Fleming Lab
2023
Devlin TA, Fleming PJ, Loza, N, Fleming KG
Generation of Unfolded Outer Membrane Protein Ensembles Targeted by Hydrodynamic Properties
(2023) Eur. Biophys. J. Online Mar 11
Devlin TA, Marx, DC, Roskopf MA, Bubb, QR, Plummer, AM, Fleming KG
FkpA Enhances Membrane Protein Folding using an Extensive Interaction Surface
(2023) Protein Science Online February 12Fleming PJ, Correia JJ, Fleming KG
Revisiting Macromolecular Hydration with HullRadSAS
(2023) Eur. Biophys. J. Online Jan 5.2022
To, P., Xia, Y. Devlin TA, Fleming KG, Fried, SD
A Proteome-Wide Map of Chaperone-Assisted Protein Refolding in the Cytosol
(2022) bioRxiv Mar 7(In Press: Proc. of the Nat. Acad. of Sci., Nov. 23, 2022 | 119(48): e2210536119 | https://doi.org/10.1073/pnas.221053611)
2021
Marx DC, Fleming KG
Local Bilayer Hydrophobicity Modulates Membrane Protein Stability
(2021) J. Am. Chem. Soc. Jan 20: 143(2):764-772Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D
De novo design of transmembrane Beta-barrels
(2021) Science Feb 19: 371:eabc81822020
Huysmans GHM, Marx DC, Radford SE, Fleming KG
Determining the Free Energies of Outer Membrane Proteins in Lipid Bilayers
(2020) Biophysics of Membrane Proteins. Methods in Molecular Biology Humana, New York, NYMarx DC, Plummer AM, Faustino, AM, Devlin, T, Roskopf, MA, Leblanc, MJ, Lessen, HJ, Amann, BT, Fleming, PJ, Krueger S, Fried, SD, Fleming KG.
SurA is a cryptically grooved chaperone that expands unfolded outer membrane proteins
(2020) Proc. Natl. Acd. Sci. USA Nov 10: 117(45):28026-28035.Marx DC, Leblanc MJ, Plummer AM, Krueger S, Fleming KG.
Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA
(2020) Protein Sci. 29(10):2043-2053.O'Brien ES, Fuglestad B, Lessen HJ, Stetz MA, Lin DW, Marques BS, Gupta K, Fleming KG, Wand AJ.
Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy
(2020) Angew. Chem. Int. Ed. Engl. 59(27):11108-11114.Alford RF, Fleming PJ, Fleming KG, Gray JJ.
Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane
(2020) Biophys. J. 118(8):2042-2055Lessen HJ, Majumdar A, Fleming KG.
Backbone Hydrogen Bond Energies in Membrane Proteins Are Insensitive to Large Changes in Local Water Concentration
(2020) J. Am. Chem. Soc. 142(13):6227-62352019
Chum AP, Shoemaker SR, Fleming PJ, Fleming KG.
Plasticity and transient binding are key ingredients of the Periplasmic Chaperone Network
(2019) Protein Science 28(7):1340-1349.2018
Fleming PJ, Fleming KG.
HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties
(2018) Biophys J. 114(4):856-869.Lessen HJ, Fleming PJ, Fleming KG, Sodt AJ.
Building Blocks of the Outer Membrane: Calculating a General Elastic Energy Model for β-Barrel Membrane Proteins
(2018) J. Chem. Theory Comput. 14(8):4487-4497.Fleming KG.
Taking deterministic control of membrane protein monomer-dimer measurements
(2018) J Gen Physiol 150(2)181-183.2017
Peterson JH, Plummer AM, Fleming KG, Bernstein HD.
Selective pressure for rapid membrane integration constrains the sequence of bacterial outer membrane proteins
(2017) Mol Microbiol 106(5)777-792.Marx DC, Fleming KG.
Influence of Protein Scaffold on Side-Chain Transfer Free Energies
(2017) Biophys J. 113(3)597-604.Mo GC, Ross B, Hertel F, Manna P, Yang X, Greenwald E, Booth C, Plummer AM, Tenner B, Chen Z, Wang Y, Kennedy EJ, Cole PA, Fleming KG, Palmer A, Jimenez R, Xiao J, Dedecker P, Zhang J.
Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution
(2017) Nat Meth 14(4)427-434.Danoff EJ, Fleming KG.
Novel Kinetic Intermediates Populated along the Folding Pathway of the Transmembrane β-Barrel OmpA
(2017) Biochemistry 56(1)47-60.2016
McDonald SK, Fleming KG
Negative charge neutralization in the loops and turns of outer membrane phospholipase A impacts folding hysteresis at neutral pH.
(2016) Biochemistry 55(44)6133-6137.Costello SM, Plummer AM, Fleming PJ, Fleming KG
Dynamic periplasmic chaperone reservoir facilitates biogenesis of outer membrane proteins
(2016) PNAS 113(33)E4794-800.Plummer AM, Fleming KG
From Chaperones to the Membrane with a BAM!
(2016) Trends Biochem Sci. 41(10):872-82.Fleming PJ, Patel DS, Wu EL, Qi Y, Yeom MS, Sousa MC, Fleming KG, Im W
BamA POTRA Domain Interacts with a Native Lipid Membrane Surface
(2016) Biophys J 110:2698-709.McDonald SK, Fleming KG
Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal
(2016) J Am Chem Soc. 138(25):7946Zaccai NR, Sandlin CW, Hoopes JT, Curtis JE, Fleming PJ, Fleming KG and Krueger S
Deuterium labeling together with contrast variation small-angle neutron scattering suggests how Skp captures and releases unfolded outer membrane proteins
(2016) Methods Enzymol 566:159-210.2015
Sandlin, CW, Zaccai NR and Fleming KG
Skp trimer formation is insensitive to ionic strength
(2015) Biochemistry 54:7059-62.Plummer AM, Gessmann D, and KG Fleming
The role of a destabilized membrane for OMP Insertion
(2015) Methods Mol Biol 1329:57-65.Plummer AM and KG Fleming
BamA Alone Accelerates Outer Membrane Protein Folding In Vitro through a Catalytic Mechanism
(2015) Biochemistry 54:6009-11.KG Fleming
A kinetic push and thermodynamic pull as driving forces for outer membrane protien sorting and folding in bacteria
(2015) Philos Trans R Soc Lond B Biol Sci 370:20150026.Danoff EJ and KG Fleming
Aqueous unfolded OmpA forms amyloid-like fibrils upon self-association
(2015) PLos One 10:e0132301.Danoff EJ and KG Fleming
Membrane defects accelerate outer membrane beta-barrel protein folding
(2015) Biochemistry 54:97-99.2014
Wu EL, Fleming PJ, Yeom MS, Widmalm G, Klauda JB, Fleming KG and W Im
E. coli outer membrane and interactions with OmpLA
(2014) Biophys J 106:2493-2502.Gessmann D, Chung YH, Danoff EJ, Plummer AM, Sandlin CW, Zaccai NR and KG Fleming
Outer membrane beta-barrel protein folding is physically controlled by periplasmic lipid head groups and BamA
(2014) PNAS 111:5878-5883.2013
Moon CP, Zaccai NR, Fleming PJ, Gessmann D and KG Fleming
Membrane protein thermodynamic stability may serve as the energy sink for sorting in the periplasm
(2013) PNAS 110:4285-4290.2012
Lees JP, Manlandro CM, Picton LK, Tan AZ, Casares S, Flanagan JM, Fleming KG and RB Hill
A designed point mutant in Fis1 disrupts dimerization and mitochondrial fission
(2012) J Mol Biol 423:143-158.O'Neill MJ, Bhakta MN, Fleming KG and A Wilks
Induced fit on heme binding to the Pseudomonas aeruginosa cytoplasmic protein (PhuS) drives interaction with heme oxygenase (HemO)
(2012) PNAS 109:5639-5644.Fleming PJ, Freites JA, Moon CP, Tobias DJ and KG Fleming
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
(2012) Biochim Biophys Acta 1818:126-134.2011
Moon CP, Kwon S and KG Fleming
Overcoming hysteresis to attain reversible equilibrium folding for outer membrane phospholipase A in phospholipid bilayers
(2011) J Mol Biol 413:484-494.Danoff EJ and KG Fleming
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 beta-barrel
(2011) Biophys Chem 159:194-204.Moon CP and KG Fleming
Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers
(2011) PNAS 108:10174-10177.Moon CP and KG Fleming
Using tryptophan fluorescence to measure the stability of membrane proteins folded in liposomes
(2011) Methods Enzymol 492:189-211.2010
Tan AE, Burgess NK, DeAndrade DS, Marold JD and KG Fleming
Self-association of unfolded outer membrane proteins
(2010) Macromol Biosci 10:763-767.2009
Pang T, Savva CG, Fleming KG, Struck DK and R Young
Structure of the lethal phage pinhole
(2009) PNAS 106:18966-18971.2008
Tan AE and KG Fleming
Outer membrane phospholipase A dimer stability does not correlate to occluded surface area
(2008) Biochemistry 47:12095-12103.Burgess NK, Dao TP, Stanley AM and KG Fleming
Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro
(2008) J Biol Chem 283:26748-26758.MacKenzie KR and KG Fleming
Association energetics of membrane spanning alpha-helices
(2008) Curr Opin Struct Biol. 18:412-419.Stanley AM and KG Fleming
The process of folding proteins into membranes: Challenges and progress
(2008) Arch Biochem Biophys 469:46-66.Burgess NK, Stanley AM and KG Fleming
Determination of membrane protein molecular weights and association equilibrium constants using sedimentation equilibrium and sedimentation velocity
(2008) Chapter 7 in Methods in Cell Biology (JJ Correia, ed) 84:181-211.2007
Duong MT, Jaszewski TM, Fleming KG, and KR MacKenzie
Changes in apparent free energy of helix-helix dimerization in a biological membrane due to point mutations
(2007) J Mol Biol 371:422-434.Stanley AM and KG Fleming
The role of a hydrogen bonding network in the transmembrane beta-barrel OMPLA
(2007) J Mol Biol 370:912-924.Stanley AM, Treubrodt AM, Chuawong P, Hendrickson TL and KG Fleming
Lipid chain selectivity by outer membrane phospholipase A
(2007) J Mol Biol 366:461-468.Ebie AZ and KG Fleming
Dimerization of the erythropoietin receptor transmembrane domain in micelles
(2007) J Mol Biol 366:517-524.2006
Stanley AM, Chuawong P, Hendrickson TL and KG Fleming
Energetics of outer membrane phospholipase A (OMPLA) dimerization
(2006) J Mol Biol 358:120-131.Kroch AE and KG Fleming
Alternate interfaces may mediate homomeric and heteromeric assembly in the transmembrane domains of SNARE proteins
(2006) J Mol Biol 357:184-194.2005
Fleming KG
Analysis of membrane proteins using analytical ultracentrifugation
(2005) Analytical Ultracentrifugation, Techniques and Methods (Scott DJ, Harding SE & Rowe AJ, eds) Royal Society of Chemistry Publishing, Cambridge, UK.Stanley AM and KG Fleming
The transmembrane domains of ErbB receptors do not dimerize strongly in micelles
(2005) J Mol Biol 347:759-772.Kobus FJ and KG Fleming
The GxxxG-containing transmembrane domain of the CCK4 oncogene does not encode preferential self-interactions
(2005) Biochemistry 44:1464-1470.2004
Doura AK and KG Fleming
Complex interactions at the helix-helix interface stabilize the glycophorin A transmembrane dimer
(2004) J Mol Biol 343:1487-1497.
Raasi S, Orlov I, Fleming KG and CM Pickart
Binding of polyubiquitin chains to ubiquitin-associated (UBA) domains of HHR23A
(2004) J Mol Biol 341:1367-1379.Doura AK, Kobus FJ, Dubrovsky L, Hibbard E and KG Fleming
Sequence context modulates the stability of a GxxxG-mediated transmembrane helix-helix dimer
(2004) J Mol Biol 341:991-998.Fleming KG*, Ren CC, Doura AK, Eisley ME, Kobus FJ and AM Stanley
*Corresponding author
Thermodynamics of glycophorin A transmembrane helix dimerization in C14 betaine micelles
(2004) Biophys Chem 108:43-49.2002
Fleming KG
Standardizing the free energy change of transmembrane helix-helix interactions
(2002) J Mol Biol 323:563-571.2001
Fleming KG* and DM Engelman
*Corresponding author
Specificity in transmembrane helix-helix interactions can define a hierarchy of stability for sequence variants
(2001) PNAS 98:14340-14344.Fleming KG* and DM Engelman
*Corresponding author
Computation and mutagenesis suggest a right-handed structure for the synaptobrevin transmembrane dimer
(2001) Proteins 45:313-317.Trombetta ES, Fleming KG and A Helenius
Quaternary and domain structure of glycoprotein processing glucosidase II
(2001) Biochemistry 40:10717-10722.Vergis JM, Bulock KG, Fleming KG and GP Beardsley
Human AICAR transformylase/IMP cyclohydrolase: A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity
(2001) J Biol Chem 276:7727-7733.2000
Fleming KG
Riding the wave: structural and energetic principles of helical membrane proteins
(2000) Current Opinion in Biotechnology (P Hensley & D Myszka, eds) 11:67-71.Fleming KG
Probing stability of helical transmembrane proteins
(2000) Energetics of Biological Macromolecules, Part C Methods Enzymol (ML Johnson & G Ackers, eds) Academic Press 323:63-77.1999
Biswas I, Ban C, Fleming KG, Qin J, Lary JW, Yphantis DA, Yang W and P Hsieh
Oligomerization of a MutS mismatch repair protein from Thermus aquaticus
(1999) J Biol Chem 274:23673-23678.Schubert C, Hirsch JA, Gurevich VV, Engelman DM, Sigler PB and KG Fleming*
*Corresponding author
Visual arrestin activity may be regulated by self-association
(1999) J Biol Chem 274:21186-21190.1998
Fleming KG
Measuring transmembrane alpha-helix energies using analytical ultracentrifugation
(1998) ChemTracts: Biological Applications of the Analytical Ultracentrifuge (JC Hanson, ed) 11:985-990.Fleming KG, Hohl TM, Yu RC, Müller SA, Wolpensinger BA, Engel A, Engelhardt H, Brünger AT, Söllner TH, and PI Hanson
A revised model for the oligomeric state of the N-ethylmaleimide-sensitive fusion protein, NSF
(1998) J Biol Chem 273:15675-15681.Fleming KG
Analysis of Membrane Protein Dimerization by Sedimentation Equilibrium
(1998) Application Information Bulletin (A Furst, ed) Beckman Coulter, Inc.Engelman DM, Fleming KG and KR MacKenzie
Helix Stability and Interactions in Membrane Proteins
(1998) Biol Skr Dan Vid Selsk 49:83-86.
O'Brien R, DeDecker B, Fleming KG, Sigler PB and JE Ladbury
The effects of salt on the TATA binding protein-DNA interaction of a hyperthermophilic archaeon
(1998) J Mol Biol 279:117-125.1997
Rodgers KK and KG Fleming
Metal-dependent structure and self-association of the RAG1 zinc-binding domain
(1997) Techniques in Protein Chemistry VIII (DK Marshak, ed) 573-584.Fleming KG, Ackerman AL and DM Engelman
The effect of point mutations on the free energy of transmembrane alpha-helix dimerization
(1997) J Mol Biol 272:266-275.1996
What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties
(1996) Protein Sci 5:1584-1593.Rodgers KK, Bu Z, Fleming KG, Schatz DG, Engelman DM and JE Coleman
A zinc-binding domain involved in the dimerization of RAG1
(1996) J Mol Biol 260:70-84.