Publications from the RAS Initiative

The NCI RAS Initiative has a "hub-and-spokes" structure, in that its scientists work both independently and in collaboration with academic and commercial entities. The list of RAS Initiative publications below reflects the balance between the public responsibilities of the National Cancer Institute and the requirements of our external partners.

Authors who names are marked with an asterisk (*) are part of the RAS Initiative.

• Discovery of BBO-8520, a first-in-class direct and covalent dual inhibitor of GTP-bound (ON) and GDP-bound (OFF) KRASG12C
  Maciag AE*, Stice JP, Wang B, Sharma AK*, Chan AH*, Lin K, Singh D, Dyba M*, Yang Y, Setoodeh S, Smith BP*, Ju JH, Jeknic S, Rabara D*, Zhang Z, Larsen EK*, Esposito D*, Denson JP*, Ranieri M, Meynardie M, Mehdizadeh S, Alexander PA*, Abreu Blanco M*, Turner DM*, Xu R, Lightstone FC, Wong KK, Stephen AG*, Wang K, Simanshu DK*, Sinkevicius KW, Nissley DV*, Wallace E, McCormick F, Beltran PJ
  Cancer Discov, Dec 2024 
  PubMed ID: 39642212

• The prominent pervasive oncogenic role and tissue-specific permissiveness of RAS gene mutations supported by DepMap high-throughput CRISPR screening data 
  Yi M*, Soppet D*, McCormick F, Nissley DV*
  Sci Rep,14(1):25452, Oct 2024
  PubMed ID: 39455841

• Two hearts beat as one: the debate over RAS dimers continues 
  Stephen AG*
  Trends Biochem Sci, Oct 2024
  PubMed ID: 39358051

• KRas4b-Calmodulin interaction with membrane surfaces: role of headgroup, acyl chain, and electrostatics 
  Shree S, McLean MA, Stephen AG*, Sligar SG
  Biochemistry, Oct 2024
  PubMed ID: 39382513

• Beyond KRAS(G12C): biochemical and computational characterization of sotorasib and adagrasib binding specificity and the critical role of H95 and Y96
  Mahran R, Kapp JN, Valtonen S, Champagne A*, Ning J, Gillette W*, Stephen AG*, Hao F, Plückthun A, Härmä H, Pantsar T, Kopra K
  ACS Chem Biol, Oct 2024
  PubMed ID: 39283696

• Targeting Ras-, Rho-, and Rab-family GTPases via a conserved cryptic pocket 
  Morstein J, Bowcut V, Fernando M, Yang Y, Zhu L, Jenkins ML, Evans JT, Guiley KZ, Peacock DM, Krahnke S*, Lin Z, Taran KA, Huang BJ, Stephen AG*, Burke JE, Lightstone FC, Shokat KM
  Cell, Sep 2024
  PubMed ID: 39255801

• Improved production of class I phosphatidylinositol 4,5-bisphosphate 3-kinase 
  Messing S*, Widmeyer SRT*, Denson JP*, Mehalko J*, Wall VE*, Drew M*, Snead K*, Hong M*, Grose C*, Esposito D*, Gillette W*
  Protein Expr Purif, 225:106582, Aug 2024
  PubMed ID: 39173964

• Functional and structural insights into RAS effector proteins
  Mozzarelli AM, Simanshu DK*, Castel P 
  Mol Cell, Aug 2024
  PubMed ID: 39025071

• Determining KRAS4B-targeting compound specificity by top-down mass spectrometry D'Ippolito RA*, Scheidemantle GM*, Rabara D*, Abreu Blanco M*, Ramakrishnan N*, Widmeyer SRT*, Messing S*, Turner D*, Maciag AE*, Stephen AG*, Esposito D*, McCormick F, Nissley DV*, DeHart CJ*
  Methods Mol Biol,2823:291-310, Jul 2024
  PubMed ID: 39052227

• Natural product graveoline modulates Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) membrane association: insights from advanced spectroscopic studiesCornilescu G*, Bindu L*, Sternicki L ,Chao FA*, Gillette WK*, Fer N*, Colombus J*, Castillo J*, Andrade Bonilla P*, Van QN*, Larsen E*, Hong M*, Burgan W*, Turbyville T*, Nissley DV*, Liu M, Quinn R, Jean-Francois FL*
  ACS Pharmacol Transl Sci,7(7):1983-1995, Jul 2024
  PubMed ID: 39022364

• KRAS: Methods and Protocols
  Stephen AG*, Esposito D*
  Methods in Molecular Biology 
  2024
  Springer

• A top-down proteomic assay to evaluate KRAS4B-compound engagement 
  D'Ippolito RA*, Rabara D*, Blanco MA*, Alberico E*, Drew MR*, Ramakrishnan N*, Sontan D*, Widmeyer SRT*, Scheidemantle GM*, Messing S*, Turner D*, Arkin M, Maciag AE*, Stephen AG*, Esposito D*, McCormick F, Nissley DV*, DeHart CJ*
  Anal Chem 2024 
  PubMed PMID: 38498381

• Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements 
  Finci LI*, Chakrabarti M*, Gulten G*, Finney J*, Grose C*, Fox T*, Yang R*, Nissley DV*, McCormick F, Esposito D*, Balius TE*, Simanshu DK* 
  Commun Biol,7(1):260 2024 
  PubMed PMID: 38431713

• Adapting recombinant bacterial alkaline phosphatase for nucleotide exchange of small GTPases
  Frank P*, Hong M*, Higgins B*, Perkins S*, Taylor T*, Wall V*, Drew M*, Waybright T*, Gillette W*, Esposito D*, Messing S* 
  Protein Expr Purif 2024
  PubMed PMID: 38395209

• Revealing the mechanism of action of a first-in-class covalent inhibitor of KRASG12C (ON) and other functional properties of oncogenic KRAS by (31)P NMR 
  Sharma AK*, Pei J, Yang Y, Dyba M*, Smith B*, Rabara D*, Larsen E*, Lightstone FC, Esposito D*, Stephen AG*, Wang B, Beltran PJ, Wallace E, Nissley DV*, McCormick F, Maciag AE*
  J Biol Chem 2024 
  PubMed PMID: 38237681

• Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane
  Shrestha R*, Carpenter TS, Van QN*, Agamasu C*, Tonelli M, Aydin F, Chen D*, Gulten G*, Glosli JN, López CA, Oppelstrup T, Neale C, Gnanakaran S, Gillette WK*, Ingólfsson HI, Lightstone FC, Stephen AG*, Streitz FH, Nissley DV*, Turbyville TJ*
  Commun Biol,7(1):242, 2024
  PubMed PMID: 38605143

• RAS and SHOC2 roles in RAF activation and therapeutic considerations
  Bonsor DA*, Simanshu DK*: 
  Ann Rev Cancer Bio, 2024
  PubMed ID: 38882927

• Ras-dependent MAPK hyperactivation by pathogenic RIT1 is a therapeutic target in myocardial hypertrophy 
  Cuevas-Navarro A, Wagner M*, Van R, Swain M*, Allison MR, Cheng A, Messing S*, Simanshu DK*,  Sale MJ, McCormick F, Stephen AG, Castel P
  Sci Adv,9(28):eadf4766 2023
  PubMed PMID: 37450595

• DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking
  Balius TE*, Tan YS*, Chakrabarti M* 
  J Comput Chem 2023
  PubMed PMID: 37743732

• Reduced dynamic complexity allows structure elucidation of an excited state of KRAS(G13D)
  Chao FA*, Chan AH*, Dharmaiah S*, Schwieters CD, Tran TH*, Taylor T*, Ramakrishnan N*, Esposito D*, Nissley DV*, McCormick F, Simanshu DK*, Cornilescu G* 
  Commun Biol,6(1):594 2023
  PubMed PMID: 37268708

• Machine learning-driven multiscale modeling: bridging the scales with a next-generation simulation infrastructure
  Ingólfsson HI, Bhatia H, Aydin F, Oppelstrup T, López CA, Stanton LG, Carpenter TS, Wong S, Di Natale F, Zhang X, Moon JY, Stanley CB, Chavez JR, Nguyen K, Dharuman G, Burns V, Shrestha R*, Goswami D*, Gulten G*, Van QN*, Ramanathan A, Van Essen B, Hengartner NW, Stephen AG*, Turbyville T*, Bremer PT, Gnanakaran S, Glosli JN, Lightstone FC, Nissley DV*, Streitz FH,
  J Chem Theory Comput 2023
  PubMed PMID: 37075065

• The Ribosomal S6 Kinase 2 (RSK2)-SPRED2 complex regulates phosphorylation of RSK substrates and MAPK signaling
  Lopez J, Bonsor DA*, Sale MJ, Urisman A, Mehalko JL*, Cabanski-Dunning M, Castel P, Simanshu DK*, McCormick F
  J Biol Chem 2023
  PubMed PMID: 37149146

• Direct modulators of K-Ras-membrane interactions
  Morstein J, Shrestha R*, Van QN*, López CA, Arora N, Tonelli M, Liang H, Chen D*, Zhou Y, Hancock JF, Stephen AG*, Turbyville TJ*, Shokat KM
  ACS Chem Biol 2023
  PubMed PMID: 37579045

• GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation
  Patel LA, Waybright TJ*, Stephen AG*, Neale C
  Comput Biol Chem,104:107835 2023
  PubMed PMID: 36893567

• Revealing KRas4b topology on the membrane surface
  Shree S, McLean MA, Stephen AG*, Sligar SG
  Biochem Biophys Res Commun,678:122-127, 2023
  PubMed PMID: 37633182

• Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties
  Whitley MJ*, Tran TH*, Rigby M*, Yi M*, Dharmaiah S*, Waybright TJ*, Ramakrishnan N*, Perkins S*, Taylor T*, Messing S*, Esposito D*, Nissley DV*, McCormick F, Stephen AG*, Turbyville T*, Cornilescu G*, Simanshu DK* 
  Sci Adv,10(7):eadj4137, 2023
  PubMed PMID: 38354232

• Allosteric regulation of switch-II domain controls KRAS oncogenicity
  Yang MH, Tran TH, Hunt B, Agnor R, Johnson CW, Shui B, Waybright TJ*, Nowak JA, Stephen AG*, Simanshu DK*, Haigis KM
  Cancer Res, 2023
  PubMed PMID: 37556505

• Destabilizing NF1 variants act in a dominant negative manner through neurofibromin dimerization
  Young LC, Goldstein de Salazar R, Han SW, Huang ZYS, Merk A*, Drew M*, Darling J*, Wall V*, Grisshammer R*, Cheng A, Allison MR, Sale MJ, Nissley DV*, Esposito D*, Ognjenovic J*, McCormick F
  Proc Natl Acad Sci U S A,120(5):e2208960120, 2023
  PubMed PMID: 36689660

• The confluence of machine learning and multiscale simulations
  Bhatia H, Aydin F, Carpenter TS, Lightstone FC, Bremer PT, Ingólfsson HI, Nissley DV*, Streitz FH
  Curr Opin Struct Biol,80:102569, 2023
  PubMed PMID: 36966691 

• Structural insights into the role of SHOC2-MRAS-PP1C complex in RAF activation
  Bonsor DA*, Simanshu DK* 
  FEBS J, 2023
  PubMed PMID: 37074066

• Consensus on the RAS dimerization hypothesis: Strong evidence for lipid-mediated clustering but not for G-domain-mediated interactions
  Simanshu DK*, Philips MR, Hancock JF
  Mol Cell, 2023
  PubMed PMID: 36990093

• RASopathy mutations provide functional insight into the BRAF cysteine-rich domain and reveal the importance of autoinhibition in BRAF regulation
  Spencer-Smith R, Terrell EM, Insinna C, Agamasu C*, Wagner ME*, Ritt DA, Stauffer J, Stephen AG*, Morrison DK
  Mol Cell. 2022;82(22):4262-76 e5
  PubMed PMID: 36347258
   
• Classical RAS proteins are not essential for paradoxical ERK activation induced by RAF inhibitors
  Lai LP*, Fer N*, Burgan W*, Wall V*, Xu B*, Soppet D*, Esposito D*, Nissley DV*, McCormick F
  Proc Natl Acad Sci U S A 2022
  PubMed PMID: 35091470
• Insights into the cross talk between effector and allosteric lobes of KRAS from methyl conformational dynamics
  Chao FA*, Dharmaiah S*, Taylor T*, Messing S*, Gillette W*, Esposito D*, Nissley DV*, McCormick F, Byrd RA, Simanshu DK*, Cornilescu G*
  J Am Chem Soc 2022
  PubMed PMID: 35213144
   
• Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
  Ingólfsson HI, Neale C, Carpenter TS, Shrestha R*, López CA, Tran TH*, Oppelstrup T, Bhatia H, Stanton LG, Zhang X, Sundram S, Di Natale F, Agarwal A, Dharuman G, Kokkila Schumacher SIL, Turbyville T*, Gulten G*, Van QN*, Goswami D*, Jean-Francois F*, Agamasu C*, Chen D*, Hettige JJ, Travers T, Sarkar S, Surh MP, Yang Y, Moody A, Liu S, Van Essen BC, Voter AF, Ramanathan A, Hengartner NW, Simanshu DK*, Stephen AG*, Bremer PT, Gnanakaran S, Glosli JN, Lightstone FC, McCormick F, Nissley DV*, Streitz FH
  Proc Natl Acad Sci USA 2022
  PubMed PMID: 34983849
   
• The tumor suppressor activity of DLC1 requires the interaction of its START domain with phosphatidylserine, PLCD1, and caveolin-1
  Sanchez-Solana B, Wang D, Qian X, Velayoudame P, Simanshu DK*, Acharya JK, Lowy DR
  Mol Cancer 2021
  PubMed PMID: 34727930
   
• NMR ¹H,¹³C, ¹⁵N backbone resonance assignments of the T35S and oncogenic T35S/Q61L mutants of human KRAS4b in the active, GppNHp-bound conformation
  Sharma AK*, Dyba M*, Tonelli M, Smith B*, Gillette WK*, Esposito D*, Nissley DV*, McCormick F, Maciag AE*
  Biomol NMR Assign 2021
  PubMed PMID: 34686998
• Recapitulation of cell-like KRAS4b membrane dynamics on complex biomimetic membranes
  Shrestha R*, Chen D*, Frank P*, Nissley DV*, Turbyville TJ*
  iScience 2021
  PubMed PMID: 35106460
   
• Polycistronic baculovirus expression of SUGT1 enables high-yield production of recombinant leucine-rich repeat proteins and protein complexes
  Snead K*, Wall V*, Ambrose H*, Esposito D*, Drew M*
  Protein Expr Purif 2022
  PubMed PMID: 35131438
   
• Virtual screening for small-molecule pathway regulators by image-profile matching
  Rohban MH, Fuller AM, Tan C, Goldstein JT, Syangtan D, Gutnick A, DeVine A, Nijsure MP, Rigby M, Sacher JR, Corsello SM, Peppler GB, Bogaczynska M, Boghossian A, Ciotti GE, Hands AT, Mekareeya A, Doan M, Gale JP, Derynck R, Turbyville T*, Boerckel JD, Singh S, Kiessling LL, Schwarz TL, Varelas X, Wagner FF, Kafri R, Eisinger-Mathason TSK, Carpenter AE
  Cell Syst. 2022;13(9):724-36 e9
  PubMed PMID: 36057257
   
• RAS at 40: Update from the RAS initiative
  Nissley DV*, McCormick F
  Cancer Discov 2022
  PubMed PMID: 35046096
   
• Exploring CRD mobility during RAS/RAF engagement at the membrane
  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.
  Biophys J. 2022;121(19):3630-50
  PubMed PMID: 35778842
   
• Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework 
  López CA, Zhang X, Aydin F, Shrestha R*, Van QN*, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D*, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH*, Chan AH*, Simanshu DK*, Nissley DV*, Streitz FH, Stephen AG*, Turbyville TJ*, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C
  J Chem Theory Comput. 2022;18(8):5025-45
  PubMed PMID: 35866871
   
• A structure is worth a thousand words: New insights for RAS and RAF regulation
  Simanshu DK*, Morrison DK
  Cancer Discov 2022
  PubMed PMID: 35046094
   
• Structure of the SHOC2-MRAS-PP1C complex provides insights into RAF activation and Noonan syndrome
  Bonsor DA*, Alexander P*, Snead K*, Hartig N, Drew M*, Messing S*, Finci LI*, Nissley DV*, McCormick F, Esposito D*, Rodriguez-Viciana P, Stephen AG*, Simanshu DK*
  Nat Struct Mol Biol. 2022;29(10):966-77
  PubMed PMID: 36175670
   
• Mapping the KRAS Proteoform Landscape in Colorectal Cancer Identifies Truncated KRAS4B that Decreases MAPK Signaling
  Adams LM, DeHart CJ*, Drown BS, Anderson LC, Bocik W, Boja ES, Hiltke TM, Hendrickson CL, Rodriguez H, Caldwell M, Vafabakhsh R, Kelleher NL  
  J Biol Chem. 2022:102768
  PubMed PMID: 36470426
• RAS interaction with Sin1 is dispensable for mTORC2assembly and activity
  Castel P, Dharmaiah S*, Sale MJ, Messing S*, Rizzuto G, Cuevas-Navarro A, Cheng A, Trnka MJ, Urisman A, Esposito D*, Simanshu DK*, McCormick F
  Proc Natl Acad Sci U S A 2020
  PubMed PMID: 34380736
   
• Refining the N-termini of the SARS-CoV-2 spike protein and its discrete receptor binding domain
  D’Ippolito RA*, Drew MR*, Mehalko J*, Snead K*, Wall V*, Putman Z*, Esposito D*, DeHart CJ*
  J Proteome Res 2021
  PubMed PMID: 34379411
   
• Sensitivity of oncogenic KRAS-expressing cells to CDK9 inhibition
  Lai LP*, Brel V, Sharma K*, Frappier J, Le-Henanf N, Vivet B, Muzet N, Schell E, Morales R, Rooney E, Basse N, Yi M*, Lacroix F, Holderfield M*, Englaro W, Marcireau C, Debussche L, Nissley DV*, McCormick F
  SLAS Discov 2021
  PubMed PMID: 33896272
   
• Production and membrane binding of N-terminally acetylated, C-terminally farnesylated and carboxymethylated KRAS4b
  Messing S*, Agamasu C*, Drew M*, DeHart CJ*, Stephen AG*, Gillette WK*
  Methods Mol Biol 2021
  PubMed PMID: 33977473
   
• The metabolic landscape of RAS-driven cancers from biology to therapy
  Mukhopadhyay S*, Vander Heiden MG, McCormick F*
  Nat Cancer 2021
  PubMed PMID: 33870211
   
• Unveiling the Dynamics of KRAS4b on Lipid Model Membranes
  Lopez CA, Agarwal A, Van QN*, Stephen AG*, Gnanakaran S.  
  J Membr Biol. 2021;254(2):201-16
  PubMed PMID: 33825026
   
• Membrane-bound KRAS approximates an entropic ensemble of configurations
  Heinrich F, Van QN*, Jean-Francois F*, Stephen AG*, Losche M.
  Biophys J. 2021;120(18):4055-66
  PubMed PMID: 34384763
   
• Development of a High-throughput NanoBRET Screening Platform to Identify Modulators of the RAS/RAF Interaction
  Durrant DE, Smith EA, Goncharova EI, Sharma N, Alexander PA*, Stephen AG*, Henrich CJ, Morrison DK
  Mol Cancer Ther. 2021;20(9):1743-54
  PubMed PMID: 34158349
   
• NMR ¹H,¹³C, ¹⁵N backbone resonance assignments of the T35S and oncogenic T35S/Q61L mutants of human KRAS4b in the active, GppNHp-bound conformation
  Sharma AK*, Dyba M*, Tonelli M, Smith B*, Gillette WK*, Esposito D*, Nissley DV*, McCormick F, Maciag AE*
  Biomol NMR Assign 2021
  PubMed PMID: 34686998
   
• Targeting eIF4A-dependent translation of KRAS signaling molecules
  Singh K, Lin J, Lecomte N, Mohan P, Gokce A, Sanghvi VR, Jiang M, Grbovic-Huezo O, Burčul A, Stark SG, Romesser PB, Chang Q, Melchor JP, Beyer RK*, Duggan M, Fukase Y, Yang G, Ouerfelli O, Viale A, de Stanchina E, Stamford AW, Meinke PT, Rätsch G, Leach SD, Ouyang Z, Wendel HG
  Cancer Res 2021
  PubMed PMID: 33632898
   
• KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation
  Tran TH*, Chan AH*, Young LC, Bindu L*, Neale C, Messing S*, Dharmaiah S*, Taylor T*, Denson JP*, Esposito D*, Nissley DV*, Stephen AG*, McCormick F*, Simanshu DK*
  Nat Commun 2021
  PubMed PMID: 33608534
   
• A practical guide to large-scale docking
  Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE*, Carlsson J, Irwin JJ, Shoichet BK
  Nat Protoc 2021
  PubMed PMID: 34561691
   
• A review of alternative promoters for optimal recombinant protein expression in baculovirus-infected insect cells
  Grose C*, Putman Z*, Esposito D*
  Protein Expr Purif 2021
  PubMed PMID: 34087362
   
• RAS nanoclusters: dynamic signaling platforms amenable to therapeutic intervention
  Van QN*, Prakash P, Shrestha R*, Balius TE*, Turbyville TJ*, Stephen AG*
  Biomolecules 2021
  PubMed PMID: 33802474
   
• Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane
  Van QN*, López CA, Tonelli M, Taylor T*, Niu B, Stanley CB, Bhowmik D, Tran TH*, Frank PH*, Messing S*, Alexander P*, Scott D, Ye X*, Drew M*, Chertov O*, Lösche M, Ramanathan A, Gross ML, Hengartner NW, Westler WM, Markley JL, Simanshu DK*, Nissley DV*, Gillette WK*, Esposito D*, McCormick F*, Gnanakaran S, Heinrich F, Stephen AG*
  Proc Natl Acad Sci U S A 2020
  PubMed PMID: 32913056
   
• Structural Insights into the SPRED1-Neurofibromin-KRAS Complex and Disruption of SPRED1-Neurofibromin Interaction by Oncogenic EGFR
  Yan W*, Markegard E, Dharmaiah S*, Urisman A, Drew M*, Esposito D*, Scheffzek K, Nissley DV*, McCormick F*, Simanshu DK*
  Cell Rep 2020
  PubMed PMID: 32697994
   
• Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD
  Travers T, López CA, Agamasu C*, Hettige JJ, Messing S*, García AE, Stephen AG*, Gnanakaran S
  Biophys J 2020
  PubMed PMID: 32649863
   
• ssGSEA score-based Ras dependency indexes derived from gene expression data reveal potential Ras addiction mechanisms with possible clinical implications
  Yi M*, Nissley DV*, McCormick F*, Stephens RM*
  Sci Rep 2020
  PubMed PMID: 32581224
   
• RAS internal tandem duplication disrupts GTPase-activating protein (GAP) binding to activate oncogenic signaling
  Nelson AC, Turbyville TJ*, Dharmaiah S*, Rigby M*, Yang R, Wang TY, Columbus J*, Stephens R*, Taylor T*, Sciacca D, Onsongo G, Sarver A, Subramanian S, Nissley DV*, Simanshu DK*, Lou E
  J Biol Chem 2020
  PubMed PMID: 32393580
   
• The frequency of Ras mutations in cancer
  Prior IA, Hood FE, Hartley JL*
  Cancer Res 2020
  PubMed PMID: 32209560
   
• Homogeneous dual-parametric coupled assay for simultaneous nucleotide exchange and KRAS/RAF-RBD interaction monitoring
  Kopra K, Vuorinen E, Abreu-Blanco M*, Wang Q, Eskonen V, Gillette W*, Pulliainen AT, Holderfield M*, Härmä H.
  Anal Chem 2020
  PubMed PMID: 32106676
   
• The small molecule BI-2852 induces a nonfunctional dimer of KRAS.
  Tran TH*, Alexander P*, Dharmaiah S*, Agamasu C*, Nissley DV*, McCormick F*, Esposito D*, Simanshu DK*, Stephen AG*, Balius TE*
  Proc Natl Acad Sci U S A 2020
  PubMed PMID: 32047043
   
• Fully Processed Recombinant KRAS4b: Isolating and Characterizing the Farnesylated and Methylated Protein
  Agamasu C*, Frank P*, Perkins S*, Waybright T*, Messing S*, Gillette W*, Stephen AG*
  J Vis Exp 2020
  PubMed PMID: 32009649
   
• Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior
  Goswami D*, Chen D*, Yang Y, Gudla PR*, Columbus J*, Worthy K*, Rigby M*, Wheeler M*, Mukhopadhyay S*, Powell K*, Burgan W*, Wall V*, Esposito D*, Simanshu D*, Lightstone FC, Nissley DV*, McCormick F*, Turbyville T*
  Elife 2020
  PubMed PMID: 31958057
   
• PDE6D Inhibitors with a New Design Principle Selectively Block K-Ras Activity
  Siddiqui FA, Alam C, Rosenqvist P, Ora M, Sabt A, Manoharan GB, Bindu L*, Okutachi S, Catillon M, Taylor T*, Abdelhafez OM, Lönnberg H, Stephen AG*, Papageorgiou AC, Virta P, Abankwa D
  ACS Omega 2019
  PubMed PMID: 31956834
   
• Undermining glutaminolysis bolsters chemotherapy while NRF2 promotes chemoresistance in KRAS-driven pancreatic cancers
  Mukhopadhyay S*, Goswami D*, Adiseshaiah PP, Burgan W*, Yi M*, Guerin TM, Kozlov SV, Nissley DV*, McCormick F*
  Cancer Res 2020
  PubMed PMID: 31911550
   
• A Massively Parallel Infrastructure for Adaptive Multiscale Simulations: Modeling RAS Initiation Pathway for Cancer
  F. Di Natale, H. Bhatia, T. S. Carpenter, C. Neale, S. Kokkila Schumacher, T. Oppelstrup, L. Stanton, X. Zhang, S. Sundram, T. R. W. Scogland, G. Dharuman, M. P. Surh, Y. Yang, C. Misale, L. Schneidenbach, C. Costa, C. Kim, B. D’Amora, S. Gnanakaran, D. V. Nissley*, F. Streitz, F. C. Lightstone, P.-T. Bremer, J. N. Glosli, H. I. Ingolfsson
  SC '19: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, Article No.: 57, 1–16.
  Winner of SC Best Paper Award
  DOI: 10.1145/3295500.3356197
   
• Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer
  Sherekar M*, Han SW, Ghirlando R, Messing S*, Drew M*, Rabara D*, Waybright T*, Juneja P, O'Neill H, Stanley CB, Bhowmik D, Ramanathan A, Subramaniam S, Nissley DV*, Gillette W*, McCormick F*, Esposito D*
  J Biol Chem 2019
  PubMed PMID: 31836666
   
• Atypical KRASG12R Mutant Is Impaired in PI3K Signaling and Macropinocytosis in Pancreatic Cancer.
  Hobbs GA, Baker NM, Miermont AM, Thurman RD, Pierobon M, Tran TH*, Anderson AO, Waters AM, Diehl JN, Papke B, Hodge RG, Klomp JE, Goodwin CM, DeLiberty JM, Wang J, Ng RWS, Gautam P, Bryant KL, Esposito D*, Campbell SL, Petricoin EF, Simanshu DK*, Aguirre AJ, Wolpin BM, Wennerberg K, Rudloff U, Cox AD, Der CJ.
  Cancer Discov 2019
  PubMed PMID: 31649109
   
• AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing
  Bhattacharya T, Brettin T, Doroshow JH, Evrard YA, Greenspan EJ, Gryshuk AL, Hoang TT, Lauzon CBV, Nissley D*, Penberthy L, Stahlberg E, Stevens R, Streitz F, Tourassi G, Xia F, Zaki G
  Front Oncol 2019
  PubMed PMID: 31632915
   
• RIT1 oncoproteins escape LZTR1-mediated proteolysis
  Castel P, Cheng A, Cuevas-Navarro A, Everman DB, Papageorge AG, Simanshu DK*, Tankka A, Galeas J, Urisman A, McCormick F.
  Science. 2019;363(6432):1226-30
  PubMed PMID: 30872527
   
• KRAS G13D sensitivity to neurofibromin-mediated GTP hydrolysis
  Rabara D*, Tran TH*, Dharmaiah S*, Stephens RM*, McCormick F*, Simanshu DK*, Holderfield M*
  Proc Natl Acad Sci U S A 2019
  PubMed PMID: 31611389
   
• Distinct Binding Preferences between Ras and Raf Family Members and the Impact on Oncogenic Ras Signaling
  Terrell EM, Durrant DE, Ritt DA, Sealover NE, Sheffels E, Spencer-Smith R, Esposito D*, Zhou Y, Hancock JF, Kortum RL, Morrison DK
  Mol Cell 2019
  PubMed PMID: 31606273
   
• Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies
  Talsania K, Mehta M, Raley C, Kriga Y, Gowda S, Grose C*, Drew M*, Roberts V*, Cheng KT, Burkett S, Oeser S, Stephens R*, Soppet D*, Chen X, Kumar P, German O, Smirnova T, Hautman C, Shetty J, Tran B, Zhao Y, Esposito D*
  Genes (Basel). 2019;10(2)
  PubMed PMID: 30678108
   
• Second harmonic generation detection of Ras conformational changes and discovery of a small molecule binder
  Donohue E, Khorsand S, Mercado G, Varney KM, Wilder PT, Yu W, MacKerell AD Jr, Alexander P*, Van QN*, Moree B, Stephen AG*, Weber DJ, Salafsky J, McCormick F*
  Proc Natl Acad Sci U S A 2019 
  PubMed PMID: 31399543
   
• PIP2 Influences the Conformational Dynamics of Membrane-Bound KRAS4b 
  McLean MA, Stephen AG*, Sligar SG
  Biochemistry 2019 
  PubMed PMID: 31339036
   
• Organization of Farnesylated, Carboxymethylated KRAS4B on Membranes
  Barklis E, Stephen AG*, Staubus AO, Barklis RL, Alfadhli A
  J Mol Biol 2019
  PubMed PMID: 31330153
   
• Structures of N-terminally processed KRAS provide insight into the role of N-acetylation 
  Dharmaiah S*, Tran TH*, Messing S*, Agamasu C*, Gillette WK*, Yan W*, Waybright T*, Alexander P*, Esposito D*, Nissley DV*, McCormick F*, Stephen AG*, Simanshu DK*
  Sci Rep 2019 
  PubMed PMID: 31324887
   
• Blockade of leukemia inhibitory factor as a therapeutic approach to KRAS driven pancreatic cancer
  Wang MT, Fer N*, Galeas J, Collisson EA, Kim SE, Sharib J, McCormick F*
  Nat Commun 2019 
  PubMed PMID: 31296870
   
• Membrane curvature sensing of the lipid-anchored K-Ras small GTPase
  Liang H, Mu H, Jean-Francois F*, Lakshman B*, Sarkar-Banerjee S, Zhuang Y, Zeng  Y, Gao W, Zaske AM, Nissley DV*, Gorfe AA, Zhao W, Zhou Y
  Life Sci Alliance 2019 
  PubMed PMID: 31296567
   
• Intercellular Transfer of Oncogenic KRAS via Tunneling Nanotubes Introduces Intracellular Mutational Heterogeneity in Colon Cancer Cells
  Desir S, Wong P, Turbyville T*, Chen D*, Shetty M, Clark C, Zhai E, Romin Y, Manova-Todorova K, Starr TK, Nissley DV, Steer CJ, Subramanian S, Lou E
  Cancers (Basel) 2019
  PubMed PMID: 31247990
   
• Production of Farnesylated and Methylated Proteins in an Engineered Insect Cell System
  Gillette W*, Frank P*, Perkins S*, Drew M*, Grose C*, Esposito D*
  Methods Mol Biol 2019
  PubMed PMID: 31152410
   
• Feasibility of using NF1-GRD and AAV for gene replacement therapy in NF1-associated tumors
  Bai RY, Esposito D*, Tam AJ, McCormick F*, Riggins GJ, Wade Clapp D, Staedtke V
  Gene Ther 2019
  PubMed PMID: 31127187
   
• New weapons to penetrate the armor: Novel reagents and assays developed at the NCI RAS Initiative to enable discovery of RAS therapeutics
  Esposito D*, Stephen AG*, Turbyville TJ*, Holderfield M*
  Semin Cancer Biol 2019
  PubMed PMID: 29432816
   
• KRAS Prenylation Is Required for Bivalent Binding with Calmodulin in a Nucleotide-Independent Manner
  Agamasu C*, Ghirlando R, Taylor T*, Messing S*, Tran TH*, Bindu L*, Tonelli M, Nissley DV*, McCormick F*, Stephen AG*
  Biophys Journal 2019
  PubMed PMID: 30846362
   
• Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane
  Lakshman B*, Messing S*, Schmid EM, Clogston JD, Gillette WK*, Esposito D*, Kessing B*, Fletcher DA, Nissley DV*, McCormick F*, Stephen AG*, Jean-Francois FL*
  J Biol Chem 2018
  PubMed ID: 30559287
   
• GradientScanSurv-An exhaustive association test method for gene expression data with censored survival outcome
  Yi M*, Zhu R, Stephens RM*
  PloS One 2018
  PubMed ID: 30517129
   
• Label-Free Time-Gated Luminescent Detection Method for the Nucleotides with Varying Phosphate Content
  Kopra K, Seppälä T, Rabara D*, Abreu-Blanco M*, Kulmala S, HolderfieldM*, Härmä H
  Sensors (Basel) 2018
  PubMed ID: 30453509
   
• The bacterial Ras/Rap1 site-specific endopeptidase RRSP cleaves Ras through an atypical mechanism to disrupt Ras-ERK signaling
  Biancucci M, Minasov G, Banerjee A, Herrera A, Woida PJ, Kieffer MB, Bindu L*, Abreu-Blanco M*, Anderson WF, Gaponenko V, Stephen AG*, Holderfield M*, Satchell KJF
  Sci Signal  2018 
  PubMed ID: 30279169
   
• Production of authentic geranylgeranylated KRAS4b using an engineered baculovirus system
  Procter L*, Grose C*, Esposito D*
  Protein Expr Purif 2018 
  PubMed ID: 29936133
   
• Direct molecular dissection of tumor parenchyma from tumor stroma in tumor xenograft using mass spectrometry-based glycoproteomics
  Ye X*, Luke BT, Wei BR, Kaczmarczyk JA, Loncarek J, Dwyer JE, Johann DJ, Saul RG, Nissley DV*, McCormick F*, Whiteley GR*, Blonder J*
  Oncotarget 2018 
  PubMed ID: 29899869
   
• Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain
  Travers T, López CA, Van QN*, Neale C, Tonelli M, Stephen AG*, Gnanakaran S
  Sci Rep 2018
  PubMed ID: 29855542
   
• Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk
  Ntai I, Fornelli L, DeHart CJ, Hutton JE, Doubleday PF, LeDuc RD, van Nispen AJ, Fellers RT, Whiteley G*, Boja ES, Rodriguez H, Kelleher NL
  Proc Natl Acad Sci USA 2018
  PubMed ID: 29610327
   
• Differential Effector Engagement by Oncogenic KRAS
  Yuan TL, Amzallag A, Bagni R*, Yi M*, Afghani S, Burgan W*, Fer N*, Strathern LA*, Powell K*, Smith B, Waters AM*, Drubin D, Thomson T, Liao R, Greninger P, Stein GT, Murchie E, Cortez E, Egan RK, Procter L*, Bess M, Cheng KT*, Lee CS, Lee LC, Fellmann C, Stephens R*, Luo J, Lowe SW, Benes CH, McCormick F*
  Cell Rep 2018
  PubMed ID: 29444439
   
• New weapons to penetrate the armor: Novel reagents and assays developed at the NCI RAS Initiative to enable discovery of RAS therapeutics
  Esposito D*, Stephen AG*, Turbyville TJ*, Holderfield M*
  Semin Cancer Biol. 2018 
  PubMed ID: 29432816
   
• Targeting RAS-driven human cancer cells with antibodies to upregulated and essential cell-surface proteins
  Martinko AJ, Truillet C, Julien O, Diaz JE, Horlbeck MA, Whiteley G*, Blonder J*, Weissman JS, Bandyopadhyay S, Evans MJ, Wells JA
  Elife 2018 
  PubMed ID: 29359686
   
• K-Ras4B Remains Monomeric on Membranes over a Wide Range of Surface Densities and Lipid Compositions
  Chung JK, Lee YK, Denson JP*, Gillette WK*, Alvarez S, Stephen AG*, Groves JT
  Biophys J. 2018 
  PubMed ID: 29320680
   
• Efforts to Develop KRAS Inhibitors
  Holderfield M*
  Cold Spring Harb Perspect Med 2018
  PubMed ID: 29101115
   
• Evaluation of the selectivity and sensitivity of isoform- and mutation-specific RAS antibodies
  Waters AM*, Ozkan-Dagliyan I, Vaseva AV, Fer N*, Strathern LA*, Hobbs GA, Tessier-Cloutier B, Gillette WK*, Bagni R*, Whiteley GR*, Hartley JL*, McCormick F*, Cox AD, Houghton PJ, Huntsman DG, Philips MR, Der CJ
  Sci Signal 2018
  PubMed ID: 28951536
   
• RAS Proteins and Their Regulators in Human Disease
  Simanshu DK*, Nissley DV*, McCormick F*
  Cell 2017
  PubMed ID: 28666118
   
• Tumor RAS Gene Expression Levels Are Influenced by the Mutational Status of RAS Genes and Both Upstream and Downstream RAS Pathway Genes
  Stephens RM*, Yi M*, Kessing B*, Nissley DV*, McCormick F*
  Cancer Inform 2017
  PubMed ID: 28634423
   
• A KRAS GTPase K104Q Mutant Retains Downstream Signaling by Offsetting Defects in Regulation
  Yin G, Kistler S, George SD, Kuhlmann N, Garvey L*, Huynh M, Bagni RK*, Lammers M, Der CJ, Campbell SL
  J Biol Chem 2017
  PubMed ID: 28154176
   
• RAS signaling: Divide and conquer
  Holderfield M*, Morrison DK
  Nat Chem Biol 2016
  PubMed ID: 27984577
   
• Comparative proteomics of a model MCF10A-KRasG12V cell line reveals a distinct molecular signature of the KRasG12V cell surface
  Ye X, Chan KC, Waters AM*, Bess M, Harned A, Wei BR, Loncarek J, Luke BT, Orsburn BC, Hollinger BD*, Stephens RM*, Bagni R*, Martinko A, Wells JA, Nissley DV*, McCormick F*, Whiteley G*, Blonder J*
  Oncotarget 2016
  PubMed ID: 27894102
   
• Inhibition of Ras/Raf/MEK/ERK Pathway Signaling by a Stress-Induced Phospho-Regulatory Circuit
  Ritt DA, Abreu-Blanco MT*, Bindu L*, Durrant DE, Zhou M, Specht SI, Stephen AG*, Holderfield M*, Morrison DK
  Mol Cell 2016
  PubMed ID: 27889448
   
• Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ
  Dharmaiah S*, Bindu L*, Tran TH*, Gillette WK*, Frank PH*, Ghirlando R, Nissley DV*, Esposito D*, McCormick F*, Stephen AG*, Simanshu DK*
  Proc Natl Acad Sci USA 2016
  PubMed ID: 27791178
   
• Single Synonymous Mutations in KRAS Cause Transformed Phenotypes in NIH3T3 Cells
  Waters AM*, Bagni R*, Portugal F*, Hartley JL*
  PLoS One 2016
  PubMed ID: 27684555
   
• Farnesylated and methylated KRAS4b: high yield production of protein suitable for biophysical studies of prenylated protein-lipid interactions
  Gillette WK*, Esposito D*, Abreu Blanco M*, Alexander P*, Bindu L*, Bittner C*, Chertov O*, Frank PH*, Grose C*, Jones JE*, Meng Z*, Perkins S*, Van Q, Ghirlando R, Fivash M*, Nissley DV*, McCormick F*, Holderfield M*, Stephen AG*
  Sci Rep 2015
  PubMed ID: 26522388
   
• Progress in targeting RAF kinases for cancer therapy
  Turbyville TJ*, Holderfield M*
  Per Med 2015
  PubMed ID: 29771643
   
• Dragging RAS back in the ring
  Stephen AG*, Esposito D*, Bagni RK*, McCormick F*
  Cancer Cell 2014
  PubMed ID: 24651010