http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

When Szent-Gyorgyi called water the “matrix of life”,1 he was echoing an old sentiment. Paracelsus in the 16th century said that “water was the matrix of the world and of all its creatures.”2 But Paracelsus’s notion of a matrixsan active substance imbued with fecund, life-giving propertiess was quite different from the picture that, until very recently, molecular biologists have tended to hold of water’s role in the chemistry of life. Although acknowledging that liquid water has some unusual and important physical and chemical propertiessits potency as a solvent, its ability to form hydrogen bonds, its amphoteric naturesbiologists have regarded it essentially as the backdrop on which life’s molecular components are arrayed. It used to be common practice, for example, to perform computer simulations of biomolecules in a vacuum. Partly this was because the computational intensity of simulating a polypeptide chain was challenging even without accounting for solvent molecules too, but it also reflected the prevailing notion that water does little more than temper or moderate the basic physicochemical interactions responsible for molecular biology. What Gerstein and Levitt said 9 years ago remains true today: “When scientists publish models of biological molecules in journals, they usually draw their models in bright colors and place them against a plain, black background”.3 Curiously, this neglect of water as an active component of the cell went hand in hand with the assumption that life could not exist without it. That was basically an empirical conclusion derived from our experience of life on Earth: environments without liquid water cannot sustain life, and special strategies are needed to cope with situations in which, because of extremes of either heat or cold, the liquid is scarce.4-6 The recent confirmation that there is at least one world rich in organic molecules on which rivers and perhaps shallow seas or bogs are filled with nonaqueous fluidsthe liquid hydrocarbons of Titan7smight now bring some focus, even urgency, to the question of whether water is indeed a * E-mail: p.ball@nature.com. Philip Ball is a science writer and a consultant editor for Nature, where he worked as an editor for physical sciences for more than 10 years. He holds a Ph.D. in physics from the University of Bristol, where he worked on the statistical mechanics of phase transitions in the liquid state. His book H2O: A Biography of Water (Weidenfeld & Nicolson, 1999) was a survey of the current state of knowledge about the behavior of water in situations ranging from planetary geomorphology to cell biology. He frequently writes about aspects of water science for both the popular and the technical media.

https://www.philipball.co.uk/images/stories/docs/pdf/ChemRev_final.pdf

Water as an Active Constituent in Cell Biology

https://www.cell.com/biophysj/pdf/S0006-3495(97)78780-0.pdf

Stretching DNA with optical tweezers

For many years, DNA gyrase was thought to be responsible both for unlinking replicated daughter chromosomes and for controlling negative superhelical tension in bacterial DNA. However, in 1990 a homolog of gyrase, topoisomerase IV, that had a potent decatenating activity was discovered. It is now clear that topoisomerase IV, rather than gyrase, is responsible for decatenation of interlinked chromosomes. Moreover, topoisomerase IV is a target of the 4-quinolones, antibacterial agents that had previously been thought to target only gyrase. The key event in quinolone action is reversible trapping of gyrase-DNA and topoisomerase IV-DNA complexes. Complex formation with gyrase is followed by a rapid, reversible inhibition of DNA synthesis, cessation of growth, and induction of the SOS response. At higher drug concentrations, cell death occurs as double-strand DNA breaks are released from trapped gyrase and/or topoisomerase IV complexes. Repair of quinolone-induced DNA damage occurs largely via recombination pathways. In many gram-negative bacteria, resistance to moderate levels of quinolone arises from mutation of the gyrase A protein and resistance to high levels of quinolone arises from mutation of a second gyrase and/or topoisomerase IV site. For some gram-positive bacteria, the situation is reversed: primary resistance occurs through changes in topoisomerase IV while gyrase changes give additional resistance. Gyrase is also trapped on DNA by lethal gene products of certain large, low-copy-number plasmids. Thus, quinolone-topoisomerase biology is providing a model for understanding aspects of host-parasite interactions and providing ways to investigate manipulation of the bacterial chromosome by topoisomerases.

DNA gyrase, topoisomerase IV, and the 4-quinolones.

Structure and reactivity of water at biomaterial surfaces

Publisher Summary This chapter focuses on the practical use of osmotic stress (OS) to measure macromolecular forces and chemical potentials. It also reviews several examples of its application. Osmotic stress is applied to a wide set of charged or electrically neutral membranes, to the arrays of muscle protein, to tobacco mosaic virus particles, to ordered arrays of DNA double helices, to sickle cell hemoglobin undergoing polymerization, to the aqueous cavities of water-in-oil liquid crystals, and to ionic channels through bilayer membranes. OS permits ascertaining the properties of boundary water under thermodynamically well-defined conditions. Three equivalent ways in which OS is consistently applied are also discussed in the chapter. The most tedious aspect of OS is getting accurate osmotic pressures of the stressing polymer solutions. The OS measurement of forces between DNA double helices demonstrates the utility of the method for examining an entire class of linear macromolecules, such as collagen triple helices and xanthan polysaccharides.

Osmotic stress for the direct measurement of intermolecular forces.

There has been much confusion recently about the relative merits of different approaches, osmotic stress, preferential interaction, and crowding, to describe the indirect effect of solutes on macromolecular conformations and reactions. To strengthen all interpretations of measurements and to forestall further unnecessary conceptual or linguistic confusion, we show here how the different perspectives all can be reconciled. Our approach is through the Gibbs-Duhem relation, the universal constraint on the number of ways it is possible to change the temperature, pressure, and chemical potentials of the several components in any thermodynamically defined system. From this general Gibbs-Duhem equation, it is possible to see the equivalence of the different perspectives and even to show the precise identity of the more specialized equations that the different approaches use.

https://www.pnas.org/content/pnas/97/8/3987.full.pdf

Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives

Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces.

Publisher Summary This chapter presents specific examples to describe procedures and use osmotic stress with maximum ease and efficiency. These examples are systems where intentionally varied water activity has revealed a connection between different functional states of proteins or other large molecules with different amounts of water associated with them. The method––osmotic stress on macromolecules–– is applied to four kinds of processes, which are (1) ionic channel opening/closing, (2) enzyme/ substrate association and turnover, (3) molecular binding, and (4) longrange interaction. Through these examples, a thermodynamic relations is developed that is useful in the interpretation of osmotic stress data. Osmotic stress experiments, in explicitly recognizing the importance of water activity, are designed to buffer it so that it is as well defined as other more familiar solution variables. Osmotic stress measurements have revealed a surprisingly large influence of water activity on macromolecular reactions and conformational transitions. It even appears that small solutes, typically thought to affect macromolecules only through direct binding, show an indirect effect through their influence on water activity.

Macromolecules and water: probing with osmotic stress.

The oxygen affinity of hemoglobin varies linearly with the chemical potential of water in the bathing medium, as seen from the osmotic effect of several neutral solutes, namely sucrose, stachyose, and two polyethyleneglycols (molecular weights of 150 and 400). The data, analyzed either by Wyman linkage equations or by Gibbs-Duhem relations, show that approximately 60 extra water molecules bind to hemoglobin during the transition from the fully deoxygenated tense (T) state to the fully oxygenated relaxed (R) state. This number, independent of the nature of the solute, agrees with the difference in water-accessible surface areas previously computed for the two conformations. The work of solvation in allosteric regulation can no longer go unrecognized.

https://science.sciencemag.org/content/sci/256/5057/655.full.pdf

Donald C. Rau

Papers

Osmotic stress for the direct measurement of intermolecular forces.

Osmotic stress, crowding, preferential hydration, and binding: A comparison of perspectives

Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces.

Macromolecules and water: probing with osmotic stress.

Protein solvation in allosteric regulation: a water effect on hemoglobin