Publications

† - equal contribution, ‡ - co-corresponding authors

2023

Brominated lipid probes expose structural asymmetries in constricted membranes.
Moss FR, Lincoff, J, Tucker M, Mohammed A, Grabe M, and Frost A.
Nat Struct Mol Biol (2023). https://doi.org/10.1038/s41594-022-00898-1

Membrane potential accelerates sugar uptake by stabilizing the outward facing conformation of the Na/glucose symporter vSGLT.
Abramson J, Khan F, Elgeti M, Grandfield S, Paz A, Naughton F, Marcoline F, Althoff T, Ermolova N, Wright E, Hubbell W, Grabe M.
Nature Communications (2023). https://doi.org/10.1038/s41467-023-43119-z

2022

Regulation of the mammalian-brain V-ATPase through ultraslow mode-switching.
Kosmidis E, Shuttle CG, Preobraschenski J, Ganzella M, Johnson PJ, Veshaguri S, Holmkvist J, Møller MP, Marantos O, Marcoline F, Grabe M, Pedersen JL, Jahn R, and Stamou D.
Nature 611, 827-834 (2022). [PDF]

Quaternary structure independent folding of voltage-gated ion channel pore domain subunits.
Arrigoni C, Lolicato M, Shaya D, Rohaim A, Findeisen F, Fong LK, Colleran CM, Dominik P, Kim SS, Schuermann JP, DeGrado WF, Grabe M, Kossiakoff AA, and Minor DL.
Nat Struct Mol Biol 29, 537–548 (2022). [PDF]

Mitochondrial uncouplers induce proton leak by activating AAC and UCP1.
Bertholet, AM, Natale, AM, Bisignano, P, Suzuki J, Fedorenko A, Hamilton J, Brustovetsky T, Kazak L, Garrity R, Chouchani ET, Brustovetsky N, Grabe M, and Kirichok Y.
Nature 606, 180–187 (2022). [PDF]

Berkeley Madonna Version 10-A simulation package for solving mathematical models.
Marcoline FV, Furth J, Nayak S, Grabe M, and Macey RI.
CPT Pharmacometrics Syst Pharmacol (2022). [PDF]

Taking the Monte-Carlo gamble: How not to buckle under the pressure!
Gomez YK†, Natale AM†, Lincoff J†, Wolgemuth CW‡, Rosenberg JM‡, and Grabe M‡.
J Comput Chem, (2022). 1. https://doi.org/10.1002/jcc.26798 [PDF]

2021

Genetically Encoded, pH-Sensitive mTFP1 Biosensor for Probing Lysosomal pH
Chin MY, Patwardhan AR, Ang KH, Wang AL, Alquezar C, Welch M, Nguyen PT, Grabe M, Molofsky AV, Arkin MR, and Kao AW.
ACS Sens. 6(6):2168-2180. (2021). [PDF]

Inroads into Membrane Physiology through Transport Nanomachines.
Stockbridge RB, Gaudet R, Grabe M, Minor DL Jr.
J Mol Biol. 433(16):167101. (2021). https://doi.org/10.1016/j.jmb.2021.167101 [PDF]

Elucidation of the molecular interactions that enable stable assembly and structural diversity in multicomponent immune receptors
Fong LK, Chalkley MJ, Tan SK, Grabe M, and DeGrado WF
Proceedings of the National Academy of Sciences 118(26), e2026318118 (2021). [PDF]

2020

Allosteric cooperation in a de novo-designed two-domain protein
Pirro F, Schmidt N, Lincoff J, Widel ZX, Polizzi NF, Liu L, Therien MJ, Grabe M, Chino M, Lombardi A, and DeGrado WF.
Proceedings of the National Academy of Sciences 117(52), 33246-33253 (2020). [PDF]

A computational model of protein induced membrane morphology with geodesic curvature driven protein-membrane interface
Zhou YC, Argudo D, Marcoline FV, and Grabe M
Journal of Computational Physics 422, 109755 (2020). [PDF]

K2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions.
Lolicato M†, Natale AM†, Abderemane-Ali F, Crottès D, Capponi S, Duman R, Wagner A, Rosenberg JM, Grabe M‡, and Minor DL‡.
Science Advances 6(44), eabc9174 (2020). [PDF | Supplement]

A kinetic mechanism for enhanced selectivity of membrane transport.
Bisignano P, Lee MA, George A, Zuckerman DM, Grabe M‡, and Rosenberg JM‡.
PLoS Computational Biology 16(7), e1007789 (2020). [PDF]

A systems-biology approach to molecular machines: Automated exploration of alternative transporter mechanisms.
George A, Bisignano P, Rosenberg JM, Grabe M, and Zuckerman DM.
PLoS Computational Biology 16(7), e1007884 (2020). [PDF]

EmrE reminds us to expect the unexpected in membrane transport.
Grabe M‡, Zuckerman DM‡, and Rosenberg JM‡.
Journal of General Physiology 152(1), e201912467 (2020). [PDF]

2019

Protons in small spaces: Discrete simulations of vesicle acidification.
Singh A, Marcoline FV‡, Veshaguri S, Kao AW, Bruchez M, Mindell JA, Stamou D, and Grabe M‡.
PLoS Computational Biology 15(12), e1007539 (2019). [PDF]

Harmonizing experimental data with modeling to predict membrane protein insertion in yeast.
Guerriero CJ, Gomez YK, Daskivich GJ, Reutter KR, Augustine AA, Weiberth KF, Nakatsukasa K, Grabe M, and Brodsky JL.
Biophysical Journal 117, 668-678 (2019). [PDF]

Biophysics at the coffee shop: lessons learned working with George Oster.
Igoshin OA, Chen J, Xing J, Liu J, Elston TC, Grabe M, Kim KS, Nirody JA, Rangamani P, Sun SX, Wang H, and Wolgemuth C.
Molecular Biology of the Cell 30, 1882-1889 (2019). [PDF]

Chemically induced vesiculation as a platform for studying TMEM16F activity.
Han TW, Ye W†, Bethel NP†, Zubia M, Kim A, Li KH, Burlingame AL, Grabe M, Jan YN, and Jan LY.
Proceedings of the National Academy of Sciences USA 116, 1309-1318 (2019). [PDF]

A multiscale model of mechanotransduction by the ankyrin chains of the NOMPC channel.
Argudo D†, Capponi S†, Bethel NP, and Grabe M.
Journal of General Physiology 151, 316-327 (2019). [PDF]

2018

Inhibitor binding mode and allosteric regulation of Na+-glucose symporters.
Bisignano P, Ghezzi C, Jo H, Polizzi NF, Althoff T, Kalyanaraman C, Friemann R, Jacobson MP, Wright EM‡, and Grabe M‡.
Nature Communications 9, 5245 (2018). [PDF]

Cilia-associated oxysterols activate Smoothened.
Raleigh, D.R, Sever N, Choksi PK, Sigg MA, Hines KM, Thompson BM, Elnatan D, Jaishankar P, Bisignano P, Garcia-Gonzalo FR, Krup AL, Eberl M, Byrne EFX, Siebold C, Wong SY, Renslo AR, Grabe M, McDonald JG, Xu L, Beachy PA, and Reiter JF.
Molecular Cell 72, 316-327 (2018). [PDF]

Entry from the lipid bilayer: a possible pathway for inhibition of a peptide G protein-coupled receptor by a lipophilic small molecule.
Bokoch MP, Jo H, Valcourt JR, Srinivasan Y, Pan AC, Capponi S, Grabe M, Dror RO, Shaw DE, DeGrado WF, and Coughlin SR.
Biochemistry 57, 5921-6044 (2018). [PDF]

Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a unique Na+ site.
Wahlgren WY, Dunevall E, North RA, Paz A, Scalise M, Bisignano P, Bengtsson-Palme J, Goyal P, Claesson E, Caing-Carlsson R, Andersson R, Beis K, Nilsson UJ, Farewell A, Pochini L, Indiveri C, Grabe M, Dobson RCJ, Abramson J, Ramaswamy S, and Friemann R.
Nature Communications 9, 1753 (2018). [PDF].

The sixth transmembrane segment Is a major gating component of the TMEM16A calcium-activated chloride channel.
Peters CJ, Gilchrist JM, Tien J, Bethel NP, Qi L, Chen T, Wang L, Jan YN, Grabe M, and Jan LY.
Neuron 97, 1063-1077 (2018). [PDF]

Protonation state of glutamate 73 regulates the formation of a specific dimeric association of mVDAC1.
Bergdoll LA, Lerch MT, Patrick JW, Belardo K, Altenbach C, Bisignano P, Laganowsky A, Grabe M, Hubbell WL, and Abramson J.
Proceedings of the National Academy of Sciences USA 115, E172-E79 (2018). [PDF]

Conformational transitions of the sodium-dependent sugar transporter, vSGLT.
Paz A, Claxton DP, Kumar JP, Kazmier K, Bisignano P, Sharma S, Nolte SA, Liwag TM, Nayak V, Wright EM, Grabe M, Mchaourab HS, and Abramson J.
Proceedings of the National Academy of Sciences USA 115, E2742-E2751 (2018). [PDF]

2017

Transmembrane helix hydrophobicity is an energetic barrier during the retrotranslocation of integral membrane ERAD substrates.
Guerriero GJ, Reutter KR, Augustine AA, Preston GM, Weiberth KF, Mackie TD, Cleveland-Rubeor HC, Bethel NP, Callenberg KM, Nakatsukasaa K, Grabe M, and Brodsky JL.
Molecular Biology of the Cell 28, 2076-2090 (2017). [PDF]

New continuum approaches for determining protein induced membrane deformations.
Argudo D, Bethel NP, Marcoline FV, Wolgemuth CW, and Grabe M.
Biophysical Journal 112, 2159-2172 (2017). [PDF]

An Assessment of How VDAC Structures Have Impacted Our Understanding of Their Function.
Bergdoll L, Grabe M, and Abramson J.
Molecular Basis for Mitochondrial Signaling (Springer Nature, Stuttgart, Germany) Chapter 6, 141-160 (2017). [PDF]

2016

Atomistic insight into lipid translocation by a TMEM16 scramblase.
Bethel NP and Grabe M.
Proceedings of the National Academy of Sciences USA 113, 14049-14054 (2016). [PDF | Supplement]

A mathematical model of osteoclast acidification during bone resorption.
Marcoline FV, Ishida Y, Mindell JA, Nayak S, and Grabe M.
Bone 93, 167-180 (2016). [PDF]

Stochastic steps in secondary active sugar transport.
Adelman JL, Ghezzi C, Bisignano P, Loo DDF, Choe S, Abramson J, Rosenberg JM, Wright EM, and Grabe M.
Proceedings of the National Academy of Sciences USA 113, E3960-E3966 (2016). [PDF | Supplement]

Direct observation of proton pumping by a eukaryotic P-type ATPase.
Veshaguri S, Christensen SM, Kemmer GC, Ghale G, Moller MP, Lohr C, Christensen AL, Justesen BH, Jorgensen IL, Schiller J, Hatzakis NS, Grabe M, Pomorski TG, and Stamou D.
Science 351, 1469-1473 (2016). [PDF]

Continuum descriptions of membranes and their interaction with proteins: towards chemically accurate models.
Argudo D†, Bethel NP†, Marcoline FV, and Grabe M.
Biochimica et Biophysica Acta - Biomembranes 1858, 1619-1634 (2016). [PDF]

2015

Membrane protein properties revealed through data-rich electrostatics calculations.
Marcoline FV†, Bethel N†, Guerriero CJ, Brodsky JL, and Grabe M.
Structure 23, 1526-1537 (2015). [PDF], Data [excel], Discussion with Dr. Milka Kostic [www]

Simulating current-voltage relationships for a single-file ion channel using the weighted ensemble method.
Adelman JL‡ and Grabe M‡.
Journal of Chemical Theory and Computation 11, 1907-1918 (2015). [PDF]

WESTPA: A portable, highly scalable software package for weighted ensemble simulation and analysis.
Zwier MC, Adelman JL, Kaus JW, Pratt AJ, Wong KF, Rego NB, Suarez E, Letteri S, Wang DW, Grabe M, Zuckerman DM, and Chong LT.
Journal of Chemical Theory and Computation 11, 800-809 (2015). [PDF]

2014

De novo design of a transmembrane Zn2+-transporting four-helix bundle.
Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M‡, Hong M‡, Grigoryan G‡, and DeGrado WF‡.
Science 346, 1520-1524 (2014). [PDF]

Cardiac BIN1 folds T-tubule membrane, controlling ion flux and limiting arrhythmia.
Hong TT†, Yang H†, Zhang SS, Cho HC, Kalashnikova M, Sun B, Zhang H, Bhargava A, Grabe M, Olgin J, Gorelik J, Marban E, Jan LY, and Shaw RM.
Nature Medicine 20, 624-632 (2014). [PDF]

Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1.
Choudhary OP†, Paz A†, Adelman JL†, Coulletier JP†, Abramson J‡, and Grabe M‡.
Nature Structural and Molecular Biology 21, 621-632 (2014). [PDF | Supplement], News & Views [PDF], Cover Image [PDF].

Antibacterial membrane attack by a pore-forming intestinal C-type lectin.
Mukherjee S, Zheng H, Derebe M, Callenberg KM, Partch CL, Rollins D, Propheter DC, Rizo J, Grabe M, Jiang QX‡, and Hooper LV‡.
Nature 505, 103-107 (2014). [PDF]

Structural determinants of water permeation through the sodium-galactose transporter vSGLT.
Adelman JL, Sheng Y, Choe S, Abramson J, Wright EM, Rosenberg JM‡, and Grabe M‡.
Biophysical Journal 106, 1280-1289 (2014). [PDF], New & Notable [PDF].

Continuum approaches to understanding ion and peptide interactions with the membrane.
Latorraca NR†, Callenberg KM†, Boyle JP, and Grabe M.
Journal of Membrane Biology 247, 395-408 (2014). [PDF]

2013

A model of lysosomal pH regulation.
Ishida Y, Nayak S, Mindell JA, and Grabe M.
Journal of General Physiology 141, 705-720 (2013). [PDF], Model file 1 [.mmd]

Simulating rare events using a Weighted Ensemble-based string method.
Adelman JL and Grabe M.
Journal of Chemical Physics 138, 044105 (2013). [PDF], Code [www]

2012

Membrane bending is critical for the stability of voltage sensor segments in the membrane.
Callenberg KM, Latorraca NR, and Grabe M.
Journal of General Physiology 140, 55-68 (2012). [PDF | Supplement]

2011

Simulations of the alternating access mechanism of the sodium symporter Mhp1.
Adelman JL, Dale AL, Zwier MC, Bhatt D, Chong LT, Zuckerman DM, and Grabe M.
Biophysical Journal 101, 2399-2407 (2011). [PDF]

Raw sewage harbors diverse viral populations.
Cantalupo PG, Calgua B, Zhao G, Hundesa A, Wier AD, Katz JP, Grabe M, Hendrix RW, Girones R, Wang D, and Pipas JM.
mBio 2, e00180-11 (2011). [PDF]

Constraint-based, homology model of the extracellular domain of the epithelial Na+ channel alpha subunit reveals a mechanism of channel activation by proteases.
Kashlan OB, Adelman JL, Okumora S, Blobner BM, Zuzek ZA, Hughey RP, Kleyman TR, and Grabe M.
Journal of Biological Chemistry 286, 649-660 (2011). [PDF]

2010

Allosteric inhibition of the epithelial Na+ channel through peptide binding at peripheral finger and thumb domains.
Kashlan OB, Boyd CR, Argyropoulos C, Okumora S, Hughey RP, Grabe M, and Kleyman TR.
Journal of Biological Chemistry 285, 35216-35223 (2010). [PDF]

Sodium release triggers galactose exit from the sodium-galactose transporter, vSGLT.
Watanabe A†, Choe S†, Chaptal V, Rosenberg JM, Wright EM, Grabe M‡, and Abramson J‡.
Nature 468, 988-991 (2010). [PDF]

Water permeation through the sodium-dependent galactose cotransporter vSGLT.
Choe S, Rosenberg JM, Abramson J, Wright EM‡, and Grabe M‡.
Biophysical Journal 99, L56-L58 (2010). [PDF | Supplement], Cover Image [JPG].

APBS membrane tool: a graphical tool for electrostatics calculations at the membrane.
Callenberg KM, Choudhary OP, de Forest GL, Gohara DW, Baker NA, and Grabe M.
PLoS ONE 5(9), e12722 (2010). [PDF]

Characterization of the PCMBS-dependent modification of KCa3.1 channel gating.
Bailey, MA, Grabe M, and Devor DC.
Journal of General Physiology 136, 367-387 (2010). [PDF]

The electrostatics of VDAC: implications for selectivity and gating.
Choudhary OP, Ujwal R, Kowallis W, Coalson R, Abramson J, and Grabe M.
Journal of Molecular Biology 396, 580-592 (2010). [PDF]

2009

Conformational dynamics of the inner pore helix of voltage-gated potassium channels.
Choe S and Grabe M.
Journal of Chemical Physics 130, 215103 (2009). [PDF]

2008

A continuum method for determining membrane protein insertion energies and the problem of charged residues.
Choe S, Hecht KA, and Grabe M.
Journal of General Physiology 131, 563-573 (2008). [PDF | Supplement | Correction]

Getting in sync with dimeric Eg5: Initiation and regulation of the processive run.
Krzysiak TC, Grabe M, and Gilbert SP.
Journal of Biological Chemistry 283, 2078-2087 (2008). [PDF]

2007

Structure prediction for the down state of a potassium channel voltage sensor.
Grabe M†, Lai HC†, Jain M, Jan YN, and Jan LY.
Nature 445, 550-553 (2007). [PDF | Supplement]

2006

Electrostatic forces in the cavity regulate K+ channel selectivity via a kinetic switch.
Grabe M, Bichet D, Qian X, Jan YN, and Jan LY.
Proceedings of the National Academy of Sciences USA 103, 14361–14366 (2006). [PDF | Supplement]

Electrostatic interactions in the channel cavity as an important determinant for potassium channel selectivity.
Bichet D, Grabe M, Jan YN, and Jan LY.
Proceedings of the National Academy of Sciences USA 103, 14355–14360 (2006). [PDF]

Accuracy of calcaneal quantitative ultrasound for identifying patients meeting the world health organizations diagnostic criteria for osteoporosis: A systematic review.
Nayak S, Olkin I, Liu H, Grabe M, Gould MK, Allen IE, Owens DK, and Bravata DM.
Annals of Internal Medicine 144, 832-841 (2006). [PDF]

2005

The S4 voltage sensor packs against the pore domain in the KAT1 voltage-gated potassium channel.
Lai HC, Grabe M, Jan YN, and Jan LY.
Neuron 47, 395-406 (2005). [PDF]

2004

A quantitative assessment of models for voltage-dependent gating of ion channels.
Grabe M, Lecar H, Jan YN, and Jan LY.
Proceedings of the National Academy of Sciences USA 101, 17640–17645 (2004). [PDF | Supplement]

2003

Electrostatic model of S4 motion in voltage-gated ion channels.
Lecar H, Larsson HP, and Grabe M.
Biophysical Journal 85, 2854-2864 (2003). [PDF]

Answers and questions from the KvAP structures.
Cohen BE†, Grabe M†, and Jan LY.
Neuron 39, 395-400 (2003). [PDF]

Protein interactions and membrane geometry.
Grabe M, Neu J, Oster G, and Nollert P.
Biophysical Journal 84, 854-868 (2003). [PDF]

2002

Biosynthesis and secretion of pituitary hormones: dynamics and regulation.
Moore HPH, Andresen JM, Eaton BA, Grabe M, Haugwitz M, Wu MM, and Machen TE.
Archives of Physiology and Biochemistry 110, 16-25 (2002). [PDF]

2001

Cystic fibrosis transmembrane conductance regulator and H+ permeability in regulation of Golgi pH.
Machen TE, Chandy G, Wu M, Grabe M, and Moore HP.
Journal of the Pancreas 2(4 Suppl), 229-236 (2001). [PDF]

Mechanisms of pH regulation in the regulated secretory pathway.
Wu MM, Grabe M, Adams S, Tsein RY, Moore HPH, and Machen TE.
Journal of Biological Chemistry 276, 33027–33035 (2001). [PDF]

Regulation of intra-Golgi pH in respiritory epithelial cells: Does CFTR regulate Golgi pH?
Chandy G, Grabe M, Moore HPH, and Machen TE.
American Journal of Physiology - Cell Physiology 281, C908-C921 (2001). [PDF]

Regulation of organelle acidity.
Grabe M and Oster G.
Journal of General Physiology 117, 329-343 (2001). [PDF | Supplement]

2000

The mechanochemistry of V-ATPase proton pumps.
Grabe M, Wang H, and Oster G.
Biophysical Journal 78, 2798-2813 (2000). [PDF]

How Fo-ATPase generates rotary torque.
Oster G, Wang H, and Grabe M.
Philosophical Transactions of the Royal Society B 355, 523-528 (2000). [PDF]

1999

Energy transduction in the sodium F-ATPase of Propionigenium modestum.
Dimroth P, Wang H, Grabe M, and Oster G.
Proceedings of the National Academy of Sciences USA 96, 4924-4929 (1999). [PDF]

1995

Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins.
Curry WB, Grabe MD, Kurnikov IV, Skourtis SS, Beratan DN, Regan JJ, Aquino AJA, Beroza P, and Onuchic JN.
Journal of Bioenergetics and Biomembranes 27, 285-293 (1995). [PDF]