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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. The presence of a regular, repeating structural motif in the IBS region of hitherto known AFP molecules, combined with the hydrophobic nature of this surface, promotes the formation of an ice-like ordering of the solvation water layer and, as a result, facilitates the process of transformation of this water layer into ice. It is, therefore, surprising that the newly discovered DUF3494 class of proteins clearly breaks out of this characteristic. In this paper, using molecular dynamics simulations, we analyze the solvation water structure of the IBS region of both DUF3494 family molecules and AFPs. As we show, although the IBS of DUF3494 molecules does not form an ice-like water structure in the solvation layer, this is compensated by the formation of the equivalent of "anchored clathrate water," in the form of a relatively large number of water molecules bound to the surface of the protein molecule and providing potential binding sites for it to the ice surface. [ABSTRACT FROM AUTHOR]

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. Our results show that the final adsorption of the AFP III molecule on the surface of ice is not achieved by chaotic diffusion movements, but it is preceded by a remote, water-mediated interaction between the IBS and the surface of ice. The key factor that determines the existence of this interaction is the ability of water molecules to spontaneously form large, high-volume aggregates that can be anchored to both the IBS of the AFP molecule and the surface of ice. The results presented in this work for AFP III are in full agreement with the ones obtained by us previously for hyperactive CfAFP, which indicates that the mechanism of the remote interaction of these molecules with ice remains unchanged despite significant differences in the molecular structure of their ice binding sites. For that reason, we can expect that also other types of AFPs interact with the ice surface according to an analogous mechanism. [ABSTRACT FROM AUTHOR]

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. In this paper, we analyze the structural properties of the solvation water in antifreeze proteins (AFPs). The results of molecular dynamics analysis with the use of various parameters related to the structure of solvation water on the protein surface are presented. We found that in the vicinity of the active region responsible for the binding of AFPs to ice, the equilibrium is clearly shifted toward the formation of "ice-like aggregates," and the solvation water has a more ordered ice-like structure. We have demonstrated that a reduction in the tendency to create "ice-like aggregates" results in a significant reduction in the antifreeze activity of the protein. We conclude that shifting the equilibrium in favor of the formation of "ice-like aggregates" in the solvation water in the active region is a prerequisite for the biological functionality of AFPs, at least for AFPs having a well-defined ice binding area. In addition, our results fully confirm the validity of the "anchored clathrate water" concept, formulated by Garnham et al. [Proc. Natl. Acad. Sci. U. S. A. 108, 7363 (2011)]. [ABSTRACT FROM AUTHOR]

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 1.7 times more often than in a hexagonal manner. When the water molecules in the ice block are more ordered, it results in the predominance of the oxygen atoms or the hydrogen atoms on the most outer part of the surface of the ice block. In this case, the hexagonal structure is formed more frequently when the supercooling of water exceeds 10 K. This phenomenon is explained by the influence of the oriented electric field, present as a consequence of the ordering of the dipoles of water molecules in the ice block. This field modifies the structure of solvation water (i.e., the layer of water in the immediate vicinity of the ice surface). We showed that the structure of solvation water predetermines the kind of the newly created layer of ice. This effect is temperature-dependent: when the temperature draws nearer to the melting point, the cubic structure becomes the prevailing form. The temperature at which the cubic and the hexagonal structures are formed with the same probabilities is equal to about 260 K. In the case of the prism plane, the new layer that is formed is always the hexagonal one, which is independent of the arrangement of water molecules in the ice block and is in agreement with previous literature data. For the basal plane, as well as for the prism plane, no evident dependence on the ordering of water molecules that constitute the ice block on the rate of crystallization can be observed. [ABSTRACT FROM AUTHOR]

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. A wild type of the protein is used, along with its three mutants, with antifreeze activities equal to 54% or 10% of the activity of the native form. The solvation water of the ice-binding surface and the rest of the protein are analyzed separately. To characterize the structure of solvation shell, parameters describing radial and angular characteristics of the mutual arrangement of the molecules were employed. They take into account short-distance (first hydration shell) or long-distance (two solvation shells) effects. The obtained results and the comparison with the results obtained previously for a hyperactive antifreeze protein from Choristoneura fumiferana lead to the conclusion that the structure and amino acid composition of the active region of the protein evolved to achieve two goals. The first one is the modification of the properties of the solvation water. The second one is the geometrical adjustment of the protein surface to the specific crystallographic plane of ice. Both of these goals have to be achieved simultaneously in order for the protein to perform its function properly. However, they seem to be independent from one another in a sense that very small antifreeze activity does not imply that properties of water become different from the ones observed for the wild type. The proteins with significantly lower activity still modify the mean properties of solvation water in a right direction, in spite of the fact that the accuracy of the geometrical match with the ice lattice is lost because of the mutations. Therefore, we do not observe any correlation between the antifreeze activity and the extent of modification of the properties of solvation water. [ABSTRACT FROM AUTHOR]

The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (Cf AFP) 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. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularly far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that--from the three analyzed solvation shells of Cf AFP--the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice. [ABSTRACT FROM AUTHOR]

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. The most striking observations concerned the temperature dependence of changes in water structure. In the case of solvation water of the ice-binding plane, the difference between the overall structural ordering of solvation water and bulk water diminished with increasing temperature; in the case of solvation water of the rest of the protein, the trend was opposite. In this respect, the solvation water of the ice-binding plane roughly resembled the hydration layer of ice. Simultaneously, the whole solvation shell of the protein displayed some features that are typical for solvation shells of many other proteins and are not encountered in the solvation water of ice. In the first place, this is an increase in density of water around the protein. The opposite is true for the solvation water of ice - it is less dense than bulk water. Therefore, even though the structure of solvation water of ice-binding plane and the structure of solvation water of ice seem to share some similarities, densitywise they differ. [ABSTRACT FROM AUTHOR]

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. The following quantities have been examined: radial distribution functions of water molecules around the investigated solutes, both local and overall characteristics of the hydrogen bond network structure (using recently elaborated method), along with estimation of the mean energy of a single hydrogen bond, and also the probability distributions which describe the orientation of a single water particle plane relatively to the center of mass of the solute molecule. As an independent method for the evaluation of the degree of changes in local structural ordering, a harmonic approximation has been adopted to estimate the absolute entropy of water. It was found that within the solvation shell of the investigated solutes, the structure of hydrogen bond network changes only slightly comparing to bulk water. Therefore, we conclude that the investigated osmolyte molecules do not disturb significantly the structure of surrounding water. This conclusion was also confirmed by calculations of the absolute entropy of water using a harmonic approximation. In the immediate vicinity of the solutes, we observe that the water-water hydrogen bonds are slightly more stable; they are slightly less distorted and a little shorter than in bulk water. Nevertheless, although this local water structure is more stable and stiffer, our results do not indicate that it is more ordered compared to bulk. Finally, the comparison of both used models of water, the fixed charge and the polarizable, leads to unambiguous conclusion that rigid (SPC) water model may be successfully used in simulations instead of polarizable (POL3), as no significant differences between these two models have been observed. [ABSTRACT FROM AUTHOR]

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. Moreover, we determine the contributions to the total entropy which originate from the first, second, and higher solvation shells. It is interesting that the limits between solvation shells are clearly visible. The first solvation shell (0.22

The entropies of simple point charge (SPC) water are calculated over a wide temperature by using the two-particle correlation function approximation. The results have shown that the first hydration shell around the water molecule has participated in 70% of the total orientational entropy of water and this rate is roughly temperature independent.

The hydration of simple formamide (F), N-methylformamide (NMF), N,N-dimethylformamide (DMF), acetamide (A), N-methylacetamide (NMA) and N,N'-dimethylacetamide (DMA) is analyzed in aqueous solutions by using Fourier transform infrared (FTIR) spectra of HDO isotopically diluted in [H.sub.2]O. The increased stability of the hydration sphere of NMA relative to DMA and of NMF relative to DMF has its origin in different geometries and also the stability of water cages containing the amides.

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. This ordering leads to positional preference of the protein relative to the ice crystal before the final attachment to the ice surface takes place, accompanied by the solidification of the interfacial water. It is possible because the solvation water of the ice-binding plane of CfAFP is susceptible to the overlapping with the solvation water of ice and is mostly changeable into ice itself. These remote interactions significantly increase efficacy of the adsorption process by facilitating the geometric adjustment of the active region of the CfAFP molecule to the ice surface. Because of the ordered nature of the water molecules at the ice-binding plane, the energy of their interactions with the ice-binding surface of the protein does not change upon the ongoing solidification of solvation water. However, the structure of the solvation water is not strictly ice-like and the growth of ice in the interfacial water is not initiated at the side of the protein. On the contrary, we find that solvation water of CfAFP solidifies slower than solvation water of ice – the solidification of interfacial water starts at the surface of ice. Moreover, in the presence of the CfAFP molecule, also solvation water of ice solidifies slower compared to the situation when the protein is not present next to the ice surface. Additionally, the presence of the protein molecule shifts the ratio of cubic to hexagonal ice that spontaneously forms at the ice surface, by introducing another layer of ordered water molecules – opposite to the ice lattice, at the other side of the crystallizing layer of water. [ABSTRACT FROM AUTHOR]

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. The possible mechanisms of these phenomena are described. The cross-correlation function of the collective velocities of surface atoms of two proteins was decomposed into the Fourier series. The amplitude spectrum displays a peak at low frequencies. Also, the results of principal component analysis suggest that the close presence of an additional protein molecule influences the high-amplitude, low-frequency modes in the most prominent way. This part of the spectrum covers biologically important protein motions. The neighbor-induced changes in the inner dynamics of the protein may be connected with the changes in the velocity power spectrum of interfacial water. The additional protein molecule changes the properties of solvation water and in this way it can influence the dynamics of the second protein. It is suggested that this phenomenon may be described, at first approximation, by a damped oscillator driven by an external random force. This model was successfully applied to conformationally rigid Choristoneura fumiferana antifreeze protein molecules. [ABSTRACT FROM AUTHOR]

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. It was studied using molecular dynamics simulations. The analyzed atoms were located at the two distant protein surfaces that were facing each other. We demonstrated that the low-frequency (ca. 2 THz and less) collective movements of these two separate sets of atoms are to some extent interdependent. Based on this finding, it can be inferred that the low frequency large-scale internal motions of these proteins are also partially interdependent. The water-mediated protein–protein interactions, which are responsible for this interdependence, have a relatively long range of at least 2 nm at room temperature. [ABSTRACT FROM AUTHOR]

The main aim of this work is to propose a rational explanationof the commonly observed phenomenon of increasing water density withinsolvation shell of proteins. We have observed that the geometry ofthe water–water hydrogen bond network within solvation layerdiffers from the one in bulk water, and it is the result of interactionsofwater molecules with protein surface. Altered geometry of the networkreflects changes in the structure of solvation water. Our explanationof the observed changes is based on model proposed by Tanaka (Tanaka,H. J. Chem. Phys.2000, 112, 799). According to this model, in liquid water exist some specialstructures formed by water molecules thanks to their unique abilityto create the branched network of hydrogen bonds. These structureshave two characteristic features: a low potential energy of internalinteractions and a large specific volume. We provide some evidencefor the supposition that deformation of the geometry of the water–waterhydrogen bond network is responsible for destabilization of thesestructures and therefore for increased local density of water. Ourmodel is constructed on the basis of the analysis of solvation waterof some specific protein, the motor head of kinesin. Subsequently,we used it for description of solvation of purely hydrophobic surface.It has been found that in this case an unoccupied space between thehydrophobic surface and neighboring solvation layer exists. It hasbeen found that thickness of this region depends on local geometryof the water–protein interface, and it is a result of maintaininga balance between water–surface interactions and water–waterinteractions. In our opinion, existence of this space region is oneof the main factors that differentiates the hydrophobic hydrationfrom hydration of the native form of kinesin. Its existence also explainswhy the density is greater for solvation water around the native formof the protein than in the vicinity of the hydrophobic surface. [ABSTRACT FROM AUTHOR]

Total vapour pressures and excess molar volumes, measured at the temperature 313.15 K, are reported for three binary mixtures (2-pyrrolidone + water), (2-pyrrolidone + methanol) and (2-pyrrolidone + ethanol). The results are compared with previously obtained data for binary mixtures (amide + A), where amide=N-methylformamide, N,N-dimethylformamide and N-methylacetamide, and A= water, methanol, and ethanol. [Copyright &y& Elsevier]

Some molecular dynamics simulations were performed for liquid TIP4P and SPC water at a constant density (1.00 g/cm3) and within the temperature range of 5–90 °C. By using harmonic approximation, both the entropy of water SH and the specific heat cv were calculated, and the results were compared to literature data. It was found that harmonic approximation overestimates absolute entropy of TIP4P water by 5.6 J/mol K (∼9.5%) at 278 K, but only by 0.4 J/mol K (∼0.5%) at 363 K. The value of the specific heat, however, is strongly underestimated: for TIP4P and SPC model, we obtain 59.5 and 56.9 J/mol K using harmonic approximation, while the correct values are 79.0 and 72.3 J/mol K, respectively. [ABSTRACT FROM AUTHOR]

A correction to the article "Structural Properties of Water: Comparison of the SPC, SPCE, TIP4P and TIP5P Models of Water" that was published in volume 123, 2005 issue is presented.

Correction for ‘Water-mediated long-range interactions between the internal vibrations of remote proteins’ by Anna Kuffel et al., Phys. Chem. Chem. Phys., 2015, 17, 6728–6733. [ABSTRACT FROM AUTHOR]

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. Even though it is difficult to define the exact structure of these aggregates, their existence alone is clearly noticeable. Moreover, these aggregates become more pronounced with the decrease of temperature. The existence of the ordered aggregates around the hydrophobic solutes complies with the concept of "icebergs" proposed by Frank and Evans.

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. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin dimer. Using the molecular dynamics method, we found that these properties are different from the ones of bulk water. The changes in structure and dynamics are visible for water beyond the first solvation layers, even for the longest analyzed distance between proteins equal to 2.0 nm. However, these changes are not always enhanced compared to the situation when only one protein surface is present. One factor that distinguishes the investigated situation from the one with a single protein is the presence of an additional electric field originating from the second protein. The tendency of vectors of dipole moments of water molecules between the proteins to follow the vectors of electric field generated by the proteins causes a distortion of the water-water hydrogen bond network. It has been shown that this distortion affects the properties of water in this region: it induces structural changes in solvation water, and leads to increased water density and increased stiffness of the water structure.

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 local values of diffusion coefficients (translational and rotational) of water adjacent to specific patches on the protein surface seem not to be correlated to the orientational ordering of hydration water, but instead they depend on spatial roughness and degree of exposure of the patch to the solvent. Finally, a relationship between the mobility of various surface atoms of the protein and the mean values of the diffusion coefficient of the adjacent water molecules has been observed. The latter finding suggests a close relationship between the dynamics of the inner kinesin movements and the behavior of solvation water which is in turn determined by the topography of the contact surface between the protein and the surrounding water molecules., (This journal is © the Owner Societies 2012)