I somehow missed a whole suite of papers in a special issue of PCCP (here) in 2010 on water in biological systems. I stumbled upon it the other day. There is too much there for me to work through every paper � suffice it to say that it covers topics ranging from water in the prebiotic evolution of DNA to water mediation of antifreeze proteins and anaesthetics, and is well worth a look.
The effort to understand hydrophobic attraction has rather overshadowed the study of interactions between hydrophilic surfaces � although, as Roland Netz and colleagues point out (E. Schneck et al., PNAS 109, 14405; 2012 � paper here), the repulsion between such surfaces, balancing out the van der Waals attraction, is ultimately what prevents biological matter from collapsing. This interaction is fairly well characterized for neutral phospholipid bilayers, but also acts between proteins, polysaccharides and nucleic acids, with exponential decay. All the same, the origins of the force, though evidently bound up with hydration, are not well understood. Netz and colleagues study it in this paper using MD simulations of zwitterionic lipid bilayers. Part of the repulsion comes from the reduction in configurational entropy of the head groups, but part is water-mediated and enthalpic, due to the expulsion of water bound to the head groups as the surfaces approach. However, at separations that allow at least 17 water molecules to hydrate each head group, the water-mediated repulsion becomes dominated by an entropic effect due to the alignment of water dipoles: at smaller separations, there is depolarization due to frustration in the dipole orientations of water molecules close to each of the two surfaces. In other words, the repulsive interaction is complex, subtle and finely tuned.
I recently saw Veronica Vaida talk about the catalytic potential of the air-water interface as a hydrophobic environment that can enhance the condensation reaction of peptide bond formation. She and Elizabeth Griffith now offer experimental support for that notion (PNAS 109, 15697; 2012 � paper here). They report IR spectroscopic evidence that leucine, as an ethyl ester, will partition to the air-water interface in a Langmuir trough, coordinate there to copper(II) ions, and undergo condensation to form peptide bonds. The prebiotic implications are clear, offering yet another reason to be interested in what goes on at this ubiquitous interface.
Alfonso De Simone at Imperial College and coworkers have investigated a nice model system for ligand binding in protein cavities: macrocyclic cucurbituril molecules, which bind a variety of hydrophobic guests very strongly (F. Biedermann et al., JACS 134, 15318; 2012 � paper here). Their simulations indicate that release of �high-energy� water in the cavity is a major driving force of binding, being favourable both enthalpically and entropically. I see that a similar conclusion is reached by C. N. Nguyen et al. in J. Chem. Phys. 137, 044101 (2012), a paper I�ve not seen beyond the abstract but which also shows that a high water density can be achieved inside these cavities despite the absence of strong solvent-cavity interactions. The paper is here.
Bob Eisenberg at Rush University and coworkers use a variational theory to probe the energetics of ion flow through protein channels (T.-L. Horng et al., J. Phys. Chem. B 116, 11422; 2012 � paper here). They say that this approach captures the electrostatic interactions that classical theories of such channels tend to ignore in their assumption of ideality of the ionic solutions. Bob�s papers always seem to contain some pungent and pertinent general comments that makes them thought-provoking (and fun) to read, viz.
�Early workers of some reputation in molecular biology, including Nobel Prize winners, attributed the secret of life to allosteric interactions of chemical signals acting on proteins and then channels. It is striking to the biologists among us that a self-consistent model of ions and side chains in channels produces strong interactions over long distances (i.e., more than 1 nm) without invoking the metaphors of vitalistic allostery. The calculations of a self-consistent variational theory of the energetics of complex fluids seem ready to replace the poetry of our ancestors� It is amusing that physicists learned to use self-consistent mathematics to analyze (control and build) complex interacting systems of holes and electrons during the same years that biologists used poetry to describe complex interacting systems of cations and anions� Certainly, a theoretical and computational approach to biology and its molecules must allow everything to interact with everything else, instead of assuming that everything is ideal and nothing interacts with nothing.�
I encountered hyaluronan recently as a polysaccharide important for the integrity of the extracellular matrix, and thus involved in skin ageing. Hydration of this macromolecule is therefore of considerable interest for skin cosmetics. Johannes Hunger at FOM Amsterdam and colleagues have used ultrafast IR and THz spectroscopy to investigate the dynamics of its hydration shell in solution, and find that around 15 waters per disaccharide unit are significantly slowed in terms of their reorientiation � a figure comparable to that found for other polysaccharides, such as dextran (J. Hunger et al., Biophys. J. 103, L10; 2012 � paper here).
A study of zwitterionic amino-acid hydration by Inigo Rodr�guez-Arteche and colleagues at the University of Pa�s Vasco in San Sebastian, Spain, indicates that, despite their large dipole moments, these ions are very well screened by water and show little tendency for dipolar alignment at moderate concentrations (I. Rodr�guez-Arteche et al., Phys. Chem. Chem. Phys. 14, 11352; 2012 � paper here). Again, and insurprisingly, the dielectric spectroscopic measurements reported here show significant slowing of water dynamics in the hydration shells.
Techniques I have never heard of before have been used by Mark Chance at Case Western Reserve and coworkers to study the structure and dynamics of protein-bound waters (S. Gupta et al., PNAS 109, 14882; 2012 � paper here). I don�t fully understand these methods, but they involve radiolytic formation of hydroxyl radicals at the protein surface, followed by diffusion of the radicals to reactive sites on the proteins and then identification by mass spectrometry. If this radiolytic method is used in O-18-enriched water, it results in selective O-18 labelling of certain residues. Time-resolved studies of O-16/O-18 exchange can then give information about water-exchange dynamics in the hydration shell. These techniques can apparently give information about the water-exchange rates for specific residues in an active-site pocket � the cases studied here are cytochrome c and ubiquitin.
I enjoyed the RSC Faraday Discussion on Hofmeister Effects in September; I gather that the proceedings will appear quite shortly, judging by the speed at which the papers were prepared. A further small advert: I have written a chapter on water in the forthcoming book Physical Chemistry in Action: Astrochemistry and Astrobiology, edited by Ian Smith, Sydney Leach and Charles Cockell and published by Springer in early November - see here.
For those who have sent me papers not mentioned here � they will be soon. I�m just getting some older things cleared first. Please do keep sending them.
The effort to understand hydrophobic attraction has rather overshadowed the study of interactions between hydrophilic surfaces � although, as Roland Netz and colleagues point out (E. Schneck et al., PNAS 109, 14405; 2012 � paper here), the repulsion between such surfaces, balancing out the van der Waals attraction, is ultimately what prevents biological matter from collapsing. This interaction is fairly well characterized for neutral phospholipid bilayers, but also acts between proteins, polysaccharides and nucleic acids, with exponential decay. All the same, the origins of the force, though evidently bound up with hydration, are not well understood. Netz and colleagues study it in this paper using MD simulations of zwitterionic lipid bilayers. Part of the repulsion comes from the reduction in configurational entropy of the head groups, but part is water-mediated and enthalpic, due to the expulsion of water bound to the head groups as the surfaces approach. However, at separations that allow at least 17 water molecules to hydrate each head group, the water-mediated repulsion becomes dominated by an entropic effect due to the alignment of water dipoles: at smaller separations, there is depolarization due to frustration in the dipole orientations of water molecules close to each of the two surfaces. In other words, the repulsive interaction is complex, subtle and finely tuned.
I recently saw Veronica Vaida talk about the catalytic potential of the air-water interface as a hydrophobic environment that can enhance the condensation reaction of peptide bond formation. She and Elizabeth Griffith now offer experimental support for that notion (PNAS 109, 15697; 2012 � paper here). They report IR spectroscopic evidence that leucine, as an ethyl ester, will partition to the air-water interface in a Langmuir trough, coordinate there to copper(II) ions, and undergo condensation to form peptide bonds. The prebiotic implications are clear, offering yet another reason to be interested in what goes on at this ubiquitous interface.
Alfonso De Simone at Imperial College and coworkers have investigated a nice model system for ligand binding in protein cavities: macrocyclic cucurbituril molecules, which bind a variety of hydrophobic guests very strongly (F. Biedermann et al., JACS 134, 15318; 2012 � paper here). Their simulations indicate that release of �high-energy� water in the cavity is a major driving force of binding, being favourable both enthalpically and entropically. I see that a similar conclusion is reached by C. N. Nguyen et al. in J. Chem. Phys. 137, 044101 (2012), a paper I�ve not seen beyond the abstract but which also shows that a high water density can be achieved inside these cavities despite the absence of strong solvent-cavity interactions. The paper is here.
Bob Eisenberg at Rush University and coworkers use a variational theory to probe the energetics of ion flow through protein channels (T.-L. Horng et al., J. Phys. Chem. B 116, 11422; 2012 � paper here). They say that this approach captures the electrostatic interactions that classical theories of such channels tend to ignore in their assumption of ideality of the ionic solutions. Bob�s papers always seem to contain some pungent and pertinent general comments that makes them thought-provoking (and fun) to read, viz.
�Early workers of some reputation in molecular biology, including Nobel Prize winners, attributed the secret of life to allosteric interactions of chemical signals acting on proteins and then channels. It is striking to the biologists among us that a self-consistent model of ions and side chains in channels produces strong interactions over long distances (i.e., more than 1 nm) without invoking the metaphors of vitalistic allostery. The calculations of a self-consistent variational theory of the energetics of complex fluids seem ready to replace the poetry of our ancestors� It is amusing that physicists learned to use self-consistent mathematics to analyze (control and build) complex interacting systems of holes and electrons during the same years that biologists used poetry to describe complex interacting systems of cations and anions� Certainly, a theoretical and computational approach to biology and its molecules must allow everything to interact with everything else, instead of assuming that everything is ideal and nothing interacts with nothing.�
I encountered hyaluronan recently as a polysaccharide important for the integrity of the extracellular matrix, and thus involved in skin ageing. Hydration of this macromolecule is therefore of considerable interest for skin cosmetics. Johannes Hunger at FOM Amsterdam and colleagues have used ultrafast IR and THz spectroscopy to investigate the dynamics of its hydration shell in solution, and find that around 15 waters per disaccharide unit are significantly slowed in terms of their reorientiation � a figure comparable to that found for other polysaccharides, such as dextran (J. Hunger et al., Biophys. J. 103, L10; 2012 � paper here).
A study of zwitterionic amino-acid hydration by Inigo Rodr�guez-Arteche and colleagues at the University of Pa�s Vasco in San Sebastian, Spain, indicates that, despite their large dipole moments, these ions are very well screened by water and show little tendency for dipolar alignment at moderate concentrations (I. Rodr�guez-Arteche et al., Phys. Chem. Chem. Phys. 14, 11352; 2012 � paper here). Again, and insurprisingly, the dielectric spectroscopic measurements reported here show significant slowing of water dynamics in the hydration shells.
Techniques I have never heard of before have been used by Mark Chance at Case Western Reserve and coworkers to study the structure and dynamics of protein-bound waters (S. Gupta et al., PNAS 109, 14882; 2012 � paper here). I don�t fully understand these methods, but they involve radiolytic formation of hydroxyl radicals at the protein surface, followed by diffusion of the radicals to reactive sites on the proteins and then identification by mass spectrometry. If this radiolytic method is used in O-18-enriched water, it results in selective O-18 labelling of certain residues. Time-resolved studies of O-16/O-18 exchange can then give information about water-exchange dynamics in the hydration shell. These techniques can apparently give information about the water-exchange rates for specific residues in an active-site pocket � the cases studied here are cytochrome c and ubiquitin.
I enjoyed the RSC Faraday Discussion on Hofmeister Effects in September; I gather that the proceedings will appear quite shortly, judging by the speed at which the papers were prepared. A further small advert: I have written a chapter on water in the forthcoming book Physical Chemistry in Action: Astrochemistry and Astrobiology, edited by Ian Smith, Sydney Leach and Charles Cockell and published by Springer in early November - see here.
For those who have sent me papers not mentioned here � they will be soon. I�m just getting some older things cleared first. Please do keep sending them.
Hello, my name is Jack Sparrow. I'm a 50 year old self-employed Pirate from the Caribbean.
No comments:
Post a Comment