Hydration dynamics of protein molecules in aqueous solution: Unity among diversity#

The influence of the hydrogen-bond network on the structure and dynamics of the RAPRKKG heptapeptide and its mutants

The structural behaviour of the RAPRKKG heptapeptide after individual or multiple mutations was inspected through molecular dynamics simulation. The nature of the mutations provided information on the flexibility of the heptapeptide and on how water molecules establish hydrogen bonds with it. The structural behaviour of the wild-type and the mutated structures were measured through the analysis of protein‒protein and protein‒solvent hydrogen bonds. The conformational behaviours of the different structures were analysed through free energy landscape analysis. The flexibility characteristics of the mutants seem to depend on the reorganization of water molecules and their static or dynamic behaviour around amino acid side chains.

Newly identified C–H⋯O hydrogen bond in histidine

Histidine C–H bonds observed in protein structures include (clockwise from top left): myoglobin, β-lactamase, and photoactive yellow protein; calculations indicate that tautomeric/protonation state influences H-bonding ability (bottom left).

Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions

The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.

Why Should Metformin Not Be Given in Advanced Kidney Disease? Potential Leads from Computer Simulations

Metformin is considered as the go-to drug in the treatment of diabetes. However, it is either prescribed in lower doses or not prescribed at all to patients with kidney problems. To find a potential explanation for this practice, we employed atomistic-level computer simulations to simulate the transport of metformin through multidrug and toxin extrusion 1 (MATE1), a protein known to play a key role in the expulsion of metformin into urine. Herein, we examine the hydrogen bonding between MATE1 and one or more metformin molecules. The simulation results indicate that metformin continuously forms and breaks off hydrogen bonds with MATE1 residues. However, the mean hydrogen bond lifetimes increase for an order of magnitude when three metformin molecules are inserted instead of one. This new insight into the metformin transport process may provide the molecular foundation behind the clinical practice of not prescribing metformin to kidney disease patients.

The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results

The biological activity of proteins depends on their three-dimensional structure, known as the native state. The main force driving the correct folding mechanism is the hydrophobic effect and when this folding kinetics is altered, aggregation phenomena intervene causing the occurrence of illnesses such as Alzheimer and Parkinson’s diseases. The other important effect is performed by water molecules and by their ability to form a complex network of hydrogen bonds whose dynamics influence the mobility of protein amino acids. In this work, we review the recent results obtained by means of spectroscopic techniques, such as Fourier Transform Infrared (FTIR) and Nuclear Magnetic Resonance (NMR) spectroscopies, on hydrated lysozyme. In particular, we explore the Energy Landscape from the thermal region of configurational stability up to that of the irreversible denaturation. The importance of the coupling between the solute and the solvent will be highlighted as well as the different behaviors of hydrophilic and hydrophobic moieties of protein amino acid residues.

Distinguishing dynamical features of water inside protein hydration layer: Distribution reveals what is hidden behind the average

Since the pioneering works of Pethig, Grant, and Wüthrich on a protein hydration layer, many studies have been devoted to find out if there are any "general and universal" characteristic features that can distinguish water molecules inside the protein hydration layer from bulk. Given that the surface itself varies from protein to protein, and that each surface facing the water is heterogeneous, search for universal features has been elusive. Here, we perform an atomistic molecular dynamics simulation in order to propose and demonstrate that such defining characteristics can emerge if we look not at average properties but the distribution of relaxation times. We present results of calculations of distributions of residence times and rotational relaxation times for four different protein-water systems and compare them with the same quantities in the bulk. The distributions in the hydration layer are unusually broad and log-normal in nature due to the simultaneous presence of peptide backbones that form weak hydrogen bonds, hydrophobic amino acid side chains that form no hydrogen bond, and charged polar groups that form a strong hydrogen bond with the surrounding water molecules. The broad distribution is responsible for the non-exponential dielectric response and also agrees with large specific heat of the hydration water. Our calculations reveal that while the average time constant is just about 2-3 times larger than that of bulk water, it provides a poor representation of the real behaviour. In particular, the average leads to the erroneous conclusion that water in the hydration layer is bulk-like. However, the observed and calculated lower value of static dielectric constant of hydration layer remained difficult to reconcile with the broad distribution observed in dynamical properties. We offer a plausible explanation of these unique properties.

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.

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.

Understanding 2D atomic resolution imaging of the calcite surface in water by frequency modulation atomic force microscopy

Frequency modulation atomic force microscopy (FM-AFM) experiments were performed on the calcite (10[Formula: see text]4) surface in pure water, and a detailed analysis was made of the 2D images at a variety of frequency setpoints. We observed eight different contrast patterns that reproducibly appeared in different experiments and with different measurement parameters. We then performed systematic free energy calculations of the same system using atomistic molecular dynamics to obtain an effective force field for the tip-surface interaction. By using this force field in a virtual AFM simulation we found that each experimental contrast could be reproduced in our simulations by changing the setpoint, regardless of the experimental parameters. This approach offers a generic method for understanding the wide variety of contrast patterns seen on the calcite surface in water, and is generally applicable to AFM imaging in liquids.

The effect of myoglobin crowding on the dynamics of water: an infrared study

Solutions containing 8 and 32 wt% myoglobin are studied by means of infrared spectroscopy, as a function of temperature (290 K and lower temperatures), in the mid- and far-infrared spectral range. Moreover, ultrafast time-resolved infrared measurements are performed at ambient temperature in the O-D stretching region. The results evidence that the vibrational properties of water remain the same in these myoglobin solutions (anharmonicity, vibrational relaxation lifetime…) and in neat water. However, the collective properties of the water molecules are significantly affected by the presence of the protein: the orientational time increases, the solid-liquid transition is affected in the most concentrated solution and the dynamical transition of the protein is observed, from the point of view of water, even in the least concentrated solution, proving that the water and myoglobin dynamics are coupled.