Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin

Globular Antifreeze Protein-Inspired Nanoparticle-Based Large-Scale T-Cell Cryoprotection System for Lymphoma Immunotherapy

Large-scale biosafe T-cell cryopreservation is required to bring T-cell therapies to the market, but it remains challenging due to the cytotoxicity of common cryoprotectants [e.g., dimethyl sulfoxide (DMSO)] and unavoidable ice injuries to cells. Herein, inspired by natural globular antifreeze proteins, we establish a biocompatible zwitterionic magnetic nanoparticle (ZMNP)-based cryoprotection system, achieving large-scale cryopreservation of T cells for lymphoma immunotherapy. ZMNPs could form a globular hydration shell to inhibit water molecule aggregation as well as ice growth, and the surficial hydration strength-antifreeze performance relationship of ZMNPs was investigated. During the thawing process, ZMNPs possessed a magnetic field-mediated nanowarming property that enabled rapid heating and also facilitated easy magnetic separation for cell recovery. These combined effects resulted in a high post-thaw viability (>80%) of large-scale T-cell cryopreservation (20 mL). Notably, post-thaw T cells exhibited similar transcript profiles to fresh cells, while up- or downregulation of 1050 genes was found in the DMSO group. In a mouse E.G7-OVA lymphoma model, ZMNP-system-cryopreserved T cells achieved a tumor suppression rate of 77.5%, twice as high as the DMSO group. This work holds great promise for the application of advanced cryopreservation techniques in the development of therapeutic cellular products.

Probing the structure of water in individual living cells

Water regulates or even governs a wide range of biological processes. Despite its fundamental importance, surprisingly little is known about the structure of intracellular water. Herein we employ a Raman micro-spectroscopy technique to uncover the composition, abundance and vibrational spectra of intracellular water in individual living cells. In three different cell types, we show a small but consistent population (~3%) of non-bulk-like water. It exhibits a weakened hydrogen-bonded network and a more disordered tetrahedral structure. We attribute this population to biointerfacial water located in the vicinity of biomolecules. Moreover, our whole-cell modeling suggests that all soluble (globular) proteins inside cells are surrounded by, on average, one full molecular layer (about 2.6 Angstrom) of biointerfacial water. Furthermore, relative invariance of biointerfacial water is observed among different single cells. Overall, our study not only opens up experimental possibilities of interrogating water structure in vivo but also provides insights into water in life.

Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences

Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.

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. 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)].

Free energy barriers for anti-freeze protein engulfment in ice: Effects of supercooling, footprint size, and spatial separation

Anti-freeze proteins (AFPs) protect organisms at freezing conditions by attaching to the ice surface and arresting its growth. Each adsorbed AFP locally pins the ice surface, resulting in a metastable dimple for which the interfacial forces counteract the driving force for growth. As supercooling increases, these metastable dimples become deeper, until metastability is lost in an engulfment event where the ice irreversibly swallows the AFP. Engulfment resembles nucleation in some respects, and this paper develops a model for the "critical profile" and free energy barrier for the engulfment process. Specifically, we variationally optimize the ice-water interface and estimate the free energy barrier as a function of the supercooling, the AFP footprint size, and the distance to neighboring AFPs on the ice surface. Finally, we use symbolic regression to derive a simple closed-form expression for the free energy barrier as a function of two physically interpretable, dimensionless parameters.

Collective Spectroscopy of Solvation Phenomena: Conflicts, Challenges, and Opportunities

Different spectroscopy types reveal different aspects of molecular processes in soft matter. In particular, collective observables can provide insights into intermolecular correlations invisible to the more popular single-particle methods. In this perspective we feature the dielectric relaxation spectroscopy (DRS) with an emphasis on the proper interpretation of this complex observable aided by computational spectroscopy. While we focus on the history and recent advances of DRS in the fields of biomolecular hydration and nanoconfinement, the discussion transcends this particular field and provides a guide for how collective spectroscopy types supported by computational decomposition can be employed to further our understanding of soft matter phenomena.

Do antifreeze proteins generally possess the potential to promote ice growth?

The binding of antifreeze proteins (AFPs) to ice needs to be mediated by interfacial water molecules. Our previous study of the effect of AFPs on the dynamics of the interfacial water of freezing at its initial stage has shown that AFPs can promote the growth of ice before binding to it. However, whether different AFPs can promote the freezing of water molecules on the basal and the prismatic surfaces of ice still needs further study. In the present contribution, five representative natural AFPs with different structures and different activities that can be adsorbed on the basal and/or prismatic surfaces of ice are investigated at the atomic level. Our results show that the phenomenon of promoting the growth of ice crystals is not universal. Only hyperactive AFPs (hypAFPs) can promote the growth of the basal plane of ice, while moderately active AFPs cannot. Moreover, this significant promotion is not observed on the prismatic plane regardless of their activity. Further analysis indicates that this promotion may result from the thicker ice/water interface of the basal plane, and the synergy of hypAFPs with ice crystals.

Influence of Aqueous Arginine Solution on Regulating Conformational Stability and Hydration Properties of the Secondary Structural Segments of a Protein at Elevated Temperatures: A Molecular Dynamics Study

The effects of aqueous arginine solution on the conformational stability of the secondary structural segments of a globular protein, ubiquitin, and the structure and dynamics of the surrounding water and arginine were examined by performing atomistic molecular dynamics (MD) simulations. Attempts have been made to identify the osmolytic efficacy of arginine solution, and its influence in guiding the hydration properties of the protein at an elevated temperature of 450 K. The similar properties of the protein in pure water at elevated temperatures were computed and compared. Replica exchange MD simulation was performed to explore the arginine solution's sensitivity in stabilizing the protein conformations for a wide range of temperatures (300-450 K). It was observed that although all the helices and strands of the protein undergo unfolding at elevated temperature in pure water, they exhibited native-like conformational dynamics in the presence of arginine at both ambient and elevated temperatures. We find that the higher free energy barrier between the folded native and unfolded states of the protein primarily arises from the structural transformation of α-helix, relative to the strands. Our study revealed that the water structure around the secondary segments depends on the nature of amino acid compositions of the helices and strands. The reorientation of water dipoles around the helices and strands was found hindered due to the presence of arginine in the solution; such hindrance reduces the possibility of exchange of hydrogen bonds that formed between the secondary segments of protein and water (PW), and as a result, PW hydrogen bonds take longer time to relax than in pure water. On the other hand, the origin of slow relaxation of protein-arginine (PA) hydrogen bonds was identified to be due to the presence of different types of protein-bound arginine molecules, where arginine interacts with the secondary structural segments of the protein through multiple/bifurcated hydrogen bonds. These protein-bound arginine formed different kinds of bridged PA hydrogen bonds between amino acid residues of the same secondary segments or among multiple bonds and helped protein to conserve its native folded form firmly.

Site-Specific Water Dynamics in the First Hydration Layer of an Anti-Freeze Glyco-Protein: A Simulation Study

Antifreeze glycoproteins (AFGPs) inhibit ice recrystallization by a mechanism remaining largely elusive. Dynamics of AFGPs’ hydration water and its involvement in the antifreeze activity, for instance, have not been identified...

What Does Time-Dependent Fluorescence Shift (TDFS) in Biomembranes (and Proteins) Report on?

The organization of biomolecules and bioassemblies is highly governed by the nature and extent of their interactions with water. These interactions are of high intricacy and a broad range of methods based on various principles have been introduced to characterize them. As these methods view the hydration phenomena differently (e.g., in terms of time and length scales), a detailed insight in each particular technique is to promote the overall understanding of the stunning “hydration world.” In this prospective mini-review we therefore critically examine time-dependent fluorescence shift (TDFS)—an experimental method with a high potential for studying the hydration in the biological systems. We demonstrate that TDFS is very useful especially for phospholipid bilayers for mapping the interfacial region formed by the hydrated lipid headgroups. TDFS, when properly applied, reports on the degree of hydration and mobility of the hydrated phospholipid segments in the close vicinity of the fluorophore embedded in the bilayer. Here, the interpretation of the recorded TDFS parameters are thoroughly discussed, also in the context of the findings obtained by other experimental techniques addressing the hydration phenomena (e.g., molecular dynamics simulations, NMR spectroscopy, scattering techniques, etc.). The differences in the interpretations of TDFS outputs between phospholipid biomembranes and proteins are also addressed. Additionally, prerequisites for the successful TDFS application are presented (i.e., the proper choice of fluorescence dye for TDFS studies, and TDFS instrumentation). Finally, the effects of ions and oxidized phospholipids on the bilayer organization and headgroup packing viewed from TDFS perspective are presented as application examples.

Hyperactive Antifreeze Proteins Promote Ice Growth before Binding to It

The antifreeze mechanism of antifreeze proteins (AFPs) evolved by organisms has been widely studied. However, detailed knowledge of the synergy between AFPs and ice crystals still remains fragmentary. In the present contribution, the cooperative effect of the hyperactive insect antifreeze protein TmAFP and ice crystals on the interfacial water during the entire process of inhibiting ice growth is systematically investigated at the atomic level and compared with its low activity mutant and a nonantifreeze protein. The results indicate a significant synergy between TmAFP and ice crystals, which enables the TmAFP to promote the ice growth before adsorbing on the surfaces of the ice crystals, while the mutant and the nonantifreeze protein cannot promote the ice growth due to the lack of this synergy. When TmAFP approaches the ice surface, the interfacial water is induced by both the AFP and the ice crystals to form the anchored clathrate motif, which binds TmAFP to the ice surface, resulting in a local increase in the curvature of the ice surface, thereby inhibiting the growth of ice. In this study, three stages, namely, promotion, adsorption, and inhibition, are observed in the complete process of TmAFP inhibiting ice growth, and the synergistic mechanism between protein and ice crystals is revealed. The results are helpful for the design of antifreeze proteins and bioinspired antifreeze materials with superior performance.

High Water Density at Non-Ice-Binding Surfaces Contributes to the Hyperactivity of Antifreeze Proteins

Antifreeze proteins (AFPs) can bind to ice nuclei thereby inhibiting their growth and their hydration shell is believed to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of four moderately-active and four hyperactive AFPs. The local water density around the ice-binding-surface (IBS) is found to be lower than that around the non-ice-binding surface (NIBS) and this difference correlates with the higher hydrophobicity of the former. While the water-density increase (with respect to bulk) around the IBS is similar between moderately-active and hyperactive AFPs, it differs around the NIBS, being higher for the hyperactive AFPs. We hypothesize that while the lower water density at the IBS can pave the way to protein binding to ice nuclei, irrespective of the antifreeze activity, the higher density at the NIBS of the hyperactive AFPs contribute to their enhanced ability in inhibiting ice growth around the bound AFPs.

THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY

Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin

Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at ∼0.1-THz frequency (10-ps timescale) at room temperature. However, the microscopic description of biomolecular functions based on various modes of protein-water-coupled motions remains elusive. A novel approach for perturbing the hydration dynamics in the subterahertz frequency range and probing them at the atomic level is therefore warranted. In this study, we investigated the effect of klystron-based, intense 0.1-THz excitation on the slow dynamics of ubiquitin using NMR-based measurements of hydrogen-deuterium exchange. We demonstrated that the subterahertz irradiation accelerated the hydrogen-deuterium exchange of the amides located in the interior of the protein and hydrophobic surfaces while decelerating this exchange in the amides located in the surface loop and short 3₁₀ helix regions. This subterahertz-radiation-induced effect was qualitatively contradictory to the increased-temperature-induced effect. Our results suggest that the heterogeneous water dynamics occurring at the protein-water interface include components that are nonthermally excited by the subterahertz radiation. Such subterahertz-excited components may be linked to the slow function-related dynamics of the protein.

Genetic Algorithm Approach for the Optimization of Protein Antifreeze Activity Using Molecular Simulations

Antifreeze proteins (AFPs) are of much interest for their ability to inhibit ice growth at low concentrations. In this work, we present a genetic algorithm for the in silico design of AFP mutants with improved antifreeze activity, measured as the predicted thermal hysteresis at a fixed concentration, ΔT_C. Central to the algorithm is our recently developed neural network method for predicting ΔT_C from molecular simulations [Kozuch et al., PNAS, 115, 13252 (2018)]. Applying the algorithm to three structurally diverse AFPs, wfAFP, rQAE, and RiAFP, we find that significantly improved mutants are discovered for rQAE and RiAFP. Testing of the optimized mutants shows an increase in ΔT_C of 0.572 ± 0.11 K (262 ± 50.6%) and 1.33 ± 0.14 K (39.9 ± 4.19%) over the native structures for rQAE and RiAFP, respectively. Structural analysis of the optimized mutants reveals that the algorithm is able to exploit two pathways for enhancing the predicted antifreeze activity of the mutants: (1) increasing the local order of surface waters by encouraging the formation of internal water channels in the protein and (2) increasing the total ice-binding area by improving the planar structure of the ice-binding surface. Additionally, analysis of all mutants explored by the algorithm reveals that a subset of residues, mainly nonpolar, are particularly helpful in improving antifreeze activity at the ice-binding surface.

Antifreeze proteins and homogeneous nucleation: On the physical determinants impeding ice crystal growth

Antifreeze proteins (AFPs) are biopolymers capable of interfering with ice growth. Their antifreeze action is commonly understood considering that the AFPs, by pinning the ice surface, force the crystal-liquid interface to bend forming an ice meniscus, causing an increase in the surface free energy and resulting in a decrease in the freezing point ΔT^max. Here, we present an extensive computational study for a model protein adsorbed on a TIP4P/Ice crystal, computing ΔT^max as a function of the average distance d between AFPs, with simulations spanning over 1 µs. First, we show that the lower the d, the larger the ΔT^max. Then, we find that the water-ice-protein contact angle along the line ΔT^max(d) is always larger than 0°, and we provide a theoretical interpretation. We compute the curvature radius of the stable solid-liquid interface at a given supercooling ΔT ≤ ΔT^max, connecting it with the critical ice nucleus at ΔT. Finally, we discuss the antifreeze capability of AFPs in terms of the protein-water and protein-ice interactions. Our findings establish a unified description of the AFPs in the contest of homogeneous ice nucleation, elucidating key aspects of the antifreeze mechanisms and paving the way for the design of novel ice-controlling materials.

Deciphering the Role of the Non-ice-binding Surface in the Antifreeze Activity of Hyperactive Antifreeze Proteins

Antifreeze proteins (AFPs) show thermal hysteresis through specific interaction with the ice crystal. Hyperactive AFPs interact with the ice surface through a threonine-rich motif present at their ice-binding surface (IBS). Ordering of water around the IBS was extensively investigated. However, the role of non-IBS in ice growth inhibition is yet to be understood completely. The present study explores the nature of hydration and its length-scale evaluation around the non-IBS for hyperactive AFPs. We observed that the hydration layer of non-IBS is liquid-like, even in highly supercooled conditions, and the nature of hydration is drastically different from the hydration pattern of non-AFP surfaces. In similar conditions, the hydration layer around the IBS is ice-like ordered. Non-IBS of the hyperactive AFP exposes toward the bulk and is able to maintain the liquid-like character of its hydration water up to 15 Å. We also find that the amino acid compositions and their spatial distribution on the non-IBS are markedly different from those of the IBS and non-AFP surfaces. These results elucidate the combined role of IBS and non-IBS in ice-growth inhibition. While IBS is required to adsorb on ice efficiently, the exposed non-IBS may prevent ice nucleation/growth on top of the bound AFPs.

Solvent dynamics play a decisive role in the complex formation of biologically relevant redox proteins

Electron transfer processes between proteins are vital in many biological systems. Yet, the role of the solvent in influencing these redox reactions remains largely unknown. In this study, terahertz-time domain spectroscopy (THz-TDS) is used to probe the collective hydration dynamics of flavoenzyme ferredoxin-NADP+-reductase (FNR), electron transfer protein ferredoxin-1 (PetF), and the transient complex that results from their interaction. Results reveal changes in the sub-picosecond hydration dynamics that are dependent upon the surface electrostatic properties of the individual proteins and the transient complex. Retarded solvent dynamics of 8-9 ps are observed for FNR, PetF, and the FNR:PetF transient complex. Binding of the FNR:PetF complex to the substrate NADP+ results in bulk-like solvent dynamics of 7 ps, showing that formation of the ternary complex is entropically favored. Our THz measurements reveal that the electrostatic interaction of the protein surface with water results in charge sensitive changes in the solvent dynamics. Complex formation between the positively charged FNR:NADP+ pre-complex and the negatively charged PetF is not only entropically favored, but in addition the solvent reorganization into more bulk-like water assists the molecular recognition process. The change in hydration dynamics observed here suggests that the interaction with the solvent plays a significant role in mediating electron transfer processes between proteins.

Hydration dynamics of proteins in reverse micelles probed by 1H-NOESY/1H-ROESY NMR and 17O-nuclear quadrupole resonance (NQR)

This study is based on extensive MD simulations of a protein in a reverse micelle to mimic the effect of confinement on biomolecules. This permits the calculation of measurable quantities appearing in NQR and Nuclear Overhauser-NMR despite the high computational effort. We address the long-standing debate about the intermolecular NOE showing that absolute quantities derived from NOESY and ROESY spectra do indeed contain considerable long-range contributions, while ratios thereof are effectively short-ranged due to almost perfect compensation effects. Based on NQR relaxation times, we predict strong rotational retardation of interstitial water between the protein and the surfactant surface. The computed NOE to ROE ratio correlates fairly with experimental results. The solvation dynamics mapped onto the protein surface reflects the spatial heterogeneity of a cell-like system with slow water dynamics in proximity to the cell wall and almost bulk-like behaviour in the water core.

Water structure and dynamics in the hydration layer of a type III anti-freeze protein

We report on a molecular dynamics study on the relation between the structure and the orientational (and hydrogen bond) dynamics of hydration water around the ocean pout AFP III anti-freeze protein. We find evidence for an increasing tetrahedral structure from the area opposite to the ice binding site (IBS) towards the protein IBS, with the strongest signal of tetrahedral structure around the THR-18 residue of the IBS. The tetrahedral structural parameter mostly positively correlates with increased reorientation decay times. Interestingly, for several key (polar) residues that are not part of the IBS but are in its vicinity, we observe a decrease of the reorientation time with increasing tetrahedral structure. A similar anti-correlation is observed for the hydrogen-bonded water molecules. These effects are enhanced at a lower temperature. We interpret these results in terms of the structure-making and structure-breaking residues. Moreover, we investigate the tetrahedral structure and dynamics of waters at a partially dehydrated IBS, and for the protein adsorbed at the air-water interface. We find that the mutation changes the preferred protein orientation upon adsorption at an air-water interface. These results are in agreement with the water-air Vibration Sum Frequency Generation spectroscopic experiments showing a strongly reduced tetrahedral signal upon mutation at the IBS.

Combined molecular dynamics and neural network method for predicting protein antifreeze activity

Antifreeze proteins (AFPs) are a diverse class of proteins that depress the kinetically observable freezing point of water. AFPs have been of scientific interest for decades, but the lack of an accurate model for predicting AFP activity has hindered the logical design of novel antifreeze systems. To address this, we perform molecular dynamics simulation for a collection of well-studied AFPs. By analyzing both the dynamic behavior of water near the protein surface and the geometric structure of the protein, we introduce a method that automatically detects the ice binding face of AFPs. From these data, we construct a simple neural network that is capable of quantitatively predicting experimentally observed thermal hysteresis from a trio of relevant physical variables. The model's accuracy is tested against data for 17 known AFPs and 5 non-AFP controls.

Toward comprehensive measurement of protein hydration dynamics: Facilitation of NMR-based methods by reverse micelle encapsulation

Protein-water interactions are a fundamental determinant of protein structure and function. Despite their importance, the molecular details of water orientations and dynamics near protein surfaces remain poorly understood, largely due to the difficulty of measuring local water mobility near the protein in a site-resolved fashion. Solution NMR-based measurement of water mobility via the nuclear Overhauser effect was presented as a method for performing comprehensive, site-resolved measurements of water dynamics many years ago. Though this approach yielded extensive insight on the dynamics and locations of waters buried within proteins, its promise for measuring surface hydration dynamics was impeded by various technical barriers. Over the past several years, however, this approach has been pursued anew with the aid of reverse micelle encapsulation of proteins of interest. The confined environment of the reverse micelle resolves many of these barriers and permits site-resolved measurement of relative water dynamics across much of the protein surface. Here, the development of this strategy for measuring hydration dynamics is reviewed with particular focus on the important remaining challenges to its widespread application.

Preordering of water is not needed for ice recognition by hyperactive antifreeze proteins

Antifreeze proteins (AFPs) inhibit ice growth in organisms living in cold environments. Hyperactive insect AFPs are particularly effective, binding ice through "anchored clathrate" motifs. It has been hypothesized that the binding of hyperactive AFPs to ice is facilitated by preordering of water at the ice-binding site (IBS) of the protein in solution. The antifreeze protein TmAFP displays the best matching of its binding site to ice, making it the optimal candidate to develop ice-like order in solution. Here we use multiresolution simulations to unravel the mechanism by which TmAFP recognizes and binds ice. We find that water at the IBS of the antifreeze protein in solution does not acquire ice-like or anchored clathrate-like order. Ice recognition occurs by slow diffusion of the protein to achieve the proper orientation with respect to the ice surface, followed by fast collective organization of the hydration water at the IBS to form an anchored clathrate motif that latches the protein to the ice surface. The simulations suggest that anchored clathrate order could develop on the large ice-binding surfaces of aggregates of ice-nucleating proteins (INP). We compute the infrared and Raman spectra of water in the anchored clathrate motif. The signatures of the OH stretch of water in the anchored clathrate motif can be distinguished from those of bulk liquid in the Raman spectra, but not in the infrared spectra. We thus suggest that Raman spectroscopy may be used to probe the anchored clathrate order at the ice-binding surface of INP aggregates.

How proteins modify water dynamics

Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by ¹⁷O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)-the integral rotational correlation time. Numerous ¹⁷O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full ¹⁷O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by ¹⁷O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for ¹⁷O MRD. By contrast, we find that the ¹⁷O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.

The spatial range of protein hydration

Proteins interact with their aqueous surroundings, thereby modifying the physical properties of the solvent. The extent of this perturbation has been investigated by numerous methods in the past half-century, but a consensus has still not emerged regarding the spatial range of the perturbation. To a large extent, the disparate views found in the current literature can be traced to the lack of a rigorous definition of the perturbation range. Stating that a particular solvent property differs from its bulk value at a certain distance from the protein is not particularly helpful since such findings depend on the sensitivity and precision of the technique used to probe the system. What is needed is a well-defined decay length, an intrinsic property of the protein in a dilute aqueous solution, that specifies the length scale on which a given physical property approaches its bulk-water value. Based on molecular dynamics simulations of four small globular proteins, we present such an analysis of the structural and dynamic properties of the hydrogen-bonded solvent network. The results demonstrate unequivocally that the solvent perturbation is short-ranged, with all investigated properties having exponential decay lengths of less than one hydration shell. The short range of the perturbation is a consequence of the high energy density of bulk water, rendering this solvent highly resistant to structural perturbations. The electric field from the protein, which under certain conditions can be long-ranged, induces a weak alignment of water dipoles, which, however, is merely the linear dielectric response of bulk water and, therefore, should not be thought of as a structural perturbation. By decomposing the first hydration shell into polarity-based subsets, we find that the hydration structure of the nonpolar parts of the protein surface is similar to that of small nonpolar solutes. For all four examined proteins, the mean number of water-water hydrogen bonds in the nonpolar subset is within 1% of the value in bulk water, suggesting that the fragmentation and topography of the nonpolar protein-water interface has evolved to minimize the propensity for protein aggregation by reducing the unfavorable free energy of hydrophobic hydration.

The geometry of protein hydration

Based on molecular dynamics simulations of four globular proteins in dilute aqueous solution, with three different water models, we examine several, essentially geometrical, aspects of the protein-water interface that remain controversial or incompletely understood. First, we compare different hydration shell definitions, based on spatial or topological proximity criteria. We find that the best method for constructing monolayer shells with nearly complete coverage is to use a 5 Šwater-carbon cutoff and a 4 Šwater-water cutoff. Using this method, we determine a mean interfacial water area of 11.1 Ų which appears to be a universal property of the protein-water interface. We then analyze the local coordination and packing density of water molecules in the hydration shells and in subsets of the first shell. The mean polar water coordination number in the first shell remains within 1% of the bulk-water value, and it is 5% lower in the nonpolar part of the first shell. The local packing density is obtained from additively weighted Voronoi tessellation, arguably the most physically realistic method for allocating space between protein and water. We find that water in all parts of the first hydration shell, including the nonpolar part, is more densely packed than in the bulk, with a shell-averaged density excess of 6% for all four proteins. We suggest reasons why this value differs from previous experimental and computational results, emphasizing the importance of a realistic placement of the protein-water dividing surface and the distinction between spatial correlation and packing density. The protein-induced perturbation of water coordination and packing density is found to be short-ranged, with an exponential decay "length" of 0.6 shells. We also compute the protein partial volume, analyze its decomposition, and argue against the relevance of electrostriction.

Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions

In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.

Revival of collective water structure and dynamics in reverse micelles brought about by protein encapsulation

A novel mechanism of depolarization in reverse micelles with zwitterionic surfactants and containing polar species but lacking ions is reported.

Macromolecular crowding and the importance of proper hydration for the structure and dynamics of protein solutions

Extensive computational studies of ubiquitin crowding with a special focus on protein hydration directly visible in dielectric spectra.

Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins

Antifreeze Proteins (AFPs) inhibit the growth of an ice crystal by binding to it. The detailed binding mechanism is, however, still not fully understood. We investigated three AFPs using Molecular Dynamics simulations in combination with Grid Inhomogeneous Solvation Theory, exploring their hydration thermodynamics. The observed enthalpic and entropic differences between the ice-binding sites and the inactive surface reveal key properties essential for proteins in order to bind ice: While entropic contributions are similar for all sites, the enthalpic gain for all ice-binding sites is lower than for the rest of the protein surface. In contrast to most of the recently published studies, our analyses show that enthalpic interactions are as important as an ice-like pre-ordering. Based on these observations, we propose a new, thermodynamically more refined mechanism of the ice recognition process showing that the appropriate balance between entropy and enthalpy facilitates ice-binding of proteins. Especially, high enthalpic interactions between the protein surface and water can hinder the ice-binding activity.

Water Dynamics in the Hydration Shells of Biomolecules

The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.

Revival of the Intermolecular Nuclear Overhauser Effect for Mapping Local Protein Hydration Dynamics

The highly heterogeneous hydration dynamics of protein-water interfaces is considered important for protein stability and dynamics, protein folding, enzymatic activity, and even drug design. The nuclear Overhauser effect (NOE) between protein and water protons is the only experimental observable which, in principle, can provide a map of locally resolved hydration dynamics. However, its utility was questioned in various theoretical studies that emphasized the contributions of long-range NOE interactions. We show by a detailed analysis based on molecular dynamics simulations that, contrary to recent claims, the protein-water NOE is an excellent observable to map local hydration dynamics at the protein surface.

In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function

Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.

Perspective: Structure and ultrafast dynamics of biomolecular hydration shells

The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.

Investigation of changes in structure and thermodynamic of spruce budworm antifreeze protein under subfreezing temperature

The aim of this theoretical work is to investigate of the changes in structure and thermodynamics of spruce budworm antifreeze protein (sbAFP) at low temperatures by using molecular dynamics simulation. The aqueous solution will form ice crystal network under the vaguely hexagonal shape at low temperature and fully represented the characteristics of hydrophobic interaction. Like ice crystal network, the cyclohexane region (including cyclohexane molecules) have enough of the characteristics of hydrophobic interaction. Therefore, in this research the cyclohexane region will be used as a representation of ice crystal network to investigate the interactions of sbAFP and ice crystal network at low temperature. The activity of sbAFP in subfreezing environment, therefore, can be clearly observed via the changes of the hydrophobic (cyclohexane region) and hydrophilic (water region) interactions. The obtained results from total energies, hydrogen bond lifetime correlation C(t), radial distribution function, mean square deviation and snapshots of sbAFP complexes indicated that sbAFP has some special changes in structure and interaction with water and cyclohexane regions at 278 K, as being transition temperature point of water molecules in sbAFP complex at low temperatures, which is more structured and support the experimental observation that the sbAFP complex becomes more rigid as the temperature is lowered.

On the coupling between the dynamics of protein and water

The solvation entropy of flexible protein regions is higher than that of rigid regions and contributes differently to the overall thermodynamic stability.

Rotational dynamics of water molecules near biological surfaces with implications for nuclear quadrupole relaxation

Based on Molecular Dynamics simulations of two different systems, the protein ubiquitin dissolved in water and an AOT reverse micelle, we present a broad analysis of the single particle rotational dynamics of water. A comprehensive connection to NQR, which is a prominent experimental method in this field, is developed, based on a reformulation of its theoretical framework. Interpretation of experimental NQR results requires a model which usually assumes that the NQR experiences retardation only in the first hydration shell. Indeed, the present study shows that this first-shell model is correct. Moreover, previous experimental retardation factors are quantitatively reproduced. All of this is seemingly contradicted by results of other methods, e.g., dielectric spectroscopy, responsible for a long-standing debate in this field. Our detailed analysis shows that NQR omits important information contained in overall water dynamics, most notably, the retardation of the water dipole axis in the electric field exerted by a biological surface.

Ice-nucleating bacteria control the order and dynamics of interfacial water

Ice-nucleating organisms play important roles in the environment. With their ability to induce ice formation at temperatures just below the ice melting point, bacteria such as Pseudomonas syringae attack plants through frost damage using specialized ice-nucleating proteins. Besides the impact on agriculture and microbial ecology, airborne P. syringae can affect atmospheric glaciation processes, with consequences for cloud evolution, precipitation, and climate. Biogenic ice nucleation is also relevant for artificial snow production and for biomimetic materials for controlled interfacial freezing. We use interface-specific sum frequency generation (SFG) spectroscopy to show that hydrogen bonding at the water-bacteria contact imposes structural ordering on the adjacent water network. Experimental SFG data and molecular dynamics simulations demonstrate that ice-active sites within P. syringae feature unique hydrophilic-hydrophobic patterns to enhance ice nucleation. The freezing transition is further facilitated by the highly effective removal of latent heat from the nucleation site, as apparent from time-resolved SFG spectroscopy.

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. 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.

Water-Mediated Dimerization of Ubiquitin Ions Captured by Cryogenic Ion Mobility-Mass Spectrometry

The dynamics, structures, and functions of most biological molecules are strongly influenced by the nature of the peptide's or protein's interaction with water. Here, cryogenic ion mobility-mass spectrometry studies of ubiquitin have directly captured a water-mediated protein-protein binding event involving hydrated, noncovalently bound dimer ions in solution, and this interaction has potential relevance to one of the most important protein-protein interactions in nature. As solvent is removed, dimer ions, viz. [2 M + 14H](14+), can be stabilized by only a few attached water molecules prior to dissociation into individual monomeric ions. The hydrophobic patch of ubiquitin formed by the side chains of Leu-8, Ile-44, and Val-70 meet all the necessary conditions for a protein-protein binding "hot spot," including the requirement for occlusion of water to nearby hydrophilic sites, and it is suggested that this interaction is responsible for formation of the hydrated noncovalent ubiquitin dimer.

Characterization of the Local Structure in Liquid Water by Various Order Parameters

A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism.