Formation of spanning water networks on protein surfaces via 2D percolation transition

The formation of spanning hydrogen-bonded water networks on protein surfaces by a percolation transition is closely connected with the onset of their biological activity. To analyze the structure of the hydration water at this important threshold, we performed the first computer simulation study of the percolation transition of water in a model protein powder and on the surface of a single protein molecule. The formation of an infinite water network in the protein powder occurs as a 2D percolation transition at a critical hydration level, which is close to the values observed experimentally. The formation of a spanning 2D water network on a single rigid protein molecule can be described by adapting the cluster analysis of conventional percolation studies to the characterization of the connectivity of the hydration water on the surface of finite objects. Strong fluctuations of the surface water network are observed close to the percolation threshold. Our simulations also furnish a microscopic picture for understanding the specific values of the experimentally observed hydration levels, where different steps of increasing mobility in the hydrated powder are observed.     

Thermal breaking of spanning water networks in the hydration shell of proteins

The presence of a spanning hydrogen-bonded network of water at the surface of biomolecules is important for their conformational stability, dynamics, and function. We have studied by computer simulations the clustering and percolation of water in the hydration shell of a small elastinlike peptide (ELP) and the medium-size protein staphylococcal nuclease (SNase), in aqueous solution. We have found that in both systems a spanning network of hydration water exists at low temperatures and breaks up with increasing temperature via a quasi-two-dimensional percolation transition. The thermal breaking of the spanning water network occurs at biologically relevant temperatures, in the temperature range, which is close to the temperature of the "inverse temperature transition" of ELP and the unfolding temperature of SNase, respectively.     

How protein surfaces induce anomalous dynamics of hydration water

Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the anomalous dynamics and water-protein interactions. For the first time we quantify the separate effect of protein topological and energetic disorder on the hydration water dynamics. When a static protein structure is simulated, we show that both types of disorder contribute to slow down water diffusion, and that allowing for protein motion, increasing the spatial dimensionality of the interface, reduces the anomalous character of hydration water. The rotation of water is, instead, altered by the energetic disorder only; indeed, when electrostatic interactions between the protein and water are switched off, water reorients even faster than in the bulk. The dynamics of water is also related to the collective structure--à voir the hydrogen bond (H-bond) network--formed by the solvent enclosing the protein surface. We show that, as expected for a full hydrated protein, when the protein surface offers pinning sites (charged or polar sites), the superficial water-water H-bond network percolates throughout the whole surface, hindering the water diffusion, whereas it does not when the protein surface lacks electrostatic interactions with water and the water diffusion is enhanced.     

Co-adsorption of surfactants and water at inorganic solid surfaces

Computer simulations of the co-adsorption of water and methanoic acid at a range of surface features of calcite and fluorite minerals have shown that the relative adsorption energies for the two minerals are reversed when solvent effects are included in the calculations, a finding which is important in the search for effective surfactant reagents in flotation techniques, which are used extensively in the mining and pharmaceutical industries and in environmental remediation processes.     

Driving forces for protein adsorption at solid surfaces

Under most conditions proteins show a strong tendency to adsorb at interfaces. The general principles underlying the interaction between proteins and solid surfaces in an aqueous environment are discussed. These principles are illustrated by experimental results obtained with well-defined systems. The approach is mainly based on thermodynamic arguments.     

Glycan–protein cross-linking mass spectrometry reveals sialic acid-mediated protein networks on cell surfaces

A cross-linking method is developed to elucidate glycan-mediated interactions between membrane proteins through sialic acids. The method provides information on previously unknown extensive glycomic interactions on cell membranes. The vast majority of membrane proteins are glycosylated with complicated glycan structures attached to the polypeptide backbone. Glycan–protein interactions are fundamental elements in many cellular events. Although significant advances have been made to identify protein–protein interactions in living cells, only modest advances have been made on glycan–protein interactions. Mechanistic elucidation of glycan–protein interactions has thus far remained elusive. Therefore, we developed a cross-linking mass spectrometry (XL-MS) workflow to directly identify glycan–protein interactions on the cell membrane using liquid chromatography-mass spectrometry (LC-MS). This method involved incorporating azido groups on cell surface glycans through biosynthetic pathways, followed by treatment of cell cultures with a synthesized reagent, N-hydroxysuccinimide (NHS)–cyclooctyne, which allowed the cross-linking of the sialic acid azides on glycans with primary amines on polypeptide backbones. The coupled peptide–glycan–peptide pairs after cross-linking were identified using the latest techniques in glycoproteomic and glycomic analyses and bioinformatics software. With this approach, information on the site of glycosylation, the glycoform, the source protein, and the target protein of the cross-linked pair were obtained. Glycoprotein–protein interactions involving unique glycoforms on the PNT2 cell surface were identified using the optimized and validated method. We built the GPX network of the PNT2 cell line and further investigated the biological roles of different glycan structures within protein complexes. Furthermore, we were able to build glycoprotein–protein complex models for previously unexplored interactions. The method will advance our future understanding of the roles of glycans in protein complexes on the cell surface.

The cell surface glycocalyx is highly interactive defined by extensive covalent and non-covalent interactions. A method for cross-linking and characterizing glycan–peptide interactions in situ is developed.     

Ab initio studies of a water layer at transition metal surfaces

This paper presents a detailed study of a water adlayer adsorbed on Pt(111) and Rh(111) surfaces using periodic density functional theory methods. The interaction between the metal surface and the water molecules is assessed from molecular dynamics simulation data and single point electronic structure calculations of selected configurations. It is argued that the electron bands around the Fermi level of the metal substrate extend over the water adlayer. As a consequence in the presence of the water layer the surface as a whole still maintains its metallic conductivity-a result of a crucial importance for understanding the process of electron transfer through the water/metal interface and electrochemical reactions in particular. Our results also indicate that there exists a weak bond between the hydrogen of the water and the Rh metal atoms as opposed to the widespread (classical) models based on purely repulsive interaction. This suggests that the commonly used classical interactions potentials adopted for large scale molecular dynamics simulations of water/metal interfaces may need revision. Two adsorption models of water on transition metals with the OH bonds pointing towards or away of the surface are also examined. It is shown that due to the very close values of their adsorption energies one should consider the real structure of water on the surface as a mixture of these simple "up" and "down" models. A model for the structure of the adsorbed water layer on Rh(111) is proposed in terms of statistical averages from molecular dynamics simulations.     

Real-time scanning tunnelling microscopy imaging of protein motion at electrode surfaces

A mutant (K27C) of the blue copper protein azurin [Eur. J. Biochem. 194 (1990) 109; J. Mol. Biol. 221 (1991) 765] for orientated immobilisation on gold surfaces was analysed by scanning tunnelling microscopy (STM) both in a resting state and following the application of a short potential pulse between the tip and sample.     

H/D isotopic exchange between water molecules at ice surfaces

H/D isotopic exchange between H(2)O and D(2)O molecules was studied at the surface of ice films at 90-140 K by the technique of Cs(+) reactive ion scattering. Ice films were deposited on a Ru(0001) substrate in different compositions of H(2)O and D(2)O and in various structures to study the kinetics of isotopic exchange. H/D exchange was very slow on an ice film at 95-100 K, even when H(2)O and D(2)O were uniformly mixed in the film. At 140 K, H/D exchange occurred in a time scale of several minutes on the uniform mixture film. Kinetic measurement gave the rate coefficient for the exchange reaction, k(140 K)=1.6(+/-0.3) x 10(-19) cm(2) molecule(-1) s(-1) and k(100 K)< or =5.7(+/-0.5) x 10(-21) cm(2) molecule(-1) s(-1) and the Arrhenius activation energy, E(a)> or =9.8 kJ mol(-1). Addition of HCl on the film to provide excess protons greatly accelerated the isotopic exchange reaction such that it went to completion very quickly at the surface. The rapid reaction, however, was confined within the first bilayer (BL) of the surface and did not readily propagate to the underlying sublayer. The isotopic exchange in the vertical direction was almost completely blocked at 95 K, and it slowly occurred only to a depth of 3 BLs from the surface at 140 K. Thus, the proton transfer was highly directional. The lateral proton transfer at the surface was attributed to the increased mobility of protonic defects at the molecularly disordered and activated surface. The slow, vertical proton transfer was probably assisted by self-diffusion of water molecules.     

Interfacial water at hydrophobic and hydrophilic surfaces: depletion versus adsorption

The structure of the water-solid interface for widely varying surface properties is investigated with Monte Carlo simulations using the SPC/E water model. Of particular interest is the relation between the wetting coefficient as a measure of the hydrophobicity of the substrate and the density depletion close to the solid surface. The substrates are modeled as rigid ordered lattices of sites that interact with water molecules through an orientation-independent Lennard-Jones potential of varying strength. Hydrophilic character is obtained by addition of polar hydroxyl groups on the substrate surface, and the influence of density, spatial distribution, and angular orientation of the polar groups on the interfacial water structure is studied.     

Aqueous peptides as experimental models for hydration water dynamics near protein surfaces

We report quasi-elastic neutron scattering experiments to contrast the water dynamics as a function of temperature for hydrophilic and amphiphilic peptides under the same level of confinement, as models for understanding hydration dynamics near chemically heterogeneous protein surfaces. We find that the hydrophilic peptide shows only a single non-Arrhenius translational process with no evidence of spatial heterogeneity unlike the amphiphilic peptide solution that exhibits two translational relaxations with an Arrhenius and non-Arrhenius dependence on temperature. Together these results provide experimental proof that heterogeneous dynamical signatures near protein surfaces arise in part from chemical heterogeneity (energy disorder) as opposed to mere topological roughness of the protein surface.     

On the number of spanning trees and normalized Laplacian of linear octagonal-quadrilateral networks

The normalized Laplacian makes a great contribution on analyzing the structure properties of nonregular graphs. Let O_n be a linear octagonal-quadrilateral network. In this article, we first concern the normalized Laplacian spectrum of O_n based on the decomposition theorem for the corresponding matrices. Then we derive the closed-term formulas of the degree-Kirchhoff index and the number of spanning trees of linear octagonal-quadrilateral networks on the basis of the relations between the roots and coefficients, respectively.     

A fluorescence method for quantitative measurements of specific protein at powder surfaces

A new method using fluorescence labelled proteins was developed to determine the quantitative amount of specific protein at the powder surface. The method is based on steady-state fluorescence measurements of pyrene labelled proteins with oxygen gas phase quenching at the powder surface. The surface load of protein was measured for spray-dried dextran powders containing bovine serum albumin (BSA). The results show a patchwise surface load of about 1.3 mg m⁻² at a concentration of 0.33% (dry weight) BSA in the powder. The patchwise surface load stays constant with increased BSA concentration in the powder.     

WATGEN: an algorithm for modeling water networks at protein-protein interfaces

Water molecules at protein-protein interfaces contribute to the close packing of atoms and ensure complementarity between the protein surfaces, as well as mediating polar interactions. Therefore, modeling of interface water is of importance in understanding the structural basis of biomolecular association. We present an algorithm, WATGEN, which predicts locations for water molecules at a protein-protein or protein-peptide interface, given the atomic coordinates of the protein and peptide. A key element of the WATGEN algorithm is the prediction of water sites that can form multiple hydrogen bonds that bridge the binding interface. Trial calculations were performed on water networks predicted by WATGEN at 126 protein-peptide interfaces (X-ray resolutions 相似文献   

High-resolution protein hydration NMR experiments: probing how protein surfaces interact with water and other non-covalent ligands

High-resolution solution NMR experiments are extremely useful to characterize the location and the dynamics of hydrating water molecules at atomic resolution. However, these methods are severely limited by undesired incoherent transfer pathways such as those arising from exchange-relayed intra-molecular cross-relaxation. Here, we review several complementary exchange network editing methods that can be used in conjunction with other types of NMR hydration experiments such as magnetic relaxation dispersion and ¹J_NC′ measurements to circumvent these limitations. We also review several recent contributions illustrating how the original solution hydration NMR pulse sequence architecture has inspired new approaches to map other types of non-covalent interactions going well beyond the initial scope of hydration. Specifically, we will show how hydration NMR methods have evolved and have been adapted to binding site mapping, ligand screening, protein-peptide and peptide-lipid interaction profiling.     

Effects of ionic strength and surface charge on protein adsorption at PEGylated surfaces

PEGylated Nb2O5 surfaces were obtained by the adsorption of poly(L-lysine)-g-poly(ethylene glycol) (PLL-g-PEG) copolymers, allowing control of the PEG surface density, as well as the surface charge. PEG (MW 2 kDa) surface densities between 0 and 0.5 nm(-2) were obtained by changing the PEG to lysine-mer ratio in the PLL-g-PEG polymer, resulting in net positive, negative and neutral surfaces. Colloid probe atomic force microscopy (AFM) was used to characterize the interfacial forces associated with the different surfaces. The AFM force analysis revealed interplay between electrical double layer and steric interactions, thus providing information on the surface charge and on the PEG layer thickness as a function of copolymer architecture. Adsorption of the model proteins lysozyme, alpha-lactalbumin, and myoglobin onto the various PEGylated surfaces was performed to investigate the effect of protein charge. In addition, adsorption experiments were performed over a range of ionic strengths, to study the role of electrostatic forces between surface charges and proteins acting through the PEG layer. The adsorbed mass of protein, measured by optical waveguide lightmode spectroscopy (OWLS), was shown to depend on a combination of surface charge, protein charge, PEG thickness, and grafting density. At high grafting density and high ionic strength, the steric barrier properties of PEG determine the net interfacial force. At low ionic strength, however, the electrical double layer thickness exceeds the thickness of the PEG layer, and surface charges "shining through" the PEG layer contribute to protein interactions with PLL-g-PEG coated surfaces. The combination of AFM surface force measurements and protein adsorption experiments provides insights into the interfacial forces associated with various PEGylated surfaces and the mechanisms of protein resistance.     

Effect of chain density and conformation on protein adsorption at PEG-grafted polyurethane surfaces

Polyurethanes were modified using monobenzyloxy polyethylene glycol (BPEG) which possesses a bulky hydrophobic benzyloxy group at one end and a hydroxyl group at the other end as a preconstructed BPEG layer, and poly(ethylene glycol) (PEG) and monomethoxyl poly(ethylene glycol) (MPEG) with various chain lengths as fillers. Our objective was to investigate the effect of PEG graft density and conformation on protein adsorption at PEGlated surface. The graft density was estimated by a chemical titration method. The combination of ATR-FTIR, AFM and titration results provide evidences that the graft density can be increased by backfilling PEG or MPEG to a BPEG layer. However, fibrinogen and albumin adsorption significantly increased on all surfaces after PEG or MPEG backfilling. We conclude that the conformation of hydrophobic benzyloxy end groups of the BPEG layer plays a key role. The benzyloxy end groups of preconstructed PEG chains stretch to the surface after PEG backfilling, which possibly accounts for the observed increase in protein adsorption. The BPEG conformation change after backfilling with PEG or MPEG was also suggested by contact angles. Additionally, protein adsorption was slightly influenced by the length of filler, suggesting a change in surface morphology.