D. Simanshu

发表

A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer.

Yuan Tian, D. Patel, V. Kim, 2014, Molecular cell.

Dicer recognizes the 5′ end of RNA for efficient and accurate processing

Hyeshik Chang, V. Narry Kim, Dinshaw J. Patel, 2011, Nature.

Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains

Yuan Tian, Dinshaw J. Patel, D. Patel, 2010, Proceedings of the National Academy of Sciences.

TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms

D. Patel, C. Joo, V. Kim, 2015, The EMBO journal.

RAS Proteins and Their Regulators in Human Disease

Frank McCormick, F. McCormick, D. Simanshu, 2017, Cell.

RIT1 oncoproteins escape LZTR1-mediated proteolysis

F. McCormick, P. Castel, D. Everman, 2019, Science.

Structural Insights into the SPRED1-Neurofibromin-KRAS Complex and Disruption of SPRED1-Neurofibromin Interaction by Oncogenic EGFR

D. Esposito, F. McCormick, K. Scheffzek, 2020, Cell reports.

Arabidopsis accelerated cell death 11, ACD11, is a ceramide-1-phosphate transfer protein and intermediary regulator of phytoceramide levels.

A. Bielawska, L. Malinina, D. Patel, 2014, Cell reports.

Atypical KRASG12R Mutant Is Impaired in PI3K Signaling and Macropinocytosis in Pancreatic Cancer.

Nicole M. Baker, E. Petricoin, D. Esposito, 2019, Cancer discovery.

Structure of the SHOC2–MRAS–PP1C complex provides insights into RAF activation and Noonan syndrome

P. Alexander, D. Esposito, F. McCormick, 2022, bioRxiv.

RAS interaction with Sin1 is dispensable for mTORC2 assembly and activity

D. Esposito, F. McCormick, M. Trnka, 2021, Proceedings of the National Academy of Sciences.

RAS internal tandem duplication disrupts GTPase-activating protein (GAP) binding to activate oncogenic signaling

Rendong Yang, Subbaya Subramanian, Ting-You Wang, 2020, The Journal of Biological Chemistry.

Structures of N-terminally processed KRAS provide insight into the role of N-acetylation

P. Alexander, D. Esposito, F. McCormick, 2019, Scientific Reports.

Insights into the Cross Talk between Effector and Allosteric Lobes of KRAS from Methyl Conformational Dynamics.

Gabriel Cornilescu, D. Esposito, F. McCormick, 2022, Journal of the American Chemical Society.

Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework.

Helgi I. Ingólfsson, Timothy S. Carpenter, Christopher B. Stanley, 2022, Journal of chemical theory and computation.

Structural basis of phosphatidylcholine recognition by the C2–domain of cytosolic phospholipase A2α

L. Malinina, D. Patel, Y. Hirano, 2019, eLife.

The glycolipid transfer protein (GLTP) domain of phosphoinositol 4-phosphate adaptor protein-2 (FAPP2): structure drives preference for simple neutral glycosphingolipids.

L. Malinina, D. Patel, S. Venyaminov, 2013, Biochimica et biophysica acta.

Crystallization and preliminary X-ray crystallographic analysis of biodegradative threonine deaminase (TdcB) from Salmonella typhimurium.

M. Murthy, D. Simanshu, H. Savithri, 2006, Acta crystallographica. Section F, Structural biology and crystallization communications.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of propionate kinase (TdcD) from Salmonella typhimurium.

D. Simanshu, M. Murthy, 2005, Acta crystallographica. Section F, Structural biology and crystallization communications.

Cloning, expression, purification and preliminary X-ray crystallographic studies of 2-methylisocitrate lyase from Salmonella typhimurium.

S. Parthasarathy, M. Murthy, D. Simanshu, 2002, Acta crystallographica. Section D, Biological crystallography.

Ras-dependent RAF-MAPK hyperactivation by pathogenic RIT1 is a therapeutic target in Noonan syndrome-associated cardiac hypertrophy

F. McCormick, M. Swain, A. Stephen, 2022, bioRxiv.

Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ.

R. Ghirlando, D. Esposito, F. McCormick, 2016, Proceedings of the National Academy of Sciences of the United States of America.

Nonvesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids

L. Malinina, D. Patel, C. Chalfant, 2013, Nature.

Phosphatidylserine Stimulates Ceramide 1-Phosphate (C1P) Intermembrane Transfer by C1P Transfer Proteins*

H. R. Bergen, L. Malinina, D. Patel, 2016, Journal of Biological Chemistry.

Structural Studies On Enzymes From Salmonella Typhimurium Involved In Propionate Metabolism: Biodegradative Threonine Deaminase, Propionate Kinase And 2-Methylisocitrate Lyase

D. Simanshu, 2006 .

Functional evaluation of tryptophans in glycolipid binding and membrane interaction by HET-C2, a fungal glycolipid transfer protein.

L. Malinina, D. Patel, H. Pike, 2018, Biochimica et biophysica acta. Biomembranes.

Structural Determination and Tryptophan Fluorescence of Heterokaryon Incompatibility C2 Protein (HET-C2), a Fungal Glycolipid Transfer Protein (GLTP), Provide Novel Insights into Glycolipid Specificity and Membrane Interaction by the GLTP Fold*

H. R. Bergen, L. Malinina, D. Patel, 2010, The Journal of Biological Chemistry.

Sphingolipid transfer proteins defined by the GLTP-fold

L. Malinina, D. Patel, Rhoderick E. Brown, 2015, Quarterly Reviews of Biophysics.

Conformational folding and stability of the HET-C2 glycolipid transfer protein fold: does a molten globule-like state regulate activity?

L. Malinina, D. Patel, S. Venyaminov, 2011, Biochemistry.

Crystal Structures of Salmonella typhimurium Biodegradative Threonine Deaminase and Its Complex with CMP Provide Structural Insights into Ligand-induced Oligomerization and Enzyme Activation*

D. Simanshu, H. Savithri, M. Murthy, 2006, Journal of Biological Chemistry.

Uridylation by TUT4 and TUT7 Marks mRNA for Degradation

D. Patel, V. Kim, S. -. Kwon, 2014, Cell.

RAS Internal Tandem Duplication Disrupts GAP-binding to Activate Oncogenic Signaling

Rendong Yang, Subbaya Subramanian, D. Simanshu, 2019, bioRxiv.

Allosteric regulation of switch-II controls K-Ras oncogenicity

A. Stephen, K. Haigis, D. Simanshu, 2022, bioRxiv.

KRAS G13D sensitivity to neurofibromin-mediated GTP hydrolysis

R. Stephens, F. McCormick, M. Holderfield, 2019, Proceedings of the National Academy of Sciences.

Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ

R. Ghirlando, D. Esposito, F. McCormick, 2016, Proceedings of the National Academy of Sciences.

Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily.

M. Murthy, D. Simanshu, H. Savithri, 2005, Journal of molecular biology.

A Structure is Worth a Thousand Words: New Insights for RAS and RAF Regulation

D. Morrison, D. Simanshu, Dhirendra K Simanshu, 2022, Cancer discovery.

KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation

D. Esposito, F. McCormick, T. Tran, 2021, Nature Communications.

Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane

Christopher B. Stanley, N. Hengartner, A. Ramanathan, 2020, Proceedings of the National Academy of Sciences.

KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation

D. Esposito, F. McCormick, T. Tran, 2020, bioRxiv.

Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins

Helgi I. Ingólfsson, Timothy S. Carpenter, A. Voter, 2020, Proceedings of the National Academy of Sciences.

The small molecule BI-2852 induces a nonfunctional dimer of KRAS

P. Alexander, D. Esposito, F. McCormick, 2020, Proceedings of the National Academy of Sciences.

Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior

Prabhakar R. Gudla, D. Esposito, F. McCormick, 2020, eLife.

INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

Christopher J. Hale, D. Patel, S. Jacobsen, 2012, Proceedings of the National Academy of Sciences.

A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo.

Julie A. Law, D. Reinberg, D. Patel, 2011, Genes & development.

dimethylation in vivo SUVH 5 SRA domain and its impact on DNA methylation and H 3 K 9 Arabidopsis A dual flip-out mechanism for 5 mC recognition by the

Julie A. Law, D. Reinberg, D. Patel, 2011 .

Structural basis of mRNA recognition and cleavage by toxin MazF and its regulation by antitoxin MazE in Bacillus subtilis.

M. Inouye, D. Patel, Jung-Ho Park, 2013, Molecular cell.

Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: Evidence for a novel Ap4A synthetic activity

D. Simanshu, H. S. Savithri, M. Murthy, 2007, Proteins.

Multimeric assembly and biochemical characterization of the Trax/Translin endonuclease complex

M. Ascano, T. Tuschl, D. Patel, 2011, Nature Structural &Molecular Biology.

Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies.

M. Murthy, Sanchari Banerjee, D. Simanshu, 2013, Biochimica et biophysica acta.

Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate

M. Murthy, D. Simanshu, H. Savithri, 2007, Journal of Biosciences.

Crystal structure of Salmonella typhimurium 2-methylisocitrate lyase (PrpB) and its complex with pyruvate and Mg(2+).

M. Murthy, D. Simanshu, M. Murthy, 2003, Biochemical and biophysical research communications.

Structures of N-terminally processed KRAS provide insight into the role of N-acetylation

P. Alexander, D. Esposito, F. McCormick, 2019, Scientific Reports.

Consensus on the RAS dimerization hypothesis: Strong evidence for lipid-mediated clustering but not for G-domain-mediated interactions.

J. Hancock, D. Simanshu, M. Philips, 2023, Molecular cell.

Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality.

M. Murthy, N. Kunishima, K. Saraboji, 2008, Acta crystallographica. Section D, Biological crystallography.

The ribosomal S6 kinase 2 (RSK2)–SPRED2 complex regulates the phosphorylation of RSK substrates and MAPK signaling

F. McCormick, P. Castel, D. Simanshu, 2023, The Journal of biological chemistry.

The tumor suppressor activity of DLC1 requires the interaction of its START domain with Phosphatidylserine, PLCD1, and Caveolin-1

J. Acharya, D. Lowy, D. Simanshu, 2021, Molecular Cancer.

Preliminary X-ray crystallographic analysis of 2-methylcitrate synthase from Salmonella typhimurium.

M. Murthy, D. Simanshu, H. Savithri, 2010, Acta crystallographica. Section F, Structural biology and crystallization communications.

Exploring CRD mobility during RAS/RAF engagement at the membrane.

Timothy S. Carpenter, P. Bremer, F. Streitz, 2022, Biophysical Journal.

Structural basis of phosphatidylcholine recognition by the 1 C 2 – domain of cytosolic phospholipase A 2 α 2 3

L. Malinina, D. Patel, Y. Hirano, 2022 .

Structural analyses of 4-phosphate adaptor protein 2 yield mechanistic insights into sphingolipid recognition by the glycolipid transfer protein family

L. Malinina, D. Patel, Rhoderick E. Brown, 2018, The Journal of Biological Chemistry.

Reduced dynamic complexity allows structure elucidation of an excited state of KRASG13D

Gabriel Cornilescu, C. Schwieters, D. Esposito, 2023, Communications biology.

RAS-dependent RAF-MAPK hyperactivation by pathogenic RIT1 is a therapeutic target in Noonan syndrome–associated cardiac hypertrophy

F. McCormick, M. Swain, A. Stephen, 2023, Science advances.

INAUGURAL ARTICLE by a Recently Elected Academy Member:Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains

D. Patel, Jinbiao Ma, Yuan Tian, 2011 .

Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements

T. E. Balius, Mayukh Chakrabarti, D. Simanshu, 2024, Communications Biology.

Phosphatidylserine Stimulates Ceramide 1-Phosphate (C1P) Intermembrane Transfer by C1P Transfer Proteins*

L. Malinina, J. Mundy, Rhoderick E. Brown, 2016, The Journal of Biological Chemistry.

INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

Christopher J. Hale, D. Patel, S. Jacobsen, 2012, Proceedings of the National Academy of Sciences.

Sphingolipid transfer proteins defined by the GLTP-fold

L. Malinina, D. Patel, Rhoderick E. Brown, 2015, Quarterly Reviews of Biophysics.

Functional and structural insights into RAS effector proteins.

P. Castel, D. Simanshu, Alessandro M. Mozzarelli, 2024, Molecular cell.