Small Molecule and Substrate Binding
Hydrogen deuterium exchange (HDX) is a very useful technique for studying the interactions between small molecule inhibitors and their target proteins. By measuring the rate of exchange of hydrogen and deuterium atoms in the protein before and after exposure to the inhibitor, we can identify the specific regions of the protein that are affected by the inhibitor binding.
This information can be used to optimize the inhibitor design, by identifying the key amino acid residues that interact with the inhibitor and designing modifications to improve binding affinity and specificity. HDX can also provide insights into the mechanism of inhibition, by revealing how the inhibitor affects the dynamics and conformational changes of the protein.
HDX-MS can also provide insights into the structural changes and dynamic behavior of proteins upon interaction with lipid membrane vesicles. This information can be used to identify the specific regions of the protein that interact with the membrane, as well as identify allosteric changes which occur upon lipid binding.
Select publications involving small molecule and substrate binding
Dr. Kevan Shokat from the University of San Diego
McGregor LM, Jenkins ML, Kerwin C, Burke JE, Shokat KM. (2017) Expanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes. Biochemistry.
Gentile DR, Rathinaswamy MK, Jenkins ML, Moss SM, Siempelkamp BD, Renslo AR, Burke JE*, Shokat KM*. Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States. (2017) Cell Chemical Biology
Nnadi CI, Jenkins ML, Gentile DR, Bateman LA, Zaidman D, Balius TE, Nomura DK, Burke JE, Shokat KM, London N. (2018). Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. J Chem Inf Model.
Dr. Thomas Leonard from Max F. Perutz Laboratories
Daniel Pokorny, Linda Truebestein, Kaelin D Fleming, John E Burke, Thomas A Leonard (2021) In vitro reconstitution of Sgk3 activation by phosphatidylinositol 3-phosphate. Journal of Biological Chemistry
Truebestein L, Hornegger H, Anrather D, Hartl M, Fleming KD, Stariha JTB, Pardon E, Steyaert J, Burke JE, Leonard TA (2021) Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediated activation. PNAS
Lučić I, Rathinaswamy MK, Truebestein L, Hamelin DJ, Burke JE, Leonard TA. (2018). Conformational sampling of membranes by Akt controls its activation and inactivation. Proc Natl Acad Sci U S A
Dr. Chambers Hughes from University of California
Castro-Falcón G, Seiler GS, Demir Ö, Rathinaswamy MK, Hamelin D, Hoffmann RM, Makowski SL, Letzel AC, Field SJ, Burke JE, Amaro RE, Hughes CC. (2018) Neolymphostin A Is a Covalent Phosphoinositide 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor That Employs an Unusual Electrophilic Vinylogous Ester. J. Med. Chem
Dr. Lina Obeid from Stony Brook University
Pulkoski-Gross MJ, Jenkins ML, Truman JP, Salama MF, Clarke CJ, Burke JE, Hannun YA, Obeid LM. (2018). An intrinsic lipid-binding interface controls sphingosine kinase 1 function. J Lipid Res
Dr. John Sondek from University of North Carolina
Edhriz Siraliev-Perez, Jordan TB Stariha, Reece M Hoffmann, Brenda RS Temple, Qisheng Zhang, Nicole Hajicek, Meredith L Jenkins, John E Burke, John Sondek (2022) Dynamics of allosteric regulation of the phospholipase C-γ isozymes upon recruitment to membranes. Elife.
Our own research
Shaw AL, Parson MAH, Truebestein L, Jenkins ML, Leonard TA, Burke JE.(2023). ATP-competitive and allosteric inhibitors induce differential conformational changes at the autoinhibitory interface of Akt1. Structure.
Rostislavleva K, Soler N, Ohashi Y, Zhang L, Pardon E, Burke JE, Masson GR, Johnson C, Steyaert J, Ktistakis NT, Williams RL. Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science. 2015 Oct 9;350(6257):aac7365.