Structural and Energetic Principles of Helical Membrane Proteins
Genome sequencing efforts are revealing that perhaps as many as 20–40% of open reading frames in complex organisms may encode proteins containing at least one helical transmembrane segment. Contrasting with the approaching tidal wave of helical membrane proteins is the fact that our understanding of the sequence-structure-function relationships for membrane proteins lags far behind that of soluble proteins. This paradox emphasizes the extensive biophysical and structural work that remains to be done in the field of helical membrane proteins.
Our research is aimed at elucidating structural and energetic principles of membrane proteins. We are especially focused on understanding the structural and energetic basis of transmembrane helix-helix recognition. Our lab takes a multidisciplinary approach to address scientific questions employing molecular biology techniques, structural studies, thermodynamic investigations and computational analysis and modeling.
Currently our research projects include:
- Structural and energetic dissection of the glycophorin A transmembrane dimer. A paradigm for transmembrane helix-helix interactions, we are probing the structural and energetic effects on dimerization of single and multiple point mutants. Our interaction studies on glycophorin A suggest the idea that specificity in helix-helix interactions for this protein may be independent of the hydrophobic environment.
- Transmembrane interactions in SNARE fusion proteins. We are using computational modeling and thermodynamics to probe the transmembrane helix-helix interactions of synaptobrevin and other SNARE proteins. Our studies on the dimerization of synaptobrevin offer an opportunity for protein engineering and design of a membrane protein as a means to understanding its structural stability.
- McDonald SK and KG Fleming (2016) “Negative charge neutralization in the loops and turns of outer membrane phospholipase A impacts folding hysteresis at neutral pH” Biochemistry In Press.
- Costello SM, Plummer AM, Fleming PJ & KG Fleming (2016) “Dynamic Periplasmic Chaperone Reservoir Facilitates Biogenesis of Outer Membrane Proteins” PNAS 113: E4794-800. PMID: 27482090; PMCID: PMC4995976.
- Plummer AM and KG Fleming (2016) “From Chaperones to the Membrane with a BAM!” Trends Biochem. Sci. 41:872-882. This article was highlighted on the cover of the October 2016 issue. PMID: 27450425; PMCID: PMC In Progress; DOI: 10.1016/j.tibs.2016.06.005.
- McDonald SK and KG Fleming (2016) “Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth-Dependence Across the Membrane Normal” J. Am Chem. Soc. 138: 7946-50. PMID: 27254476; PMCID: 4927395; DOI: 10.1021/jacs.6b03460.
- Fleming PJ, Patel DS, Wu EL, Qi Y, Yeom MS, Sousa MC, Fleming KG and W Im (2016) “BamA POTRA Domain Interacts with a Native Lipid Membrane Surface” Biophys. J. 110: 2698-2709. PMID: 27332128; PMCID: PMC4919588 DOI: 10.1016/j.bpj.2016.05.010.
- Zaccai NR, Sandlin CW, Hoopes JT, Curtis JE, Fleming PJ, Fleming KG and S Krueger (2016) “Deuterium labeling together with contrast variation small-angle neutron scattering suggests how Skp captures and releases unfolded outer membrane proteins” (2015) Methods Enzymol 566 159-210. PMID: 26791979; PMCID: PMC4913355; DOI: 10.1016/bs.mie.2015.06.041
- Sandlin CW, Zaccai NR and KG Fleming (2015) “Skp trimer formation is insensitive to ionic strength” Biochemistry 54: 7059-7062. PMID: 26579730; PMCID: PMC4905700; DOI: 10.1021/acs.biochem.5b00806
- Plummer AM*, Gessmann D* and KG Fleming (2015) “The Role of a Destabilized membrane for OMP Insertion” Methods Mol. Biol. 1329: 57-65. PMID: 26427676: PMCID: N/A. *Joint First Authors.
- Plummer AM and KG Fleming (2015) “BamA Alone Accelerates Outer Membrane Protein Folding In Vitro through a Catalytic Mechanism” Biochemistry 54: 6009-6011. PMID: 26394056; PMCID: PMC4613867.
- Danoff EJ and KG Fleming (2015) “Aqueous, Unfolded OmpA Forms Amyloid-Like Fibrils Upon Self-Association” PLos ONE 10: e0132301. PMID: 26196893; PMCID: PMC4509890
- Fleming KG (2015) “A kinetic push and thermodynamic pull as driving forces for outer membrane protein sorting and folding in bacteria” Phil Trans R Soc Lond B Biol Sci 370: 1679. PMID: 26370938;
- Danoff EJ and KG Fleming (2015) “Membrane defects accelerate outer membrane -barrel protein folding” Biochem 54: 97-99. PMID: 25513891; PMCID: PMC4303321.
- Wu EL, Fleming PJ, Yeom MS, Widmalm G, Klauda JB, Fleming KG and W Im (2014) “E coli Outer Membrane and Interactions with OmpLA” Biophys. J. 106: 2493. PMID: 24896129; PMCID: PMC4052237.
- Gessmann D, Chung YH, Danoff EJ, Plummer AM, Sandlin CW, Zaccai NR and KG Fleming (2014) “Outer membrane -barrel protein folding is physically controlled by periplasmic lipid head groups and BamA” PNAS 111: 5878-93. PMID: 24715731; PMCID: PMC4000854.
- Fleming KG (2014) “Energetics of Membrane Protein Folding” Ann Rev Biophys 43: 233-55. PMID: 24895854; PMCID Pending.
- Moon CP, Zaccai NR, Fleming PJ, Gessmann D and KG Fleming (2013) “Membrane protein thermodynamic stability may serve as the energy sink for sorting in the periplasm” PNAS 110: 4285-4290. PMID: 23440211; PMCID: PMC3600475.
- Lees JPB, Manlandro CM, Picton LK, Ebie Tan AZ, Casares S, Flanagan JM, Fleming KG and RB Hill (2012) “A designed point mutant in Fis1 disrupts dimerization and mitochondrial fission” J. Mol. Biol. 423: 143-158 PMID: 22789569; PMCID: PMC3456991.
- O’Neill MJ, Bhakta MN, Fleming KG and A Wilks (2012) “Induced Fit on Heme Binding to the Pseudomonas aeruginosa Cytoplasmic Protein (PhuS) Drives Interaction with Heme Oxygenase (HemO)” PNAS 109: 5639-5644. PMID: 22451925; PMCID: PMC3326490.
- Buchanan SK, Yamashita Y and KG Fleming (2012) “Structure and folding of outer membrane proteins” in Comprehensive Biophysics eds. EH Egelman and LK Tamm, Oxford: Academic Press Vol 5: 139-163.
- Moon CP, Kwon S and KG Fleming (2011) “Overcoming hysteresis to attain reversible equilibrium folding for outer membrane phospholipase A in phospholipid bilayers” J. Mol. Biol. 413: 484-494. PMID: 21888919; PMCID: PMC3193555.
- Fleming PJ, Freites JA, Moon CP, Tobias DJ and KG Fleming (2011) “Outer membrane phospholipase A in phospholipid bilayers: A model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers” BBA Biomembranes 1818: 126-134. PMID: 21816133; PMCID: PMC3233656.
- Danoff EJ and KG Fleming (2011) “The soluble, periplasmic domain of OmpA folds as an independent unit and displays chaperone activity by reducing the self-association propensity of the unfolded OmpA transmembrane -barrel” Biophys. Chem. 159: 194-204. PMID 21782315; PMC3169180.
- Moon CP and Fleming KG (2011) “From the Cover: Side-chain hydrophobicity scale derived from transmembrane protein folding in lipid bilayers” PNAS 108: 10174-10177. PMID 21606332; PMC3121867.