J. Burke

发表

Accurate prediction of protein structures and interactions using a 3-track neural network

Gyu Rie Lee, J. H. Pereira, N. Grishin, 2021, Science.

Conformational sampling of membranes by Akt controls its activation and inactivation

John E. Burke, David J. Hamelin, Thomas A. Leonard, 2018, Proceedings of the National Academy of Sciences.

Using Hydrogen/Deuterium Exchange Mass Spectrometry to Define the Specific Interactions of the Phospholipase A2 Superfamily with Lipid Substrates, Inhibitors, and Membranes*

E. Dennis, J. Burke, Jian Cao, 2012, The Journal of Biological Chemistry.

Phospholipase A2 Biochemistry

E. Dennis, J. Burke, 2009, Cardiovascular Drugs and Therapy.

The substrate specificity of the human TRAPPII complex’s Rab-guanine nucleotide exchange factor activity

U. Dalwadi, C. Yip, J. Burke, 2020, Communications biology.

Vesicular and non-vesicular transport feed distinct glycosylation pathways in the Golgi

Roger L. Williams, S. d'Auria, A. Varriale, 2013, Nature.

Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne

P. R. Elliott, H. Ovaa, J. Burke, 2016, Nature.

Integrated Structural Modeling of Full-Length LRH-1 Reveals Inter-domain Interactions Contribute to Receptor Structure and Function.

J. Meiler, J. Burke, C. Seacrist, 2020, Structure.

An overview of hydrogen deuterium exchange mass spectrometry (HDX-MS) in drug discovery

J. Burke, M. Jenkins, G. Masson, 2017, Expert opinion on drug discovery.

Dynamic steps in receptor tyrosine kinase mediated activation of class IA phosphoinositide 3-kinases (PI3K) captured by H/D exchange (HDX-MS)

John E. Burke, Roger L. Williams, J. Burke, 2013, Advances in biological regulation.

Defining how oncogenic and developmental mutations of PIK3R1 alter the regulation of class IA phosphoinositide 3-kinases

M. Rathinaswamy, J. Burke, M. Boulanger, 2019, bioRxiv.

Defining How Oncogenic and Developmental Mutations of PIK3R1 Alter the Regulation of Class IA Phosphoinositide 3-Kinases.

M. Rathinaswamy, J. Burke, M. Boulanger, 2019, Structure.

The Molecular Basis of Aichi Virus 3A Protein Activation of Phosphatidylinositol 4 Kinase IIIβ, PI4KB, through ACBD3.

J. Burke, M. Jenkins, J. McPhail, 2017, Structure.

Conformational disruption of PI3Kδ regulation by immunodeficiency mutations in PIK3CD and PIK3R1

Braden D. Siempelkamp, J. Burke, M. Jenkins, 2017, Proceedings of the National Academy of Sciences.

Regulation of PI3K by PKC and MARCKS: Single-Molecule Analysis of a Reconstituted Signaling Pathway.

Roger L. Williams, J. Burke, J. Falke, 2016, Biophysical journal.

Molecular determinants of PI3Kγ-mediated activation downstream of G-protein–coupled receptors (GPCRs)

Roger L. Williams, A. Bresnick, J. Backer, 2013, Proceedings of the National Academy of Sciences.

Dynamics of the Phosphoinositide 3-Kinase p110δ Interaction with p85α and Membranes Reveals Aspects of Regulation Distinct from p110α

Roger L. Williams, J. Burke, O. Perisic, 2011, Structure.

Dynamics of the Phosphoinositide 3-Kinase p110δ Interaction with p85α and Membranes Reveals Aspects of Regulation Distinct from p110α

Roger L. Williams, J. Burke, O. Perisic, 2011, Structure.

Novel roles of phosphoinositides in signaling, lipid transport, and disease.

J. Burke, Gerald R. V. Hammond, 2020, Current opinion in cell biology.

PKD autoinhibition in trans regulates activation loop autophosphorylation in cis

T. Leonard, J. Burke, A. Hausser, 2022, bioRxiv.

Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediated activation

T. Leonard, E. Pardon, J. Steyaert, 2021, Proceedings of the National Academy of Sciences.

Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediated activation

T. Leonard, E. Pardon, J. Steyaert, 2021, Proceedings of the National Academy of Sciences.

Characterization of the c10orf76‐PI4KB complex and its necessity for Golgi PI4P levels and enterovirus replication

J. Burke, T. Balla, F. V. van Kuppeveld, 2019, EMBO reports.

Phospholipase A 2 Biochemistry

E. Dennis, J. Burke, 2010 .

Microsoft Word-WFA_Manuscript_Aug_10_2016_Final_2.docx

J. Burke, M. Gilbert, M. Jenkins, 2016 .

Structure and inhibition of Cryptococcus neoformans sterylglucosidase to develop antifungal agents

M. Del Poeta, J. Burke, R. Rizzo, 2021, Nature Communications.

Molecular insight into the autoinhibition of a master regulator of lipid signalling in human disease

J. Burke, 2020, EBioMedicine.

Potent and selective fluoroketone inhibitors of group VIA calcium-independent phospholipase A2.

E. Dennis, J. Burke, Y. Hsu, 2010, Journal of medicinal chemistry.

Design and Structural Characterization of Potent and Selective Inhibitors of Phosphatidylinositol 4 Kinase IIIβ.

K. Shokat, J. Glenn, J. Burke, 2016, Journal of medicinal chemistry.

The intrinsically disordered tails of PTEN and PTEN-L have distinct roles in regulating substrate specificity and membrane activity

Roger L. Williams, J. Burke, O. Perisic, 2015, The Biochemical journal.

Recognition of protein-linked glycans as a determinant of peptidase activity

J. Burke, M. Gilbert, W. Wakarchuk, 2017, Proceedings of the National Academy of Sciences.

Type III phosphatidylinositol 4 kinases: structure, function, regulation, signalling and involvement in disease.

J. Burke, G. L. Dornan, J. McPhail, 2016, Biochemical Society transactions.

A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond

J. Burke, W. Wakarchuk, A. Boraston, 2022, The Journal of biological chemistry.

Overview Pulmonary - Allergy, Dermatological, Gastrointestinal & Arthritis: Bradykinin receptor antagonists

J. Burke, J. Cheronis, E. Whalley, 1995 .

Phospholipase A 2 structure/function, mechanism, and signaling 1

E. Dennis, J. Burke, 2009 .

A Phospholipid Substrate Molecule Residing in the Membrane Surface Mediates Opening of the Lid Region in Group IVA Cytosolic Phospholipase A2*

Virgil L. Woods, E. Dennis, J. Burke, 2008, Journal of Biological Chemistry.

Calcium Binding Rigidifies the C2 Domain and the Intradomain Interaction of GIVA Phospholipase A2 as Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry*

Virgil L. Woods, E. Dennis, J. Burke, 2008, Journal of Biological Chemistry.

ATP-competitive and allosteric inhibitors induce differential conformational changes at the autoinhibitory interface of Akt

T. Leonard, J. Burke, M. Jenkins, 2022, bioRxiv.

Biochemical Characterization of the TINTIN Module of the NuA4 Complex Reveals Allosteric Regulation of Nucleosome Interaction

U. Dalwadi, C. Yip, J. Burke, 2022, Molecular and cellular biology.

Biochemical insight into novel Rab-GEF activity of the mammalian TRAPPIII complex

U. Dalwadi, C. Yip, J. Burke, 2021, bioRxiv.

Activation of phospholipase C β by Gβγ and Gαq involves C-terminal rearrangement to release auto-inhibition

J. Burke, G. Tall, M. Jenkins, 2019, bioRxiv.

Novel PIK3CD mutations affecting N-terminal residues of p110δ cause activated PI3Kδ syndrome (APDS) in humans.

Braden D. Siempelkamp, J. McElwee, J. Burke, 2017, The Journal of allergy and clinical immunology.

Beyond PI3Ks: targeting phosphoinositide kinases in disease

J. Burke, B. Emerling, Gerald R. V. Hammond, 2022, Nature Reviews Drug Discovery.

Group IVA cytosolic phospholipase A2 (cPLA2alpha) and integrin alphaIIbbeta3 reinforce each other's functions during alphaIIbbeta3 signaling in platelets.

E. Dennis, Takao Shimizu, N. Prévost, 2008, Blood.

Group IVA cytosolic phospholipase A2 (cPLA2 ) and integrin IIb 3 reinforce each other’s functions during IIb 3 signaling in platelets

E. Dennis, Takao Shimizu, N. Prévost, 2008 .

Probing Protein-Membrane Interactions and Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS).

David J. Hamelin, J. Burke, R. Hoffmann, 2021, Methods in molecular biology.

Oncogenic mutations of PIK3CA lead to increased membrane recruitment driven by reorientation of the ABD, p85 and C-terminus

M. Rathinaswamy, J. Burke, M. Jenkins, 2022, bioRxiv.

Design and study of Bi[1,8]naphthyridine ligands as potential photooxidation mediators in Ru(II) polypyridyl aquo complexes.

J. Burke, R. Thummel, Feiyue Wu, 2004, Inorganic chemistry.

Methods in the Study of PTEN Structure: X-Ray Crystallography and Hydrogen Deuterium Exchange Mass Spectrometry.

Roger L. Williams, J. Burke, G. Masson, 2016, Methods in molecular biology.

Molecular basis for the recruitment of the Rab effector protein WDR44 by the GTPase Rab11

T. Leonard, J. Burke, M. Jenkins, 2022, The Journal of biological chemistry.

Deconvolution of Buparlisib's mechanism of action defines specific PI3K and tubulin inhibitors for therapeutic intervention

D. Fabbro, M. Zvelebil, Roger L. Williams, 2017, Nature Communications.

Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry.

Virgil L. Woods, J. Mccammon, E. Dennis, 2009, Journal of the American Chemical Society.

Diversity-oriented synthesis yields novel multistage antimalarial inhibitors

Benito Munoz, Stuart L. Schreiber, Takashi Yoshinaga, 2016, Nature.

Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments

Jie Zheng, Albert J R Heck, Christoph Borchers, 2019, Nature Methods.

UCT943, a Next-Generation Plasmodium falciparum PI4K Inhibitor Preclinical Candidate for the Treatment of Malaria

R. Price, K. Chibale, Dale Taylor, 2018, Antimicrobial Agents and Chemotherapy.

Palmitoylation targets the calcineurin phosphatase to the phosphatidylinositol 4-kinase complex at the plasma membrane

A. Gingras, M. Cyert, Jagoree Roy, 2021, Nature Communications.

Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110α (PIK3CA)

Glenn R Masson, John E Burke, Oscar Vadas, 2012, Proceedings of the National Academy of Sciences.

Interaction of group IA phospholipase A2 with metal ions and phospholipid vesicles probed with deuterium exchange mass spectrometry.

Virgil L. Woods, E. Dennis, J. Burke, 2008, Biochemistry.

Molecular Basis for Recognition of the Cancer Glycobiomarker, LacdiNAc (GalNAc[β1→4]GlcNAc), by Wisteria floribunda Agglutinin*

J. Burke, M. Gilbert, H. van Faassen, 2016, The Journal of Biological Chemistry.

Structural Basis for Activation and Inhibition of Class I Phosphoinositide 3-Kinases

John E. Burke, Oscar Vadas, Roger L. Williams, 2011, Science Signaling.

Rommie E. Amaro, M. Rathinaswamy, J. Burke, 2021, eLife.

Connecting with an old partner in a new way.

Roger L. Williams, J. Burke, 2013, Cancer cell.

Molecular Mechanisms of Human Disease Mediated by Oncogenic and Primary Immunodeficiency Mutations in Class IA Phosphoinositide 3-Kinases

J. Burke, G. L. Dornan, 2018, Front. Immunol..

Expanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes.

K. Shokat, J. Burke, L. M. McGregor, 2017, Biochemistry.

Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex

Roger L. Williams, C. Sachse, J. Burke, 2016, Autophagy.

Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes

Jan Steyaert, John E. Burke, Yohei Ohashi, 2015, Science.

Structural Basis for Regulation of Phosphoinositide Kinases and Their Involvement in Human Disease.

J. Burke, 2018, Molecular cell.

Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States.

Kevan M. Shokat, Steven M. Moss, John E. Burke, 2017, Cell chemical biology.

Class I phosphoinositide 3-kinase (PI3K) regulatory subunits and their roles in signaling and disease.

M. Rathinaswamy, J. Burke, 2019, Advances in biological regulation.

Drugging the Phosphoinositide 3-Kinase (PI3K) and Phosphatidylinositol 4-Kinase (PI4K) Family of Enzymes for Treatment of Cancer, Immune Disorders, and Viral/Parasitic Infections.

J. Burke, J. McPhail, J. A. McPhail, 2020, Advances in experimental medicine and biology.

G Protein–Coupled Receptor–Mediated Activation of p110β by Gβγ Is Required for Cellular Transformation and Invasiveness

Roger L. Williams, R. Taussig, A. Bresnick, 2012, Science Signaling.

Protein – Coupled Receptor – Mediated Activation of p 110 b by G bg Is Required for Cellular Transformation and Invasiveness

Roger L. Williams, R. Taussig, A. Bresnick, 2012 .

Synergy in activating class I PI3Ks.

Roger L. Williams, J. Burke, 2015, Trends in biochemical sciences.

A single discrete Rab5-binding site in phosphoinositide 3-kinase β is required for tumor cell invasion

David J. Hamelin, Zahra Erami, A. Bresnick, 2019, The Journal of Biological Chemistry.

Structure of the phosphoinositide 3-kinase p110γ-p101 complex reveals molecular mechanism of GPCR activation

Scott D. Hansen, E. Pardon, J. Steyaert, 2021, bioRxiv.

Structure of the phosphoinositide 3-kinase p 110 gp 101 2 complex reveals molecular mechanism of GPCR activation 3

Scott D. Hansen, E. Pardon, Carson Adams, 2021 .

Structure of the phosphoinositide 3-kinase (PI3K) p110γ-p101 complex reveals molecular mechanism of GPCR activation

Scott D. Hansen, E. Pardon, J. Steyaert, 2021, Science advances.

Rommie E. Amaro, M. Rathinaswamy, J. Burke, 2020, bioRxiv.

The middle lipin domain adopts a membrane-binding dimeric protein fold

J. Burke, K. Reue, M. Airola, 2021, Nature communications.

The middle lipin (M-Lip) domain is a new dimeric protein fold that binds membranes

J. Burke, K. Reue, M. Airola, 2021, bioRxiv.

E. coli and Sf9 contaminant databases to increase efficiency of tandem mass spectrometry peptide identification in structural mass spectrometry experiments.

J. Burke, M. Jenkins, Joseph M Dobbs, 2020, Journal of the American Society for Mass Spectrometry.

Dynamic structural biology at the protein membrane interface

John E Burke, J. Burke, 2019, The Journal of Biological Chemistry.

Probing the dynamic regulation of peripheral membrane proteins using hydrogen deuterium exchange-MS (HDX-MS).

J. Burke, O. Vadas, 2015, Biochemical Society transactions.

Crystal structure of a lipin/Pah phosphatidic acid phosphatase

J. Burke, K. Reue, M. Airola, 2020, Nature Communications.

Neolymphostin A Is a Covalent Phosphoinositide 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor That Employs an Unusual Electrophilic Vinylogous Ester.

Rommie E. Amaro, David J. Hamelin, M. Rathinaswamy, 2018, Journal of medicinal chemistry.

Accurate prediction of protein structures and interactions using a 3-track neural network

Gyu Rie Lee, J. H. Pereira, D. Baker, 2021, Science.

Crystal structure of an archaeal CorB magnesium transporter

B. Roux, J. Burke, G. Kozlov, 2021, Nature Communications.

Molecular mechanisms of PI4K regulation and their involvement in viral replication

J. Burke, McPhail Jacob A, 2022, Traffic.

Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11

K. Shokat, Roger L. Williams, J. Burke, 2016, Protein science : a publication of the Protein Society.

pH Biosensing by PI4P Regulates Cargo Sorting at the TGN.

C. Borchers, J. Burke, G. Smits, 2020, Developmental cell.

Activation of the essential kinase PDK1 by phosphoinositide-driven trans-autophosphorylation

T. Leonard, J. Burke, Kaelin D. Fleming, 2021, Nature Communications.

An intrinsic lipid-binding interface controls sphingosine kinase 1 function[S]

Y. Hannun, J. Burke, L. Obeid, 2018, Journal of Lipid Research.

Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα

M. Gstaiger, J. Burke, M. Wymann, 2022, Journal of the American Chemical Society.

In vitro reconstitution of Sgk3 activation by phosphatidylinositol 3-phosphate

T. Leonard, J. Burke, Kaelin D. Fleming, 2021, The Journal of biological chemistry.

In vitro reconstitution of Sgk3 activation by phosphatidylinositol-3-phosphate

T. Leonard, J. Burke, Kaelin D. Fleming, 2021, bioRxiv.

Structures of PI4KIIIβ complexes show simultaneous recruitment of Rab11 and its effectors

Kevan M. Shokat, John E. Burke, K. Shokat, 2014, Science.

Probing the Architecture, Dynamics, and Inhibition of the PI4KIIIα/TTC7/FAM126 Complex.

David J. Hamelin, U. Dalwadi, C. Yip, 2018, Journal of molecular biology.

Investigating how intrinsically disordered regions contribute to protein function using HDX-MS.

J. Burke, M. Jenkins, M. A. Parson, 2022, Biochemical Society transactions.

Palmitoylation Targets the Calcineurin Phosphatase to the Phosphatidylinositol 4‐kinase Complex at the Plasma Membrane

A. Gingras, M. Cyert, Jagoree Roy, 2022, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Characterization of the Golgi c10orf76-PI4KB complex, and its necessity for Golgi PI4P levels and enterovirus replication

J. Burke, T. Balla, F. V. van Kuppeveld, 2019, bioRxiv.

Using Hydrogen-Deuterium Exchange Mass Spectrometry to Examine Protein-Membrane Interactions.

J. Burke, M. Jenkins, O. Vadas, 2017, Methods in enzymology.

The function of phosphatidylinositol 5-phosphate 4-kinase γ (PI5P4Kγ) explored using a specific inhibitor that targets the PI5P-binding site

Roger L. Williams, J. Burke, D. Maloney, 2014, The Biochemical journal.

Localizing the Membrane Binding Region of Group VIA Ca2+-independent Phospholipase A2 Using Peptide Amide Hydrogen/Deuterium Exchange Mass Spectrometry*

Virgil L. Woods, E. Dennis, J. Burke, 2009, The Journal of Biological Chemistry.

PKCβ Phosphorylates PI3Kγ to Activate It and Release It from GPCR Control

Emilio Hirsch, John E. Burke, Roger L. Williams, 2013, PLoS biology.

Structural and mechanistic insights into the function of the unconventional class XIV myosin MyoA fromToxoplasma gondii.

David J. Hamelin, J. Burke, D. Warshaw, 2018 .

Structural and mechanistic insights into the function of the unconventional class XIV myosin MyoA from Toxoplasma gondii

David J. Hamelin, J. Burke, D. Warshaw, 2018, Proceedings of the National Academy of Sciences of the United States of America.

The comparison of 8-hydroxyquinoline, tropolone, and acetylacetone as mediators in the labelling of polymorphonuclear leucocytes with indium-111: A functional study

J. Burke, P. Wyeth, S. Roath, 2004, European Journal of Nuclear Medicine.

Dissecting the molecular assembly of the Toxoplasma gondii MyoA motility complex

J. Burke, D. Warshaw, G. Ward, 2017, The Journal of Biological Chemistry.

Discovery and Preclinical Characterization of 5-[4,6-Bis({3-oxa-8-azabicyclo[3.2.1]octan-8-yl})-1,3,5-triazin-2-yl]-4-(difluoromethyl)pyridin-2-amine (PQR620), a Highly Potent and Selective mTORC1/2 Inhibitor for Cancer and Neurological Disorders.

D. Fabbro, M. Zvelebil, W. Löscher, 2018, Journal of medicinal chemistry.

HDX-MS-optimized approach to characterize nanobodies as tools for biochemical and structural studies of class IB phosphoinositide 3-kinases.

E. Pardon, J. Steyaert, M. Rathinaswamy, 2021, Structure.

HDX-MS optimized approach to characterize nanobodies as tools for biochemical and structural studies of class IB phosphoinositide 3-kinases

E. Pardon, J. Steyaert, M. Rathinaswamy, 2021, bioRxiv.

Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5

David J. Hamelin, J. Burke, E. Hirsch, 2018, Nature Communications.

Crystal structure of a bacterial CNNM magnesium transporter

B. Roux, J. Burke, G. Kozlov, 2021, bioRxiv.

( S)-4-(Difluoromethyl)-5-(4-(3-methylmorpholino)-6-morpholino-1,3,5-triazin-2-yl)pyridin-2-amine (PQR530), a Potent, Orally Bioavailable, and Brain-Penetrable Dual Inhibitor of Class I PI3K and mTOR Kinase.

D. Fabbro, J. Burke, M. Wymann, 2019, Journal of medicinal chemistry.

The juxtamembrane linker in neutral sphingomyelinase-2 functions as an intramolecular allosteric switch that activates the enzyme

David J. Hamelin, Y. Hannun, M. García-Díaz, 2019, The Journal of Biological Chemistry.

Structural Basis for Inhibitor Potency and Selectivity of Plasmodium falciparum Phosphatidylinositol 4-kinase Inhibitors.

S. Fienberg, C. Eyermann, K. Chibale, 2020, ACS infectious diseases.

Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29

S. Withers, J. Burke, O. Salama-Alber, 2018, The Journal of Biological Chemistry.

Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange

Daniel Zaidman, Nir London, John E Burke, 2018, J. Chem. Inf. Model..

Regulation of a Coupled MARCKS-PI3K Lipid Kinase Circuit by Calmodulin: Single-Molecule Analysis of a Membrane-Bound Signaling Module.

Roger L. Williams, J. Burke, J. Falke, 2016, Biochemistry.

Dynamics of allosteric regulation of the phospholipase C-γ isozymes upon recruitment to membranes

J. Sondek, J. Burke, M. Jenkins, 2022, bioRxiv.

Molecular mechanism of activation of class IA phosphoinositide 3-kinases (PI3Ks) by membrane-localized HRas

Braden D. Siempelkamp, M. Rathinaswamy, J. Burke, 2017, The Journal of Biological Chemistry.

Molecular basis for differential activation of p101 and p84 complexes of PI3Kγ by Ras and GPCRs

Roger L. Williams, M. Rathinaswamy, U. Dalwadi, 2022, bioRxiv.

Abstract 671: BKM120-mediated G2 arrest: Structural and functional segregation of off-target action and PI3K inhibition

D. Fabbro, M. Zvelebil, Roger L. Williams, 2015 .

Allosteric activation of PI3Kα by oncogenic mutations

Roger L. Williams, J. Burke, O. Perisic, 2013, Oncotarget.