Department of Materials Science, University of Patras, 26504 Rio Patras, Greece, Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vass. Constantinou Avenue, 116 35 Athens, Greece, Institut de Biologie Moleculaire et Cellulaire, UPR9021 CNRS, Immunologie et Chimie Therapeutiques, 67084 Strasbourg, France, and Dipartimento di Scienze Farmaceutiche, Universita di Trieste, Piazzale Europa 1, 34127 Trieste, Italy

Chemistry of Carbon Nanotubes

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

CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc.

CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations

https://www.cell.com/biophysj/pdf/S0006-3495(09)00791-7.pdf

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

Carbon nanotube applications for tissue engineering.

Confinement can induce unusual behavior in the properties of matter. Using molecular dynamics simulations, we show here that water confined to carbon nanotubes of a critical size under ambient conditions (1 bar, 300 K) can undergo a transition into a state having icelike mobility with an amount of hydrogen bonding similar to that in liquid water. The onset of this behavior occurs rapidly, raising the possibility that confinement inside nanotubes, and perhaps even buckyballs, can provide an environment in which the dynamics of phase changes may be studied directly by simulation. Moreover, because of a variety of evidence suggesting that water ordering may modulate proton conductance via a “proton wire” hydrogen bonding network, the ability to modulate water ordering with geometry suggests a possible mechanism for a switchable nanoscale semiconductor.

Anomalously Immobilized Water: A New Water Phase Induced by Confinement in Nanotubes

Cholesterol-induced modifications in lipid bilayers: a simulation study.

Molecular dynamics simulations were used to study ionic flow in carbon nanotubes with the goal of using carbon nanotubes as artificial protein channels found in cell membranes. Previous simulations show that water and molten ions enter carbon nanotubes spontaneously. Our simulations show that ion occupancy in a carbon nanotube solvated in an electrolyte is very low for a (16,16) uncapped tube. When partial charges were placed on the rim atoms of the tube and an external electric field was applied, it was found that the ion occupancy increased significantly. To mimic an ion channel in a membrane, functional groups were attached at the ends and the tube was placed in a slab. The functionalized tube was found to conduct ions in the presence of an electric field. It is also shown that cationic or anionic selectivity could be obtained by symmetrical placement of the functional groups.

R. Jay Mashl

Papers

Anomalously Immobilized Water: A New Water Phase Induced by Confinement in Nanotubes

Cholesterol-induced modifications in lipid bilayers: a simulation study.

Electrolytic Transport in Modified Carbon Nanotubes

Sphingomyelin-Cholesterol Domains in Phospholipid Membranes: Atomistic Simulation

Structure of Sphingomyelin Bilayers: A Simulation Study