Water Determines the Structure and Dynamics of Proteins

Fast-field-cycling NMR at very low magnetic fields: water molecular dynamic biomarkers of glioma cell invasion and migration

Our objective was to study NMR relaxometry of glioma invasion/migration at very low field (<2 mT) by fast-field-cycling NMR (FFC-NMR) and to decipher the pathophysiological processes of glioma that are responsible for relaxation changes in order to open a new diagnostic method that can be extended to imaging. The phenotypes of two new glioma mouse models, Glio6 and Glio96, were characterized by T_2w -MRI, HE histology, Ki-67 immunohistochemistry (IHC) and CXCR4 RT-qPCR, and were compared with the U87 model. R₁ dispersions of glioma tissues were acquired at low field (0.1 mT-0.8 T) ex vivo and were fitted with Lorentzian and power-law models to extract FFC biomarkers related to the molecular dynamics of water. In order to decipher relaxation changes, three main invasion/migration pathophysiological processes were studied: hypoxia, H₂ O₂ function and the water-channel aquaporin-4 (AQP4). Glio6 and Glio96 were characterized with invasion/migration phenotype and U87 with high cell proliferation as a solid glioma. At very low field, invasion/migration versus proliferation was characterized by a decrease in the relaxation-rate constant (ΔR₁  ≈ -32% at 0.1 mT) and correlation time (≈-40%). These decreases corroborated the AQP4-IHC overexpression (Glio6/Glio96: +92%/+46%), suggesting rapid transcytolemmal water exchange, which was confirmed by the intracellular water-lifetime τ_IN decrease (Δτ_IN  ≈ -30%). In functional experiments, AQP4 expression, τ_IN and the relaxation-rate constant at very low field were all found to be sensitive to hypoxia and to H₂ O₂ stimuli. At very low field the role of water exchanges in relaxation modulation was confirmed, and for the first time it was linked to the glioma invasion/migration and to its main pathophysiological processes: hypoxia, H₂ O₂ redox signaling and AQP4 expression. The method appears appropriate to evaluate the effect of drugs that can target these pathophysiological mechanisms. Finally, FFC-NMR operating at low field is demonstrated to be sensitive to invasion glioma phenotype and can be straightforwardly extended to FFC-MRI as a new cancer invasion imaging method in the clinic.

Tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS): a promising analytical method for investigating heterogenous samples

Ion mobility spectrometry/mass spectrometry (IMS/MS) is widely used to study various levels of protein structure. Here, we review the current state of affairs in tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS). Two different tTIMS/MS instruments are discussed in detail: the first tTIMS/MS instrument, constructed from coaxially aligning two TIMS devices; and an orthogonal tTIMS/MS configuration that comprises an ion trap for irradiation of ions with UV photons. We discuss the various workflows the two tTIMS/MS setups offer and how these can be used to study primary, tertiary, and quaternary structures of protein systems. We also discuss, from a more fundamental perspective, the processes that lead to denaturation of protein systems in tTIMS/MS and how to soften the measurement so that biologically meaningful structures can be characterised with tTIMS/MS. We emphasize the concepts underlying tTIMS/MS to underscore the opportunities tandem-ion mobility spectrometry methods offer for investigating heterogeneous samples.

Water clusters and density fluctuations in liquid water based on extended hierarchical clustering methods

The microscopic structures of liquid water at ambient temperatures remain a hot debate, which relates with structural and density fluctuations in the hydrogen bond network. Here, we use molecular dynamics simulations of liquid water to study the properties of three-dimensional cage-like water clusters, which we investigate using extended graph-based hierarchical clustering methods. The water clusters can cover over 95% of hydrogen bond network, among which some clusters maximally encompass thousands of molecules extending beyond 3.0 nm. The clusters imply fractal behaviors forming percolating networks and the morphologies of small and large clusters show different scaling rules. The local favored clusters and the preferred connections between adjacent clusters correspond to lower energy and conformational entropy depending on cluster topologies. Temperature can destroy large clusters into small ones. We show further that the interior of clusters favors high-density patches. The water molecules in the small clusters, inside which are the void regarded as hydrophobic objects, have a preference for being more tetrahedral. Our results highlight the properties and changes of water clusters as the fundamental building blocks of hydrogen bond networks. In addition, the water clusters can elucidate structural and density fluctuations on different length scales in liquid water.

Water Dynamics in Cancer Cells: Lessons from Quasielastic Neutron Scattering

The severity of the cancer statistics around the globe and the complexity involving the behavior of cancer cells inevitably calls for contributions from multidisciplinary areas of research. As such, materials science became a powerful asset to support biological research in comprehending the macro and microscopic behavior of cancer cells and untangling factors that may contribute to their progression or remission. The contributions of cellular water dynamics in this process have always been debated and, in recent years, experimental works performed with Quasielastic neutron scattering (QENS) brought new perspectives to these discussions. In this review, we address these works and highlight the value of QENS in comprehending the role played by water molecules in tumor cells and their response to external agents, particularly chemotherapy drugs. In addition, this paper provides an overview of QENS intended for scientists with different backgrounds and comments on the possibilities to be explored with the next-generation spectrometers under construction.

Spatially Resolved Hydration Thermodynamics in Biomolecular Systems

Water is essential for the structure, dynamics, energetics, and thus the function of biomolecules. It is a formidable challenge to elicit, in microscopic detail, the role of the solvation-related driving forces of biomolecular processes, such as the enthalpy and entropy contributions to the underlying free-energy landscape. In this Perspective, we discuss recent developments and applications of computational methods that provide a spatially resolved map of hydration thermodynamics in biomolecular systems and thus yield atomic-level insights to guide the interpretation of experimental observations. An emphasis is on the challenge of quantifying the hydration entropy, which requires characterization of both the motions of the biomolecules and of the water molecules in their surrounding.

Hydration Dynamics of Model Peptides with Different Hydrophobic Character

The multi-scale dynamics of aqueous solutions of the hydrophilic peptide N-acetyl-glycine-methylamide (NAGMA) have been investigated through extended frequency-range depolarized light scattering (EDLS), which enables the broad-band detection of collective polarizability anisotropy fluctuations. The results have been compared to those obtained for N-acetyl-leucinemethylamide (NALMA), an amphiphilic peptide which shares with NAGMA the same polar backbone, but also contains an apolar group. Our study indicates that the two model peptides induce similar effects on the fast translational dynamics of surrounding water. Both systems slow down the mobility of solvating water molecules by a factor 6–8, with respect to the bulk. Moreover, the two peptides cause a comparable far-reaching spatial perturbation extending to more than two hydration layers in diluted conditions. The observed concentration dependence of the hydration number is explained considering the random superposition of different hydration shells, while no indication of solute aggregation phenomena has been found. The results indicate that the effect on the dynamics of water solvating the amphiphilic peptide is dominated by the hydrophilic backbone. The minor impact of the hydrophobic moiety on hydration features is consistent with structural findings derived by Fourier transform infrared (FTIR) measurements, performed in attenuated total reflectance (ATR) configuration. Additionally, we give evidence that, for both systems, the relaxation mode in the GHz frequency range probed by EDLS is related to solute rotational dynamics. The rotation of NALMA occurs at higher timescales, with respect to the rotation of NAGMA; both processes are significantly slower than the structural dynamics of hydration water, suggesting that solute and solvent motions are uncoupled. Finally, our results do not indicate the presence of super-slow water (relaxation times in the order of tens of picoseconds) around the peptides investigated.

Desiccation‐tolerance and globular proteins adsorb similar amounts of water

When exposed to desiccation stress, extremotolerant organisms from all domains of life produce protective disordered proteins with the potential to inform the design of excipients for formulating biologics and industrial enzymes. However, the mechanism(s) of desiccation protection remain largely unknown. To investigate the role of water sorption in desiccation protection, we use thermogravimetric analysis to study water adsorption by two desiccation-tolerance proteins, cytosolic abundant heat soluble protein D from tardigrades and late embryogenesis abundant protein 4 from the anhydrobiotic midge Polypedilum vanderplanki, and, as a control, the globular B1 domain of staphylococcal protein G. All samples adsorb similar amounts of water, suggesting that modulated water retention is not responsible for dehydration protection by desiccation-tolerance proteins.

Critical In-Plane Density of Polyelectrolyte Brush for the Ordered Hydrogen-Bonded Structure of Incorporated Water

A polymer electrolyte brush is a reasonable platform to confine water molecules within a nanoscopic area to study their role in the function of interacting media because of their adjustable nanospace and charge by changing the in-plane density and side chains of the brush. Here, we demonstrate how the in-plane spacing of cationic polymer brush chains, poly[2-(methacryloyloxy)ethyltrimethylammonium chloride] (PMTAC), affects the hydrogen bond configuration of incorporated water using soft X-ray emission spectroscopy. At the critical in-plane density σ = 0.30 chains/nm² of PMTAC, tetrahedrally coordinated water molecules started to melt into distorted or broken hydrogen-bonded configurations. Considering the charge on the quaternary ammonium cations, the electric field required to form a tetrahedrally coordinated hydrogen-bonded configuration was estimated as ∼500 kV cm^-1 and is effective up to ∼1 nm from the surface of the polymer chain. These findings are useful for designing specific interface properties and the resultant surface function of polyelectrolyte-based materials.

Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics

We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polymers, as they can be precisely synthesized with a variety of sidechain chemistries. We examine water behavior near a set of peptoid oligomers in which the number and placement of nonpolar versus polar sidechains are systematically varied. To do this, we leverage a new computational workflow enabling accurate sampling of polypeptoid conformations. We find that the hydration waters are less dense, are more tetrahedral, and have slower dynamics compared to bulk water. The magnitude of these shifts increases with the number of nonpolar groups. We also find that shifts in the water structure and dynamics are strongly correlated, suggesting that experimental insight into the dynamics of hydration water obtained by Overhauser dynamic nuclear polarization (ODNP) also contains information about water structural properties. We then demonstrate the ability of ODNP to probe site-specific dynamics of hydration water near these model peptoid systems.

On the influence of water on THz vibrational spectral features of molecular crystals

The nanoscale structure of molecular assemblies plays a major role in many (μ)-biological mechanisms. Molecular crystals are one of the most simple of these assemblies and are widely used in a variety of applications from pharmaceuticals and agrochemicals, to nutraceuticals and cosmetics. The collective vibrations in such molecular crystals can be probed using terahertz spectroscopy, providing unique characteristic spectral fingerprints. However, the association of the spectral features to the crystal conformation, crystal phase and its environment is a difficult task. We present a combined computational-experimental study on the incorporation of water in lactose molecular crystals, and show how simulations can be used to associate spectral features in the THz region to crystal conformations and phases. Using periodic DFT simulations of lactose molecular crystals, the role of water in the observed lactose THz spectrum is clarified, presenting both direct and indirect contributions. A specific experimental setup is built to allow the controlled heating and corresponding dehydration of the sample, providing the monitoring of the crystal phase transformation dynamics. Besides the observation that lactose phases and phase transformation appear to be more complex than previously thought - including several crystal forms in a single phase and a non-negligible water content in the so-called anhydrous phase - we draw two main conclusions from this study. Firstly, THz modes are spread over more than one molecule and require periodic computation rather than a gas-phase one. Secondly, hydration water does not only play a perturbative role but also participates in the facilitation of the THz vibrations.

Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques

Water often plays a key role in protein structure, molecular recognition, and mediating protein-ligand interactions. Thus, free energy calculations must adequately sample water motions, which often proves challenging in typical MD simulation time scales. Thus, the accuracy of methods relying on MD simulations ends up limited by slow water sampling. Particularly, as a ligand is removed or modified, bulk water may not have time to fill or rearrange in the binding site. In this work, we focus on several molecular dynamics (MD) simulation-based methods attempting to help rehydrate buried water sites: BLUES, using nonequilibrium candidate Monte Carlo (NCMC); grand, using grand canonical Monte Carlo (GCMC); and normal MD. We assess the accuracy and efficiency of these methods in rehydrating target water sites. We selected a range of systems with varying numbers of waters in the binding site, as well as those where water occupancy is coupled to the identity or binding mode of the ligand. We analyzed the rehydration of buried water sites in binding pockets using both clustering of trajectories and direct analysis of electron density maps. Our results suggest both BLUES and grand enhance water sampling relative to normal MD and grand is more robust than BLUES, but also that water sampling remains a major challenge for all of the methods tested. The lessons we learned for these methods and systems are discussed.

Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena

Molecular dynamics simulation is the most popular computational technique for investigating the structural and dynamical behaviour of proteins, in search of the molecular basis of their function. Far from being a completely settled field of research, simulations are still evolving to best capture the essential features of the atomic interactions that govern a protein's inner motions. Modern force fields are becoming increasingly accurate in providing a physical description adequate to this purpose, and allow us to model complex biological systems under fairly realistic conditions. Furthermore, the use of accelerated sampling techniques is improving our access to the observation of progressively larger molecular structures, longer time scales, and more hidden functional events. In this review, the basic principles of molecular dynamics simulations and a number of key applications in the area of protein science are summarized, and some of the most important results are discussed. Examples include the study of the structure, dynamics and binding properties of 'difficult' targets, such as intrinsically disordered proteins and membrane receptors, and the investigation of challenging phenomena like hydration-driven processes and protein aggregation. The findings described provide an overall picture of the current state of this research field, and indicate new perspectives on the road ahead to the upcoming future of molecular simulations.

Site-directed fluorescence approaches to monitor the structural dynamics of proteins using intrinsic Trp and labeled with extrinsic fluorophores

Comprehensive understanding of a protein’s function depends on having reliable, sophisticated tools to study protein structural dynamics in physiologically-relevant conditions. Here, we present an effective, robust step-by-step protocol to monitor the structural dynamics (including hydration dynamics) of a protein utilizing various site-directed fluorescence (SDFL) approaches. This protocol should be widely applicable for studying soluble proteins, intrinsically-disordered proteins, and membrane proteins.

For complete details on the use and execution of this protocol, please refer to Das et al. (2020), Das and Raghuraman (2021), and Chatterjee et al. (2021).

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A step-by-step protocol to monitor the structural dynamics of proteins using SDFL

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Applicable to proteins with intrinsic Trp and labeled with extrinsic fluorophores

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This protocol should be widely applicable for soluble and membrane proteins

Molecular dynamics simulations of structural and dynamical aspects of DNA hydration water

Water is a remarkable liquid, both because of it is intriguing but also because of its importance. Water plays a key role on the structure and function of biological molecules, but on the other hand also the structure and dynamics of water are deeply influenced by its interactions with biological molecules, specially at low temperatures, where water's anomalies are enhanced. Here we present extensive molecular dynamics simulations of water hydrating a oligonucleotide down to very low temperatures (supercooled water), comparing four water models and analyzing the water structure and dynamics in different domains: water in the minor groove, water in the major groove and bulk water. We found that the water in the grooves is slowed down by the interactions with the nucleic acid and a hints of a dynamic transition regarding translational and orientational dynamics were found, specially for the water models TIP4P/2005 and TIP4P-Ew, which also showed the closest agreement with available experimental data. The behavior of water in such extreme conditions is relevant for the study of cryopreservation of biological tissues.

The origin and impact of bound water around intrinsically disordered proteins

Proteins and water couple dynamically over a wide range of time scales. Motivated by their central role in protein function, protein-water dynamics and thermodynamics have been extensively studied for structured proteins, where correspondence to structural features has been made. However, properties controlling intrinsically disordered protein (IDP)-water dynamics are not yet known. We report results of megahertz-to-terahertz dielectric spectroscopy and molecular dynamics simulations of a group of IDPs with varying charge content along with structured proteins of similar size. Hydration water around IDPs is found to exhibit more heterogeneous rotational and translational dynamics compared with water around structured proteins of similar size, yielding on average more restricted dynamics around individual residues of IDPs, charged or neutral, compared with structured proteins. The on-average slower water dynamics is found to arise from excess tightly bound water in the first hydration layer, which is related to greater exposure to charged groups. The more tightly bound water to IDPs correlates with the smaller hydration shell found experimentally, and affects entropy associated with protein-water interactions, the contribution of which we estimate based on the dielectric measurements and simulations. Water-IDP dynamic coupling at terahertz frequencies is characterized by the dielectric measurements and simulations.

From Protein Design to the Energy Landscape of a Cold Unfolding Protein

Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein-water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ∼0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.

Investigating Crystalline Protein Suspension Formulations of Pembrolizumab from MAS NMR Spectroscopy

Developing biological formulations to maintain the chemical and structural integrity of therapeutic antibodies remains a significant challenge. Monoclonal antibody (mAb) crystalline suspension formulation is a promising alternative for high concentration subcutaneous drug delivery. It demonstrates many merits compared to the solution formulation to reach a high concentration at the reduced viscosity and enhanced stability. One main challenge in drug development is the lack of high-resolution characterization of the crystallinity and stability of mAb microcrystals in the native formulations. Conventional analytical techniques often cannot evaluate structural details of mAb microcrystals in the native suspension due to the presence of visible particles, relatively small crystal size, high protein concentration, and multicomponent nature of a liquid formulation. This study demonstrates the first high-resolution characterization of mAb microcrystalline suspension using magic angle spinning (MAS) NMR spectroscopy. Crystalline suspension formulation of pembrolizumab (Keytruda, Merck & Co., Inc., Kenilworth, NJ 07033, U.S.) is utilized as a model system. Remarkably narrow ¹³C spectral linewidth of approximately 29 Hz suggests a high order of crystallinity and conformational homogeneity of pembrolizumab crystals. The impact of thermal stress and dehydration on the structure, dynamics, and stability of these mAb crystals in the formulation environment is evaluated. Moreover, isotopic labeling and heteronuclear ¹³C and ¹⁵N spectroscopies have been utilized to identify the binding of caffeine in the pembrolizumab crystal lattice, providing molecular insights into the cocrystallization of the protein and ligand. Our study provides valuable structural details for facilitating the design of crystalline suspension formulation of Keytruda and demonstrates the high potential of MAS NMR as an advanced tool for biophysical characterization of biological therapeutics.

The Seed and the Metabolism Regulation

Simple Summary

Seeds are the reproductive units of higher plants. They have a significant place in agriculture and plant diversity maintenance. Because they are dehydrated, they can remain viable in the environment for centuries. This review explores the dry seed as a metabolically inactive organism, but well organized to protect its components and enter intensive repair to restore metabolic activities upon imbibition for the completion of germination. Metabolism regulation is also critical for the most important seed traits, dormancy, and ageing recovery capacity.

Abstract

The seed represents a critical stage in the life cycle of flowering plants. It corresponds to a dry structure carrying the plant embryo in dormant or quiescent state. Orthodox seeds possess a very low water content, preventing biochemical reactions, especially respiration. If the desiccation of living organisms leads to a loss of homeostasis, structure, and metabolism, the seeds go through it successfully thanks to their structure, cellular organization, and growth regulation. Seeds set up a certain number of sophisticated molecules to protect valuable macromolecules or organelles from dehydration/rehydration cycles. Moreover, dormancy takes place in a coordinated process with environmental cues in order to ensure embryo development at the most appropriate conditions for the establishment of the new plant. Moreover, repair processes are programmed to be ready to operate to maximize germination success and seed longevity. This review focuses on the physiology of the seed as related to hydration forces, respiration, and biochemical reactions in the transition from thermodynamically undefined dry state to self-sustained living system. Such processes are of importance for basic knowledge of the regulation of metabolism of living organisms, but also for the control of germination in the context of climate change due to global warming.

Decoding the Kinetic Pathways toward a Lipid/DNA Complex of Alkyl Alcohol Cationic Lipids Formed in a Microfluidic Channel

Complexes of cationic liposomes with DNA have emerged as promising nonviral vectors for delivering genetic information into cells for gene therapy. Kinetics of the liposome/DNA complex (lipoplex) formation on a millisecond time scale are studied by monitoring time evolution of fluorescence of 8-anilino-1-naphthalene sulfonic acid (ANS) and ethidium bromide (EtBr) in a continuous flow microfluidic channel coupled to a fluorescence microscope. The formation of lipoplexes between calf thymus DNA and liposomes based on two novel cationic lipids (Lip1810 and Lip1814) are found to follow a two-step process with kinetic constants for the Lip1814/DNA complex (k₁ = 1120-1383 s^-1, k₂ = 0.227-1.45 s^-1) being significantly different from those (k₁ = 68.53-98.5 s^-1, k₂ = 32.3-60.19 s^-1) corresponding to formation of the Lip1810/DNA complex. The kinetic pathway leading to the formation of Lip1814/DNA complex is diffusion-controlled whereas the formation of Lip1810/DNA complex occurs by a conformational rearrangement-controlled pathway. The observed difference in the kinetics of lipoplex formation likely originates from different structures of the lipid/DNA complexes.

Seeking Solvation: Exploring the Role of Protein Hydration in Silk Gelation

The mechanism by which arthropods (e.g., spiders and many insects) can produce silk fibres from an aqueous protein (fibroin) solution has remained elusive, despite much scientific investigation. In this work, we used several techniques to explore the role of a hydration shell bound to the fibroin in native silk feedstock (NSF) from Bombyx mori silkworms. Small angle X-ray and dynamic light scattering (SAXS and DLS) revealed a coil size (radius of gyration or hydrodynamic radius) around 12 nm, providing considerable scope for hydration. Aggregation in dilute aqueous solution was observed above 65 °C, matching the gelation temperature of more concentrated solutions and suggesting that the strength of interaction with the solvent (i.e., water) was the dominant factor. Infrared (IR) spectroscopy indicated decreasing hydration as the temperature was raised, with similar changes in hydration following gelation by freezing or heating. It was found that the solubility of fibroin in water or aqueous salt solutions could be described well by a relatively simple thermodynamic model for the stability of the protein hydration shell, which suggests that the affected water is enthalpically favoured but entropically penalised, due to its reduced (vibrational or translational) dynamics. Moreover, while the majority of this investigation used fibroin from B. mori, comparisons with published work on silk proteins from other silkworms and spiders, globular proteins and peptide model systems suggest that our findings may be of much wider significance.

Influence of protic ionic liquids on hydration of glycine based peptides

The structure of water, especially around the solute is thought to play an important role in many biological and chemical processes. Water-peptide and cosolvent-peptide interactions are crucial in determining the structure and function of protein molecules. In this work, we present the H-bonding analysis for model peptides like glycyl-glycine (gly-gly), glycine-ւ-valine (gly-val), glycyl-ւ-leucine (gly-leu) and triglycine (trigly) and triethylammonium based carboxylate protic ionic liquids (PILs) in aqueous solutions as well as for peptides in ∼0.2 mol·L^-1 of aqueous PIL solutions in the spectral range of 7800-5500 cm^-1 using Fourier transform near-infrared (FT-NIR) spectroscopy at 298.15 K. The hydration numbers for peptides and PILs were obtained using NIR method of simultaneous estimation of hydration spectrum and hydration number of a solute dissolved in water. The H-bond of water molecules around peptides and PILs are found to be stronger and shorter than those in pure liquid water. We observe that the hydration shell around zwitterions is a clathrate-like cluster of water in which ions entrap. Watery network analysis confirms that singly H-bonded species or NHBs changes to partial or distorted ice-like structures of water in the hydration shell of PILs. The overall water H-bonding in the hydration sphere of PILs increases in the order TEAF < TEAA < TEAG < TEAPy ≈ TEAP < TEAB. The influence of PILs on hydration behavior of peptides is explored in terms of H-bonding, cooperativity, hydrophobicity, water structural changes, ionic interactions etc.

Model Folded Hydrophobic Polymers Reside in Highly Branched Voids

By using advanced data analysis techniques, we characterize the shape of the voids surrounding model polymers of different sizes in water, observed in molecular dynamics simulations. We find that even when the model polymer is folded, the voids are extremely rough, with branches that can extend to over 1 nm away from the polymer. Water molecules in contact with the void retain close-to-bulk properties in terms of local structure. The branches disappear, and the voids start resembling the quasispherical shape predicted by dewetting theory only when they surround particles with a radius ∼1 nm, well above the size occupied by a folded hydrophobic polymer. Our results provide fresh insights into the microscopic origins of the vapor-like interfaces underlying dewetting and drying transitions.

Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents

Biocatalysis in organic solvents (OSs) is very appealing for the industry in producing bulk and/or fine chemicals, such as pharmaceuticals, biodiesel, and fragrances. The poor performance of enzymes in OSs (e.g., reduced activity, insufficient stability, and deactivation) negates OSs' excellent solvent properties. Molecular dynamics (MD) simulations provide a complementary method to study the relationship between enzymes dynamics and the stability in OSs. Here we describe computational procedure for MD simulation of enzymes in OSs with an example of Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO) cosolvent with software GROMACS. We discuss main essential practical issues considered (such as choice of force field, parameterization, simulation setup, and trajectory analysis). The core part of this protocol (enzyme-OS system setup, analysis of structural-based and solvation-based observables) is transferable to other enzymes and any OS systems. Combining with experimental studies, the obtained molecular knowledge is most likely to guide researchers to access rational protein engineering approaches to tailor OS resistant enzymes and expand the scope of biocatalysis in OS media. Finally, we discuss potential solutions to overcome the remaining challenges of computational biocatalysis in OSs and briefly draw future directions for further improvement in this field.

Hydration Shell Model for Expeditious and Reliable Individual Hydrogen Bond Energies in Large Water Clusters

Recently, we have developed and tested a method, based on the molecular tailoring approach (MTA-based) to directly estimate the individual hydrogen bond (HB) energies in molecular clusters. Application of this...

Recent developments on bismuth oxyhalide-based functional nanomaterials for biomedical applications

Multifunctional bismuth oxyhalide (BiOX, X = F, Cl, Br, and I) nanomaterials have great potential advantages in medical diagnostic and therapeutic applications. Pure BiOX nanomaterials have some limitations such as...

Water adsorption in porous organic crystals of adamantane-bearing macrocycles

Adamantane-based macrocycles with pyrazine or tetrazine units afforded porous crystals with distinct surface properties of 1D pores, which captured multiple water molecules from the air or liquid water in a single-crystal-to-single-crystal fashion.

Single-particle and collective excitations of polar water molecules confined in nano-pores within cordierite crystal lattice

Recently, the low-temperature phase of water molecules confined within nanocages formed by the crystalline lattice of water-containing cordierite crystals was reported to comprise domains with ferroelectrically ordered dipoles within the...

Experimental mapping of short-wavelength phonons in proteins

Phonons are quasi-particles, observed as lattice vibrations in periodic materials, that often dampen in the presence of structural perturbations. Nevertheless, phonon-like collective excitations exist in highly complex systems, such as proteins, although the origin of such collective motions has remained elusive. Here we present a picture of temperature and hydration dependence of collective excitations in green fluorescent protein (GFP) obtained by inelastic neutron scattering. Our results provide evidence that such excitations can be used as a measure of flexibility/softness and are possibly associated with the protein’s activity. Moreover, we show that the hydration water in GFP interferes with the phonon propagation pathway, enhancing the structural rigidity and stability of GFP.

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Quantum phenomena in biology have long fascinated people around the world

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This work presents a direct experimental observation of phonons, the quantum vibrations in a protein

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The collective excitations or phonons in proteins were detected by utilizing inelastic neutron scattering technique at Oak Ridge National Laboratory

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Our results illustrate the flexibility-activity relationship in proteins by mapping the temperature and hydration dependence of these collective excitations

The role of conformational dynamics on the activity of polymer-conjugated CalB in organic solvents

A perennial interest in enzyme catalysis has been expanding its applicability from aqueous phase where enzymes are naturally evolved to organic solvents in which the majority of industrial chemical synthesis...

Terahertz circular polarization sensing for protein denaturation based on a twisted dual-layer metasurface

Protein denaturation has very important research value in nutrition, biomedicine, and the food industry, which is caused by the changes in the molecular structure of the protein. Since the collective vibrational and torsional modes of protein molecules are within the terahertz (THz) frequency range, THz spectroscopy can characterize the protein denaturation with several advantages of non-contact, label-free, real-time, and non-destructive. Therefore, we proposed a reflective THz time-domain polarization spectroscopy sensing method, and use a flexible twisted dual-layer metasurface film as a sensor to realize the thermal denaturation sensing, concentration sensing, and types identification of protein aqueous solutions. The experiment tested three proteins (bovine serum albumin, whey protein, and ovalbumin), and the results show that: for the thermal denaturation sensing, its detection sensitivity can reach 6.30 dB/% and the detection accuracy is 0.77%; for the concentration sensing, the detection sensitivity and detection accuracy reach 52.9 dB·mL/g and 3.6·10^-5 g/mL, respectively; in addition, different protein types can be distinguished by the difference of the circular polarization spectra.

Accurate Machine Learning Prediction of Protein Circular Dichroism Spectra with Embedded Density Descriptors

A data-driven approach to simulate circular dichroism (CD) spectra is appealing for fast protein secondary structure determination, yet the challenge of predicting electric and magnetic transition dipole moments poses a substantial barrier for the goal. To address this problem, we designed a new machine learning (ML) protocol in which ordinary pure geometry-based descriptors are replaced with alternative embedded density descriptors and electric and magnetic transition dipole moments are successfully predicted with an accuracy comparable to first-principle calculation. The ML model is able to not only simulate protein CD spectra nearly 4 orders of magnitude faster than conventional first-principle simulation but also obtain CD spectra in good agreement with experiments. Finally, we predicted a series of CD spectra of the Trp-cage protein associated with continuous changes of protein configuration along its folding path, showing the potential of our ML model for supporting real-time CD spectroscopy study of protein dynamics.

Key role of a structural water molecule for the specificity of 14F7-An antitumor antibody targeting the NeuGc GM3 ganglioside

Tumor-associated glycolipids such as NeuGc GM3 are auspicious molecular targets in antineoplastic therapies and vaccine strategies. 14F7 is a monoclonal IgG1 with high clinical potential in cancer immunotherapy as it displays extraordinary specificity for NeuGc GM3, while it does not recognize the very similar, ubiquitous NeuAc GM3. Here we present the 2.3 Å crystal structure of the 14F7 antigen-binding domain (14F7 scFv) in complex with the NeuGc GM3 trisaccharide. Modeling analysis and previous mutagenesis data suggest that 14F7 may also bind to an alternative NeuGc GM3 conformation, not observed in the crystal structure. The most intriguing finding, however, was that a water molecule centrally placed in the complementarity-determining region directly mediates the specificity of 14F7 to NeuGc GM3. This has profound impact on the complexity of engineering in the binding site and provides an excellent example of the importance in understanding the water structure in antibody-antigen interactions.

Comparing the Expense and Accuracy of Methods to Simulate Atomic Vibrations in Rubrene

Atomic vibrations can inform about materials properties from hole transport in organic semiconductors to correlated disorder in metal-organic frameworks. Currently, there are several methods for predicting these vibrations using simulations, but the accuracy-efficiency tradeoffs have not been examined in depth. In this study, rubrene is used as a model system to predict atomic vibrational properties using six different simulation methods: density functional theory, density functional tight binding, density functional tight binding with a Chebyshev polynomial-based correction, a trained machine learning model, a pretrained machine learning model called ANI-1, and a classical forcefield model. The accuracy of each method is evaluated by comparison to the experimental inelastic neutron scattering spectrum. All methods discussed here show some accuracy across a wide energy region, though the Chebyshev-corrected tight-binding method showed the optimal combination of high accuracy with low expense. We then offer broad simulation guidelines to yield efficient, accurate results for inelastic neutron scattering spectrum prediction.

Probing the Bovine Hemoglobin Adsorption Process and its Influence on Interfacial Water Structure at the Air-Water Interface

*These authors contributed equally to this work.The molecular-level insight of protein adsorption and its kinetics at interfaces is crucial because of its multifold role in diverse fundamental biological processes and applications. In the present study, the sum frequency generation (SFG) vibrational spectroscopy has been employed to demonstrate the adsorption process of bovine hemoglobin (BHb) protein molecules at the air-water interface at interfacial isoelectric point of the protein. It has been observed that surface coverage of BHb molecules significantly influences the arrangement of the protein molecules at the interface. The time-dependent SFG studies at two different frequencies in the fingerprint region elucidate the kinetics of protein denaturation process and its influence on the hydrogen-bonding network of interfacial water molecules at the air-water interface. The initial growth kinetics suggests the synchronized behavior of protein adsorption process with the structural changes in the interfacial water molecules. Interestingly, both the events carry similar characteristic time constants. However, the conformational changes in the protein structure due to the denaturation process stay for a long time, whereas the changes in water structure reconcile quickly. It is revealed that the protein denaturation process is followed by the advent of strongly hydrogen-bonded water molecules at the interface. In addition, we have also carried out the surface tension kinetics measurements to complement the findings of our SFG spectroscopic results.

Supercooled nano-droplets of water confined in hydrophobic rubber

Hydrophobic elastomers are capable of absorbing a small amount of water that forms droplets around hydrophilic sites. These systems allow the study of confinement effects by a hydrophobic environment on the dynamics and thermodynamic behaviour of water molecules. The freezing-melting properties and the dynamics of water inside nano-droplets in butyl rubber are affected, as revealed by differential scanning calorimetry (DSC) and deuterium nuclear magnetic resonance (²H-NMR). Upon cooling down, all water crystalizes with a bimodal droplet population (d_a = 3.4 nm and d_b = 4.4 nm) in a temperature range associated with the droplet size distribution. However, the melting temperature is not shifted according to the Gibbs-Thomson equation. The relative decrease of the ²H-NMR longitudinal magnetization is not a single exponential and, by inverse Laplace transformation, it was deduced to be bimodal in agreement with the DSC measurements (T_1,a ∼ 10 ms and T_1,b ∼ 200 ms). The deduced correlation time of molecular reorientation is longer than that of bulk water and the behaviour with temperature follows the Vogel-Fulcher-Tammann (VFT) equations with a changing fragility as the droplet size is reduced when reducing hydration.

Accelerated Vibrational Energy Relaxation of Water in Alkaline Environments

We observe that hydrated hydroxide ions introduce an additional relaxation channel for the vibrational relaxation of the OD vibrations of HDO molecules in aqueous NaOH solutions. This additional relaxation path involves resonant (Förster) vibrational energy transfer from the excited OD vibration to OH stretch vibrations of hydrated OH^– complexes. This energy transfer constitutes an efficient mechanism for dissipation of the OD vibrational energy, as the accepting OH stretch vibrations show an extremely rapid subsequent relaxation with a time constant of <200 fs. We find that the Förster energy transfer is characterized by a Förster radius of 2.8 ± 0.2 Å.

Less-Ordered Hydration Shell around Poly(N,N-diethylacrylamide) Is Insensitive to the Clouding Transition

Raman multivariate curve resolution (Raman-MCR) is applied to examine how the hydration shell around poly(N,N-diethylacrylamide) (PDEAM) changes upon heating, in comparison with poly(N-isopropylacrylamide) (PNIPAM), both of which undergo a clouding transition near room temperature. We report that PDEAM possesses a less-ordered and smaller hydration shell than PNIPAM. Furthermore, the PDEAM hydration-shell structure is insensitive to the occurrence of clouding, indicating the coil-globule transition and aggregation of multiple chains can be achieved without the hydration-shell structural transformation.

Phospholipids dock SARS-CoV-2 spike protein via hydrophobic interactions: a minimal in-silico study of lecithin nasal spray therapy

Understanding the physical and chemical properties of viral infections at molecular scales is a major challenge for the scientific community more so with the outbreak of global pandemics. There is currently a lot of effort being placed in identifying molecules that could act as putative drugs or blockers of viral molecules. In this work, we computationally explore the importance in antiviral activity of a less studied class of molecules, namely surfactants. We employ all-atoms molecular dynamics simulations to study the interaction between the receptor-binding domain of the SARS-CoV-2 spike protein and the phospholipid lecithin (POPC), in water. Our microsecond simulations show a preferential binding of lecithin to the receptor-binding motif of SARS-CoV-2 with binding free energies significantly larger than [Formula: see text]. Furthermore, hydrophobic interactions involving lecithin non-polar tails dominate these binding events, which are also accompanied by dewetting of the receptor binding motif. Through an analysis of fluctuations in the radius of gyration of the receptor-binding domain, its contact maps with lecithin molecules, and distributions of water molecules near the binding region, we elucidate molecular interactions that may play an important role in interactions involving surfactant-type molecules and viruses. We discuss our minimal computational model in the context of lecithin-based liposomal nasal sprays as putative mitigating therapies for COVID-19.

Molecular dynamic investigation of ethanol-water mixture by terahertz-induced Kerr effect

The terahertz Kerr effect (TKE) spectroscopy provides time-resolved measurement of low-frequency molecular motions of liquids. Here, the intense broadband terahertz (THz) pulses resonantly excite multiple molecular modes in pure ethanol and ethanol-water mixtures. For pure ethanol, the obtained unipolar TKE response contains the molecular relaxation information extending over tens of picoseconds, which originates from the coupling between the permanent molecular dipole moment of ethanol and the THz electric field. For ethanol-water mixtures with different molar proportions, the results observed on the sub-picosecond time scale can always be divided into the linear superposition of the TKE signals of pure ethanol and water. Under the observation time window over tens of picoseconds (after 1 picosecond), the relative molecular contribution of ethanol in the mixture changes nonlinearly with the increase of water molecules, implying the complex structural perturbation of ethanol hydrogen bond network in the mixture. This work provides a new perspective for further investigation on the hydrogen bond network structure and dynamics in aqueous amphiphilic solutions.

Energy relaxation dynamics of hydrogen-bonded OH vibration conjugated with free OH bond at an air/water interface

Vibrational energy relaxation dynamics of the excited hydrogen-bonded (H-bonded) OH conjugated with free OH (OD) at an air/water (for both pure water and isotopically diluted water) interface are elucidated via non-equilibrium ab initio molecular dynamics (NE-AIMD) simulations. The calculated results are compared with those of the excited H-bonded OH in bulk liquid water reported previously. In the case of pure water, the relaxation timescale (vibrational lifetime) of the excited H-bonded OH at the interface is T₁ = 0.13 ps, which is slightly larger than that in the bulk (T₁ = 0.11 ps). Conversely, in the case of isotopically diluted water, the relaxation timescale of T₁ = 0.74 ps in the bulk decreases to T₁ = 0.26 ps at the interface, suggesting that the relaxation dynamics of the H-bonded OH are strongly dependent on the surrounding H-bond environments particularly for the isotopically diluted conditions. The relaxation paths and their rates are estimated by introducing certain constraints on the vibrational modes except for the target path in the NE-AIMD simulation to decompose the total energy relaxation rate into contributions to possible relaxation pathways. It is found that the main relaxation pathway in the case of pure water is due to intermolecular OH⋯OH vibrational coupling, which is similar to the relaxation in the bulk. In the case of isotopically diluted water, the main pathway is due to intramolecular stretch and bend couplings, which show more efficient relaxation than in the bulk because of strong H-bonding interactions specific to the air/water interface.

Water's Variable Role in Protein Stability Uncovered by Liquid-Observed Vapor Exchange NMR

Water is essential to protein structure and stability, yet our understanding of how water shapes proteins is far from thorough. Our incomplete knowledge of protein-water interactions is due in part to a long-standing technological inability to assess experimentally how water removal impacts local protein structure. It is now possible to obtain residue-level information on dehydrated protein structures via liquid-observed vapor exchange (LOVE) NMR, a solution NMR technique that quantifies the extent of hydrogen-deuterium exchange between unprotected amide protons of a dehydrated protein and D₂O vapor. Here, we apply LOVE NMR, Fourier transform infrared spectroscopy, and solution hydrogen-deuterium exchange to globular proteins GB1, CI2, and two variants thereof to link mutation-induced changes in the dehydrated protein structure to changes in solution structure and stability. We find that a mutation that destabilizes GB1 in solution does not affect its dehydrated structure, whereas a mutation that stabilizes CI2 in solution makes several regions of the protein more susceptible to dehydration-induced unfolding, suggesting that water is primarily responsible for the destabilization of the GB1 variant but plays a stabilizing role in the CI2 variant. Our results indicate that changes in dehydrated protein structure cannot be predicted from changes in solution stability alone and demonstrate the ability of LOVE NMR to uncover the variable role of water in protein stability. Further application of LOVE NMR to other proteins and their variants will improve the ability to predict and modulate protein structure and stability in both the hydrated and dehydrated states for applications in medicine and biotechnology.

Real-time observation of photoionization-induced water migration dynamics in 4-methylformanilide-water by picosecond time-resolved infrared spectroscopy and ab initio molecular dynamics simulations

A novel time-resolved pump-probe spectroscopic approach that enables to keep high resolution in both the time and energy domain, nanosecond excitation-picosecond ionization-picosecond infrared probe (ns-ps-ps TRIR) spectroscopy, has been applied to the trans-4-methylformanilide-water (4MetFA-W) cluster. Water migration dynamics from the CO to the NH binding site in a peptide linkage triggered by photoionization of 4MetFA-W is directly monitored by the ps time evolution of IR spectra, and the presence of an intermediate state is revealed. The time evolution is analyzed by rate equations based on a four-state model of the migration dynamics. Time constants for the initial to the intermediate and hot product and to the final product are obtained. The acceleration of the dynamics by methyl substitution and the strong contribution of intracluster vibrational energy redistribution in the termination of the solvation dynamics is suggested. This picture is well confirmed by the ab initio on-the-fly molecular dynamics simulations. Vibrational assignments of 4MetFA and 4MetFA-W in the neutral (S₀ and S₁) and ionic (D₀) electronic states measured by ns IR dip and electron-impact IR photodissociation spectroscopy are also discussed prior to the results of time-resolved spectroscopy.

Accurate Prediction of Hydration Sites of Proteins Using Energy Model With Atom Embedding

We propose a method based on neural networks to accurately predict hydration sites in proteins. In our approach, high-quality data of protein structures are used to parametrize our neural network model, which is a differentiable score function that can evaluate an arbitrary position in 3D structures on proteins and predict the nearest water molecule that is not present. The score function is further integrated into our water placement algorithm to generate explicit hydration sites. In experiments on the OppA protein dataset used in previous studies and our selection of protein structures, our method achieves the highest model quality in terms of F1 score, compared to several previous studies.

Lanthanide-dependent coordination interactions in lanmodulin: a 2D IR and molecular dynamics simulations study

The biological importance of lanthanides, and the early lanthanides (La³⁺-Nd³⁺) in particular, has only recently been recognized, and the structural principles underlying selective binding of lanthanide ions in biology are not yet well established. Lanmodulin (LanM) is a novel protein that displays unprecedented affinity and selectivity for lanthanides over most other metal ions, with an uncommon preference for the early lanthanides. Its utilization of EF-hand motifs to bind lanthanides, rather than the Ca²⁺ typically recognized by these motifs in other proteins, has led it to be used as a model system to understand selective lanthanide recognition. Two-dimensional infrared (2D IR) spectroscopy combined with molecular dynamics simulations were used to investigate LanM's selectivity mechanisms by characterizing local binding site geometries upon coordination of early and late lanthanides as well as calcium. These studies focused on the protein's uniquely conserved proline residues in the second position of each EF-hand binding loop. We found that these prolines constrain the EF-hands for strong coordination of early lanthanides. Substitution of this proline results in a more flexible binding site to accommodate a larger range of ions but also results in less compact coordination geometries and greater disorder within the binding site. Finally, we identify the conserved glycine in the sixth position of each EF-hand as a mediator of local binding site conformation and global secondary structure. Uncovering fundamental structure-function relationships in LanM informs the development of synthetic biology technologies targeting lanthanides in industrial applications.

Stabilizing Role of Water Solvation on Anion-π Interactions in Proteins

In this work, anion-π interactions between sulfate groups (SO₄ ^2-) and protein aromatic amino acids (AAs) (histidine protonated (HisP), histidine neutral (HisN), tyrosine (Tyr), tryptophan (Trp), and phenylalanine (Phe)) in an aqueous environment have been analyzed using quantum chemical (QC) calculations and molecular dynamics (MD) simulations. Sulfates can occur naturally in solution and can be contained in biomolecules playing relevant roles in their biological function. In particular, the presence of sulfate groups in glycosaminoglycans such as heparin and heparan sulfate has been shown to be relevant for protein and cellular communication and, consequently, for tissue regeneration. Therefore, anion-π interactions between sulfate groups and aromatic residues represent a relevant aspect to investigate. QC results show that such an anion-π mode of interaction between SO₄ ^2- and aromatic AAs is only possible in the presence of water molecules, in the absence of any other cooperative non-covalent interactions. Protonated histidine stands out in terms of its enhancement in the magnitude of interaction strength on solvation. Other AAs such as non-protonated histidine, tyrosine, and phenylalanine can stabilize anion-π interactions on solvation, albeit with weak interaction energy. Tryptophan does not exhibit any anion-π mode of interaction with SO₄ ^2-. The order of magnitude of the interaction of aromatic AAs with SO₄ ^2- on microsolvation is HisP > HisN > Tyr > Trp > Phe. Atoms in molecules (AIM) analysis illustrates the significance of water molecules in stabilizing the divalent SO₄ ^2- anion over the π surface of the aromatic AAs. MD simulation analysis shows that the order of magnitude of the interaction of SO₄ ^2- with aromatic AAs in macroscopic solvation is HisP > HisN, Tyr, Trp > Phe, which is very much in line with the QC results. Spatial distribution function analysis illustrates that protonated histidine alone is capable of establishing the anion-π interaction with SO₄ ^2- in the solution phase. This study sheds light on the understanding of anion-π interactions between SO₄ ^2- and aromatic AAs such as His and Tyr observed in protein crystal structures and the significance of water molecules in stabilizing such interactions, which is not feasible otherwise.

Orientations and water dynamics of photoinduced secondary charge-separated states for magnetoreception by cryptochrome

In the biological magnetic compass, blue-light photoreceptor protein of cryptochrome is thought to conduct the sensing of the Earth's magnetic field by photoinduced sequential long-range charge-separation (CS) through a cascade of tryptophan residues, W_A(H), W_B(H) and W_C(H). Mechanism of generating the weak-field sensitive radical pair (RP) is poorly understood because geometries, electronic couplings and their modulations by molecular motion have not been investigated in the secondary CS states generated prior to the terminal RP states. In this study, water dynamics control of the electronic coupling is revealed to be a key concept for sensing the direction of weak magnetic field. Geometry and exchange coupling (singlet-triplet energy gap: 2J) of photoinduced secondary CS states composed of flavin adenine dinucleotide radical anion (FAD^-•) and radical cation W_B(H)^+• in the cryptochrome DASH from Xenopus laevis were clarified by time-resolved electron paramagnetic resonance. We found a time-dependent energetic disorder in 2J and was interpreted by a trap CS state capturing one reorientated water molecule at 120 K. Enhanced electron-tunneling by water-libration was revealed for the terminal charge-separation event at elevated temperature. This highlights importance of optimizing the electronic coupling for regulation of the anisotropic RP yield on the possible magnetic compass senses.

Emergence of Electric Fields at the Water-C12E6 Surfactant Interface

We study the properties of the interface of water and the surfactant hexaethylene glycol monododecyl ether (C12E6) with a combination of heterodyne-detected vibrational sum frequency generation (HD-VSFG), Kelvin-probe measurements, and molecular dynamics (MD) simulations. We observe that the addition of the hydrogen-bonding surfactant C12E6, close to the critical micelle concentration (CMC), induces a drastic enhancement in the hydrogen bond strength of the water molecules close to the interface, as well as a flip in their net orientation. The mutual orientation of the water and C12E6 molecules leads to the emergence of a broad (∼3 nm) interface with a large electric field of ∼1 V/nm, as evidenced by the Kelvin-probe measurements and MD simulations. Our findings may open the door for the design of novel electric-field-tuned catalytic and light-harvesting systems anchored at the water-surfactant-air interface.

Contributions of higher-order proximal distribution functions to solvent structure around proteins

The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein myoglobin in the P6 crystal unit cell. Molecular dynamics simulations are performed, and solvent density distributions around the solute molecules are compared with the results from different pDF reconstruction models. It is shown that the next-nearest-neighbor modification significantly improves the reconstruction of the solvent number density distribution in concave regions and between solute molecules. The probability densities are then used to calculate the solute-solvent non-bonded interaction energies including van der Waals and electrostatic, which are found to be in good agreement with the simulated values.