Extending the applicability of the O-ring theory to protein–DNA complexes

Many biological processes depend on protein-based interactions, which are governed by central regions with higher binding affinities, the hot-spots. The O-ring theory or the “Water Exclusion” hypothesis states that the more deeply buried central regions are surrounded by areas, the null-spots, whose role would be to shelter the hot-spots from the bulk solvent. Although this theory is well-established for protein–protein interfaces, its applicability to other protein interfaces remains unclear. Our goal was to verify its applicability to protein–DNA interfaces. We performed Molecular Dynamics simulations in explicit solvent of several protein–DNA complexes and measured a variety of solvent accessible surface area (SASA) features, as well as, radial distribution functions of hot-spots and null-spots. Our aim was to test the influence of water in their coordination sphere. Our results show that hot-spots tend to have fewer water molecules in their neighborhood when compared to null-spots, and higher values of ΔSASA, which confirms their occlusion from solvent. This study provides evidence in support of the O-ring theory with its applicability to a new type of protein-based interface: protein–DNA.     

Protein–protein interface prediction based on hexagon structure similarity

Studies on protein–protein interaction are important in proteome research. How to build more effective models based on sequence information, structure information and physicochemical characteristics, is the key technology in protein–protein interface prediction. In this paper, we study the protein–protein interface prediction problem. We propose a novel method for identifying residues on interfaces from an input protein with both sequence and 3D structure information, based on hexagon structure similarity. Experiments show that our method achieves better results than some state-of-the-art methods for identifying protein–protein interface. Comparing to existing methods, our approach improves F-measure value by at least 0.03. On a common dataset consisting of 41 complexes, our method has overall precision and recall values of 63% and 57%. On Benchmark v4.0, our method has overall precision and recall values of 55% and 56%. On CAPRI targets, our method has overall precision and recall values of 52% and 55%.     

Dynamics of protein and mixed protein/surfactant adsorption layers at the water/fluid interface

The adsorption behaviour of proteins and systems mixed with surfactants of different nature is described. In the absence of surfactants the proteins mainly adsorb in a diffusion controlled manner. Due to lack of quantitative models the experimental results are discussed partly qualitatively. There are different types of interaction between proteins and surfactant molecules. These interactions lead to protein/surfactant complexes the surface activity and conformation of which are different from those of the pure protein. Complexes formed with ionic surfactants via electrostatic interaction have usually a higher surface activity, which becomes evident from the more than additive surface pressure increase. The presence of only small amounts of ionic surfactants can significantly modify the structure of adsorbed proteins. With increasing amounts of ionic surfactants, however, an opposite effect is reached as due to hydrophobic interaction and the complexes become less surface active and can be displaced from the interface due to competitive adsorption. In the presence of non-ionic surfactants the adsorption layer is mainly formed by competitive adsorption between the compounds and the only interaction is of hydrophobic nature. Such complexes are typically less surface active than the pure protein. From a certain surfactant concentration of the interface is covered almost exclusively by the non-ionic surfactant. Mixed layers of proteins and lipids formed by penetration at the water/air or by competitive adsorption at the water/chloroform interface are formed such that at a certain pressure the components start to separate. Using Brewster angle microscopy in penetration experiments of proteins into lipid monolayers this interfacial separation can be visualised. A brief comparison of the protein adsorption at the water/air and water/n-tetradecane shows that the adsorbed amount at the water/oil interface is much stronger and the change in interfacial tension much larger than at the water/air interface. Also some experimental data on the dilational elasticity of proteins at both interfaces measured by a transient relaxation technique are discussed on the basis of the derived thermodynamic model. As a fast developing field of application the use of surface tensiometry and rheometry of mixed protein/surfactant mixed layers is demonstrated as a new tool in the diagnostics of various diseases and for monitoring the progress of therapies.     

Geometric similarity between protein–RNA interfaces

A new method is described to measure the geometric similarity between protein–RNA interfaces quantitatively. The method is based on a procedure that dissects the interface geometry in terms of the spatial relationships between individual amino acid nucleotide pairs. Using this technique, we performed an all‐on‐all comparison of 586 protein–RNA interfaces deposited in the current Protein Data Bank, as the result, an interface–interface similarity score matrix was obtained. Based upon this matrix, hierarchical clustering was carried out which yielded a complete clustering tree for the 586 protein–RNA interfaces. By investigating the organizing behavior of the clustering tree and the SCOP classification of protein partners in complexes, a geometrically nonredundant, diverse data set (representative data set) consisting of 45 distinct protein–RNA interfaces was extracted for the purpose of studying protein–RNA interactions, RNA regulations, and drug design. We classified protein–RNA interfaces into three types. In type I, the families and interface structural classes of the protein partners, as well as the interface geometries are all similar. In type II, the interface geometries and the interface structural classes are similar, whereas the protein families are different. In type III, only the interface geometries are similar but the protein families and the interface structural classes are distinct. Furthermore, we also show two new RNA recognition themes derived from the representative data set. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

The effect of methylation on the hydrogen-bonding and stacking interaction of nucleic acid bases

Methylated nucleosides play an important role in DNA/RNA function, and may affect republication by interrupting the base-pairing and base-stacking. In order to investigate the effect of methylation on the interaction between nucleic acid bases, this work presents the hydrogen-bonding and stacking interactions between 5-methylcytosine and guanine (G), cytosine (C) and G, 1-methyladenine and thymine (T), as well as adenine and T. Geometry optimization and potential energy surface scan have been performed for the involved complexes by MP2 calculations. The interaction energies, which were corrected for the basis-set superposition error by the full Boys–Bernardi counterpoise correction scheme, were used to evaluate the interaction intensity of these nucleic acid bases. The atoms in molecules theory and natural bond orbital analysis have been performed to study the hydrogen bonds in these complexes. The result shows that the methyl substitute contributes the stability to these complexes because it enhances either the hydrogen bonding or the staking interaction between nucleic acid bases studied.     

DNA—metal(ii) ion—phosphatidylcholine complexes: structure calculations and stability estimates by molecular mechanics

The structures and formation energies of nucleic acid—phospholipid complexes both in the absence and in the presence of Mg²⁺ ions were calculated taking double-stranded trinucleoside diphosphates NpNpN or heptanucleotides ApAp(NpNpN)pApA, composed of 64 possible combinations of genetic code, and phosphatidylcholine as model compounds. The dependence of intramolecular interactions on the primary structure of nucleic acid molecules and on the presence of a cationic bridge was revealed. The formation energies and structure of oligonucleotides were found by molecular mechanics calculations with the AMBER force field. The structures of phospholipid and MgCl₂ molecules were calculated by the semiempirical PM3 method, while the energies of phospholipid—oligonucleotide complexes were calculated by the molecular mechanics method. Calculations of complexes were carried our with consideration of solvation effects. Considerable gain in the formation energy of triple complexes (13–14 kcal mol⁻¹) is achieved due to the presence of the electroneural metal bridge. A tendency toward increasing the stability of triple complexes containing guanosine-and cytidine-enriched triplets was revealed. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2068–2071, November, 1999.     

Synthesis and crystal structures of sterically tuned ether functionalized NHC–silver(I) complexes: antibacterial and nucleic acid interaction studies

A series of new imidazolium salts (1–4) as N-heterocyclic carbene (NHC) precursors have been synthesized by successive N-alkylation method. Reactions of these salts with Ag₂O by varying the metal to salt ratio forms a series of new Ag(I)–NHC complexes (5–8). All compounds were characterized by physico-chemical and spectroscopic techniques. The molecular structures of 1 and 5 were characterized by single-crystal X-ray diffraction analysis. A comparative investigation of the bacterial growth inhibition potential of the salts and respective complexes indicates that 5–8 displayed good antibacterial activities on Staphylococcus aureus (ATCC 12600) and Escherichia coli (ATCC 11303) compared with the salts. Furthermore, it was observed that with increase in chain length at N-positions, the antibacterial activities also increased. Nuclease activity of the reported salts and Ag(I)–NHC complexes with nucleic acids (DNA and RNA) were also studied using agarose gel electrophoresis; the results show that the compounds do not have any apparent interaction with nucleic acids in the absence of hydrogen peroxide (H₂O₂). However, 5 and 8 were efficient in promoting the cleavage of nucleic acids in the presence of H₂O₂.     

Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA : Protein Complexes

A nonredundant dataset of ∼300 high (up to 2.5 Å) resolution X-ray structures of RNA : protein complexes were analyzed for hydrogen bonds between amino-acid residues and canonical ribonucleotides (rNs). The identified 17100 contacts were classified based on the identity (rA, rC, rG or rU) and interacting fragment (base, sugar, or ribose) of the rN, the nature (polar or nonpolar) and interacting moiety (main chain or side chain) of the amino-acid residue, as well as the rN and amino-acid atoms participating in the hydrogen bonding. 80 possible hydrogen-bonding combinations (4 (rNs)×20 (amino acids)) involve a wide variety of RNA and protein types and are present in multiple occurrences in almost all PDB files. Comparison with the analogously-selected DNA:protein complexes reveals that the absence of 2′-OH group in DNA mainly accounts for the differences in DNA:protein and RNA : protein hydrogen bonding. Search for intrinsically-stable base:amino acid pairs containing single or multiple hydrogen bonds reveals 37 unique pairs, which may act as well-defined RNA : protein interaction motifs. Overall, our work collectively analyzes the largest set of nucleic acid-protein hydrogen bonds to date, and therefore highlights several trends that may help frame structural rules governing the physiochemical characteristics of RNA : protein recognition.     

Molecular simulation of protein adsorption and conformation at gas-liquid,liquid–liquid and solid–liquid interfaces

The adsorption of proteins at surfaces and interfaces is important in a wide range of industries. Understanding and controlling the conformation of adsorbed proteins at surfaces is critical to stability and function in many technological applications including foods and biomedical testing kits or sensors. Studying adsorbed protein conformation is difficult experimentally and so over the past few decades researchers have turned to computer simulation methods to give information at the atomic level on this important area. In this review we summarize some of the significant simulation work over the past four years at both fluid (liquid–liquid and gas–liquid interfaces) and solid–liquid interfaces. Of particular significance is the work on surfactant proteins such as fungal hydrophobins, ranspumin-2 from the túngara frog and the bacteria protein BslA. These have evolved unique structures impart very high surface-active properties to the molecules. A highlight is the elucidation of the clam-shell unhinging mechanism of ranspumin-2 adsorption to the gas–liquid interface that is responsible for its adsorption to and stabilization of the air bubbles in túngara frog foam nests.     

Weighted edge based clustering to identify protein complexes in protein–protein interaction networks incorporating gene expression profile

Protein complex detection from protein–protein interaction (PPI) network has received a lot of focus in recent years. A number of methods identify protein complexes as dense sub-graphs using network information while several other methods detect protein complexes based on topological information. While the methods based on identifying dense sub-graphs are more effective in identifying protein complexes, not all protein complexes have high density. Moreover, existing methods focus more on static PPI networks and usually overlook the dynamic nature of protein complexes. Here, we propose a new method, Weighted Edge based Clustering (WEC), to identify protein complexes based on the weight of the edge between two interacting proteins, where the weight is defined by the edge clustering coefficient and the gene expression correlation between the interacting proteins. Our WEC method is capable of detecting highly inter-connected and co-expressed protein complexes. The experimental results of WEC on three real life data shows that our method can detect protein complexes effectively in comparison with other highly cited existing methods.Availability: The WEC tool is available at http://agnigarh.tezu.ernet.in/~rosy8/shared.html.     

Structure and Orientation of Tetracarboxylic Acids at Oil–Water Interfaces

Fouling caused by tetracarboxylic acids in transport and separation process chains involving petroemulsions occurs when the interfacial concentration of tetraacids becomes large enough for calcium ions in the water phase to “crosslink” the adsorbed tetraacid molecules and form a precipitate. At present, the structure and orientation of tetraacid molecules at oil–water interfaces, which influences the precipitation behavior, has not been studied in detail. In this work, molecular dynamics simulations of indigenous and synthetic tetracarboxylic acid compounds are presented to describe the structure and spatial orientation of tetraacid molecules at oil–water interfaces. Molecular distributions relative to the oil–water dividing surface along with the length and orientation angle distributions of the acidic arm groups are presented. The probability distributions determined here that describe the tetraacids at an oil–water interface can be employed to reconstruct the density of carboxylic acid groups at the oil–water interface. The interfacial carboxylic acid density can be employed to determine the fraction of adsorbed tetraacid molecules that are “crosslinked” with calcium ions based on the distances between carboxylic acid groups. The simulations presented also form a basis to calculate interfacial molecular areas and virial coefficients to employ in molecular mixed monolayer adsorption isotherms.     

Charged versus Neutral Hydrogen‐Bonded Complexes: Is There a Difference in the Nature of the Hydrogen Bonds?

A theoretical study on some carboxylic acid dimers formed by positively or negatively charged molecules has been carried out by using DFT methods. The resulting dimers possess either a charge of +2 or ?2. In addition, the corresponding neutral complexes have also been considered. The electron density distribution described by the atoms in molecules and the natural bond orbital methods, as well as the electric field maps of the systems, have been analyzed and compared without finding significant differences between the neutral and ionic complexes. The interaction energy along the dissociation path of the charged dimers shows both a local minimum and a local maximum, defining a stability region between them. When this energetic profile is recalculated by removing the repulsion between the charged groups, it resembles to those of the neutral molecules. Hence, the characteristics of the charged dimers are similar to those of the neutral ones: the addition of a repulsion term for the charged groups permits to retrieve the energetic profiles dependence with the distance in the charged system. The interacting quantum atom (IQA) method has been used to calculate the interaction energy terms, including the classic Coulombic term between the whole molecules and the corresponding of the carboxylic acid groups. The IQA results show repulsive electrostatic interactions when the whole molecules are considered in the ionic complexes, but attractive ones between the carboxylic groups in both neutral and ionic complexes.     

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank,which uses dihedral angles as independent variables

We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein–DNA complex, a protein–tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.     

Role of interfacial water on protein adsorption at cross-linked polyethylene oxide interfaces

Sum frequency generation (SFG) vibrational spectroscopy was used to study the structure of water at cross-linked PEO film interfaces in the presence of human serum albumin (HSA) protein. Although PEO is charge neutral, the PEO film/water interface exhibited an SFG signal of water similar to that of a highly charged water/silica interface, signifying the presence of ordered water. Ordered water molecules were observed not only at the water/PEO interface, but also within the PEO film. It indicates that the PEO and water form an ordered hydrogen-bonded network extending from the bulk PEO film into liquid water, which can provide an energy barrier for protein adsorption. Upon exposure to the protein solution, the SFG spectra of water at the water/PEO interface remained nearly unperturbed. For comparison, the SFG spectra of water/silica and water/polystyrene interfaces were also studied with and without HSA in the solution. The SFG spectra of the interfacial water were correlated with the amount of protein adsorbed on the surfaces using fluorescence microscopy, which showed that the amount of protein adsorbed on the PEO film was about 10 times less than that on a polystyrene film and 3 times less than that on silica.     

Individually double minimum-distance definition of protein–RNA binding residues and application to structure-based prediction

Identifying protein–RNA binding residues is essential for understanding the mechanism of protein–RNA interactions. So far, rigid distance thresholds are commonly used to define protein–RNA binding residues. However, after investigating 182 non-redundant protein–RNA complexes, we find that it would be unsuitable for a certain amount of complexes since the distances between proteins and RNAs vary widely. In this work, a novel definition method was proposed based on a flexible distance cutoff. This method can fully consider the individual differences among complexes by setting a variable tolerance limit of protein–RNA interactions, i.e. the double minimum-distance by which different distance thresholds are achieved for different complexes. In order to validate our method, a comprehensive comparison between our flexible method and traditional rigid methods was implemented in terms of interface structure, amino acid composition, interface area and interaction force, etc. The results indicate that this method is more reasonable because it incorporates the specificity of different complexes by extracting the important residues lost by rigid distance methods and discarding some redundant residues. Finally, to further test our double minimum-distance definition strategy, we developed a classifier to predict those binding sites derived from our new method by using structural features and a random forest machine learning algorithm. The model achieved a satisfactory prediction performance and the accuracy on independent data sets reaches to 85.0%. To the best of our knowledge, it is the first prediction model to define positive and negative samples using a flexible cutoff. So the comparison analysis and modeling results have demonstrated that our method would be a very promising strategy for more precisely defining protein–RNA binding sites.     

Surface‐Guided Formation of an Organocobalt Complex

Organocobalt complexes represent a versatile tool in organic synthesis as they are important intermediates in Pauson–Khand, Friedel–Crafts, and Nicholas reactions. Herein, a single‐molecule‐level investigation addressing the formation of an organocobalt complex at a solid–vacuum interface is reported. Deposition of 4,4′‐(ethyne‐1,2‐diyl)dibenzonitrile and Co atoms on the Ag(111) surface followed by annealing resulted in genuine complexes in which single Co atoms laterally coordinated to two carbonitrile groups undergo organometallic bonding with the internal alkyne moiety of adjacent molecules. Alternative complexation scenarios involving fragmentation of the precursor were ruled out by complementary X‐ray photoelectron spectroscopy. According to density functional theory analysis, the complexation with the alkyne moiety follows the Dewar–Chatt–Duncanson model for a two‐electron‐donor ligand where an alkyne‐to‐Co donation occurs together with a strong metal‐to‐alkyne back‐donation.     

Energy Landscape of Aptamer/Protein Complexes Studied by Single‐Molecule Force Spectroscopy

Aptamers are single‐stranded nucleic acid molecules selected in vitro to bind to a variety of target molecules. Aptamers bound to proteins are emerging as a new class of molecules that rival commonly used antibodies in both therapeutic and diagnostic applications. With the increasing application of aptamers as molecular probes for protein recognition, it is important to understand the molecular mechanism of aptamer–protein interaction. Recently, we developed a method of using atomic force microscopy (AFM) to study the single‐molecule rupture force of aptamer/protein complexes. In this work, we investigate further the unbinding dynamics of aptamer/protein complexes and their dissociation‐energy landscape by AFM. The dependence of single‐molecule force on the AFM loading rate was plotted for three aptamer/protein complexes and their dissociation rate constants, and other parameters characterizing their dissociation pathways were obtained. Furthermore, the single‐molecule force spectra of three aptamer/protein complexes were compared to those of the corresponding antibody/protein complexes in the same loading‐rate range. The results revealed two activation barriers and one intermediate state in the unbinding process of aptamer/protein complexes, which is different from the energy landscape of antibody/protein complexes. The results provide new information for the study of aptamer–protein interaction at the molecular level.     

Design of composite films and ultrathin membranes of interpolymer complexes

The formation of stoichiometric interpolymer complexes (IPCs) between the poly(vinyl ether) of ethyleneglycol and the copolymer of acrylic acid–butyl vinyl ether, between copolymers of vinyl ether of ethyleneglycol–butyl vinyl ether, and the copolymer of acrylic acid–vinylbutyl ether is demonstrated by conductimetric, potentiometric, viscometric and spectroturbidimetric methods in aqueous solution. The swelling/deswelling behavior of composite films derived from the IPC has been studied in water, alcohol and water–alcohol mixtures, depending on various factors. The formation of polyelectrolyte complexes (PECs) between the copolymer of acrylic acid–vinyl butyl ether and poly(vinyl ether of monoethanolamine) on a dimeric interface of water–butanol has been studied by the potentiometric method. The kinetics of PEC formation on a dimeric interface was measured and the activation energy of this process was calculated. Copyright © 2000 John Wiley & Sons, Ltd.     

Development of non‐bonded interaction parameters between graphene and water using particle swarm optimization

New Lennard‐Jones parameters have been developed to describe the interactions between atomistic model of graphene, represented by REBO potential, and five commonly used all‐atom water models, namely SPC, SPC/E, SPC/Fw, SPC/Fd, and TIP3P/Fs by employing particle swarm optimization (PSO) method. These new parameters were optimized to reproduce the macroscopic contact angle of water on a graphene sheet. The calculated line tension was in the order of 10⁻¹¹ J/m for the droplets of all water models. Our molecular dynamics simulations indicate the preferential orientation of water molecules near graphene–water interface with one O H bond pointing toward the graphene surface. Detailed analysis of simulation trajectories reveals the presence of water molecules with ≤∼1, ∼2, and ∼4 hydrogen bonds at the surface of air–water interface, graphene–water interface, and bulk region of the water droplet, respectively. Presence of water molecules with ≤∼1 and ∼2 hydrogen bonds suggest the existence of water clusters of different sizes at these interfaces. The trends observed in the libration, bending, and stretching bands of the vibrational spectra are closely associated with these structural features of water. The inhomogeneity in hydrogen bond network of water at the air–water and graphene–water interface is manifested by broadening of the peaks in the libration band for water present at these interfaces. The stretching band for the molecules in water droplet shows a blue shift as compared to the pure bulk water, which conjecture the presence of weaker hydrogen bond network in a droplet. © 2017 Wiley Periodicals, Inc.