scholarly journals A structural model of the active ribosome-bound membrane protein insertase YidC

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Stephan Wickles ◽  
Abhishek Singharoy ◽  
Jessica Andreani ◽  
Stefan Seemayer ◽  
Lukas Bischoff ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Structural Model ◽  
Cytoplasmic Membrane ◽  
Membrane Surface ◽  
Single Copy ◽  
Protein Insertion ◽  
Versus Protein ◽  
Membrane Protein Insertion ◽  
Translational Mode ◽  
Dynamics Simulations

The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.

scholarly journals A Continuum Method for Determining Membrane Protein Insertion Energies and the Problem of Charged Residues

2008 ◽  
Vol 131 (6) ◽  
pp. 563-573 ◽  
Author(s):  
Seungho Choe ◽  
Karen A. Hecht ◽  
Michael Grabe
Keyword(s):  
Membrane Protein ◽  
Protein Complexes ◽  
Computational Cost ◽  
Atomistic Simulations ◽  
Protein Insertion ◽  
Membrane Protein Insertion ◽  
Membrane Protein Complexes ◽  
Dynamics Simulations ◽  
Charged Peptides ◽  
Continuum Theories

Continuum electrostatic approaches have been extremely successful at describing the charged nature of soluble proteins and how they interact with binding partners. However, it is unclear whether continuum methods can be used to quantitatively understand the energetics of membrane protein insertion and stability. Recent translation experiments suggest that the energy required to insert charged peptides into membranes is much smaller than predicted by present continuum theories. Atomistic simulations have pointed to bilayer inhomogeneity and membrane deformation around buried charged groups as two critical features that are neglected in simpler models. Here, we develop a fully continuum method that circumvents both of these shortcomings by using elasticity theory to determine the shape of the deformed membrane and then subsequently uses this shape to carry out continuum electrostatics calculations. Our method does an excellent job of quantitatively matching results from detailed molecular dynamics simulations at a tiny fraction of the computational cost. We expect that this method will be ideal for studying large membrane protein complexes.

Structure of YidC from Thermotoga maritima and its implications for YidC‐mediated membrane protein insertion

2018 ◽  
Vol 32 (5) ◽  
pp. 2411-2421 ◽  
Author(s):  
Yanlong Xin ◽  
Yan Zhao ◽  
Jiangge Zheng ◽  
Haizhen Zhou ◽  
Xuejun Cai Zhang ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Thermotoga Maritima ◽  
Protein Insertion ◽  
Membrane Protein Insertion

Membrane protein import in yeast mitochondria

2000 ◽  
Vol 28 (4) ◽  
pp. 495-499 ◽  
Author(s):  
K. Tokatlidis ◽  
S. Vial ◽  
P. Luciano ◽  
M. Vergnolle ◽  
S. Clémence
Keyword(s):  
Membrane Protein ◽  
Molecular Mechanism ◽  
Protein Import ◽  
Mitochondrial Matrix ◽  
Yeast Mitochondria ◽  
Inner Membrane ◽  
Protein Insertion ◽  
The Past ◽  
Membrane Protein Insertion ◽  
Membrane Bound

The protein import pathway that targets proteins to the mitochondrial matrix has been extensively characterized in the past 15 years. Variations of this import pathway account for the sorting of proteins to other compartments as well, but the insertion of integral inner membrane proteins lacking a presequence is mediated by distinct translocation machinery. This consists of a complex of Tim9 and Tim10, two homologous, Zn2+-binding proteins that chaperone the passage of the hydrophobic precursor across the aqueous inter-membrane space. The precursor is then targeted to another, inner-membrane-bound, complex of at least five subunits that facilitates insertion. Biochemical and genetic experiments have identified the key components of this process; we are now starting to understand the molecular mechanism. This review highlights recent advances in this new membrane protein insertion pathway.

scholarly journals Membrane Protein Insertion into and Compatibility with Biomimetic Membranes

2017 ◽  
Vol 1 (7) ◽  
pp. 1700053 ◽  
Author(s):  
Tingwei Ren ◽  
Mustafa Erbakan ◽  
Yuexiao Shen ◽  
Eduardo Barbieri ◽  
Patrick Saboe ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Protein Insertion ◽  
Biomimetic Membranes ◽  
Membrane Protein Insertion
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