Literature DB >> 30692197

Dynamic structural biology at the protein membrane interface.

John E Burke1.   

Abstract

Since I started doing scientific research, I've been fascinated by the interplay of protein structure and dynamics and how they together mediate protein function. A particular area of interest has been in understanding the mechanistic basis of how lipid-signaling enzymes function on membrane surfaces. In this award lecture article, I will describe my laboratory's studies on the structure and dynamics of lipid-signaling enzymes on membrane surfaces. This is important, as many lipid-signaling enzymes are regulated through dynamic regulatory mechanisms that control their enzymatic activity. This article will discuss my continued enthusiasm in using a synergistic application of hydrogen-deuterium exchange MS (HDX-MS) with other structural biology techniques to probe the mechanistic basis for how membrane-localized signaling enzymes are regulated and how these approaches can be used to understand how they are misregulated in disease. I will discuss specific examples of how we have used HDX-MS to study phosphoinositide kinases and the protein kinase Akt. An important focus will be on a description of how HDX-MS can be used as a powerful tool to optimize the design of constructs for X-ray crystallography and EM. The use of a diverse toolbox of biophysical methods has revealed novel insight into the complex and varied regulatory networks that control the function of lipid-signaling enzymes and enabled unique insight into the mechanics of membrane recruitment.
© 2019 Burke.

Entities:  

Keywords:  Akt; Akt PKB; HDX–MS; PI3K; PI3K/Akt; PI4K; hydrogen-deuterium exchange mass spectrometry; lipid signaling; phosphatidylinositide 3-kinase (PI3K); phosphatidylinositol kinase; phosphoinositide; protein dynamics

Mesh:

Substances:

Year:  2019        PMID: 30692197      PMCID: PMC6422078          DOI: 10.1074/jbc.AW118.003236

Source DB:  PubMed          Journal:  J Biol Chem        ISSN: 0021-9258            Impact factor:   5.157


  79 in total

1.  Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS.

Authors:  Dennis Pantazatos; Jack S Kim; Heath E Klock; Raymond C Stevens; Ian A Wilson; Scott A Lesley; Virgil L Woods
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-08       Impact factor: 11.205

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

Authors:  Cameron J Powell; Raghavendran Ramaswamy; Anne Kelsen; David J Hamelin; David M Warshaw; Jürgen Bosch; John E Burke; Gary E Ward; Martin J Boulanger
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-22       Impact factor: 11.205

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

Authors:  Christel Brunschwig; Nina Lawrence; Dale Taylor; Efrem Abay; Mathew Njoroge; Gregory S Basarab; Claire Le Manach; Tanya Paquet; Diego Gonzàlez Cabrera; Aloysius T Nchinda; Carmen de Kock; Lubbe Wiesner; Paolo Denti; David Waterson; Benjamin Blasco; Didier Leroy; Michael J Witty; Cristina Donini; James Duffy; Sergio Wittlin; Karen L White; Susan A Charman; Maria Belén Jiménez-Díaz; Iñigo Angulo-Barturen; Esperanza Herreros; Francisco Javier Gamo; Rosemary Rochford; Dalu Mancama; Theresa L Coetzer; Mariëtte E van der Watt; Janette Reader; Lyn-Marie Birkholtz; Kennan C Marsh; Suresh M Solapure; John E Burke; Jacob A McPhail; Manu Vanaerschot; David A Fidock; Paul V Fish; Peter Siegl; Dennis A Smith; Grennady Wirjanata; Rintis Noviyanti; Ric N Price; Jutta Marfurt; Kigbafori D Silue; Leslie J Street; Kelly Chibale
Journal:  Antimicrob Agents Chemother       Date:  2018-08-27       Impact factor: 5.191

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

Authors:  Gillian L Dornan; Jacob A McPhail; John E Burke
Journal:  Biochem Soc Trans       Date:  2016-02       Impact factor: 5.407

Review 5.  Using hydrogen/deuterium exchange mass spectrometry to define the specific interactions of the phospholipase A2 superfamily with lipid substrates, inhibitors, and membranes.

Authors:  Jian Cao; John E Burke; Edward A Dennis
Journal:  J Biol Chem       Date:  2012-12-03       Impact factor: 5.157

6.  Dominant-activating germline mutations in the gene encoding the PI(3)K catalytic subunit p110δ result in T cell senescence and human immunodeficiency.

Authors:  Carrie L Lucas; Hye Sun Kuehn; Fang Zhao; Julie E Niemela; Elissa K Deenick; Umaimainthan Palendira; Danielle T Avery; Leen Moens; Jennifer L Cannons; Matthew Biancalana; Jennifer Stoddard; Weiming Ouyang; David M Frucht; V Koneti Rao; T Prescott Atkinson; Anahita Agharahimi; Ashleigh A Hussey; Les R Folio; Kenneth N Olivier; Thomas A Fleisher; Stefania Pittaluga; Steven M Holland; Jeffrey I Cohen; Joao B Oliveira; Stuart G Tangye; Pamela L Schwartzberg; Michael J Lenardo; Gulbu Uzel
Journal:  Nat Immunol       Date:  2013-10-28       Impact factor: 25.606

Review 7.  An overview of hydrogen deuterium exchange mass spectrometry (HDX-MS) in drug discovery.

Authors:  Glenn R Masson; Meredith L Jenkins; John E Burke
Journal:  Expert Opin Drug Discov       Date:  2017-08-17       Impact factor: 6.098

8.  Targeting Plasmodium PI(4)K to eliminate malaria.

Authors:  Case W McNamara; Marcus Cs Lee; Chek Shik Lim; Siau Hoi Lim; Jason Roland; Oliver Simon; Bryan Ks Yeung; Arnab K Chatterjee; Susan L McCormack; Micah J Manary; Anne-Marie Zeeman; Koen J Dechering; Tr Santha Kumar; Philipp P Henrich; Kerstin Gagaring; Maureen Ibanez; Nobutaka Kato; Kelli L Kuhen; Christoph Fischli; Advait Nagle; Matthias Rottmann; David M Plouffe; Badry Bursulaya; Stephan Meister; Lucia Rameh; Joerg Trappe; Dorothea Haasen; Martijn Timmerman; Robert W Sauerwein; Rossarin Suwanarusk; Bruce Russell; Laurent Renia; Francois Nosten; David C Tully; Clemens Hm Kocken; Richard J Glynne; Christophe Bodenreider; David A Fidock; Thierry T Diagana; Elizabeth A Winzeler
Journal:  Nature       Date:  2013-11-27       Impact factor: 49.962

9.  Conformational sampling of membranes by Akt controls its activation and inactivation.

Authors:  Iva Lučić; Manoj K Rathinaswamy; Linda Truebestein; David J Hamelin; John E Burke; Thomas A Leonard
Journal:  Proc Natl Acad Sci U S A       Date:  2018-04-09       Impact factor: 11.205

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

Authors:  Oscar Vadas; Hashem A Dbouk; Aliaksei Shymanets; Olga Perisic; John E Burke; Widian F Abi Saab; Bassem D Khalil; Christian Harteneck; Anne R Bresnick; Bernd Nürnberg; Jonathan M Backer; Roger L Williams
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-04       Impact factor: 11.205

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  2 in total

Review 1.  Hydrogen-Deuterium Exchange Mass-Spectrometry of Secondary Active Transporters: From Structural Dynamics to Molecular Mechanisms.

Authors:  Moshe Giladi; Daniel Khananshvili
Journal:  Front Pharmacol       Date:  2020-02-19       Impact factor: 5.810

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

Authors:  Weijing Gu; Shujuan Gao; Huan Wang; Kaelin D Fleming; Reece M Hoffmann; Jong Won Yang; Nimi M Patel; Yong Mi Choi; John E Burke; Karen Reue; Michael V Airola
Journal:  Nat Commun       Date:  2021-08-05       Impact factor: 14.919

  2 in total

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