrated. Electronic supplementary material The online version of this article (doi:10.1186/s12860-015-0078-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Katarzyna Plak
- Department of Cell Biochemistry, University of Groningen, Nijenborgh 7, Groningen, AG 9747, The Netherlands. .,Current address: BIOTEC center, Technical University Dresden, Tatzberg 47/49, 01307, Dresden, Germany.
| | - Henderikus Pots
- Department of Cell Biochemistry, University of Groningen, Nijenborgh 7, Groningen, AG 9747, The Netherlands.
| | - Peter J M Van Haastert
- Department of Cell Biochemistry, University of Groningen, Nijenborgh 7, Groningen, AG 9747, The Netherlands.
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Nijenborgh 7, Groningen, AG 9747, The Netherlands.
| |
Collapse
|
46
|
Nussinov R, Tsai CJ, Muratcioglu S, Jang H, Gursoy A, Keskin O. Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation. Expert Rev Proteomics 2015; 12:669-82. [DOI: 10.1586/14789450.2015.1100079] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
47
|
Ritchie AW, Webb LJ. Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations. J Phys Chem B 2015; 119:13945-57. [PMID: 26375183 DOI: 10.1021/acs.jpcb.5b06888] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological function emerges in large part from the interactions of biomacromolecules in the complex and dynamic environment of the living cell. For this reason, macromolecular interactions in biological systems are now a major focus of interest throughout the biochemical and biophysical communities. The affinity and specificity of macromolecular interactions are the result of both structural and electrostatic factors. Significant advances have been made in characterizing structural features of stable protein-protein interfaces through the techniques of modern structural biology, but much less is understood about how electrostatic factors promote and stabilize specific functional macromolecular interactions over all possible choices presented to a given molecule in a crowded environment. In this Feature Article, we describe how vibrational Stark effect (VSE) spectroscopy is being applied to measure electrostatic fields at protein-protein interfaces, focusing on measurements of guanosine triphosphate (GTP)-binding proteins of the Ras superfamily binding with structurally related but functionally distinct downstream effector proteins. In VSE spectroscopy, spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment. By performing this experiment repeatedly throughout a protein-protein interface, an experimental map of measured electrostatic fields generated at that interface is determined. These data can be used to rationalize selective binding of similarly structured proteins in both in vitro and in vivo environments. Furthermore, these data can be used to compare to computational predictions of electrostatic fields to explore the level of simulation detail that is necessary to accurately predict our experimental findings.
Collapse
Affiliation(s)
- Andrew W Ritchie
- Department of Chemistry, Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology, The University of Texas at Austin , 105 East 24th Street STOP A5300, Austin, Texas 78712, United States
| |
Collapse
|
48
|
Rugbjerg P, Knuf C, Förster J, Sommer MOA. Recombination-stable multimeric green fluorescent protein for characterization of weak promoter outputs inSaccharomyces cerevisiae. FEMS Yeast Res 2015; 15:fov085. [DOI: 10.1093/femsyr/fov085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2015] [Indexed: 01/26/2023] Open
|
49
|
Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O. The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas. Mol Cancer Res 2015; 13:1265-73. [PMID: 26085527 PMCID: PMC4572916 DOI: 10.1158/1541-7786.mcr-15-0165] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/09/2015] [Indexed: 12/14/2022]
Abstract
KRAS4B is a highly oncogenic splice variant of the KRAS isoform. It is the only isoform associated with initiation of adenocarcinomas. Insight into why and how KRAS4B can mediate ductal adenocarcinomas, particularly of the pancreas, is vastly important for its therapeutics. Here we point out the overlooked critical role of calmodulin (CaM). Calmodulin selectively binds to GTP-bound K-Ras4B; but not to other Ras isoforms. Cell proliferation and growth require the MAPK (Raf/MEK/ERK) and PI3K/Akt pathways. We propose that Ca(2+)/calmodulin promote PI3Kα/Akt signaling, and suggest how. The elevated calcium levels clinically observed in adenocarcinomas may explain calmodulin's involvement in recruiting and stimulating PI3Kα through interaction with its n/cSH2 domains as well as K-Ras4B; importantly, it also explains why K-Ras4B specifically is a key player in ductal carcinomas, such as pancreatic (PDAC), colorectal (CRC), and lung cancers. We hypothesize that calmodulin recruits and helps activate PI3Kα at the membrane, and that this is the likely reason for Ca(2+)/calmodulin dependence in adenocarcinomas. Calmodulin can contribute to initiation/progression of ductal cancers via both PI3Kα/Akt and Raf/MEK/ERK pathways. Blocking the K-Ras4B/MAPK pathway and calmodulin/PI3Kα binding in a K-Ras4B/calmodulin/PI3Kα trimer could be a promising adenocarcinoma-specific therapeutic strategy.
Collapse
Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI at Frederick, Frederick, Maryland. Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Serena Muratcioglu
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI at Frederick, Frederick, Maryland
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| |
Collapse
|
50
|
Rugbjerg P, Myling-Petersen N, Sommer MOA. Flexible metabolic pathway construction using modular and divisible selection gene regulators. Metab Eng 2015; 31:189-97. [PMID: 26303342 DOI: 10.1016/j.ymben.2015.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 01/09/2023]
Abstract
Genetic selections are important to biological engineering. Although selectable traits are limited, currently each trait only permits simultaneous introduction of a single DNA fragment. Complex pathway and strain construction however depends on rapid, combinatorial introduction of many genes that encode putative pathway candidates and homologs. To triple the utility of existing selection genes, we have developed divisible selection in Saccharomyces cerevisiae. Here, independent DNA fragments can be introduced and selected for simultaneously using a set of split hybrid transcription factors composed of parts from Escherichia coli LexA and Herpes simplex VP16 to regulate one single selectable phenotype of choice. Only when co-expressed, these split hybrid transcription factors promote transcription of a selection gene, causing tight selection of transformants containing all desired DNA fragments. Upon transformation, 94% of the selected colonies resulted strictly from transforming all three modules based on ARS/CEN plasmids. Similarly when used for chromosome integration, 95% of the transformants contained all three modules. The divisible selection system acts dominantly and thus expands selection gene utility from one to three without any genomic pre-modifications of the strain. We demonstrate the approach by introducing the fungal rubrofusarin polyketide pathway at a gene load of 11 kb distributed on three different plasmids, using a single selection trait and one yeast transformation step. By tripling the utility of existing selection genes, the employment of divisible selection improves flexibility and freedom in the strain engineering process.
Collapse
Affiliation(s)
- Peter Rugbjerg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, DK-2970 Hørsholm, Denmark.
| | - Nils Myling-Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, DK-2970 Hørsholm, Denmark.
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, DK-2970 Hørsholm, Denmark.
| |
Collapse
|