Abstract
Life-as-we-know-it could not exist without water. In fact, living cells survive in environments mainly constituted by water. Cellular shape and functionality are determined by the presence of both the plasma and the cytoplasmic membrane, which define all the necessary compartments for the organization of the cellular matter, as well as to prevent mixing of the cell with its external environment. To this aim, living organisms typically exploit biological lipids, amphiphile molecules comprising a strongly polar head group and one or more long hydrocarbon tails. In aqueous solutions, these amphiphilic molecules tend to aggregate driven by ’like-to-like’ interactions that are usually referred to as the hydrophobic effect. Within this general framework, water is unique because it forms hydrogen bonds with itself as well as with the polar moiety of the amphiphilic molecule. While this marvelous balance is the result of millions of years of evolution, it is possible to imagine that a different type of life could be achieved in different biological environments under different conditions, such as those present in other planets of our universe. Although water has been detected in various thermodynamic states in our solar system, an alternative scenario suggests the possibility of using polarity-inverted membranes in non-polar solvents, such as the hydrocarbons frequently found in earth-like systems. Motivated by this idea, a number of related studies have recently been conducted. In this contribution, I will describe recent efforts by our group along these lines, as well as the possibility of leveraging on recent achievements of AlphaFold that highlighted the power of data-driven approaches hinging on artificial intelligence/machine learning techniques.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Board, Space Studies and National Academies of Sciences, Engineering, and Medicine and others: An Astrobiology Strategy for the Search for Life in the Universe. National Academies Press (2019)
Malaterre, C., Jeancolas, C., Nghe, P.: The origin of life: what is the question? Astrobiology 22(7), 851–862 (2022)
MultiMedia LLC: NASA Astrobiology Strategy (2015). https://astrobiology.nasa.gov/nai/media/medialibrary/2015/10/NASA_Astrobiology_Strategy_2015_151008.pdf
OoLEN, Asche, S., Bautista, C., Boulesteix, D., Champagne-Ruel, A., Mathis, C., Markovitch, O., Peng, Z., Adams, A., Dass, A.V., Buch, A., Camprubi, E., Colizzi, E.S., Colón-Santos, S., Dromiack, H., Estrova, V., Garcia, A., Grimaud, G., Halpern, A., Harrison, S.A., Jordan, S.F., Jia, T.Z., Kahana, A., Kolchinsky, A., Moron-Garcia, O., Mizuuchi, R., Nan, J., Orlova, Y., Pearce, B.K.D., Paschek, K., Preiner, M., Pinna, S., Rodríguez-Román, E., Schwander, L., Sharma, S., Smith, H.B., Vieira, A., Xavier, J.C.: What it takes to solve the Origin(s) of life: an integrated review of techniques (2023). https://doi.org/10.48550/arXiv.2308.11665
Warren, A.O., Kite, E.S.: Narrow range of early habitable Venus scenarios permitted by modeling of oxygen loss and radiogenic argon degassing. Proc. Natl. Acad. Sci. 120(11), e2209751120 (2023)
Open AI: ChatGPT (2023). https://chat.openai.com/auth/login
Finkelstein, A.V., Ptitsyn, O.: Protein Physics: A Course of Lectures. Elsevier (2016)
Vologodskii, A.: Biophysics of DNA. Cambridge University Press (2015)
Andersen, O.S., Koeppe, R.E.: Bilayer thickness and membrane protein function: an energetic perspective. Annu. Rev. Biophys. Biomol. Struct. 36, 107–130 (2007)
Ball, P.: H2O: A Biography of Water. Hachette UK (2015)
ECLT-NICHE: WATER-The strangest liquid (2022). https://www.unive.it/data/33113/25/57974
Hansen, J.P., McDonald, I.R.: Theory of Simple Liquids: With Applications to Soft Matter. Academic Press (2013)
Tanford, C.: Contribution of hydrophobic interactions to the stability of the globular conformation of proteins. J. Am. Chem. Soc. 84(22), 4240–4247 (1962)
De Gennes, P.G.: Scaling Concepts in Polymer Physics. Cornell University Press (1979)
Flory, P.: Statistical Mechanics of Chain Molecules. Interscience Publishers (1969). https://books.google.it/books?id=EDZRAAAAMAAJ
Journaux, B., Pakhomova, A., Collings, I.E., Petitgirard, S., Boffa Ballaran, T., Brown, J.M., Vance, S.D., Chariton, S., Prakapenka, V.B., Huang, D., et al.: On the identification of hyperhydrated sodium chloride hydrates, stable at icy moon conditions. Proc. Natl. Acad. Sci. 120(9), e2217125120 (2023)
McKay, C.P., Smith, H.D.: Possibilities for methanogenic life in liquid methane on the surface of titan. Icarus 178(1), 274–276 (2005)
Palmer, M.Y., Cordiner, M.A., Nixon, C.A., Charnley, S.B., Teanby, N.A., Kisiel, Z., Irwin, P.G., Mumma, M.J.: ALMA detection and astrobiological potential of vinyl cyanide on titan. Sci. Adv. 3(7), e1700022 (2017)
Liu, K., Zheng, L., Liu, Q., de Vries, J.W., Gerasimov, J.Y., Herrmann, A.: Nucleic acid chemistry in the organic phase: from functionalized oligonucleotides to DNA side chain polymers. J. Am. Chem. Soc. 136(40), 14255–14262 (2014)
Arcella, A., Portella, G., Collepardo-Guevara, R., Chakraborty, D., Wales, D.J., Orozco, M.: Structure and properties of DNA in apolar solvents. J. Phys. Chem. B 118(29), 8540–8548 (2014)
Wolynes, P.G.: Biomolecular folding in vacuo!!!(?). Proc. Natl. Acad. Sci. 92(7), 2426–2427 (1995)
Hartsough, D.S., Merz, K.M., Jr.: Protein dynamics and solvation in aqueous and nonaqueous environments. J. Am. Chem. Soc. 115(15), 6529–6537 (1993)
Nick Pace, C., Trevino, S., Prabhakaran, E., Martin Scholtz, J.: Protein structure, stability and solubility in water and other solvents. Philos. Trans. R. Soc. Lond. Ser. B: Biol. Sci. 359(1448), 1225–1235 (2004)
Soares, C.M., Teixeira, V.H., Baptista, A.M.: Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies. Biophys. J. 84(3), 1628–1641 (2003)
Klibanov, A.M.: Improving enzymes by using them in organic solvents. Nature 409(6817), 241–246 (2001)
Griffiths, T.R., Pugh, D.C.: Correlations among solvent polarity scales, dielectric constant and dipole moment, and a means to reliable predictions of polarity scale values from cu. Coord. Chem. Rev. 29(2), 129–211 (1979). https://doi.org/10.1016/S0010-8545(00)82109-8, www.sciencedirect.com/science/article/pii/S0010854500821098
Hayashi, T., Yasuda, S., Škrbić, T., Giacometti, A., Kinoshita, M.: Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail. J. Chem. Phys. 147(12) (2017)
Roth, R., Harano, Y., Kinoshita, M.: Morphometric approach to the solvation free energy of complex molecules. Phys. Rev. Lett. 97(7), 078101 (2006)
Hayashi, T., Inoue, M., Yasuda, S., Petretto, E., Škrbić, T., Giacometti, A., Kinoshita, M.: Universal effects of solvent species on the stabilized structure of a protein. J. Chem. Phys. 149(4) (2018)
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucl. Acids Res. 28(1), 235–242 (2000)
Bank, P.D.: Protein Data Bank (2023). https://www.rcsb.org/
Carrer, M., Škrbić, T., Bore, S.L., Milano, G., Cascella, M., Giacometti, A.: Can polarity-inverted surfactants self-assemble in nonpolar solvents? J. Phys. Chem. B 124(29), 6448–6458 (2020)
Chaikin, P.M., Lubensky, T.C., Witten, T.A.: Principles of Condensed Matter Physics, vol. 10. Cambridge University Press, Cambridge (1995)
Marrink, S.J., Lindahl, E., Edholm, O., Mark, A.E.: Simulation of the spontaneous aggregation of phospholipids into bilayers. J. Am. Chem. Soc. 123(35), 8638–8639 (2001)
Facchin, M., Scarso, A., Selva, M., Perosa, A., Riello, P.: Towards life in hydrocarbons: aggregation behaviour of “reverse” surfactants in cyclohexane. RSC Adv. 7(25), 15337–15341 (2017)
Dongmo, C.J.F., Carrer, M., Houvet, M., Škrbić, T., Graziano, G., Giacometti, A.: Can the roles of polar and non-polar moieties be reversed in non-polar solvents? Phys. Chem. Chem. Phys. 22(44), 25848–25858 (2020)
Dongmo, C.J.F., Giacometti, A.: Solvent quality and solvent polarity in polypeptides. Phys. Chem. Chem. Phys. 25(6), 4839–4853 (2023)
Rubinstein, M., Colby, R.H.: Polymer Physics (Chemistry). Oxford University Press, 1st edn. (2003). http://amazon.com/o/ASIN/019852059X/
Huang, Y., Cheng, S.: Chain conformations and phase separation in polymer solutions with varying solvent quality. J. Polym. Sci. 59(22), 2819–2831 (2021)
Heidt, A.: Astrobiologists train an AI to find life on mars. Nature (2023)
Warren-Rhodes, K., Cabrol, N.A., Phillips, M., Tebes-Cayo, C., Kalaitzis, F., Ayma, D., Demergasso, C., Chong-Diaz, G., Lee, K., Hinman, N., et al.: Orbit-to-ground framework to decode and predict biosignature patterns in terrestrial analogues. Nat. Astron. 7(4), 406–422 (2023)
Callaway, E.: It will change everything: DeepMind’s AI makes gigantic leap in solving protein structures. Nature 588(7837), 203–205 (2020)
Team, A.: Alphafold: a solution to a 50-year-old grand challenge in biology (2021)
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al.: Highly accurate protein structure prediction with AlphaFold. Nature 596(7873), 583–589 (2021)
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G.R., Wang, J., Cong, Q., Kinch, L.N., Schaeffer, R.D., et al.: Accurate prediction of protein structures and interactions using a three-track neural network. Science 373(6557), 871–876 (2021)
Thorp, H.H.: Proteins, Proteins Everywhere (2021)
Moore, P.B., Hendrickson, W.A., Henderson, R., Brunger, A.T.: The protein-folding problem: not yet solved. Science 375(6580), 507–507 (2022)
Chen, S.J., Hassan, M., Jernigan, R.L., Jia, K., Kihara, D., Kloczkowski, A., Kotelnikov, S., Kozakov, D., Liang, J., Liwo, A., et al.: Protein folds vs. protein folding: differing questions, different challenges. Proc. Natl. Acad. Sci. 120(1), e2214423119 (2023)
AlphaFold, D.M.: AlphaFold Protein Structure Database (2023). https://alphafold.ebi.ac.uk/
Akdel, M., Pires, D.E., Pardo, E.P., Jänes, J., Zalevsky, A.O., Mészáros, B., Bryant, P., Good, L.L., Laskowski, R.A., Pozzati, G., et al.: A structural biology community assessment of alphafold2 applications. Nat. Struct. Mol. Biol. 29(11), 1056–1067 (2022)
Communication, E.: AlphaFold applications—a community assessment (2022). https://www.embl.org/news/science/alphafold-community-applications/
Acknowledgements
The work presented in this contribution has been obtained in collaboration with many collaborators to whom I am very grateful. Many discussions with the members of the European Center for Living Technologies (ECLT) are also greatly acknowledged.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Giacometti, A. (2024). Can Life Exist Without Water? A Data-Driven Approach. In: Cortesi, A. (eds) Space Data Management. Studies in Big Data, vol 141. Springer, Singapore. https://doi.org/10.1007/978-981-97-0041-7_6
Download citation
DOI: https://doi.org/10.1007/978-981-97-0041-7_6
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-97-0040-0
Online ISBN: 978-981-97-0041-7
eBook Packages: Intelligent Technologies and RoboticsIntelligent Technologies and Robotics (R0)