Relevance of Earth-Bound Extremophiles in the Search for Extraterrestrial Life.

The recent discovery of extrasolar Earth-like planets that orbit in their habitable zone of their system, and the latest clues of the presence of liquid water in the subsurface of Mars and in the subglacial ocean of Jupiter's and Saturn's moons, has reopened debates about habitability and limits of life. Although liquid water, widely accepted as an absolute requirement for terrestrial life, may be present in other bodies of the solar system or elsewhere, physical and chemical conditions, such as temperature, pressure, and salinity, may limit this habitability. However, extremophilic microorganisms found in various extreme terrestrial environments are adapted to thrive in permanently extreme ranges of physicochemical conditions.

Behavior of Hydrated Lipid Bilayers at Cryogenic Temperatures.

Neutron diffraction was used to study the behavior of water present in phospholipid multilamellar stacks from 1,2-dimyristoyl--glycero-3-phosphatidylcholine (DMPC) at cryogenic temperatures. Evidence was found for the existence of a highly viscous phase of water that exists between 180 and 220 K based on the observation that water can leave the intermembrane space at these low temperatures. Similar measurements are described in the literature for purple membrane (PM) samples.

Surviving salt fluctuations: stress and recovery in Halobacterium salinarum, an extreme halophilic Archaeon.

Halophilic proteins subjected to below about 15% salt in vitro denature through misfolding, aggregation and/or precipitation. Halobacteria, however, have been detected in environments of fluctuating salinity such as coastal salterns and even around fresh water springs in the depths of the Dead Sea. In order to identify the underlying mechanisms of low salt survival, we explored the reactivation capacity of Halobacterium (Hbt) salinarum sub-populations after incubation in low salt media and recovery in physiological salt.

Molecular dynamics in cells: A neutron view.

Experiments to characterize intracellular molecular dynamics in vivo are discussed following a description of the incoherent neutron scattering method. Work reviewed includes water diffusion in bacteria, archaea, red blood cells, brain cells and cancer cells, and the role of proteome molecular dynamics in adaptation to physiological temperature and pressure, and in response to low salt stress in an extremophile. A brief discussion of the potential links between neutron scattering results and MD simulations on in-cell dynamics concludes the review.

Solution scattering approaches to dynamical ordering in biomolecular systems.

Clarification of solution structure and its modulation in proteins and protein complexes is crucially important to understand dynamical ordering in macromolecular systems. Small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS) are among the most powerful techniques to derive structural information. Recent progress in sample preparation, instruments and software analysis is opening up a new era for small-angle scattering.

On the quest for the elusive mechanism of action of daptomycin: Binding, fusion, and oligomerization.

Daptomycin, sold under the trade name CUBICIN, is the first lipopeptide antibiotic to be approved for use against Gram-positive organisms, including a number of highly resistant species. Over the last few decades, a number of studies have tried to pinpoint the mechanism of action of daptomycin. These proposed modes of action often have points in common (e.

Mobility of a Mononucleotide within a Lipid Matrix: A Neutron Scattering Study.

An essential question in studies on the origins of life is how nucleic acids were first synthesized and then incorporated into compartments about 4 billion years ago. A recent discovery is that guided polymerization within organizing matrices could promote a non-enzymatic condensation reaction allowing the formation of RNA-like polymers, followed by encapsulation in lipid membranes. Here, we used neutron scattering and deuterium labelling to investigate 5'-adenosine monophosphate (AMP) molecules captured in a multilamellar phospholipid matrix.

A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion.

The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an integrative approach combining small-angle neutron scattering (SANS), low-resolution electron microscopy and biophysical analyses we determined the arrangement of the proteins and lipids within the super-complex. The results guided the placement of X-ray structures of individual HTL components and allowed the proposal of a model of the functional translocon.

The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering.

Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the 'lubricant' for the conformational fluctuations required for biological activity.

Neutrons describe ectoine effects on water H-bonding and hydration around a soluble protein and a cell membrane.

Understanding adaptation to extreme environments remains a challenge of high biotechnological potential for fundamental molecular biology. The cytosol of many microorganisms, isolated from saline environments, reversibly accumulates molar concentrations of the osmolyte ectoine to counterbalance fluctuating external salt concentrations. Although they have been studied extensively by thermodynamic and spectroscopic methods, direct experimental structural data have, so far, been lacking on ectoine-water-protein interactions.

Self-assembly Controls Self-cleavage of HHR from ASBVd (-): a Combined SANS and Modeling Study.

In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-).

Molecular adaptation and salt stress response of Halobacterium salinarum cells revealed by neutron spectroscopy.

Halobacterium salinarum is an extreme halophile archaeon with an absolute requirement for a multimolar salt environment. It accumulates molar concentrations of KCl in the cytosol to counterbalance the external osmotic pressure imposed by the molar NaCl. As a consequence, cytosolic proteins are permanently exposed to low water activity and highly ionic conditions.

Dynamic footprint of sequestration in the molecular fluctuations of osteopontin.

The sequestration of calcium phosphate by unfolded proteins is fundamental to the stabilization of biofluids supersaturated with respect to hydroxyapatite, such as milk, blood or urine. The unfolded state of osteopontin (OPN) is thought to be a prerequisite for this activity, which leads to the formation of core-shell calcium phosphate nanoclusters. We report on the structures and dynamics of a native OPN peptide from bovine milk, studied by neutron spectroscopy and small-angle X-ray and neutron scattering.

Molecular Dynamics Simulations of a Powder Model of the Intrinsically Disordered Protein Tau.

The tau protein, whose aggregates are involved in Alzheimer's disease, is an intrinsically disordered protein (IDP) that regulates microtubule activity in neurons. An IDP lacks a single, well-defined structure and, rather, constantly exchanges among multiple conformations. In order to study IDP dynamics, the combination of experimental techniques, such as neutron scattering, and computational techniques, such as molecular dynamics (MD) simulations, is a powerful approach.

Thermal fluctuations in amphipol A8-35 particles: a neutron scattering and molecular dynamics study.

Amphipols are a class of polymeric surfactants that can stabilize membrane proteins in aqueous solutions as compared to detergents. A8-35, the best-characterized amphipol to date, is composed of a polyacrylate backbone with ~35% of the carboxylates free, ~25% grafted with octyl side-chains, and ~40% with isopropyl ones. In aqueous solutions, A8-35 self-organizes into globular particles with a molecular mass of ~40 kDa.

Picosecond dynamics in haemoglobin from different species: a quasielastic neutron scattering study.

Background: Dynamics in haemoglobin from platypus (Ornithorhynchus anatinus), chicken (Gallus gallus domesticus) and saltwater crocodile (Crocodylus porosus) were measured to investigate response of conformational motions on the picosecond time scale to naturally occurring variations in the amino acid sequence of structurally identical proteins.

Methods: Protein dynamics was measured using incoherent quasielastic neutron scattering. The quasielastic broadening was interpreted first with a simple single Lorentzian approach and then by using the Kneller-Volino Brownian dynamics model.

Correlation between supercoiling and conformational motions of the bacterial flagellar filament.

The bacterial flagellar filament is a very large macromolecular assembly of a single protein, flagellin. Various supercoiled states of the filament exist, which are formed by two structurally different conformations of flagellin in different ratios. We investigated the correlation between supercoiling of the protofilaments and molecular dynamics in the flagellar filament using quasielastic and elastic incoherent neutron scattering on the picosecond and nanosecond timescales.

Perspectives in biological physics: the nDDB project for a neutron Dynamics Data Bank for biological macromolecules.

Neutron spectroscopy provides experimental data on time-dependent trajectories, which can be directly compared to molecular dynamics simulations. Its importance in helping us to understand biological macromolecules at a molecular level is demonstrated by the results of a literature survey over the last two to three decades. Around 300 articles in refereed journals relate to neutron scattering studies of biological macromolecular dynamics, and the results of the survey are presented here.

Dynamics measured by neutron scattering correlates with the organization of bioenergetics complexes in natural membranes from hyperthermophile and mesophile bacteria.

Various models on membrane structure and organization of proteins and complexes in natural membranes emerged during the last years. However, the lack of systematic dynamical studies to complement structural investigations hindered the establishment of a more complete picture of these systems. Elastic incoherent neutron scattering gives access to the dynamics on a molecular level and was applied to natural membranes extracted from the hyperthermophile Aquifex aeolicus and the mesophile Wolinella succinogenes bacteria.

Change of dynamics of raft-model membrane induced by amyloid-β protein binding.

While the steady-state existence in the size and shape of liquid-ordered microdomains in cell membranes, the so-called "lipid rafts", still remain the subject of debate, glycosphingolipid-cholesterol rich regions in plasma membranes have been considered to have a function as platforms for signaling and sorting. In addition, recent spectroscopic studies show that the interaction between monosialoganglioside and amyloid beta (Aβ protein promotes the transition of Aβ from the native structure to the cross-beta fold in amyloid aggregates. However, there is few evidence on the dynamics of "lipid rafts" membranes.

Neutron scattering: a tool to detect in vivo thermal stress effects at the molecular dynamics level in micro-organisms.

In vivo molecular dynamics in Halobacterium salinarum cells under stress conditions was measured by neutron scattering experiments coupled with microbiological characterization. Molecular dynamics alterations were detected with respect to unstressed cells, reflecting a softening of protein structures consistent with denaturation. The experiments indicated that the neutron scattering method provides a promising tool to study molecular dynamics modifications in the proteome of living cells induced by factors altering protein folds.

Hydration shells with a pinch of salt.

The discovery of extreme halophile microorganisms in the Dead Sea, which are specifically dependent on a multimolar salt environment to survive, stimulated major developments in biology and physical chemistry. The minireview focuses on the molecular level. After a brief introduction to the history of halophile studies, protein and nucleic acid solvent interactions and their influence on macromolecular structure stabilization and dynamics are discussed.

A polymer surfactant corona dynamically replaces water in solvent-free protein liquids and ensures macromolecular flexibility and activity.

The observation of biological activity in solvent-free protein-polymer surfactant hybrids challenges the view of aqueous and nonaqueous solvents being unique promoters of protein dynamics linked to function. Here, we combine elastic incoherent neutron scattering and specific deuterium labeling to separately study protein and polymer motions in solvent-free hybrids. Myoglobin motions within the hybrid are found to closely resemble those of a hydrated protein, and motions of the polymer surfactant coating are similar to those of the hydration water, leading to the conclusion that the polymer surfactant coating plasticizes protein structures in a way similar to hydration water.

Dynamical coupling of intrinsically disordered proteins and their hydration water: comparison with folded soluble and membrane proteins.

Hydration water is vital for various macromolecular biological activities, such as specific ligand recognition, enzyme activity, response to receptor binding, and energy transduction. Without hydration water, proteins would not fold correctly and would lack the conformational flexibility that animates their three-dimensional structures. Motions in globular, soluble proteins are thought to be governed to a certain extent by hydration-water dynamics, yet it is not known whether this relationship holds true for other protein classes in general and whether, in turn, the structural nature of a protein also influences water motions.