Wiedemann, N. & Pfanner, N. Mitochondrial machineries for protein import and assembly. Annu. Rev. Biochem. 86, 685–714 (2017).
Hansen, K. G. & Herrmann, J. M. Transport of proteins into mitochondria. Protein J. 38, 330–342 (2019).
Callegari, S., Cruz-Zaragoza, L. D. & Rehling, P. From TOM to the TIM23 complex—handing over of a precursor. Biol. Chem. 401, 709–721 (2020).
Schmidt, O., Pfanner, N. & Meisinger, C. Mitochondrial protein import: from proteomics to functional mechanisms. Nat. Rev. Mol. Cell Biol. 11, 655–667 (2010).
Araiso, Y., Imai, K. & Endo, T. Structural snapshot of the mitochondrial protein import gate. FEBS J. 288, 5300–5310 https://doi.org/10.1111/febs.15661 (2020).
Kubrich, M. et al. The polytopic mitochondrial inner membrane proteins MIM17 and MIM23 operate at the same preprotein import site. FEBS Lett. 349, 222–228 (1994).
Lohret, T. A., Jensen, R. E. & Kinnally, K. W. Tim23, a protein import component of the mitochondrial inner membrane, is required for normal activity of the multiple conductance channel, MCC. J. Cell Biol. 137, 377–386 (1997).
Truscott, K. N. et al. A presequence- and voltage-sensitive channel of the mitochondrial preprotein translocase formed by Tim23. Nat. Struct. Biol. 8, 1074–1082 (2001).
Meinecke, M. et al. Tim50 maintains the permeability barrier of the mitochondrial inner membrane. Science 312, 1523–1526 (2006).
Alder, N. N., Jensen, R. E. & Johnson, A. E. Fluorescence mapping of mitochondrial TIM23 complex reveals a water-facing, substrate-interacting helix surface. Cell 134, 439–450 (2008).
Denkert, N. et al. Cation selectivity of the presequence translocase channel Tim23 is crucial for efficient protein import. eLife 6, e28324 https://doi.org/10.7554/eLife.28324 (2017).
Chacinska, A. et al. Mitochondrial presequence translocase: switching between TOM tethering and motor recruitment involves Tim21 and Tim17. Cell 120, 817–829 (2005).
van der Laan, M. et al. Pam17 is required for architecture and translocation activity of the mitochondrial protein import motor. Mol. Cell. Biol. 25, 7449–7458 (2005).
Ieva, R. et al. Mgr2 functions as lateral gatekeeper for preprotein sorting in the mitochondrial inner membrane. Mol. Cell 56, 641–652 (2014).
Yamamoto, H. et al. Tim50 is a subunit of the TIM23 complex that links protein translocation across the outer and inner mitochondrial membranes. Cell 111, 519–528 (2002).
Chacinska, A. et al. Mitochondrial translocation contact sites: separation of dynamic and stabilizing elements in formation of a TOM–TIM–preprotein supercomplex. EMBO J. 22, 5370–5381 (2003).
Mokranjac, D., Bourenkov, G., Hell, K., Neupert, W. & Groll, M. Structure and function of Tim14 and Tim16, the J and J-like components of the mitochondrial protein import motor. EMBO J. 25, 4675–4685 (2006).
D’Silva, P. R., Schilke, B., Hayashi, M. & Craig, E. A. Interaction of the J-protein heterodimer Pam18/Pam16 of the mitochondrial import motor with the translocon of the inner membrane. Mol. Biol. Cell 19, 424–432 (2008).
Mokranjac, D. et al. Role of Tim50 in the transfer of precursor proteins from the outer to the inner membrane of mitochondria. Mol. Biol. Cell 20, 1400–1407 (2009).
Josyula, R., Jin, Z., Fu, Z. & Sha, B. Crystal structure of yeast mitochondrial peripheral membrane protein Tim44p C-terminal domain. J. Mol. Biol. 359, 798–804 (2006).
Sim, S. I., Chen, Y. & Park, E. Structural basis of mitochondrial protein import by the TIM complex. Preprint at bioRxiv https://doi.org/10.1101/2021.10.10.463828 (2021).
Demishtein-Zohary, K. et al. Role of Tim17 in coupling the import motor to the translocation channel of the mitochondrial presequence translocase. eLife 6, e22696 https://doi.org/10.7554/eLife.22696 (2017).
Demishtein-Zohary, K., Marom, M., Neupert, W., Mokranjac, D. & Azem, A. GxxxG motifs hold the TIM23 complex together. FEBS J. 282, 2178–2186 (2015).
Ting, S. Y., Schilke, B. A., Hayashi, M. & Craig, E. A. Architecture of the TIM23 inner mitochondrial translocon and interactions with the matrix import motor. J. Biol. Chem. 289, 28689–28696 (2014).
Ting, S. Y., Yan, N. L., Schilke, B. A. & Craig, E. A. Dual interaction of scaffold protein Tim44 of mitochondrial import motor with channel-forming translocase subunit Tim23. eLife 6, e23609 https://doi.org/10.7554/eLife.23609 (2017).
Schiller, D., Cheng, Y. C., Liu, Q., Walter, W. & Craig, E. A. Residues of Tim44 involved in both association with the translocon of the inner mitochondrial membrane and regulation of mitochondrial Hsp70 tethering. Mol. Cell. Biol. 28, 4424–4433 (2008).
Schilke, B. A., Hayashi, M. & Craig, E. A. Genetic analysis of complex interactions among components of the mitochondrial import motor and translocon in Saccharomyces cerevisiae. Genetics 190, 1341–1353 (2012).
Weiss, C. et al. Domain structure and lipid interaction of recombinant yeast Tim44. Proc. Natl Acad. Sci. USA 96, 8890–8894 (1999).
Tamura, Y. et al. Identification of Tam41 maintaining integrity of the TIM23 protein translocator complex in mitochondria. J. Cell Biol. 174, 631–637 (2006).
Kutik, S. et al. The translocator maintenance protein Tam41 is required for mitochondrial cardiolipin biosynthesis. J. Cell Biol. 183, 1213–1221 (2008).
Qi, L. et al. Cryo-EM structure of the human mitochondrial translocase TIM22 complex. Cell Res. 31, 369–372 (2021).
Zhang, Y. et al. Structure of the mitochondrial TIM22 complex from yeast. Cell Res. 31, 366–368 (2021).
Dekker, P. J. et al. The Tim core complex defines the number of mitochondrial translocation contact sites and can hold arrested preproteins in the absence of matrix Hsp70-Tim44. EMBO J. 16, 5408–5419 (1997).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Humphreys, I. R. et al. Computed structures of core eukaryotic protein complexes. Science 374, eabm4805 (2021).
Lee, S. et al. The Mgr2 subunit of the TIM23 complex regulates membrane insertion of marginal stop-transfer signals in the mitochondrial inner membrane. FEBS Lett. 594, 1081–1087 (2020).
Gebert, M. et al. Mgr2 promotes coupling of the mitochondrial presequence translocase to partner complexes. J. Cell Biol. 197, 595–604 (2012).
Tamura, Y. et al. Tim23–Tim50 pair coordinates functions of translocators and motor proteins in mitochondrial protein import. J. Cell Biol. 184, 129–141 (2009).
Geissler, A. et al. The mitochondrial presequence translocase: an essential role of Tim50 in directing preproteins to the import channel. Cell 111, 507–518 (2002).
Gevorkyan-Airapetov, L. et al. Interaction of Tim23 with Tim50 is essential for protein translocation by the mitochondrial TIM23 complex. J. Biol. Chem. 284, 4865–4872 (2009).
Dayan, D. et al. A mutagenesis analysis of Tim50, the major receptor of the TIM23 complex, identifies regions that affect its interaction with Tim23. Sci. Rep. 9, 2012 (2019).
Singha, U. K. et al. Protein translocase of mitochondrial inner membrane in Trypanosoma brucei. J. Biol. Chem. 287, 14480–14493 (2012).
Pyrihova, E. et al. A single Tim translocase in the mitosomes of Giardia intestinalis illustrates convergence of protein import machines in anaerobic eukaryotes. Genome Biol. Evol. 10, 2813–2822 (2018).
Chaudhuri, M. et al. Tim17 updates: a comprehensive review of an ancient mitochondrial protein translocator. Biomolecules 10, 1643 https://doi.org/10.3390/biom10121643 (2020).
Schneider, A. Mitochondrial protein import in trypanosomatids: variations on a theme or fundamentally different? PLoS Pathog. 14, e1007351 (2018).
Wu, X. & Rapoport, T. A. Translocation of proteins through a distorted lipid bilayer. Trends Cell Biol. 31, 473–484 (2021).
Ramesh, A. et al. A disulfide bond in the TIM23 complex is crucial for voltage gating and mitochondrial protein import. J. Cell Biol. 214, 417–431 (2016).
Martin, J., Mahlke, K. & Pfanner, N. Role of an energized inner membrane in mitochondrial protein import. Delta psi drives the movement of presequences. J. Biol. Chem. 266, 18051–18057 (1991).
Turakhiya, U. et al. Protein import by the mitochondrial presequence translocase in the absence of a membrane potential. J. Mol. Biol. 428, 1041–1052 (2016).
McIsaac, R. S. et al. Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae. Mol. Biol. Cell 22, 4447–4459 (2011).
Lee, M. E., DeLoache, W. C., Cervantes, B. & Dueber, J. E. A highly characterized yeast toolkit for modular, multipart assembly. ACS Synth. Biol. 4, 975–986 (2015).
Lin, A. et al. Utilization of a strongly inducible DDI2 promoter to control gene expression in Saccharomyces cerevisiae. Front. Microbiol. 9, 2736 (2018).
Meisinger, C., Pfanner, N. & Truscott, K. N. Isolation of yeast mitochondria. Methods Mol. Biol. 313, 33–39 (2006).
Meyer, L. et al. A simplified workflow for monoclonal antibody sequencing. PLoS ONE 14, e0218717 (2019).
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
Tegunov, D. & Cramer, P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods 16, 1146–1152 (2019).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D Struct. Biol. 74, 531–544 (2018).
Terwilliger, T. C., Sobolev, O. V., Afonine, P. V. & Adams, P. D. Automated map sharpening by maximization of detail and connectivity. Acta Crystallogr. D Struct. Biol. 74, 545–559 (2018).
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).
Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98, 10037–10041 (2001).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
Krishnamurthy, M. et al. Caught in the act: covalent cross-linking captures activator–coactivator interactions in vivo. ACS Chem. Biol. 6, 1321–1326 (2011).
Varadi, M. et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50, D439–D444 (2022).
Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv https://doi.org/10.1101/2021.10.04.463034 (2022).
Schneiter, R. et al. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis of the lipid molecular species composition of yeast subcellular membranes reveals acyl chain-based sorting/remodeling of distinct molecular species en route to the plasma membrane. J. Cell Biol. 146, 741–754 (1999).
Zinser, E. et al. Phospholipid synthesis and lipid composition of subcellular membranes in the unicellular eukaryote Saccharomyces cerevisiae. J. Bacteriol. 173, 2026–2034 (1991).
Schlame, M., Ren, M., Xu, Y., Greenberg, M. L. & Haller, I. Molecular symmetry in mitochondrial cardiolipins. Chem. Phys. Lipids 138, 38–49 (2005).
van Meer, G., Voelker, D. R. & Feigenson, G. W. Membrane lipids: where they are and how they behave. Nat. Rev. Mol. Cell Biol. 9, 112–124 (2008).
Wu, E. L. et al. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J. Comput. Chem. 35, 1997–2004 (2014).
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).
Horvath, S. E. & Daum, G. Lipids of mitochondria. Prog. Lipid Res. 52, 590–614 (2013).
Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods 14, 71–73 (2017).
Klauda, J. B. et al. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J. Phys. Chem. B 114, 7830–7843 (2010).
Phillips, J. C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020).
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: an N⋅log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993).
Balusek, C. et al. Accelerating membrane simulations with hydrogen mass repartitioning. J. Chem. Theory Comput. 15, 4673–4686 (2019).
Zorova, L. D. et al. Mitochondrial membrane potential. Anal. Biochem. 552, 50–59 (2018).
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
Romo, T. D., Leioatts, N. & Grossfield, A. Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations. J. Comput. Chem. 35, 2305–2318 (2014).
Romo, T. D. & Grossfield, A. LOOS: an extensible platform for the structural analysis of simulations. Annu. Int. Conf. IEEE Eng. Med. Biol. Soc. 2332–2335 (2009).
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
van der Laan, M. et al. A role for Tim21 in membrane-potential-dependent preprotein sorting in mitochondria. Curr. Biol. 16, 2271–2276 (2006).
Tucker, K. & Park, E. Cryo-EM structure of the mitochondrial protein-import channel TOM complex at near-atomic resolution. Nat. Struct. Mol. Biol. 26, 1158–1166 (2019).
Ieva, R. et al. Mitochondrial inner membrane protease promotes assembly of presequence translocase by removing a carboxy-terminal targeting sequence. Nat. Commun. 4, 2853 (2013).
Gotzke, H. et al. The ALFA-tag is a highly versatile tool for nanobody-based bioscience applications. Nat. Commun. 10, 4403 (2019).
More News
Author Correction: Bitter taste receptor activation by cholesterol and an intracellular tastant – Nature
Audio long read: How does ChatGPT ‘think’? Psychology and neuroscience crack open AI large language models
Ozempic keeps wowing: trial data show benefits for kidney disease