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2020
A kinetic mechanism for enhanced selectivity of membrane transport
Bisignano, Lee, George, Zuckerman, Grabe‡, and Rosenberg‡
PLoS Computational Biology (in press) [not available].
‡ - co-corresponding authors
A systems-biology approach to molecular machines: Automated exploration of alternative transporter mechanisms
George, Bisignano, Rosenberg, Grabe, and Zuckerman
PLoS Computational Biology (in press) [not available].
‡ - co-corresponding authors
EmrE reminds us to expect the unexpected in membrane transport
Grabe‡, Zuckerman‡, and Rosenberg‡
Journal of General Physiology 152(1):e201912467 [PDF].
‡ - co-corresponding authors
2019
Protons in small spaces: Discrete simulations of vesicle acidification
Singh, Marcoline‡, Veshaguri, Kao, Bruchez, Mindell, Stamou, and Grabe‡
PLoS Computational Biology 15(12):e1007539 [www].
‡ - co-corresponding authors
Harmonizing experimental data with modeling to predict membrane protein insertion in yeast
Guerriero, Gomez, Daskivich, Reutter, Augustine, Weiberth, Nakatsukasa, Grabe, and Brodsky
Biophysical Journal 117:668-678 [PDF].
Biophysics at the coffee shop: lessons learned working with George Oster.
O.A. Igoshin, J. Chen, J. Xing, J. Liu, T.C. Elston, M. Grabe, K.S. Kim, J.A. Nirody, P. Rangamani, S.X. Sun, H. Wang, and C. Wolgemuth.
mBoc 30:1882-1889 [PDF].
Chemically induced vesiculation as a platform for studying TMEM16F activity.
T.W. Han, W. Ye†, N.P. Bethel†, M. Zubia, A. Kim, K.H. Li, A.L. Burlingame, M. Grabe, Y.N. Jan, and L.Y. Jan.
PNAS 116:1309-1318 [PDF].
† - equal contributors
A multiscale model of mechanotransduction by the ankyrin chains of the NOMPC channel.
Argudo, D.†, S. Capponi†, N.P. Bethel, and M. Grabe.
J. Gen. Physiol. 151:316-327 [PDF].
† - co-first authors
2018
Inhibitor binding mode and allosteric regulation of Na+-glucose symporters.
Bisignano, P., C. Ghezzi, H. Jo, N. Polizzi, A. Thorsten, C. Kalyanaraman, R Friemann, MP. Jacobson, E.M. Wright‡, and M. Grabe‡.
Nature Comm. [www].
‡ - co-corresponding authors
Cilia-associated oxysterols activate Smoothened
Raleigh, D.R, ... P. Bisignano, ... , M. Grabe, J.G. McDonald, L. Xu, P.A. Beachy, and J.F. Reiter.
Molecular Cell 72:316-327 [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.
Bichemistry 57:5921-6044 [PDF].
Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a unique Na+ site.
Wahlgren, W.Y., E. Dunevall, R.A. North, A. Paz, M. Scalise, P. Bisignano, J. Bengtsson-Palme, P. Goyal, E. Claesson, R. Caing-Carlsson, R. Andersson, K. Beis, U.J. Nilsson, A. Farewell, L. Pochini, C. Indiveri, M. Grabe, R.C.J. Dobson,12, J. Abramson, S. Ramaswamy, and R. Friemann.
Nature Comm. 9:1753 [PDF].
The Sixth Transmembrane Segment Is a Major Gating Component of the TMEM16A Calcium-Activated Chloride Channel.
Peters C.J., J.M. Gilchrist, J. Tien, N.P. Bethel, L. Qi, T. Chen, L. Wang, Y.N. Jan, M. Grabe, and L.Y. Jan.
Neuron 97:1063-1077 [PDF].
Protonation state of glutamate 73 regulates the formation of a specific dimeric association of mVDAC1.
Bergdoll, L.A., M.T. Lerch, J.W. Patrick, K. Belardo, C. Altenbach, P. Bisignano, A. Laganowsky, M. Grabe, W.L. Hubbell, and J. Abramson.
Proc. Natl. Acad. Sci. USA E172-E79 [PDF].
Conformational transitions of the sodium-dependent sugar transporter, vSGLT.
Paz, A., D.P. Claxton, J.P. Kumar, K. Kazmier, P. Bisignano, S. Sharma, S.A. Nolte, T.M. Liwag, V. Nayak, E.M. Wright, M. Grabe, H.S. Mchaourab, and J. Abramson.
Proc. Natl. Acad. Sci. USA 115:E2742-E2751 [PDF].
2017
Transmembrane helix hydrophobicity is an energetic barrier during the retrotranslocation of integral membrane ERAD substrates.
Guerriero, G.J., K.R. Reutter, A.A. Augustine, G.M. Preston, K.F. Weiberth, T.D. Mackie, H.C. Cleveland-Rubeor, N.P. Bethel, K.M. Callenberg, K. Nakatsukasaa, M. Grabe, and J.L. Brodsky.
Mol. Biol. Cell. 28:2076-2090 [PDF].
New continuum approaches for determining protein induced membrane deformations.
Argudo, D., N.P. Bethel, F.V. Marcoline, C.W. Wolgemuth, and M. Grabe.
Biophys. J. 112:2159-2172 [PDF].
An Assessment of How VDAC Structures Have Impacted Our Understanding of Their Function.
Bergdoll L., M. Grabe, and J. Abramson.
Molecular Basis for Mitochondrial Signaling (Springer Nature, Stuttgart, Germany) Chapter 6:141-160 [PDF].
2016
Atomistic insight into lipid translocation by a TMEM16 scramblase.
Bethel, N. and M. Grabe.
Proc. Natl. Acad. Sci. USA 113:14049-14054 [PDF].
A mathematical model of osteoclast acidification during bone resorption.
Marcoline, F.V., Y. Ishida, J.A. Mindell, S. Nayak, and M. Grabe.
Bone 93: 167-180 [PDF].
Stochastic steps in secondary active sugar transport.
Adelman, J.L., C. Ghezzi, P. Bisignano, D.D.F. Loo, S. Choe, J. Abramson, J.M. Rosenberg, E.M. Wright, and M. Grabe.
Proc. Natl. Acad. Sci. USA 113: E3960-E3966 [PDF].
Direct observation of proton pumping by a eukaryotic P-type ATPase.
Veshaguri, S, S.M. Christensen, G.C. Kemmer, G. Ghale, M.P. Moller, C. Lohr, A.L. Christensen, B.H. Justesen, I.L. Jorgensen, J. Schiller, N.S. Hatzakis, M. Grabe, T.G. Pomorski, and D. Stamou.
Science 351: 1469-1473 [PDF].
Continuum descriptions of membranes and their interaction with proteins: towards chemically accurate models.
Argudo, D.†, N. Bethel†, F.V. Marcoline, and M. Grabe.
BBA - Biomembranes 1858:1619-1634 [PDF].
† - co-first authors
2015
Membrane protein properties revealed through data-rich electrostatics calculations.
Marcoline, F.V.†, N. Bethel†, C.J. Guerriero, J.L. Brodsky, and M. Grabe.
Structure 23: 1526-1537 [PDF], Spread Sheet [excel], Discussion with Dr. Milka Kostic [www].
† - co-first authors
Simulating current-voltage relationships for a single-file ion channel using the weighted ensemble method.
Adelman, J.L.‡ and M. Grabe‡.
J. Comp. Theory Chem. 11: 1907-1918 [PDF].
‡ - co-corresponding authors
WESTPA: A portable, highly scalable software package for weighted ensemble simulation and analysis.
Zwier, M.C., J.L. Adelman, J.W. Kaus, A.J. Pratt, K.F. Wong, N.B. Rego, E. Suarez, S. Letteri, D.W. Wang, M. Grabe, D.M. Zuckerman, and L.T. Chong.
J. Comp. Theory Chem. 11: 800-809 [PDF].
2014
De novo design of a transmembrane Zn2+-transporting four-helix bundle.
Joh, N.H., T. Wang, M.P. Bhate, R. Acharya, Y. Wu, M. Grabe‡, M. Hong‡, G. Grigoryan‡, and W.F. DeGrado‡.
Science 346: 1520-1524 [PDF].
‡ - co-corresponding authors
Cardiac BIN1 folds T-tubule membrane, controlling ion flux and limiting arrhythmia.
Hong, TT.†, H. Yang†, S.S. Zhang, H.C. Cho, M.Kalashnikova, B. Sun, H. Zhang, A. Bhargava, M. Grabe, J. Olgin, J. Gorelik, E. Marban, L.Y. Jan, and R.M. Shaw.
Nat. Med. 20: 624-632 [PDF].
Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1.
Choudhary, O.P.†, A. Paz†, J.L. Adelman†, J.P. Coulletier†, J. Abramson‡, and M. Grabe‡.
Nat. Struct. Mol. Bio. 21: 621-632 [PDF], News & Views [PDF], Cover Image [image].
† - co-first authors, ‡ - co-corresponding authors
Antibacterial membrane attack by a pore-forming intestinal C-type lectin.
Mukherjee, S., H. Zheng, M. Derebe, K.M. Callenberg, C.L. Partch, D. Rollins, D.C. Propheter, J. Rizo, M. Grabe, Q.X. Jiang‡, and L.V. Hooper‡.
Nature 505: 103-107 [www].
‡ - co-corresponding authors
Structural determinants of water permeation through the sodium-galactose transporter vSGLT.
Adelman, J.L., Y. Sheng, Y., S. Choe, J. Abramson, E. Wright, J.M. Rosenberg‡, and M. Grabe‡.
Biophys. J.. 106: 1280-1289 [PDF], New & Notable [PDF].
‡ - co-corresponding authors
Continuum approaches to understanding ion and peptide interactions with the membrane.
Latorraca, N.R.†, K.M. Callenberg†, J.P. Boyle, and M. Grabe.
J. Memb. Bio. 247: 395-408 [PDF].
† - co-first authors
2013
A model of lysosomal pH regulation.
Ishida, Y., S. Nayak, J.A. Mindell, and M. Grabe.
J. Gen. Physiol. 141: 705-720 [PDF].
Simulating rare events using a Weighted Ensemble-based string method.
Adelman, J.L. and M. Grabe.
J. Chem. Phys. 138, 044105 [PDF | code].
2012
Membrane bending is critical for the stability of voltage sensor segments in the membrane.
Callenberg, K.M., N.R. Latorraca, and M. Grabe.
J. Gen. Physiol. 140: 55-68 [PDF].
2011
Simulations of the alternating access mechanism of the sodium symporter Mhp1.
Adelman, J.L., A.L. Dale, M.C. Zwier, D. Bhatt, L.T. Chong, D.M. Zuckerman, and M. Grabe.
Biophys. J. 101: 2399-2407 [PDF].
Raw sewage harbors diverse viral populations.
Cantalupo, P.G., B. Calgua, G. Zhao, A. Hundesa, A.D. Wier, J.P. Katz, M. Grabe, R.W. Hendrix, R. Girones, D. Wang, and J.M. Pipas.
mBio 2: e00180-11 [www].
Constraint-based, homology model of the extracellular domain of the epithelial Na+ channel alpha subunit reveals a mechanism of channel activation by proteases.
Kashlan, O.B., J.L. Adelman, S. Okumora, B.M. Blobner, Z.A. Zuzek, R.P. Hughey, T.R. Kleyman, and M. Grabe.
J. Biol. Chem. 286: 649-660 [PDF].
2010
Allosteric inhibition of the epithelial Na+ channel through peptide binding at peripheral finger and thumb domains.
Kashlan, O.B., C.R. Boyd, C. Argyropoulos, S. Okumora, R.P. Hughey, M. Grabe, and T.R. Kleyman.
J. Biol. Chem. 285: 35216-35223 [PDF].
Sodium release triggers galactose exit from the sodium-galactose transporter, vSGLT.
Watanabe, A.†, S. Choe†, V. Chaptal, J.M. Rosenberg, E.M. Wright, M. Grabe‡, and J. Abramson‡.
Nature 468: 988-991 [PDF].
† - co-first authors, ‡ - co-corresponding authors
Water permeation through the sodium-dependent galactose cotransporter vSGLT.
Choe, S., J.M. Rosenberg, J. Abramson, E.M. Wright‡, and M. Grabe‡.
Biophys. J. 99: L56-L58 [PDF], Cover Image [image].
‡ - co-corresponding authors
APBS membrane tool: a graphical tool for electrostatics calculations at the membrane.
Callenberg, K.M., O.P. Choudhary, G.L. de Forest, D.W. Gohara, N.A. Baker, and M. Grabe.
PLoS ONE 5(9):e12722 [www].
Characterization of the PCMBS-dependent modification of KCa3.1 channel gating.
Bailey, M.A., M. Grabe, and D.C. Devor.
J. Gen. Physiol. 136: 367-387 [PDF].
The electrostatics of VDAC: implications for selectivity and gating.
Choudhary, O.P., R. Ujwal, W. Kowallis, R. Coalson, J. Abramson, and M. Grabe.
J. Mol. Biol. 396: 580-592 [PDF].
2009
Conformational dynamics of the inner pore helix of voltage-gated potassium channels.
Choe, S. and M. Grabe.
J. Chem. Phys. 130: 215103 [PDF].
2008
A continuum method for determining membrane protein insertion energies and the problem of charged residues.
Choe, S., K.A. Hecht, and M. Grabe.
J. Gen. Physiol. 131: 563 [PDF | Supplement].
Getting in sync with dimeric Eg5: Initiation and regulation of the processive run.
Krzysiak, T.C., M. Grabe, and S.P. Gilbert.
J. Biol. Chem. 283: 2078 [PDF].
2007
Structure prediction for the down state of a potassium channel voltage sensor.
Grabe, M.†, H.C. Lai†, M. Jain, Y.N. Jan, and L.Y. Jan.
Nature 445: 550 [PDF | Supplement].
2006
Electrostatic forces in the cavity regulate K+ channel selectivity via a kinetic switch.
Grabe, M., D. Bichet, X. Qian, Y.N. Jan, and L.Y. Jan.
Proc. Natl. Acad. Sci. USA 103: 14361 [PDF | Supplement].
Electrostatic interactions in the channel cavity as an important determinant for potassium channel selectivity.
Bichet, D., M. Grabe, Y.N. Jan, and L.Y. Jan.
Proc. Natl.Acad. Sci. USA 103: 14355 [PDF | Supplement].
Accuracy of calcaneal quantitative ultrasound for identifying patients meeting the world health organizations diagnostic criteria for osteoporosis: A systematic review.
Nayak, S., I. Olkin, H. Liu, M. Grabe, M.K. Gould, I.E. Allen, D.K. Owens, and D.M. Bravata.
Ann. Inter. Med. 144: 832 [PDF].
2005
The S4 voltage sensor packs against the pore domain in the KAT1 voltage-gated potassium channel.
Lai, H.C., M. Grabe, Y.N. Jan, and L.Y. Jan.
Neuron 47: 395 [PDF].
2004
A quantitative assessment of models for voltage-dependent gating of ion channels.
Grabe, M., H. Lecar, Y.N. Jan, and L.Y. Jan.
Proc. Natl. Acad. Sci. USA 101: 17640 [PDF | Supplement].
2003
Electrostatic model of S4 motion in voltage-gated ion channels.
Lecar, H., H.P. Larsson, and M. Grabe.
Biophys. J. 85: 2854 [PDF].
Answers and questions from the KvAP structures.
Grabe, M.†, B.E. Cohen†, and L.Y. Jan.
Neuron 39: 395 [PDF].
Protein interactions and membrane geometry.
Grabe, M., J. Neu, G. Oster, and P. Nollert.
Biophys. J. 84: 854 [PDF].
2002
Biosynthesis and secretion of pituitary hormones: dynamics and regulation.
Moore, H.-P.H., J.M. Anderson, B.A. Eaton, M. Grabe, M. Haugwitz, M.M. Wu, and T.E. Machen.
Arch. Physiol. Biochem. 110: 16 [PDF].
2001
Cystic fibrosis transmembrane conductance regulator and H+ permeability in regulation of Golgi pH.
Machen, T.E., G. Chandy, M. Wu, M. Grabe, and H.P. Moore.
J. Pancreas. 2(4 Suppl): 229 [PDF].
Mechanisms of pH regulation in the regulated secretory pathway.
Wu, M., M. Grabe, S. Adams, R. Tsein, H.P. Moore, and T. Machen.
J. Biol. Chem. 276: 33027 [PDF].
Regulation of intra-Golgi pH in respirotary epithelial cells: Does CFTR regulate Golgi pH?
Chandy, G., M. Grabe, H.P. Moore, and T. Machen.
Am. J. Physiol. 281: C908 [PDF].
Regulation of organelle acidity.
Grabe, M. and G. Oster.
J. Gen. Physiol. 117: 329 [PDF | Supplement].
2000
The mechanochemistry of V-ATPase proton pumps.
Grabe, M., H. Wang, and G. Oster.
Biophys. J. 78(6): 2798 [PDF].
How Fo-ATPase generates rotary torque.
Oster, G., H. Wang, and M. Grabe.
B: Phil. Trans. Roy. Soc. 355: 523 [PDF].
1999
Energy transduction in the sodium F-ATPase of Propionigenium modestum.
Dimroth, P., H. Wang, M. Grabe, and G. Oster.
Proc. Natl. Acad. Sci. USA 96: 4924 [PDF].
1995
Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins.
Curry, W.B., M.D. Grabe, I.V. Kurnikov, S.S. Skourtis, D.N. Beratan, J.J. Regan, A.J.A. Aquino, P. Beroza, and J.N. Onuchic.
J. Bioenerg. Biomem. 27: 285 [PDF]. |
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