Molecular Creation (logo) A Story of Natural Molecular Evolution from Atoms and Water to the living Cell




1.    E. Schrodinger, What is Life? with Mind and Matter (Cambridge University Press, 1944 and 1967).

2.    J. D. Watson, The Double Helix (A Signet Book, The New American Library, 1968).

3.    M. F. Chaplin, Nature Rev. Mol. Cell Biol. 7: 861-866 (2006). Do we underestimate the importance of water in cell biology? See also, N. R. Pace, Cell 65: 531-534 (1991). Origin of Life – Facing up to the physical setting. Also, J. Glanz, Science 276: 505 (1997). Cell Biology: Force-Carrying Web Pervades Living Cells. Also, A. Kaufmann, The Origins of Order: Self Organization and Selection in Evolution. (Oxford University Press, Inc., 1992). Also, P. Ball, Chem. Rev. 108(1): 74 (2008). Water as an active constituent in cell biology.

4.   H. E. Stanley et al. J. Phys. Condens. Matter 21(50): 504105-504118 (2009). Heterogeneities in Confined Water and Protein Hydration Water. Also, P. Gallo et al. Chem. Reviews 116: 7463-7500 (2016). Water: A Tale of Two Liquids.

 5.    H. S. Frank, Science 169: 635 (1970). The Structure of Ordinary Water. See also, F. Franks (ed.) Water – A Comprehensive Treatise. (Plenum, 1972). Also, D. Eisenberg and W. Kauzmann, Structure and Properties of Water. (Oxford University Press, 1969). Also, D. P. Stevenson, Structural Chemistry and Molecular Biology. (Freeman, 1968).  Also, P. G. Kosolik and I. M. Svishchev, Science 265: 1219 (1994). Spatial Structure in Liquid Water.  Also, N. Vinogradov and R. H. Linnell, Hydrogen Bonding (Van Nostrand Reinhold, 1971).

 6.    E. D. Isaacs, et al., Physical Rev. Letters 82(3): 600 (1999). Covalency of the Hydrogen Bond in Ice: A Direct X-Ray Measurement.  See also, J. Grdadolnik, F. Merzel and F. Avbelj, Proc. Natl. Acad. Sci. USA 114(2): 322-327 (2017). Origin of hydrophobicity and enhanced hydrogen bond strength near hydrophobic surfaces. (Covalent hydrogen-bonding in water adjacent to hydrophobic surfaces.)

 7.    C. Y. Lee, J. A. McCammon and P. J. Rossky, J. Chem. Phys. 80(9): 4448 (1984). The structure of liquid water at extended hydrophobic surfaces. Also, L. F. Scatena, M. G. Brown, and G. L. Richmond, Science 292: 908-9125 (2001). Water at hydrophobic surfaces: Weak Hydrogen Bonding and Strong Orientational Effects. See also, J. M. Rogers and J. D. Weeks, Proc. Nat. Acad. Sci. USA, 105(49): 19136-19141 (2008). Interplay of Local Hydrogen-Bonding and Long-Ranged Dipolar Forces in Simulations of Confined Water.

 8.    A. J. Patel, P. Varilly, S. N. Jamadagni, M. F. Hagan, D. Chandler and S. Garde,  J. Phys. Chem. B 116(8): 2498 (2012). Sitting on the Edge: How Biomolecules use Hydrophobicity to Tune their Interactions and Functions. See also, D. Chandler, Nature 437: 640 (2005). Interfaces and the Driving Force of Hydrophobic Assembly.  Also, B. J. Berne, J. D. Weeks and R. Zhou. Ann. Rev. Phys. Chem. 60: 85-103 (2009). Dewetting and Hydrophobic Interaction in Physical and Biological Systems.  Also, S-Y. Sheu and D-Y. Yang. J. Phys. Chem. 114(49): 16558-16566 (2010). Determination of Protein Surface Hydration Shell Free Energy of Water Motion. 

Also, S. Ebbinghaus et. al. Proc. Natl. Acad. Sci. USA 104(52): 20749-20752  (2007). An Extended Dynamic Hydration Shell Around Proteins Also, N. V. Nucci, M. S. Pometun and A. J. Wand, Nature Structural and Site Biology 18: 245-249 (2011). Site-resolved measurement of water-protein interactions by solution NMR. Also, R. L. Baldwin and G. D. Rose, Proc. Natl. Acad. Sci. USA 113(44): 12462-12466 (2016). How the hydrophobic factor drives protein folding.

 9.     H. Eyring and M. S. Jhon, Significant Liquid Structures (John Wiley and Sons. 1969) p.115. The Domain Theory of the Dielectric Constant of H-Bonded Liquids. Theoretical Study and Molecular Dynamics Simulation.

 10.   J. Minbiao M. Odelius and K. J. Gaffney, Science 328: 1003-1005 (2010). Large Angular Jump Mechanism observed for hydrogen-bond exchange in aqueous perchlorate solution. See also, D. Lange and J. T. Hynes, Proc. Nat. Acad. Sci. USA 104: 11167 (2007). Reorientation Dynamics of Water Molecules in Anionic Hydration Shells. Also, J. L. Skinner, Science 328: 985-986 (2010). Following the Motions of Water Molecules in Aqueous Solutions. Also, J. D. Cruzan et. al., Science 271: 59 (1996). Quantifying Hydrogen Bond Cooperativity in Water. Also, N. E. Tuckerman, D. Marx, D. Klein and M. Parrinello, Science 275: 817 (1997).  On the Quantum Nature of the Shared Proton in Hydrogen Bonds.

 11.  J. C. Collins, Biomolecular Evolution from Water to the Molecules of Life. (Molecular Presentations, 2014).

 12.  Y. Zubavicus and M. Grunze, Science 304: 974-976 (2004). New Insights into the Structure of Water with Ultrafast probes. Also, R. Hoyland and L. B. Kier, Theor. Chim. Acta. 15: 1-11 (1969). Molecular orbital calculations for hydrogen-bonded forms of water. See also, J. Del Bene and J. A. Pople, J. Chem. Phys. 52: 48-61 (1970). Theory of Molecular Interactions: Molecular Orbital Studies of Water.

 13.  A. Tokmakoff, Science 317: 54-55 (2007). Shining light on the rapidly-evolving structure of water.

 14.  A. H. Narten and H. A. Levy, Water – A Comprehensive Treatise (Plenum Press,    1972) pp. 311-332. Surface of Liquid Water: Scattering of X-rays.

 15.  M. Fung, Science 190: 800-802 (1975). Orientation of water in striated frog muscle.  See also, J. R. Grigera and H. J. C. Berendsen, Biopolymers 18(1): 47-52 (1978). The molecular detail of collagen hydration. .Also, C. B Anfinsen Science 181: 223-230 (1973). Principles governing the folding of proteins. Also, D. E.Woessner and B. S. Snowden, Jr., Ann. N. Y. Acad. Sci. 204: 113-124  (1973). A pulsed NMR study of dynamics and ordering of water in interfacial systems. Also, J. Bella, B. Brodsky and H. R. Berman, Structure 3(9): 893-906 (1995). Hydration structure of collagen.

 16.   J. L. Ranck, L. Mateu, D. M. Sadler, A. Tardieu, T. Gulik-Krzywicki and V. Luzzati, J. Mol. Biol. 85: 249 (1974). Order-disorder conformational transitions of hydrocarbon chains of lipids.

 17.  R. Lumry and S. Rajender, Biopolymers 9: 1125-1227 (1970). Entropy-Entropy Compensation Phenomena in Water Solutions of Proteins and Small Molecules: A Ubiquitous Property of Water.

 18.  G. E. Joyce, Sci. Am. 260: 90 (1992). Directed Molecular Evolution.  See also, A. C. Wilson, Sci. Amer. 253: 164 (1985). The molecular basis of evolution.  Also, G. W. Robinson and C. H. Cho, Biophys. J. 77: 3311-3318 (1999). The Role of Water in Protein Unfolding.

 19.  C. A. Chatzidimitriou-Dreismann et al., Physical Review Letters, 1 August (2003).  See also, F. Sanders, Discover, Nov. 10, 2003. Where is the H in H20? Also, C. A. Chatzidimitriou-Dreismann, Physica. B. 385(1): 1 (2006). Attosecond Quantum Entanglement in Neutron Compton Scattering from Water in the KeV Range.

 20.   E. Schrodinger, Math. Proc. of the Cambridge Phil. Soc. 31(04): 555 (1935). Discussion of the probability relations between separate systems.

 21.   J. V. Howarth, R. D. Keynes and J. M. Ritchie, J. Physiol. 194: 745 (1968). Heat released from nerve membrane during depolarization. See also, D.–G. Margineau and E. Schoffeniels, Proc. Natl. Acad. Sci. USA 74(9): 3810-3812 (1977). Molecular events and energy changes during the action potential.  Also, L. B. Cohen, B. Hille and R. D. Keynes, J. Physiol. 211: 495 (1970). Increased order in nerve membrane depolarization. Also, D. Debanne, E. Campanac, D. Bialowas, E. Carlier and G. Alcaraz, Physiological Reviews 91(2): 555 (2011). Axon Physiology. Also, M. Prats, J. Teissie and J. Tocanne, Letters to Nature 322: 756 (1986). Lateral proton conduction at lipid-water interfaces.

 22.  Butlerow, Ann. 120: 295 (1861). Sugars from formaldehyde.

 23.  J. U. Neff , Ann. 403: 204-383 (1914). Dissociation Processes in the Sugar Group. Part 3. Also, C. R. Nollar, Chemistry of Organic Compounds (W. B. Saunders Company, 1951). p. 218 and 354

 24.  D. C. Youvan and B. L. Mars, Sci. Amer. 256: 42-48 (1987). Molecular Mechanisms of Photosynthesis.

 25.  A. Szent-Gyorgi, The living State (Academic Press, 1972).

 26.   Mayer and A. Hallbrucker, Nature 325: 601 (1987). Cubic ice from liquid water.  See also, A. K. Soper, Science 297: 1288 (2002). Water and Ice.

 27.  B. Kamb, Structural Chemistry and Molecular Biology, (Freeman, 1968) pp. 507-542. Ice Polymorphism and the Structure of Water.

 28.  D-S. Yang and A.H. Zewail, Proc. Nat. Acad. Sci. USA 106(11): 4122-4126 (2009). Ordered water structure at hydrophobic graphite interfaces observed by 4D ultrafast electron crystallography. Also, C-Y. Ruan, V. A. Lobastov, F. Vigliotti, S. Chen and A. H. Zewail, Science 304: 80-84 (2004). Ultrafast Electron Crystallography of Interfacial Water.

 29.  J. C. Collins, The Matrix of Life. (Molecular Presentations, 1991). See also, E. J. Ariens, Molecular Pharmacology (Academic Press, New York, 1964). See also, L. B. Kier, Molecular Orbital Theory in Drug Research (Academic Press, New York, 1965). Also, K. J. Brunings and P. Lindgren (eds.) Modern Concepts in the Relationship between Structure and Pharmacological Activity (MacMillan, 1971).

 30.  T. L. Blundell, J. F.  Cutfield, S. M. Cutfield, E. K. Dodson, G. G. Dodson, G. G. Hodgkin, D. A. Mercola and M. Vijayan, Nature 231: 506 (1971). Atomic positions in rhombahedral 2-zinc insulin crystals.

 31.  C. W. Ward and M. C. Lawrence, BioEssays 31(4): 422 (2009). Ligand-induced    activation of the insulin receptor.

 32.  E. Conway, Ann. Rev. Phys. Chem. 17: 481 (1966). Electrolyte Solutions: Solvation and Structural Effects.  See also, P. M. Wiggins, J. Theor. Biol. 32: 131 (1971). Water structure as a determinant of ion distribution in living tissue. Also, C. F. Hazelwood, (ed.) Ann. N.Y. Acad. Sci. 204 (1973). Physicochemical state of ions and water in living tissues and model systems. Also, B. Hribar, N. T. Southhall, V. Vlachy and K. A. Dill, J. Am. Chem. Soc. 124: 12302-12311 (2004). How ions affect the structure of water.

 33.   O. F. Mohammed, D. Pines, J. Dreyer, E. Pines and E. T. J. Nibbering, Science 310:  83 (2005). Sequential Proton Transfer through Bridges in Acid-Base Reactions. See also, M. G. Brown, J. G. Loeser and R. J. Saykally, Science 271: 59 (1996). Quantifying Hydrogen-bond Cooperativity in Water.  Also, A. J. Horsewell, N. H. Jones and R. Caciuffo, Science 291: 100 (2001). Evidence for coherent proton tunneling in a hydrogen bond network. Also, J. Lin, H. A. Balabin and D. H. Beratan, Science 310: 1311 (2005). The Nature of Aqueous Tunneling Pathways.  Also, H. J. Bakker and H.-K. Niehuys, Science 297: 587 (2002). Delocalization of Protons in Liquid Water. See also, B. Weber et. al., Science 335: 64 (2012). Ohm’s Law Survives at the Atomic Scale. Also, E. Frier, S. Wolf and K. Gerwert, Proc. Nat. Acad. Sci. USA 108(28): 11435-11439 (2011). Proton transfer via transient linear water-molecule chain in membrane protein.

 34.  S. H. Kim, Advan. Enzymol. 246: 279 (1978). Three-dimensional structure of transfer RNA and its functional implications.

 35.   M. A. Rould, J. J. Perona, D. Soll and T. A. Steitz, Science 246: 1135-1142 (1989). Structure of E. coli glutamyl-tRNA sythetase complexed with tRNAgln and ATP.

 36.  N. Sharon, Sci. Amer. 245(5): 90-93 (1980). Carbohydrates. See also, D. A. Rees, Polysaccharide Shapes (Wiley, 1977).

 37.  G. O. Phillips, Chem. in Brit. 1006 (1989). Rediscovering Cellulose.

 38.  J. M. Harvey, M. C. R. Symons and R. J. Naftalin, Nature 261: 435 (1976). Proton magnetic resonance study of the hydration of glucose.

 39.  R. H. Marchessault and P. R. Sundararajan, Adv. in Carb. Chem. and Biochem. 33: 387 1976). Molecular complexes in starch.

 40.  B. H. Patel, C. Percivalle, D. J. Ritso, C. D. Duffy and J. D. Sutherland, Nature Chemistry 7: 301-307 (2015). Common origins of RNA, protein and lipid precursors in cyanosulfidic protometabolism. See also, R. F. Service, Science 347: 1298 (2015). Origin-Of-Life puzzle cracked.

 41.  T. Kulakovskaya, Biochem. and Physiology 1(2): 107 (2012). Inorganic Pyrophosphates: Jack Of All Trades.

 42.  O. Kennard et al., Proc. Royal Soc. London 325: 401 (1971). The crystal and Molecular Structure of Adenosine Triphosphate. Also, R. J. P. Williams, Eur. J. Biochem. 57: 135 (1975). Quantitative determination of the conformation of ATP in aqueous solution.

 43   T. R. Cech, Sci. Amer. 255(5): 6465 (1986). RNA as an Enzyme.

 44.  G. Wachtershauser, Proc. Natl. Acad. Sci. USA 87(1): 200-204 (1990). Evolution of the First Metabolic Cycles.

 45.  R. Hernandez and J. A. Piccirilli, Nature Chemistry 5: 360-362 (2013). Chemical origins of life: Prebiotic RNA unstruck.

 46.  M. Illangasekare, G. Sanchez, T. Nickles and M. Yarus, Science 267: 643 (1995).   Aminoacyl-t-RNA synthesis catalyzed by a ribonucleic acid.

 47.  R. Benne and P. Sloof, Biosystems 21(1): 51-68 (1987). Evolution of the mitochondrial protein synthetic machinery.

 48.   P. Y. Chou and G. D. Fasman, Biochemistry 13: 222 (1974). Prediction of protein conformation.

 49.  L. Pauling, R. B. Corey and H. R. Branson, Proc. Natl. Acad. Sci. USA 37: 205-211  (1951). The Structure of Proteins. Two Hydrogen-bonded Helical Configurations of Polypeptide Chain. See also, L. Pauling and R. B. Corey, Proc. Natl. Acad. Sci. USA 37: 251-256 (1951). The Pleated Sheet. A New Layer Configuration of Polypeptide Chains.

 50.  S. L. Miller and L. E. Orgel, The Origins of Life on Earth (Prentice-Hall, Englewood Cliffs, NJ, 1974).  See also, D. J. Brooks, J. R. Fresco, A. M. Lesk and M. Singh, Mol. Biol. Evol. 19(10): 1645-1655 (202). Evolution of Amino Acids.

 51. A. S. Sprin, Ribosomal Structure and Protein Synthesis (Benjamin-Cummings, 1986).

 52. M. Shtilerman, G. H. Lorimer and S. W. Englander, Science 284: 822-824 (1999). Chaperone Function: Folding by Forced Unfolding.

 53.   F. A. Quiocho and W. N. Lipscomb, Adv. In Protein Chem. 25: 1 (1971). Carboxypeptidase A. See also, W. N. Lipscomb, Ann. Rev. Biochem. 52: 17 (1983). Structure and Catalysis of Carboxypeptidase A.

 54.  W. N. Lipscomb, Proc. Robert A. Welch Fund. Conf. Chem. Res. 15: 140-141 (1971). Catalysis of Carboxypeptidase A.

 55.  J. D. Watson and F. H. C. Crick, Nature 171: 737-738 (1953). Molecular structure of nucleic acid. A structure of deoxyribonucleic acid.  See also, R. Franklin and R. G. Gosling, Nature 171: 740-741 (1953). Molecular Configuration in Sodium Thymonucleate.

 56. B. Gu, F. S. Zhang, Z. P. Wang and H. Y. Zhou, Phys, Rev. Lett. 100: 88104 (2008).   Solvent-induced DNA conformational transition.  See also, W. Fuller, T. Forsyth and A. Mahendrasingam, Phil. Trans. R. Soc. Lond. B259: 1237-1248 (2004). Water- DNA Interactions as studied by X-ray and neutron fiber diffraction.  Also, P. Auffinger and E. Westhof, J. Mol. Biol. 268: 118-136 (1997). Water and Ion Binding around RNA and DNA.  Also, V. Makarov, B. M. Pettitt and M. Feig, Acc. Chem. Res. 35: 376-384 (2002). Solvation and hydration of proteins and nucleic acids: A Theoretical simulation and experiment. Also, S. Pal, P. K. Maiti and B. Bagchi, J. Phys.: Condens. Matter 17: S4317-S4331 (2005). Anisotropic and sub-diffusive water motion at the surface of DNA.  Also, S. K. Pal, L. Zhao, T. Xia and A. H. Zewail, Proc. Nat. Acad. Sci. USA 140(24): 13746 (2003). Ultrafast Hydration of DNA.

57.  B. Alberts, Molecular Biology of the Cell (Garland Science, New York, 2002).

 58.  D. J. Hanahan, Lipid Chemistry (John Wiley and Sons Inc. New York and London, 1960).

59.  M. S. Bretscher, Sci. Amer. 253(4): 100-108 (1985). The Molecules of the Cell Membrane. J. K. Wright, R. Seckler, and P. Overath, Ann. Res. Biochem. 55: 225-148 (1986).  Molecular aspects of sugar ion cotransport. 

60.  S. J. Singer and G. L. Nicolson, Science 175: 720-731 (1972). The fluid mosaic model of the structure of cell membranes. See also, D. Chapman and D. F. H. Wallach (eds.) Biological Membranes (Academic Press, New York, 1973). Also, D. E. Green (eds.) Annal. N. Y. Acad. Sci. 195 (1975). Biological Membrane Structure and Function.

61. G. Lagaly, Angew. Chem. Int. Ed. Engl. 15: 575-580 (1976). Kink-block and gauche-block structures of biomolecular films.  See also, S. J. Opella, J. P. Yesinowski and J. S. Waugh, Proc. Natl. Acad. Sci. USA 73(11): 3812 (1976). NMR description of molecular motion and phase separations of cholesterol in lecithin dispersions.  Also, P. T. Inglefield, K. A. Lindblom and A. M. Gottlieb, Biocimica et Biophysica Acta water lamellar phase.  Also, G. L. Jandrasiak and J. C. Mendible,  Biochimica. et Biophysica Acta. 424: 149 (1976). The Phospholipid Head-Group Orientation: Effect on Hydration and Electrical Conductance.

62. D. Eisenberg, Ann. Rev. Biochem. 53: 595-623 (1984). Three-dimensional structure of membrane and surface proteins.

63.  D. L. D. Caspar and D. A. Kirschner, Nature New Biology 231: 46 (1971). Myelin membrane structure at 10A resolution.

64.  N. Unwin, J. Mol. Biol. 346: 967 (2005). Refined structure of nicotinic acetylcholine receptor at 4A resolution.

65. R. Henderson and P. N. T. Unwin, Naure 257: 28-32 (1975). Three-dimensional model of purple membrane.  See also, Z. Zhang, J. Tan, Y. Zhang and F. Liu, Curr. Res. Photosynth. 1: 205 (1990).  Significance of water molecules in keeping the structural integrity of purple membrane.  Also, R. E. Blakenship, Photosynth. Res. 33: 91-111 (1992). Origin and early evolution of photosynthesis.

66. U. W. Junge and D. J. Muller, Science 333: 704-705 (2011). Seeing a Molecular Motor Work.

67. W. R. Nes and M. L. McKean, Biochemistry of Steroids and other Isopentenoids (University Park Press, 1977).

68. R. Breton et al., Protein Sci. 15(5): 987 (2006). Comparison of crystal structures of human androgen receptor ligand-binding domain with various agonist level molecular determinants responsible for bonding affinity.

69. G. N. Ling, C. Miller and M. M. Ochsenfeld, Ann, NY Acad. of Sci. 204: 6-47 (1973).  Physicochemical state of ions and water in living Tissues and Model  Systems.

70. H. E. Huxley, Sci. Amer. 213(6): 18 (1965). The Mechanism of Muscle Contraction.     See also, R. Cooke, Crit. Rev. in Biochem. 21(1): 53 (1986). The Mechanism of Muscle Contraction.

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