Solvation of molecules from the family of "domain of unknown function" 3494 and their ability to bind to ice.

In 2012, the molecular structure of a new, broad class of ice-binding proteins, classified as "domain of unknown function" (DUF) 3494, was described for the first time. These proteins have a common tertiary structure and are characterized by a very wide spectrum of antifreeze activity (from weakly active to hyperactive). The ice-binding surface (IBS) region of these molecules differs significantly in its structure from the IBS of previously known antifreeze proteins (AFPs), showing a complete lack of regularity and high hydrophilicity.

Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice.

Using molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water, which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation and distance relative to the surface of ice, which enables the effective binding (via hydrogen bonds) of the molecule with the nascent ice surface.

Mechanism of antifreeze protein functioning and the "anchored clathrate water" concept.

In liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case, the interactions of water molecules with the protein surface shift the equilibrium of the process.

Revealing the Frank-Evans "Iceberg" Structures within the Solvation Layer around Hydrophobic Solutes.

Using computer simulations, the structural properties of solvation water of three model hydrophobic molecules, methane and two fullerenes (C60 and C80), were studied. Systems were simulated at temperatures in the range of 250-298 K. By analyzing both the local ordering of the molecules of water in the solvation layers and the structure of hydrogen bond network, it is shown that in the solvation layer of hydrophobic molecules, ordered aggregates consisting of water molecules are formed.

Role of the Solvation Water in Remote Interactions of Hyperactive Antifreeze Proteins with the Surface of Ice.

Most protein molecules do not adsorb onto ice, one of the exceptions being so-called antifreeze proteins. In this paper, we describe that there is a force pushing an antifreeze protein molecule away from the ice surface when it is not oriented with its ice-binding plane toward the ice and that this pushing force may be also present even when the protein is oriented with its ice-binding plane toward the ice. This force is absent only when certain specific distance criteria are met, regarding the surface of ice and the protein.

Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface.

Using computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent.

The accretion of the new ice layer on the surface of hexagonal ice crystal and the influence of the local electric field on this process.

The process of creation of a new layer of ice on the basal plane and on the prism plane of a hexagonal ice crystal is analyzed. It is demonstrated that the ordering of water molecules in the already existing crystal affects the freezing. On the basal plane, when the orientations of water molecules in the ice block are random, the arrangement of the new layer in a cubic manner is observed more frequently-approximately 1.

Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity.

Water molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel pout) is investigated.

Correction: Water-mediated long-range interactions between the internal vibrations of remote proteins.

Correction for 'Water-mediated long-range interactions between the internal vibrations of remote proteins' by Anna Kuffel et al., Phys. Chem.

Water-mediated influence of a crowded environment on internal vibrations of a protein molecule.

The influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected.

Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein.

The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism.

Water-mediated long-range interactions between the internal vibrations of remote proteins.

It is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer.

Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein.

Many hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were analyzed and compared with the properties of solvation water present at the surface of ice.

Properties of water in the region between a tubulin dimer and a single motor head of kinesin.

A kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions.

Why the solvation water around proteins is more dense than bulk water.

The main aim of this work is to propose a rational explanation of the commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that the geometry of the water-water hydrogen bond network within solvation layer differs from the one in bulk water, and it is the result of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the structure of solvation water.

The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein.

A single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water.

The hydrogen bond network structure within the hydration shell around simple osmolytes: urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model.

Despite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind, we determine two main aims of this work as follows: description of the water-water hydrogen bond network structure within the solvation layer around solute molecules (urea, trimethylamine-N-oxide, and tetramethylurea), and also comparison of rigid simple point charges (SPC) and polarizable (POL3) models of water.

Structural properties of hydration shell around various conformations of simple polypeptides.

In this paper we investigate structural properties of water within the solvation shell around the peptide core created by a well-defined conformation of polypeptide chain. The following secondary structures are investigated: linear (straight chain), and three helices PII (polyproline-like), 3(10), and alpha. We propose using the two-particle contribution to entropy as a rational measure of the water structural ordering within the solvation layer.

Effects of urea and trimethylamine-N-oxide on the properties of water and the secondary structure of hen egg white lysozyme.

The influence of urea and trimethylamine-N-oxide (TMAO) on the structure of water and secondary structure of hen egg white lysozyme (HEWL) has been investigated. The hydration of these osmolytes was studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H(2)O. The difference spectra procedure was applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO.

Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide.

Several conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer-the first solvation shell-around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.

Two-particle entropy and structural ordering in liquid water.

Entropies of simple point charge (SPC) water were calculated over the temperature range 278-363 K using the two-particle correlation function approximation. Then, the total two-particle contribution to the entropy of the system was divided into three parts, which we call translational, configurational, and orientational. The configurational term describes the contribution to entropy, which originates from spatial distribution of surrounding water molecules (treated as points, represented by the center of mass) around the central one.

Hydration of simple amides. FTIR spectra of HDO and theoretical studies.

The hydration of formamide (F), N-methylformamide (NMF), N,N-dimethylformamide (DMF), acetamide (A), N-methylacetamide (NMA), and N,N-dimethylacetamide (DMA) has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure has been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To facilitate the interpretation of obtained spectral results, DFT calculations of aqueous amide clusters were performed.

Structural properties of water: comparison of the SPC, SPCE, TIP4P, and TIP5P models of water.

Molecular-dynamics simulations were carried out for the SPC, SPCE, TIP4P, and TIP5P models of water at 298 K. From these results we determine the following quantities: the absolute entropy using the two-particle approximation, the mean lifetime of the hydrogen bond, the mean number of hydrogen bonds per molecule, and the mean energy of the hydrogen bond. From the entropy calculations we find that nearly all contributions to the total entropy originates from the orientation effects.