Understanding mitochondria and the utility of optimization as a canonical framework for identifying and modeling mitochondrial pathways

References

Adiele, R.C. and Adiele, C.A. (2019). Metabolic defects in multiple sclerosis. Mitochondrion 44: 7–14, https://doi.org/10.1016/j.mito.2017.12.005.Search in Google Scholar PubMed

Alimohamadi, H. and Rangamani, P. (2018). Modeling membrane curvature generation due to membrane–protein interactions. Biomolecules 8: 120, https://doi.org/10.3390/biom8040120.Search in Google Scholar PubMed PubMed Central

Baker, N., Patel, J., and Khacho, M. (2019). Linking mitochondrial dynamics, cristae remodeling and supercomplex formation: how mitochondrial structure can regulate bioenergetics. Mitochondrion 49: 259–268, https://doi.org/10.1016/j.mito.2019.06.003.Search in Google Scholar PubMed

Balazsi, G., van Oudenaarden, A., and Collins, J.J. (2011). Cellular decision making and biological noise: from microbes to mammals. Cell 144: 910–925, https://doi.org/10.1016/j.cell.2011.01.030.Search in Google Scholar PubMed PubMed Central

Banga, J.R. (2008). Optimization in computational systems biology. BMC Syst. Biol. 2: 47, https://doi.org/10.1186/1752-0509-2-47.Search in Google Scholar PubMed PubMed Central

Barberis, S.D. (2019). Wiring optimization explanation in neuroscience: what is special about it? THEORIA 34, https://doi.org/10.1387/theoria.18148.Search in Google Scholar

Barbot, M. and Meinecke, M. (2016). Reconstitutions of mitochondrial inner membrane remodeling. J. Struct. Biol. 196: 20–28, https://doi.org/10.1016/j.jsb.2016.07.014.Search in Google Scholar PubMed

Bassereau, P., Jin, R., Baumgart, T., Deserno, M., Dimova, R., Frolov, V.A., Bashkirov, P.V., Grubmüller, H., Jahn, R., Risselada, H.J., et al.. (2018). The 2018 biomembrane curvature and remodeling roadmap. J. Phys. D Appl. Phys. 51: 343001, https://doi.org/10.1088/1361-6463/aacb98.Search in Google Scholar PubMed PubMed Central

Beard, D.A. (2005). A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation. PLoS Comput. Biol. 1: e36, https://doi.org/10.1371/journal.pcbi.0010036.Search in Google Scholar PubMed PubMed Central

Benard, G., Bellance, N., James, D., Parrone, P., Fernandez, H., Letellier, T., and Rossignol, R. (2007). Mitochondrial bioenergetics and structural network organization. J. Cell Sci. 120: 838–848, https://doi.org/10.1242/jcs.03381.Search in Google Scholar PubMed

Benaroya, H. (2020). Brain energetics, mitochondria, and traumatic brain injury. Rev. Neurosci. 31: 363–390, https://doi.org/10.1515/revneuro-2019-0086.Search in Google Scholar PubMed

Benaroya, H. and Bernold, L. (2008). Engineering of lunar bases. Acta Astronaut. 62: 277–299, https://doi.org/10.1016/j.actaastro.2007.05.001.Search in Google Scholar

Benaroya, H., Nagurka, M.L., and Han, S.M. (2018). Mechanical vibration: analysis, uncertainties, and control, 4th ed. Boca Raton, FL: CRC Press, Taylor & Francis Group.10.1201/9781315118369Search in Google Scholar

Bertram, R., Gram Pedersen, M., Luciani, D.S., and Sherman, A. (2006). A simplified model for mitochondrial ATP production. J. Theor. Biol. 243: 575–586, https://doi.org/10.1016/j.jtbi.2006.07.019.Search in Google Scholar PubMed

Bossy-Wetzel, E. and Green, D.R. (1999). Caspases induce cytochrome c release from mitochondria by activating cytosolic factors. J. Biol. Chem. 274: 17484–17490, https://doi.org/10.1074/jbc.274.25.17484.Search in Google Scholar PubMed

Brown, A.E. and Discher, D.E. (2009). Conformational changes and signaling in cell and matrix physics. Curr. Biol. 19: R781–R789, https://doi.org/10.1016/j.cub.2009.06.054.Search in Google Scholar PubMed PubMed Central

Brown, M.F. (2012). Curvature forces in membrane lipid–protein interactions. Biochemistry 51: 9782–9795, https://doi.org/10.1021/bi301332v.Search in Google Scholar PubMed PubMed Central

Buhlman, L.M. (Ed.) (2016). Mitochondrial mechanisms of degeneration and repair in Parkinson’s disease. Cham, Switzerland: Springer Nature.10.1007/978-3-319-42139-1Search in Google Scholar

Caicedo, A., Zambrano, K., Sanon, S., Luis Velez, J., Montalvo, M., Jara, F., Moscoso, S.A., Velez, P., Maldonado, A., and Velarde, G. (2021). The diversity and coexistence of extracellular mitochondria in circulation: a friend or foe of the immune system. Mitochondrion 58: 270–284, https://doi.org/10.1016/j.mito.2021.02.014.Search in Google Scholar PubMed

Cairns, C.B., Walther, J., Harken, A.H., and Banerjee, A. (1998). Mitochondrial oxidative phosphorylation thermodynamic efficiencies reflect physiological organ roles. Am. J. Physiol. Regul. Integr. Comp. Physiol. 274: 1376–1383, https://doi.org/10.1152/ajpregu.1998.274.5.R1376.Search in Google Scholar PubMed

Calvetti, D. and Somersalo, E. (2015). Life sciences through mathematical models. Rend. Lincei. 26: 193–201, https://doi.org/10.1007/s12210-015-0422-5.Search in Google Scholar

Calvetti, D. and Somersalo, E. (2019). Brain energy metabolism. In: Encyclopedia of computational neuroscience. Springer Science+Business Media, LLC, part of Springer Nature, New York, pp. 1–19.10.1007/978-1-4614-7320-6_100673-1Search in Google Scholar

Canham, P.B. (1970). The minimum energy of bending as a possible explanation of the biconcave shape of the human red blood cell. J. Theor. Biol. 26: 61–81, https://doi.org/10.1016/s0022-5193(70)80032-7.Search in Google Scholar

Cenini, G., Lloret, A., and Cascella, R. (2019). Oxidative stress in neurodegenerative diseases: from a mitochondrial point of view. Oxid. Med. Cell. Longev. 2019: 2105607, https://doi.org/10.1155/2019/2105607.Search in Google Scholar PubMed PubMed Central

Chauhan, A., Vera, J., and Wolkenhauer, O. (2014). The systems biology of mitochondrial fission and fusion and implications for disease and aging. Biogerontology 15: 1–12, https://doi.org/10.1007/s10522-013-9474-z.Search in Google Scholar PubMed

Chen, B.L., Hall, D.H., and Chklovskii, D.B. (2006). Wiring optimization can relate neuronal structure and function. Proc. Natl. Acad. Sci. U.S.A. 103: 4723–4728, https://doi.org/10.1073/pnas.0506806103.Search in Google Scholar PubMed PubMed Central

Chen, Y., Meyer, J.N., Hill, H.Z., Lange, G., Condon, M.R., Klein, J.C., Ndirangu, D., and Falvo, M.J. (2017). Role of mitochondrial DNA damage and dysfunction in veterans with Gulf War illness. PLoS One 12: e0184832, https://doi.org/10.1371/journal.pone.0184832.Search in Google Scholar PubMed PubMed Central

Cogliati, S., Enriquez, J.A., and Scorrano, L. (2016). Mitochondrial cristae: where beauty meets functionality. Trends Biochem. Sci. 41: 261–273, https://doi.org/10.1016/j.tibs.2016.01.001.Search in Google Scholar PubMed

Cohen, B.H. and Gold, D.R. (2001). Mitochondrial cytopathy in adults – what we know so far. Cleve. Clin. J. Med. 68: 625–642, https://doi.org/10.3949/ccjm.68.7.625.Search in Google Scholar PubMed

Colina‐Tenorio, L., Horten, P., Pfanner, N., and Rampelt, H. (2020). Shaping the mitochondrial inner membrane in health and disease. J. Intern. Med. 287: 645–664, https://doi.org/10.1111/joim.13031.Search in Google Scholar PubMed

Correia, S.C. and Moreira, P.I. (2018). Role of mitochondria in neurodegenerative diseases: the dark side of the “energy factory”. In: Mitochondrial biology and experimental therapeutics. Springer International Publishing AG, part of Springer Nature, Switzerland, pp. 213–239.10.1007/978-3-319-73344-9_11Search in Google Scholar

Csordas, G., Weaver, D., and Hajnoczky, G. (2018). Endoplasmic reticulum-mitochondrial contactology: structure and signaling functions. Trends Cell Biol. 28: 523–540, https://doi.org/10.1016/j.tcb.2018.02.009.Search in Google Scholar PubMed PubMed Central

Denn, M.M. (1969). Optimization by variational methods. New York: McGraw-Hill.Search in Google Scholar

Diogo, C.V., Yambire, K.F., Fernandez Mosquera, L., Branco, F.T., and Raimundo, N. (2018). Mitochondrial adventures at the organelle society. Biochem. Biophys. Res. Commun. 500: 87–93, https://doi.org/10.1016/j.bbrc.2017.04.124.Search in Google Scholar PubMed PubMed Central

Dorn, G.W.2nd and Maack, C. (2013). SR and mitochondria: calcium cross-talk between kissing cousins. J. Mol. Cell. Cardiol. 55: 42–49, https://doi.org/10.1016/j.yjmcc.2012.07.015.Search in Google Scholar PubMed

Doyle, F.J.3rd and Stelling, J. (2006). Systems interface biology. J. R. Soc. Interface 3: 603–616, https://doi.org/10.1098/rsif.2006.0143.Search in Google Scholar PubMed PubMed Central

Drapaca, C.S. (2015). An electromechanical model of neuronal dynamics using Hamilton’s principle. Front. Cell. Neurosci. 9: 271, https://doi.org/10.3389/fncel.2015.00271.Search in Google Scholar PubMed PubMed Central

Duchen, M.R. (2004). Mitochondria in health and disease: perspectives on a new mitochondrial biology. Mol. Aspect. Med. 25: 365–451, https://doi.org/10.1016/j.mam.2004.03.001.Search in Google Scholar PubMed

Dudkina, N.V., Eubel, H., Keegstra, W., Boekema, E.J., and Braun, H.P. (2005). Structure of a mitochondrial supercomplex formed by respiratory-chain complexes I and III. Proc. Natl. Acad. Sci. U. S. A. 102: 3225–3229, https://doi.org/10.1073/pnas.0408870102.Search in Google Scholar PubMed PubMed Central

Dudkina, N.V., Kouril, R., Peters, K., Braun, H.P., and Boekema, E.J. (2010). Structure and function of mitochondrial supercomplexes. Biochim. Biophys. Acta 1797: 664–670, https://doi.org/10.1016/j.bbabio.2009.12.013.Search in Google Scholar PubMed

Eisner, V., Picard, M., and Hajnoczky, G. (2018). Mitochondrial dynamics in adaptive and maladaptive cellular stress responses. Nat. Cell Biol. 20: 755–765, https://doi.org/10.1038/s41556-018-0133-0.Search in Google Scholar PubMed PubMed Central

El-Hattab, A.W. and Scaglia, F. (2016). Mitochondrial cytopathies. Cell Calcium 60: 199–206, https://doi.org/10.1016/j.ceca.2016.03.003.Search in Google Scholar PubMed

Elbaz, Y. and Schuldiner, M. (2011). Staying in touch: the molecular era of organelle contact sites. Trends Biochem. Sci. 36: 616–623, https://doi.org/10.1016/j.tibs.2011.08.004.Search in Google Scholar

Elfawy, H.A. and Das, B. (2019). Crosstalk between mitochondrial dysfunction, oxidative stress, and age related neurodegenerative disease: etiologies and therapeutic strategies. Life Sci. 218: 165–184, https://doi.org/10.1016/j.lfs.2018.12.029.Search in Google Scholar

Emam, S. and Lacarbonara, W. (2022). A review on buckling and postbuckling of thin elastic beams. Eur. J. Mech. Solid. 92, https://doi.org/10.1016/j.euromechsol.2021.104449.Search in Google Scholar

Farmer, T., Naslavsky, N., and Caplan, S. (2018). Tying trafficking to fusion and fission at the mighty mitochondria. Traffic 19: 569–577, https://doi.org/10.1111/tra.12573.Search in Google Scholar

Feng, Q. and Kornmann, B. (2018). Mechanical forces on cellular organelles. J. Cell Sci. 131, https://doi.org/10.1242/jcs.218479.Search in Google Scholar

Filadi, R. and Pizzo, P. (2020). Mitochondrial calcium handling and neurodegeneration: when a good signal goes wrong. Curr. Opin. Physiol. 17: 224–233, https://doi.org/10.1016/j.cophys.2020.08.009.Search in Google Scholar

Frey, T.G. and Mannella, C.A. (2000). The internal structure of mitochondria. Trends Biochem. Sci. 25: 319–324, https://doi.org/10.1016/s0968-0004(00)01609-1.Search in Google Scholar

Friedman, J.R., Lackner, L.L., West, M., Dibenedetto, J.R., Nunnari, J., and Voeltz, G.K. (2011). ER tubules mark sites of mitochondrial division. Science 334: 358–362, https://doi.org/10.1126/science.1207385.Search in Google Scholar PubMed PubMed Central

Galloway, C.A., Lee, H., and Yoon, Y. (2012). Mitochondrial morphology-emerging role in bioenergetics. Free Radic. Biol. Med. 53: 2218–2228, https://doi.org/10.1016/j.freeradbiomed.2012.09.035.Search in Google Scholar PubMed PubMed Central

Galluzzi, L., Morselli, E., Kepp, O., Vitale, I., Rigoni, A., Vacchelli, E., Michaud, M., Zischka, H., Castedo, M., and Kroemer, G. (2010). Mitochondrial gateways to cancer. Mol. Aspect. Med. 31: 1–20, https://doi.org/10.1016/j.mam.2009.08.002.Search in Google Scholar PubMed

Genova, M.L. and Lenaz, G. (2013). A critical appraisal of the role of respiratory supercomplexes in mitochondria. Biol. Chem. 394: 631–639, https://doi.org/10.1515/hsz-2012-0317.Search in Google Scholar PubMed

Ghochani, M., Nulton, J.D., Salamon, P., Frey, T.G., Rabinovitch, A., and Baljon, A.R. (2010). Tensile forces and shape entropy explain observed crista structure in mitochondria. Biophys. J. 99: 3244–3254, https://doi.org/10.1016/j.bpj.2010.09.038.Search in Google Scholar PubMed PubMed Central

Giorgi, C., De Stefani, D., Bononi, A., Rizzuto, R., and Pinton, P. (2009). Structural and functional link between the mitochondrial network and the endoplasmic reticulum. Int. J. Biochem. Cell Biol. 41: 1817–1827, https://doi.org/10.1016/j.biocel.2009.04.010.Search in Google Scholar PubMed PubMed Central

Glancy, B., Willingham, T.B., Kim, Y., and Katti, P. (2020). The functional impact of mitochondrial structure across subcellular scales. Front. Physiol. 11: 541040, https://doi.org/10.3389/fphys.2020.541040.Search in Google Scholar PubMed PubMed Central

Golshani-Hebroni, S. (2016). Mg++ requirement for MtHK binding, and Mg++ stabilization of mitochondrial membranes via activation of MtHK & MtCK and promotion of mitochondrial permeability transition pore closure: a hypothesis on mechanisms underlying Mg++’s antioxidant and cytoprotective effects. Gene 581: 1–13, https://doi.org/10.1016/j.gene.2015.12.046.Search in Google Scholar PubMed

Goriely, A., Geers, M.G., Holzapfel, G.A., Jayamohan, J., Jerusalem, A., Sivaloganathan, S., Squier, W., van Dommelen, J.A., Waters, S., and Kuhl, E. (2015). Mechanics of the brain: perspectives, challenges, and opportunities. Biomech. Model. Mechanobiol. 14: 931–965, https://doi.org/10.1007/s10237-015-0662-4.Search in Google Scholar PubMed PubMed Central

Guillemin, A. and Stumpf, M.P.H. (2021). Noise and the molecular processes underlying cell fate decision-making. Phys. Biol. 18: 011002, https://doi.org/10.1088/1478-3975/abc9d1.Search in Google Scholar PubMed

Guillen-Gosalbez, G. and Sorribas, A. (2009). Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses. BMC Bioinf. 10: 386, https://doi.org/10.1186/1471-2105-10-386.Search in Google Scholar PubMed PubMed Central

Gupta, S., Kass, G.E., Szegezdi, E., and Joseph, B. (2009). The mitochondrial death pathway: a promising therapeutic target in diseases. J. Cell Mol. Med. 13: 1004–1033, https://doi.org/10.1111/j.1582-4934.2009.00697.x.Search in Google Scholar PubMed PubMed Central

Hasenstaub, A., Otte, S., Callaway, E., and Sejnowski, T.J. (2010). Metabolic cost as a unifying principle governing neuronal biophysics. Proc. Natl. Acad. Sci. U.S.A. 107: 12329–12334, https://doi.org/10.1073/pnas.0914886107.Search in Google Scholar PubMed PubMed Central

Henne, W.M. (2016). Organelle remodeling at membrane contact sites. J. Struct. Biol. 196: 15–19, https://doi.org/10.1016/j.jsb.2016.05.003.Search in Google Scholar PubMed PubMed Central

Hildebrand, F.B. (1965). Methods of applied mathematics, 2nd ed. Englewood Cliffs, NJ: Prentice-Hall.Search in Google Scholar

Hood, D.A., Memme, J.M., Oliveira, A.N., and Triolo, M. (2019). Maintenance of skeletal muscle mitochondria in health, exercise, and aging. Annu. Rev. Physiol. 81: 19–41, https://doi.org/10.1146/annurev-physiol-020518-114310.Search in Google Scholar PubMed

Ikon, N. and Ryan, R.O. (2017). Cardiolipin and mitochondrial cristae organization. Biochim. Biophys. Acta Biomembr. 1859: 1156–1163, https://doi.org/10.1016/j.bbamem.2017.03.013.Search in Google Scholar PubMed PubMed Central

Javier-Torrent, M., Zimmer-Bensch, G., and Nguyen, L. (2021). Mechanical forces orchestrate brain development. Trends Neurosci. 44: 110–121, https://doi.org/10.1016/j.tins.2020.10.012.Search in Google Scholar PubMed

John, G.B., Shang, Y., Li, L., Renken, C., Mannella, C.A., Selker, J.M.L., Rangell, L., Bennett, M.J., and Zha, J. (2005). The mitochondrial inner membrane protein mitofilin controls cristae morphology. Mol. Biol. Cell 16: 1543–1554, https://doi.org/10.1091/mbc.e04-08-0697.Search in Google Scholar PubMed PubMed Central

Joubert, F. and Puff, N. (2021). Mitochondrial cristae architecture and functions: lessons from minimal model systems. Membranes 11, https://doi.org/10.3390/membranes11070465.Search in Google Scholar PubMed PubMed Central

Kembro, J.M., Aon, M.A., Winslow, R.L., O’Rourke, B., and Cortassa, S. (2013). Integrating mitochondrial energetics, redox and ROS metabolic networks: a two-compartment model. Biophys. J. 104: 332–343, https://doi.org/10.1016/j.bpj.2012.11.3808.Search in Google Scholar PubMed PubMed Central

Kembro, J.M., Cortassa, S., and Aon, M.A. (2014). Complex oscillatory redox dynamics with signaling potential at the edge between normal and pathological mitochondrial function. Front. Physiol. 5: 257, https://doi.org/10.3389/fphys.2014.00257.Search in Google Scholar PubMed PubMed Central

Klecker, T., Bockler, S., and Westermann, B. (2014). Making connections: interorganelle contacts orchestrate mitochondrial behavior. Trends Cell Biol. 24: 537–545, https://doi.org/10.1016/j.tcb.2014.04.004.Search in Google Scholar PubMed

Kondadi, A.K., Anand, R., and Reichert, A.S. (2020). Cristae membrane dynamics – a paradigm change. Trends Cell Biol. 30: 923–936, https://doi.org/10.1016/j.tcb.2020.08.008.Search in Google Scholar PubMed

Kornmann, B. (2013). The molecular hug between the ER and the mitochondria. Curr. Opin. Cell Biol. 25: 443–448, https://doi.org/10.1016/j.ceb.2013.02.010.Search in Google Scholar PubMed

Kornmann, B. and Walter, P. (2010). ERMES-mediated ER-mitochondria contacts: molecular hubs for the regulation of mitochondrial biology. J. Cell Sci. 123: 1389–1393, https://doi.org/10.1242/jcs.058636.Search in Google Scholar PubMed PubMed Central

Koslik, H.J., Hamilton, G., and Golomb, B.A. (2014). Mitochondrial dysfunction in Gulf war illness revealed by 31Phosphorus magnetic resonance spectroscopy: a case-control study. PLoS One 9: e92887, https://doi.org/10.1371/journal.pone.0092887.Search in Google Scholar PubMed PubMed Central

Kraus, S. (2001). Mitochondria – structure and role in respiration. In: Encyclopedia of life sciences. Nature Publishing Group, Springer, Switzerland.10.1038/npg.els.0001380Search in Google Scholar

Kremling, A. and Saez-Rodriguez, J. (2007). Systems biology – an engineering perspective. J. Biotechnol. 129: 329–351, https://doi.org/10.1016/j.jbiotec.2007.02.009.Search in Google Scholar PubMed

Kroemer, G. (1997). Mitochondrial implication in apoptosis. Towards an endosymbiont hypothesis of apoptosis evolution. Cell Death Differ. 4: 443–456, https://doi.org/10.1038/sj.cdd.4400266.Search in Google Scholar PubMed

Kubota, T., Shindo, Y., Tokuno, K., Komatsu, H., Ogawa, H., Kudo, S., Kitamura, Y., Suzuki, K., and Oka, K. (2005). Mitochondria are intracellular magnesium stores: investigation by simultaneous fluorescent imagings in PC12 cells. Biochim. Biophys. Acta Mol. Cell Res. 1744: 19–28, https://doi.org/10.1016/j.bbamcr.2004.10.013.Search in Google Scholar PubMed

Kuhlbrandt, W. (2015). Structure and function of mitochondrial membrane protein complexes. BMC Biol. 13: 89, https://doi.org/10.1186/s12915-015-0201-x.Search in Google Scholar PubMed PubMed Central

Kurt, B. and Topal, T. (2013). Mitochondrial disease. Dis. Mol. Med. 1, https://doi.org/10.5455/dmm.20130107125901.Search in Google Scholar

Laadhari, A., Misbah, C., and Saramito, P. (2010). On the equilibrium equation for a generalized biological membrane energy by using a shape optimization approach. Phys. Nonlinear Phenom. 239: 1567–1572, https://doi.org/10.1016/j.physd.2010.04.001.Search in Google Scholar

Lackner, L.L. (2014). Shaping the dynamic mitochondrial network. BMC Biol. 12: 10, https://doi.org/10.1186/1741-7007-12-35.Search in Google Scholar PubMed PubMed Central

Lanczos, C. (1986). The variational principles of mechanics, 4th ed. New York: Dover Publications.Search in Google Scholar

Lemonde, H. and Rahman, S. (2015). Inherited mitochondrial disease. Paediatr. Child Health 25: 133–138, https://doi.org/10.1016/j.paed.2014.11.002.Search in Google Scholar

Lim, C.T., Zhou, E.H., and Quek, S.T. (2006). Mechanical models for living cells – a review. J. Biomech. 39: 195–216, https://doi.org/10.1016/j.jbiomech.2004.12.008.Search in Google Scholar PubMed

Lucia, U. (2015). Bioengineering thermodynamics of biological cells. Theor. Biol. Med. Model. 12: 29, https://doi.org/10.1186/s12976-015-0024-z.Search in Google Scholar PubMed PubMed Central

Magnus, G. and Keizer, J. (1997). Minimal model of beta-cell mitochondrial Ca ion handling. Model.Physiol.: C717–C733, https://doi.org/10.1152/ajpcell.1997.273.2.c717.Search in Google Scholar

Magnus, G. and Keizer, J. (1998a). Model of Beta-cell mitochondrial calcium handling and electrical activity – I – cytoplasmic variables. Model.Physiol.: C1158–C1173, https://doi.org/10.1152/ajpcell.1998.274.4.c1158.Search in Google Scholar

Magnus, G. and Keizer, J. (1998b). Model of beta-cell mitochondrial calcium handling and electrical activity – II – mitochondrial variables. Model.Physiol.: C1174–C1184, https://doi.org/10.1152/ajpcell.1998.274.4.c1174.Search in Google Scholar PubMed

Mannella, C.A. (2000). Introduction – our changing views of mitochondria. J. Bioenerg. Biomembr. 32: 1–4, https://doi.org/10.1023/a:1005562109678.10.1023/A:1005562109678Search in Google Scholar

Mannella, C.A. (2006a). The relevance of mitochondrial membrane topology to mitochondrial function. Biochim. Biophys. Acta 1762: 140–147, https://doi.org/10.1016/j.bbadis.2005.07.001.Search in Google Scholar PubMed

Mannella, C.A. (2006b). Structure and dynamics of the mitochondrial inner membrane cristae. Biochim. Biophys. Acta 1763: 542–548, https://doi.org/10.1016/j.bbamcr.2006.04.006.Search in Google Scholar PubMed

Mannella, C.A. (2008). Structural diversity of mitochondria: functional implications. Ann. N. Y. Acad. Sci. 1147: 171–179, https://doi.org/10.1196/annals.1427.020.Search in Google Scholar PubMed PubMed Central

Mannella, C.A. (2020). Consequences of folding the mitochondrial inner membrane. Front. Physiol. 11: 536, https://doi.org/10.3389/fphys.2020.00536.Search in Google Scholar

Mannella, C.A., Lederer, W.J., and Jafri, M.S. (2013). The connection between inner membrane topology and mitochondrial function. J. Mol. Cell. Cardiol. 62: 51–57, https://doi.org/10.1016/j.yjmcc.2013.05.001.Search in Google Scholar

Mannella, C.A., Pfeiffer, D.R., Bradshaw, P.C., Moraru, I.I., Slepchenko, B., Loew, L.M., Hsieh, C.e., Buttle, K., and Marko, M. (2001). Topology of the mitochondrial inner membrane: dynamics and bioenergetic implications. IUBMB Life 52: 93–100, https://doi.org/10.1080/15216540152845885.Search in Google Scholar

Marchi, S., Patergnani, S., and Pinton, P. (2014). The endoplasmic reticulum-mitochondria connection: one touch, multiple functions. Biochim. Biophys. Acta 1837: 461–469, https://doi.org/10.1016/j.bbabio.2013.10.015.Search in Google Scholar

Merolle, L., Cappadone, C., Farruggia, G., Marraccini, C., Sargenti, A., Colanardi, A., and Iotti, S. (2014). Intracellular magnesium content changes during mitochondria-mediated apoptosis: in depth study of early events on mitochondrial membrane potential. J. Biol. Res. 87: 41, https://doi.org/10.4081/jbr.2014.2139.Search in Google Scholar

Moeendarbary, E. and Harris, A.R. (2014). Cell mechanics: principles, practices, and prospects. Wiley Interdiscip. Rev. Syst. Biol. Med. 6: 371–388, https://doi.org/10.1002/wsbm.1275.Search in Google Scholar

Morava, E. and Kozicz, T. (2013). Mitochondria and the economy of stress (mal)adaptation. Neurosci. Biobehav. Rev. 37: 668–680, https://doi.org/10.1016/j.neubiorev.2013.02.005.Search in Google Scholar

Moshkforoush, A., Ashenagar, B., Tsoukias, N.M., and Alevriadou, B.R. (2019). Modeling the role of endoplasmic reticulum-mitochondria microdomains in calcium dynamics. Sci. Rep. 9: 17072, https://doi.org/10.1038/s41598-019-53440-7.Search in Google Scholar

Mottaghi, S. and Benaroya, H. (2015). Design of a lunar surface structure. I: design configuration and thermal analysis. J. Aero. Eng. 28, https://doi.org/10.1061/(asce)as.1943-5525.0000382.Search in Google Scholar

Murley, A. and Nunnari, J. (2016). The emerging network of mitochondria-organelle contacts. Mol. Cell. 61: 648–653, https://doi.org/10.1016/j.molcel.2016.01.031.Search in Google Scholar PubMed PubMed Central

Nielsen, J. (2007). Principles of optimal metabolic network operation. Mol. Syst. Biol. 3: 126, https://doi.org/10.1038/msb4100169.Search in Google Scholar PubMed PubMed Central

Nielsen, J., Gejl, K.D., Hey-Mogensen, M., Holmberg, H.C., Suetta, C., Krustrup, P., Elemans, C.P.H., and Ortenblad, N. (2017). Plasticity in mitochondrial cristae density allows metabolic capacity modulation in human skeletal muscle. J. Physiol. 595: 2839–2847, https://doi.org/10.1113/jp273040.Search in Google Scholar

Niyazov, D.M., Kahler, S.G., and Frye, R.E. (2016). Primary mitochondrial disease and secondary mitochondrial dysfunction: importance of distinction for diagnosis and treatment. Mol. Syndromol. 7: 122–137, https://doi.org/10.1159/000446586.Search in Google Scholar PubMed PubMed Central

Ormazabal, A., Casado, M., Molero-Luis, M., Montoya, J., Rahman, S., Aylett, S.-B., Hargreaves, I., Heales, S., and Artuch, R. (2015). Can folic acid have a role in mitochondrial disorders? Drug Discov. Today 20: 1349–1354, https://doi.org/10.1016/j.drudis.2015.07.002.Search in Google Scholar PubMed

Osellame, L.D., Blacker, T.S., and Duchen, M.R. (2012). Cellular and molecular mechanisms of mitochondrial function. Best Pract. Res. Clin. Endocrinol. Metabol. 26: 711–723, https://doi.org/10.1016/j.beem.2012.05.003.Search in Google Scholar PubMed PubMed Central

Pagliuso, A., Cossart, P., and Stavru, F. (2018). The ever-growing complexity of the mitochondrial fission machinery. Cell. Mol. Life Sci. 75: 355–374, https://doi.org/10.1007/s00018-017-2603-0.Search in Google Scholar PubMed PubMed Central

Panchal, K. and Tiwari, A.K. (2019). Mitochondrial dynamics, a key executioner in neurodegenerative diseases. Mitochondrion 47: 151–173, https://doi.org/10.1016/j.mito.2018.11.002.Search in Google Scholar PubMed

Panda, S., Behera, S., Alam, M.F., and Syed, G.H. (2021). Endoplasmic reticulum & mitochondrial calcium homeostasis: the interplay with viruses. Mitochondrion 58: 227–242, https://doi.org/10.1016/j.mito.2021.03.008.Search in Google Scholar PubMed PubMed Central

Patel, P.K., Shirihai, O., and Huang, K.C. (2013). Optimal dynamics for quality control in spatially distributed mitochondrial networks. PLoS Comput. Biol. 9: e1003108, https://doi.org/10.1371/journal.pcbi.1003108.Search in Google Scholar PubMed PubMed Central

Petridou, N.I., Spiro, Z., and Heisenberg, C.P. (2017). Multiscale force sensing in development. Nat. Cell Biol. 19: 581–588, https://doi.org/10.1038/ncb3524.Search in Google Scholar PubMed

Polo, C.C., Fonseca-Alaniz, M.H., Chen, J.H., Ekman, A., McDermott, G., Meneau, F., Krieger, J.E., and Miyakawa, A.A. (2020). Three-dimensional imaging of mitochondrial cristae complexity using cryo-soft X-ray tomography. Sci. Rep. 10: 21045, https://doi.org/10.1038/s41598-020-78150-3.Search in Google Scholar

Qi, H., Li, L., and Shuai, J. (2015). Optimal microdomain crosstalk between endoplasmic reticulum and mitochondria for Ca2+ oscillations. Sci. Rep. 5: 7984, https://doi.org/10.1038/srep07984.Search in Google Scholar

Quintana-Cabrera, R., Mehrotra, A., Rigoni, G., and Soriano, M.E. (2018). Who and how in the regulation of mitochondrial cristae shape and function. Biochem. Biophys. Res. Commun. 500: 94–101, https://doi.org/10.1016/j.bbrc.2017.04.088.Search in Google Scholar

Racay, P. (2008). Effect of magnesium on calcium-induced depolarisation of mitochondrial transmembrane potential. Cell Biol. Int. 32: 136–145, https://doi.org/10.1016/j.cellbi.2007.08.024.Search in Google Scholar

Raffaello, A., Mammucari, C., Gherardi, G., and Rizzuto, R. (2016). Calcium at the center of cell signaling: interplay between endoplasmic reticulum, mitochondria, and lysosomes. Trends Biochem. Sci. 41: 1035–1049, https://doi.org/10.1016/j.tibs.2016.09.001.Search in Google Scholar

Rampelt, H., Zerbes, R.M., van der Laan, M., and Pfanner, N. (2017). Role of the mitochondrial contact site and cristae organizing system in membrane architecture and dynamics. Biochim. Biophys. Acta Mol. Cell Res. 1864: 737–746, https://doi.org/10.1016/j.bbamcr.2016.05.020.Search in Google Scholar

Ramsay, D.S. and Woods, S.C. (2014). Clarifying the roles of homeostasis and allostasis in physiological regulation. Psychol. Rev. 121: 225–247, https://doi.org/10.1037/a0035942.Search in Google Scholar

Raven, J.A. (2021). Determinants, and implications, of the shape and size of thylakoids and cristae. J. Plant Physiol. 257: 153342, https://doi.org/10.1016/j.jplph.2020.153342.Search in Google Scholar

Reddy, J.N. (2017). Energy principles and variational methods in applied mechanics, 3rd ed. New York: John Wiley & Sons, Incorporated.Search in Google Scholar

Renken, C., Siragusa, G., Perkins, G., Washington, L., Nulton, J., Salamon, P., and Frey, T.G. (2002). A thermodynamic model describing the nature of the crista junction: a structural motif in the mitochondrion. J. Struct. Biol. 138: 137–144, https://doi.org/10.1016/s1047-8477(02)00012-6.Search in Google Scholar

Roberts, R.C. (2017). Postmortem studies on mitochondria in schizophrenia. Schizophr. Res. 187: 17–25, https://doi.org/10.1016/j.schres.2017.01.056.Search in Google Scholar PubMed PubMed Central

Rossi, M.J. and Pekkurnaz, G. (2019). Powerhouse of the mind: mitochondrial plasticity at the synapse. Curr. Opin. Neurobiol. 57: 149–155, https://doi.org/10.1016/j.conb.2019.02.001.Search in Google Scholar

Saa, A. and Siqueira, K.M. (2013). Modeling the ATP production in mitochondria. Bull. Math. Biol. 75: 1636–1651, https://doi.org/10.1007/s11538-013-9862-1.Search in Google Scholar

Schechter, R.S. (1967). The variational method in engineering. New York: McGraw-Hill.Search in Google Scholar

Schmiedel, J., Jackson, S., Schafer, J., and Reichmann, H. (2003). Mitochondrial cytopathies. J. Neurol. 250: 267–277, https://doi.org/10.1007/s00415-003-0978-3.Search in Google Scholar

Schuetz, R., Kuepfer, L., and Sauer, U. (2007). Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol. 3: 119, https://doi.org/10.1038/msb4100162.Search in Google Scholar

Schwarz, T.L. (2013). Mitochondrial trafficking in neurons. Cold Spring Harbor Perspect. Biol. 5, https://doi.org/10.1101/cshperspect.a011304.Search in Google Scholar

Segawa, M., Wolf, D.M., Hultgren, N.W., Williams, D.S., van der Bliek, A.M., Shackelford, D.B., Liesa, M., and Shirihai, O.S. (2020). Quantification of cristae architecture reveals time-dependent characteristics of individual mitochondria. Life Sci. Alliance 3, https://doi.org/10.26508/lsa.201900620.Search in Google Scholar

Shaughnessy, D.T., McAllister, K., Worth, L., Haugen, A.C., Meyer, J.N., Domann, F.E., Van Houten, B., Mostoslavsky, R., Bultman, S.J., Baccarelli, A.A., et al.. (2014). Mitochondria, energetics, epigenetics, and cellular responses to stress. Environ. Health Perspect. 122: 1271–1278, https://doi.org/10.1289/ehp.1408418.Search in Google Scholar

Simcox, E.M. and Reeve, A.K. (2016). An introduction to mitochondria, their structure and functions. In: Mitochondrial dysfunction in neurodegenerative disorders. Springer International Publishing, Switzerland, pp. 3–30.10.1007/978-3-319-28637-2_1Search in Google Scholar

Singh, S., Singh, T.G., Rehni, A.K., Sharma, V., Singh, M., and Kaur, R. (2021). Reviving mitochondrial bioenergetics: a relevant approach in epilepsy. Mitochondrion 58: 213–226, https://doi.org/10.1016/j.mito.2021.03.009.Search in Google Scholar

Skulachev, V.P. (2001). Mitochondrial filaments and clusters as intracellular power transmitting cables. Trends Biochem. Sci. 26: 23–29, https://doi.org/10.1016/s0968-0004(00)01735-7.Search in Google Scholar

Spagnuolo, M. and Andreaus, U. (2018). A targeted review on large deformations of planar elastic beams: extensibility, distributed loads, buckling and post-buckling. Math. Mech. Solid 24: 258–280, https://doi.org/10.1177/1081286517737000.Search in Google Scholar

Stear, E.B. (1973). Systems theory aspects of physiological systems. IFAC Proc. Vol. 6: 496–500, https://doi.org/10.1016/s1474-6670(17)68074-1.Search in Google Scholar

Stephan, T., Bruser, C., Deckers, M., Steyer, A.M., Balzarotti, F., Barbot, M., Behr, T.S., Heim, G., Hubner, W., Ilgen, P., et al.. (2020). MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation. EMBO J. 39: e104105, https://doi.org/10.15252/embj.2019104105.Search in Google Scholar PubMed PubMed Central

Stroud, D.A., Oeljeklaus, S., Wiese, S., Bohnert, M., Lewandrowski, U., Sickmann, A., Guiard, B., van der Laan, M., Warscheid, B., and Wiedemann, N. (2011). Composition and topology of the endoplasmic reticulum-mitochondria encounter structure. J. Mol. Biol. 413: 743–750, https://doi.org/10.1016/j.jmb.2011.09.012.Search in Google Scholar PubMed

Sutherland, W.J. (2005). The best solution. Nature 435: 569, https://doi.org/10.1038/435569a.Search in Google Scholar PubMed

Takeuchi, A. and Matsuoka, S. (2020). Integration of mitochondrial energetics in heart with mathematical modelling. J. Physiol. 598: 1443–1457, https://doi.org/10.1113/jp276817.Search in Google Scholar PubMed

Tauchert, T.R. (1974). Energy principles in structural mechanics. New York: McGraw-Hill.Search in Google Scholar

Tee, S.Y., Bausch, A.R., and Janmey, P.A. (2009). The mechanical cell. Curr. Biol. 19: R745–R748, https://doi.org/10.1016/j.cub.2009.06.034.Search in Google Scholar PubMed PubMed Central

Tyler, W.J. (2012). The mechanobiology of brain function. Nat. Rev. Neurosci. 13: 867–878, https://doi.org/10.1038/nrn3383.Search in Google Scholar PubMed

Tzameli, I. (2012). The evolving role of mitochondria in metabolism. Trends Endocrinol. Metabol. 23: 417–419, https://doi.org/10.1016/j.tem.2012.07.008.Search in Google Scholar PubMed

Vakifahmetoglu-Norberg, H., Ouchida, A.T., and Norberg, E. (2017). The role of mitochondria in metabolism and cell death. Biochem. Biophys. Res. Commun. 482: 426–431, https://doi.org/10.1016/j.bbrc.2016.11.088.Search in Google Scholar PubMed

van der Bliek, A.M., Shen, Q., and Kawajiri, S. (2013). Mechanisms of mitochondrial fission and fusion. Cold Spring Harbor Perspect. Biol. 5, https://doi.org/10.1101/cshperspect.a011072.Search in Google Scholar PubMed PubMed Central

van der Laan, M., Bohnert, M., Wiedemann, N., and Pfanner, N. (2012). Role of MINOS in mitochondrial membrane architecture and biogenesis. Trends Cell Biol. 22: 185–192, https://doi.org/10.1016/j.tcb.2012.01.004.Search in Google Scholar PubMed

Vanhauwaert, R., Bharat, V., and Wang, X. (2019). Surveillance and transportation of mitochondria in neurons. Curr. Opin. Neurobiol. 57: 87–93, https://doi.org/10.1016/j.conb.2019.01.015.Search in Google Scholar PubMed

Venkateswaran, N., Sekhar, S., Thirupatchur Sanjayasarathy, T., Krishnan, S.N., Kabaleeswaran, D.K., Ramanathan, S., Narayanasamy, N., Jagathrakshakan, S.S., and Vignesh, S.R. (2012). Energetics based spike generation of a single neuron: simulation results and analysis. Front. Neuroenerget. 4: 2, https://doi.org/10.3389/fnene.2012.00002.Search in Google Scholar PubMed PubMed Central

Vinogradskaya, I.S., Kuznetsova, T.G., and Suprunenko, E.A. (2014). Mitochondrial network of skeletal muscle fiber, 69. Moscow University Biological Sciences Bulletin, Moscow, pp. 57–66.10.3103/S009639251402014XSearch in Google Scholar

Wai, T. and Langer, T. (2016). Mitochondrial dynamics and metabolic regulation. Trends Endocrinol. Metabol. 27: 105–117, https://doi.org/10.1016/j.tem.2015.12.001.Search in Google Scholar PubMed

Wallace, D.C. (2005). A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine. Annu. Rev. Genet. 39: 359–407, https://doi.org/10.1146/annurev.genet.39.110304.095751.Search in Google Scholar PubMed PubMed Central

Wang, Q., Qian, W., Xu, X., Bajpai, A., Guan, K., Zhang, Z., Chen, R., Flamini, V., and Chen, W. (2019). Energy-mediated machinery drives cellular mechanical allostasis. Adv. Mater. 31: e1900453, https://doi.org/10.1002/adma.201900453.Search in Google Scholar PubMed

Wang, Y., Zhang, X.S., and Chen, L. (2010). Optimization meets systems biology. BMC Syst. Biol. 4(Suppl. 2): S1, https://doi.org/10.1186/1752-0509-4-S2-S1.Search in Google Scholar PubMed PubMed Central

Westermann, B. (2010). Mitochondrial fusion and fission in cell life and death. Nat. Rev. Mol. Cell Biol. 11: 872–884, https://doi.org/10.1038/nrm3013.Search in Google Scholar PubMed

Westermann, B. (2012). Bioenergetic role of mitochondrial fusion and fission. Biochim. Biophys. Acta 1817: 1833–1838, https://doi.org/10.1016/j.bbabio.2012.02.033.Search in Google Scholar

Wilson, E.L. and Metzakopian, E. (2021). ER-mitochondria contact sites in neurodegeneration: genetic screening approaches to investigate novel disease mechanisms. Cell Death Differ. 28: 1804–1821, https://doi.org/10.1038/s41418-020-00705-8.Search in Google Scholar

Wolf, D.M., Segawa, M., Kondadi, A.K., Anand, R., Bailey, S.T., Reichert, A.S., van der Bliek, A.M., Shackelford, D.B., Liesa, M., and Shirihai, O.S. (2019). Individual cristae within the same mitochondrion display different membrane potentials and are functionally independent. EMBO J. 38: e101056, https://doi.org/10.15252/embj.2018101056.Search in Google Scholar

Wolf, F.I., Torsello, A., Fasanella, S., and Cittadini, A. (2003). Cell physiology of magnesium. Mol. Aspect. Med. 24: 11–26, https://doi.org/10.1016/s0098-2997(02)00088-2.Search in Google Scholar

Wolkenhauer, O. and Mesarovic, M. (2005). Feedback dynamics and cell function: why systems biology is called Systems Biology. Mol. Biosyst. 1: 14–16, https://doi.org/10.1039/b502088n.Search in Google Scholar PubMed

Wolkenhauer, O., Ullah, M., Wellstead, P., and Cho, K.H. (2005). The dynamic systems approach to control and regulation of intracellular networks. FEBS Lett. 579: 1846–1853, https://doi.org/10.1016/j.febslet.2005.02.008.Search in Google Scholar PubMed

Yang, X., Heinemann, M., Howard, J., Huber, G., Iyer-Biswas, S., Le Treut, G., Lynch, M., Montooth, K.L., Needleman, D.J., Pigolotti, S., et al. (2021). Physical bioenergetics: energy fluxes, budgets, and constraints in cells. Proc. Natl. Acad. Sci. U. S. A. 118, https://doi.org/10.1073/pnas.2026786118.Search in Google Scholar PubMed PubMed Central

Youle, R.J. and Van Der Bliek, A.M. (2012). Mitochondrial fission, fusion, and stress. Science 337: 1062–1065, https://doi.org/10.1126/science.1219855.Search in Google Scholar PubMed PubMed Central

Yu, S.B. and Pekkurnaz, G. (2018). Mechanisms orchestrating mitochondrial dynamics for energy homeostasis. J. Mol. Biol. 430: 3922–3941, https://doi.org/10.1016/j.jmb.2018.07.027.Search in Google Scholar PubMed PubMed Central

Zhang, L., Trushin, S., Christensen, T.A., Bachmeier, B.V., Gateno, B., Schroeder, A., Yao, J., Itoh, K., Sesaki, H., Poon, W.W., et al. (2016). Altered brain energetics induces mitochondrial fission arrest in Alzheimer’s disease. Sci. Rep. 6: 18725, https://doi.org/10.1038/srep18725.Search in Google Scholar PubMed PubMed Central

Zhong-can, O.Y. and Helfrich, W. (1989). Bending energy of vesicle membranes: general expressions for the first, second, and third variation of the shape energy and applications to spheres and cylinders. Phys. Rev. A Gen. Phys. 39: 5280–5288, https://doi.org/10.1103/physreva.39.5280.Search in Google Scholar PubMed

Zick, M. and Reichert, A.S. (Eds.) (2011). Mitochondria in cellular domains. John Wiley & Sons, New York.10.1002/9781118015759.ch6Search in Google Scholar

Zorov, D.B., Isaev, N.K., Plotnikov, E.Y., Silachev, D.N., Zorova, L.D., Pevzner, I.B., Morosanova, M.A., Jankauskas, S.S., Zorov, S.D., and Babenko, V.A. (2013). Perspectives of mitochondrial medicine. Biochemistry 78: 979–990, https://doi.org/10.1134/s0006297913090034.Search in Google Scholar