Only 75 membrane protein structures had been solved to high resolution by the close of 2003. Because alpha-helical membrane proteins account for ~30% of genome sequences, predicting from amino acid sequence the three-dimensional structures of these proteins is an important goal. Such predictions require understanding two fundamental issues: mechanisms of the biological assembly of MPs by the SecY/Sec61 (translocon) complex and the principles of the physical stability of MPs in their natural lipid bilayer milieu.
The specific aims of this proposal address aspects of both issues as follows: (1) Decipher the """"""""code"""""""" embedded in membrane protein amino acid sequences that determines whether or not a polypeptide segment is integrated into the endoplasmic reticulum membrane by the Sec61 complex as a transmembrane helix. This work will expand a first draft 'biological' hydrophobicity scale obtained using an in vitro system based upon cotranslational insertion of model proteins into microsomes. (2) Gain insights into translocon function using molecular dynamics simulations of the SecY complex from M. jannaschii, for which the crystallographic structure has been determined recently. These simulations will allow manipulation of the translocon structure in the bilayer environment as a means of learning how the translocon may open and close to release TM helices into the bilayer. (3) Establish an experiment-based interfacial hydrophobicity scale for describing the interactions of polypeptide segments with the interface regions of bilayers formed from ER lipids. This is important because the translocon, presumably in concert with the lipid bilayer, distinguishes between the bilayer's hydrocarbon core and interfacial regions. (4) Clarify the physical basis for translocon-assisted insertion into membranes of (1) short TM helices (-12 amino acids) and (2) a model S4 helix voltage-sensor peptide from the KvAP voltage-gated K+ channel. The information obtained will help us understand how to predict the topology and structure of unusual membrane proteins, such as the CIC chloride channel. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM074637-01A1
Application #
7105886
Study Section
Special Emphasis Panel (ZRG1-BCMB-B (02))
Program Officer
Chin, Jean
Project Start
2006-03-01
Project End
2010-02-28
Budget Start
2006-03-01
Budget End
2007-02-28
Support Year
1
Fiscal Year
2006
Total Cost
$367,962
Indirect Cost
Name
University of California Irvine
Department
Physiology
Type
Schools of Medicine
DUNS #
046705849
City
Irvine
State
CA
Country
United States
Zip Code
92697
Ulmschneider, Jakob P; Smith, Jeremy C; White, Stephen H et al. (2018) The importance of the membrane interface as the reference state for membrane protein stability. Biochim Biophys Acta Biomembr 1860:2539-2548
Gumbart, James C; Ulmschneider, Martin B; Hazel, Anthony et al. (2018) Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method. J Membr Biol 251:345-356
Ulmschneider, Martin B; Ulmschneider, Jakob P; Freites, J Alfredo et al. (2017) Transmembrane helices containing a charged arginine are thermodynamically stable. Eur Biophys J 46:627-637
Chen, Yuanyuan; Capponi, Sara; Zhu, Lu et al. (2017) YidC Insertase of Escherichia coli: Water Accessibility and Membrane Shaping. Structure 25:1403-1414.e3
Capponi, Sara; Freites, J Alfredo; Tobias, Douglas J et al. (2016) Interleaflet mixing and coupling in liquid-disordered phospholipid bilayers. Biochim Biophys Acta 1858:354-62
Grønberg, Christina; Sitsel, Oleg; Lindahl, Erik et al. (2016) Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport. Biophys J 111:2417-2429
Cymer, Florian; von Heijne, Gunnar; White, Stephen H (2015) Mechanisms of integral membrane protein insertion and folding. J Mol Biol 427:999-1022
Lorch, Sebastian; Capponi, Sara; Pieront, Florian et al. (2015) Dynamic Carboxylate/Water Networks on the Surface of the PsbO Subunit of Photosystem II. J Phys Chem B 119:12172-81
Capponi, Sara; Heyden, Matthias; Bondar, Ana-Nicoleta et al. (2015) Anomalous behavior of water inside the SecY translocon. Proc Natl Acad Sci U S A 112:9016-21
White, Stephen H (2015) The messy process of guiding proteins into membranes. Elife 4:

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