Dr. Michael Grabe

Genetics
K. Arndt
T.-L. Ashman
G. Campbell
D. Chapman
G. Hatfull
J. Hildebrand
L. Jacobson
S. Kalisz
J. Martens
V. Oke
W. Saunders
B. Stronach
S. Tonsor
R. Wood

Microbiology
G. Hatfull
R. Hendrix
J. Lawrence
V. Oke
J. Pipas
M. Popa
I. Campbell
R.L. Duda
S. Godfrey

Molecular Biology
K. Arndt
J. Franzen
P. Grabowski
G. Hatfull
R. Hendrix
L. Jen-Jacobson
J. Martens
C. Peebles
J. Pipas
J. Rosenberg
A. Schwacha
C. Walsh

Plant Biology
T.-L. Ashman
W. Carson
S. Kalisz
V. Oke
C. Partanen
S. Tonsor
B. Traw

Science Education
A. Bledsoe
K. Curto
L. Daniels
S. Godfrey
N. Kaufmann
C. LaFave
J. Newman
E. Polinko
M. Popa
L. Roberts
T. Seiflein
R. Sherwin
A. Slinskey Legg

Structural Biology
M. Grabe
J. Hempel
R. Hendrix
L. Jen-Jacobson
J. Rosenberg
A. VanDemark

Former Faculty

Photo of Dr.
Grabe

Computational Modeling of Molecular and Cellular Systems

Assistant Professor

Dr. Grabe received his Ph.D. in 2002 with George Oster at the University of California, Berkeley, performed his postdoctoral studies with Lily Jan at the University of California, San Francisco, and joined the Department in 2006.

Currently, Dr. Grabe is accepting graduate students in his laboratory. Dr. Grabe is accepting undergraduate researchers, and does sponsor students in other laboratories.

Professional Interests - Publications - Contact Information - Lab Personnel

Professional Interests of Michael Grabe

Our lab uses computational methods to understand biological phenomena. We are primarily interested in ion transport across cellular membranes. We wish to understand the molecular workings of ion channels and transporters as well as how these proteins work together to regulate ion homeostasis in organelles such as the lysosome and Golgi. We are also interested in the role that membrane proteins have in controlling the intrinsic shape of organelles.

Fig. 1. a,KAT1 expressing yeast grown on low K⁺ media. The F207D mutation compromises the channel's ability to open resulting in lack of growth. The double mutant channel resues yeast growth. b, S4 is pictured in the down state and the up state based on the Kv1.2 structure. Dashed lines indicate the extent of the movement of the C-terminal end. The inner helices (S6) of the central pore are blue, and the S5 segments grey.

Opening of voltage-gated ion channels.
Voltage-gated potassium (Kv) channels are essential for fundamental biological activities such as the beating of our hearts and mental cognition. The interplay of voltage-gated channels generates the action potential responsible for carrying information throughout the nervous system. The channel's ability to switch between on and off states in response to changes in membrane voltage is required for transmission. The highly charged S4 segment of voltage-gated ion channels forms the principle component of the voltage-sensing domain, the portion of the protein that confers voltage sensitivity to this class of channels. This segment traverses the membrane electric field in response to changes in membrane potential leading to channel opening. In a recent set of studies, we employed conditional lethal/second-site suppressor yeast screens to determine the transmembrane packing of the voltage sensor in the down state (Lai et al. 2005). We identified residues in close proximity by first finding mutations that destroy the channel's ability to rescue yeast growth (F207D) followed by the identification of second-site suppressor mutations that restore the channel's ability to open and conduct potassium (S179H+F207D in Fig. 1a). We constructed a down state model of the channel using six pairs of interacting residues as structural constraints and verified this model by engineering suppressor mutations based on spatial considerations. A comparison of our down state model to the up state Kv1.2 crystal structure solved by Roderick MacKinnon's lab suggests that the S4 segment undergoes a large motion during gating (see the green helix in Fig. 1b in the two distinct positions). One of the outstanding questions is how such motions lead to channel opening. The study of this problem is an ongoing project in the lab.

Fig. 2.On the left we see a model of the Kir3.2 channel and the location of the S177G mutation (red) that destroys selectivity. V188D restores selectivity (lower green residue). Current traces show that the S177G channel permeates Na⁺, but the double mutant does not.

Ion selectivity and permeation.
Potassium channels selectively permit the passage of potassium ions while suppressing the flow of other ions. Generally, this selectivity is attributed to a narrow stretch of the channel known as the selectivity filter. However, channels are long pores with spatially distinct ion binding sites that must all be traversed during ion permeation. In a series of papers, we showed that selectivity of mutant Kir3.2 (GIRK2) channels can be substantially amplified by introducing acidic residues into the cavity, a binding site below the selectivity filter (Bichet et al. 2006, Grabe et al. 2006). We used continuum electrostatic calculations along with multi-ion, kinetic models to understand how mutations (red and green residues in Fig. 2) affect the macroscopic properties of the channel, such as selectivity. Kinetic models derived from such molecular calculations demonstrate that non-selective electrostatic stabilization of cations in the cavity can amplify channel selectivity independently of the selectivity filter. This non-intuitive result highlights the dependence of channel properties on the entire channel architecture, and it suggests that selectivity may not be fully understood by focusing on thermodynamic considerations of ion dehydration and the energetics of the selectivity filter solely. That said, there are open questions about how ion selectivity arises in the selectivity filter, and we are using computational methods to probe how single point mutations outside the selectivity filter destroy selectivity.

Publication Archive
20 Citations
18 Abstracts
17 PDFs

Recent Publications of Michael Grabe

Choe, S., K.A. Hecht, and M. Grabe (2008) A continuum method for determining membrane protein insertion energies and the problem of charged residues. J. Gen. Physiol. :In Press

Krzysiak, T.C., M. Grabe, and S.P. Gilbert (2007) Getting in sync with dimeric Eg5: Initiation and regulation of the processive run. J. Biol. Chem. 283:2078-2087 (PDF Reprint: 607 kb)

Grabe, M., H.C. Lai, M. Jain, Y.N. Jan, and L.Y. Jan (2007) Structure prediction for the down state of a potassium channel voltage sensor. Nature 445:550-553

Nayak, S., I. Olkin, H. Liu, M. Grabe, M.K. Gould, I.E. Allen, D.K. Owens, and D.M. Bravata (2006) Accuracy of Calcaneal quantitative ultrasound for identifying patients meeting the world health organizations diagnostic criteria for osteoporosis: A systematic review. Ann. Inter. Med. 144:832-841 (PDF Reprint: 466 kb)

Grabe, M., D. Bichet, X. Qian, Y.N. Jan, and L.Y. Jan (2006) K⁺ channel selectivity depends on kinetic as well as thermodynamic factors. Proc. Natl. Acad. Sci., USA 103:14361-14366 (PDF Reprint: 1.9 MB)

Bichet, D., M. Grabe, Y.N. Jan, and L.Y. Jan (2006) Electrostatic interactions in the channel cavity as an important determinant of potassium channel selectivity. Proc. Natl. Acad. Sci., USA 103:14355-14360 (PDF Reprint: 1.2 MB)

Lai, H.C., M. Grabe, Y.N. Jan, and L.Y. Jan (2005) The S4 voltage sensor packs against the pore domain in the KAT1 voltage-gated potassium channel. Neuron 47:395-406 (PDF Reprint: 659 kb)

Grabe, M., H. Lecar, Y.N. Jan, and L.Y. Jan (2004) A quantitative assessment of models for voltage-dependent gating of ion channels. Proc. Natl. Acad. Sci., USA 101:17640-17645 (PDF Reprint: 522 kb)

Grabe, M., J. Neu, G. Oster, and P. Nollert (2003) Protein interactions and membrane geometry. Biophys. J. 84:854-868 (PDF Reprint: 375 kb)

Cohen, B.E., M. Grabe, and L.Y. Jan (2003) Answers and questions from the KvAP structures. Neuron 39:395-400 (PDF Reprint: 314 kb)

Lecar, H., H.P. Larsson, and M. Grabe (2003) Electrostatic model of S4 motion in voltage-gated ion channels. Biophys. J. 85:2854-2864 (PDF Reprint: 375 kb)

Moore, H.P., J.M. Andresen, B.A. Eaton, M. Grabe, M. Haugwitz, M.M. Wu, and T.E. Machen (2002) Biosynthesis and secretion of pituitary hormones: dynamics and regulation. Arch. Physiol. Biochem. 110:16-25 (PDF Reprint: 139 kb)

Grabe, M., and G. Oster (2001) Regulation of organelle acidity. J. Gen. Physiol. 117:329-344 (PDF Reprint: 366 kb)

Wu, M.M., M. Grabe, S. Adams, R.Y. Tsien, H.P. Moore, and T.E. Machen (2001) Mechanisms of pH regulation in the regulated secretory pathway. J. Biol. Chem. 276:33027-33035 (PDF Reprint: 314 kb)

Chandy, G., M. Grabe, H.P. Moore, and T.E. Machen (2001) Regulation of intra-Golgi pH in respirotary epithelial cells: Does CFTR regulate Golgi pH? Am. J. Physiol. Cell Ph. 281:C908-C921 (PDF Reprint: 758 kb)

How to Contact Michael Grabe

US Mail
University of Pittsburgh
Department of Biological Sciences
242 Crawford Hall
4249 Fifth Avenue
Pittsburgh, PA 15260

Phone, FAX, Internet
Office : (412) 624-4266
Lab :
FAX : (412) 624-4759
Email : mdgrabe@pitt.edu
Web : http://mgrabe1.bio.pitt.edu/~mgrabe/

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