Interaction of Squid (Dosidicus giga) Mantle Protein with a Mixtures of Potato and Corn Starch in an Extruded Snack,as Characterized by FTIR and DSC

The majority of snacks expanded by extrusion (SEE) are made with vegetable sources, to improve their nutritional content; it has been proposed to incorporate squid (Dosidicus gigas), due to its high protein content, low price and high availability. However, the interaction of proteins of animal origin with starch during extrusion causes negative effects on the sensory properties of SEE, so it is necessary to know the type of protein–carbohydrate interactions and their effect on these properties. The objective of this research was to study the interaction of proteins and carbohydrates of SEE elaborated with squid mantle, potato and corn. The nutritional composition and protein digestibility were evaluated, Fourier transform infrared (FTIR) and Differential Scanning Calorimetry (DSC) were used to study the formation of protein–starch complexes and the possible regions responsible for their interactions. The SEE had a high protein content (40–85%) and biological value (>93%). The melting temperature (Tm) was found between 145 and 225 °C; the Tm values in extruded samples are directly proportional to the squid content. The extrusion process reduced the amine groups I and II responsible for the protein–protein interaction and increased the O-glucosidic bonds, so these bonds could be responsible for the protein–carbohydrate interactions.     

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.     

Designing a Useful Lipid Raft Model Membrane for Electrochemical and Surface Analytical Studies

A model biomimetic system for the study of protein reconstitution or drug interactions should include lipid rafts in the mixed lipid monolayer, since they are usually the domains embedding membrane proteins and peptides. Four model lipid films composed of three components: 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), cholesterol (Chol) and sphingomyelin (SM) mixed in different molar ratios were proposed and investigated using surface pressure measurements and thermodynamic analysis of the monolayers at the air–water interface and imaged by Brewster angle microscopy. The ternary monolayers were transferred from the air–water onto the gold electrodes to form bilayer films and were studied for the first time by electrochemical methods: alternative current voltammetry and electrochemical impedance spectroscopy and imaged by atomic force microscopy. In excess of DOPC, the ternary systems remained too liquid for the raft region to be stable, while in the excess of cholesterol the layers were too solid. The layers with SM in excess lead to the formation of Chol:SM complexes but the amount of the fluid matrix was very low. The equimolar content of the three components lead to the formation of a stable and well-organized assembly with well-developed raft microdomains of larger thickness, surrounded by the more fluid part of the bilayer. The latter is proposed as a convenient raft model membrane for further physicochemical studies of interactions with drugs or pollutants or incorporation of membrane proteins.     

Ab Initio Molecular Dynamics Simulations of the Interaction between Organic Phosphates and Goethite

Today’s fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future, and therefore effective P use is crucial to avoid food shortage. A substantial amount of P from fertilizers gets adsorbed onto soil minerals to become unavailable to plants. Understanding P interaction with these minerals would help efforts that improve P efficiency. To this end, we performed a molecular level analysis of the interaction of common organic P compounds (glycerolphosphate (GP) and inositol hexaphosphate (IHP)) with the abundant soil mineral (goethite) in presence of water. Molecular dynamics simulations are performed for goethite–IHP/GP–water complexes using the multiscale quantum mechanics/molecular mechanics method. Results show that GP forms monodentate (M) and bidentate mononuclear (B) motifs with B being more stable than M. IHP interacts through multiple phosphate groups with the 3M motif being most stable. The order of goethite–IHP/GP interaction energies is GP M < GP B < IHP M < IHP 3M. Water is important in these interactions as multiple proton transfers occur and hydrogen bonds are formed between goethite–IHP/GP complexes and water. We also present theoretically calculated infrared spectra which match reasonably well with frequencies reported in literature.     

Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding

Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a powerful tool to predict both the pose and energetics of such ligands. Thus, the use of molecular simulation may provide insight into aberrant molecular interactions in diseases and, from a drug design perspective, may allow for the employment of less wet lab resources than traditional in vitro compound screening approaches. With regard to basic research questions, molecular simulation can support the understanding of the exact molecular interaction and binding mode. Here, we focus on examples targeting RNA–protein complexes in neurodegenerative diseases and viral infections. These examples illustrate that the strategy is rather general and could be applied to different pharmacologically relevant approaches. We close this study by outlining one of these approaches, namely the light-controllable association of small molecules with RNA, as an emerging approach in RNA-targeting therapy.     

Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease

Computational analysis of protein–ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse of the potential of a small organic molecule to be a ligand to the binding site of a protein target. Available scoring functions, such as in docking programs, all rely on equations that sum each type of protein–ligand interactions in order to predict the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. Electrostatic interactions constitute one of the most important part of total interactions between macromolecules. Unlike dispersion forces, they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In this study, complexes of HIV-1 protease with inhibitor molecules (JE-2147 and darunavir) were analyzed by using charge densities from the transferable aspherical-atom University at Buffalo Databank (UBDB). Moreover, we analyzed the electrostatic interaction energy for an ensemble of structures, using molecular dynamic simulations to highlight the main features of electrostatic interactions important for binding affinity.     

Complexes of Formaldehyde and α-Dicarbonyls with Hydroxylamine: FTIR Matrix Isolation and Theoretical Study

The interactions of formaldehyde (FA), glyoxal (Gly) and methylglyoxal (MGly) with hydroxylamine (HA) isolated in solid argon and nitrogen were studied using FTIR spectroscopy and ab initio methods. The spectra analysis indicates the formation of two types of hydrogen-bonded complexes between carbonyl and hydroxylamine in the studied matrices. The cyclic planar complexes are stabilized by O–H⋯O(C), and C–H⋯N interactions and the nonplanar complexes are stabilized by O–H⋯O(C) bond. Formaldehyde was found to form with hydroxylamine, the cyclic planar complex and methylglyoxal, the nonplanar one in both argon and nitrogen matrices. In turn, glyoxal forms with hydroxylamine the most stable nonplanar complex in solid argon, whereas in solid nitrogen, both types of the complex are formed.     

Compressed images for affinity prediction (CIFAP): a study on predicting binding affinities for checkpoint kinase 1 protein inhibitors

Analyses of known protein–ligand interactions play an important role in designing novel and efficient drugs, contributing to drug discovery and development. Recently, machine learning methods have proven useful in the design of novel drugs, which utilize intelligent techniques to predict the outcome of unknown protein–ligand interactions by learning from the physical and geometrical properties of known protein–ligand interactions. The aim of this study is to work through a specific example of a novel computational method, namely compressed images for affinity prediction (CIFAP), in which binding affinities for structurally related ligands in complexes with human checkpoint kinase 1 (CHK1) are predicted. The CIFAP algorithm presented here relates published pIC ₅₀ values of 57 compounds, derived from a thienopyridine pharmacophore, in complexes with CHK1 to their two‐dimensional (2D) electrostatic potential images compressed in orthogonal dimensions. Patterns obtained from the 2D images are then used as inputs in regression and learning algorithms such as support vector regression (SVR) and adaptive neuro‐fuzzy inference system (ANFIS) methods to validate the experimental pIC ₅₀ values. This study revealed that the 2D image pixels in the vicinity of bound ligand surfaces provide more relevant information to make correlations with the empirical pIC ₅₀ values. As compared with ANFIS, SVR gave rise to the lowest root mean square errors and the greatest correlations, suggesting that SVR could be a plausible choice of machine learning methods in predicting binding affinities by CIFAP. Copyright © 2013 John Wiley & Sons, Ltd.     

Triarylborane Dyes as a Novel Non-Covalent and Non-Inhibitive Fluorimetric Markers for DPP III Enzyme

Novel dyes were prepared by simple “click CuAAC” attachment of a triarylborane–alkyne to the azide side chain of an amino acid yielding triarylborane dye 1 which was conjugated with pyrene (dye 2) forming a triarylborane–pyrene FRET pair. In contrast to previous cationic triarylboranes, the novel neutral dyes interact only with proteins, while their affinity to DNA/RNA is completely abolished. Both the reference triarylborane amino acid and triarylborane–pyrene conjugate bind to BSA and the hDPP III enzyme with high affinities, exhibiting a strong (up to 100-fold) fluorescence increase, whereby the triarylborane–pyrene conjugate additionally retained FRET upon binding to the protein. Furthermore, the triarylborane dyes, upon binding to the hDPP III enzyme, did not impair its enzymatic activity under a wide range of experimental conditions, thus being the first non-covalent fluorimetric markers for hDPP III, also applicable during enzymatic reactions with hDPP III substrates.     

Cyanovirin-N Binds Viral Envelope Proteins at the Low-Affinity Carbohydrate Binding Site without Direct Virus Neutralization Ability

Glycan-targeting antibodies and pseudo-antibodies have been extensively studied for their stoichiometry, avidity, and their interactions with the rapidly modifying glycan shield of influenza A. Broadly neutralizing antiviral agents bind in the same order when they neutralize enveloped viruses regardless of the location of epitopes to the host receptor binding site. Herein, we investigated the binding of cyanovirin-N (CV–N) to surface-expressed glycoproteins such as those of human immunodeficiency virus (HIV) gp120, hemagglutinin (HA), and Ebola (GP)1,2 and compared their binding affinities with the binding response to the trimer-folded gp140 using surface plasmon resonance (SPR). Binding-site knockout variants of an engineered dimeric CV–N molecule (CVN2) revealed a binding affinity that correlated with the number of (high-) affinity binding sites. Binding curves were specific for the interaction with N-linked glycans upon binding with two low-affinity carbohydrate binding sites. This biologically active assembly of a domain-swapped CVN2, or monomeric CV–N, bound to HA with a maximum K_D of 2.7 nM. All three envelope spike proteins were recognized at a nanomolar K_D, whereas binding to HIV neutralizing 2G12 by targeting HA and Ebola GP1,2 was measured in the µM range and specific for the bivalent binding scheme in SPR. In conclusion, invariant structural protein patterns provide a substrate for affinity maturation in the membrane-anchored HA regions, as well as the glycan shield on the membrane-distal HA top part. They can also induce high-affinity binding in antiviral CV–N to HA at two sites, and CVN2 binding is achieved at low-affinity binding sites.     

A–X⋯σ Interactions—Halogen Bonds with σ-Electrons as the Lewis Base Centre

CCSD(T)/aug-cc-pVTZ//ωB97XD/aug-cc-pVTZ calculations were performed for halogen-bonded complexes. Here, the molecular hydrogen, cyclopropane, cyclobutane and cyclopentane act as Lewis base units that interact through the electrons of the H–H or C–C σ-bond. The FCCH, ClCCH, BrCCH and ICCH species, as well as the F₂, Cl₂, Br₂ and I₂ molecular halogens, act as Lewis acid units in these complexes, interacting through the σ-hole localised at the halogen centre. The Quantum Theory of Atoms in Molecules (QTAIM), the Natural Bond Orbital (NBO) and the Energy Decomposition Analysis (EDA) approaches were applied to analyse these aforementioned complexes. These complexes may be classified as linked by A–X···σ halogen bonds, where A = C, X (halogen). However, distinct properties of these halogen bonds are observed that depend partly on the kind of electron donor: dihydrogen, cyclopropane, or another cycloalkane. Examples of similar interactions that occur in crystals are presented; Cambridge Structural Database (CSD) searches were carried out to find species linked by the A–X···σ halogen bonds.     

Anion Binding Properties of Alkynylplatinum(II) Complexes with Amide-Functionalized Terpyridine: Host–Guest Interactions and Fluoride Ion-Induced Deprotonation

Molecular sensors able to detect ions are of interest due to their potential application in areas such as pollutant sequestration. Alkynylplatinum(II) terpyridine complexes with an amide-based receptor moiety have been synthesized and characterized. Their anion binding properties based on host–guest interactions have been examined with the use of UV-vis absorption and emission spectral titration studies. Spectral changes were observed for both complexes upon the addition of spherical and nonspherical anions. Their titration profiles were shown to be in good agreement with theoretical results predicting a 1:1 binding model, and the binding constants were determined from the experimental data. Drastic color changes from yellow to orange–red were observed for one of the complexes upon titration with fluoride (F⁻) ion in acetone. These changes were ascribed to the deprotonation of the amide functionalities induced by F⁻ ion, and this was confirmed by the restoration of spectral changes upon addition of trifluoroacetic acid to the F⁻ ion–complex mixture as well as by electrospray ionization mass spectrometry (ESI-MS) data.     

Binding Free Energy (BFE) Calculations and Quantitative Structure–Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 (smHDAC8) Inhibitors

Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identification and development of novel lead compounds. In this study, we explore the binding modes of a series of benzhydroxamates derivatives developed as histone deacetylase inhibitors of Schistosoma mansoni histone deacetylase (smHDAC) using molecular docking and binding free energy (BFE) calculations. The developed docking protocol was able to correctly reproduce the experimentally established binding modes of resolved smHDAC8–inhibitor complexes. However, as has been reported in former studies, the obtained docking scores weakly correlate with the experimentally determined activity of the studied inhibitors. Thus, the obtained docking poses were refined and rescored using the Amber software. From the computed protein–inhibitor BFE, different quantitative structure–activity relationship (QSAR) models could be developed and validated using several cross-validation techniques. Some of the generated QSAR models with good correlation could explain up to ~73% variance in activity within the studied training set molecules. The best performing models were subsequently tested on an external test set of newly designed and synthesized analogs. In vitro testing showed a good correlation between the predicted and experimentally observed IC₅₀ values. Thus, the generated models can be considered as interesting tools for the identification of novel smHDAC8 inhibitors.     

Detection and characterization of nonspecific,sparsely populated binding modes in the early stages of complexation

A method is proposed to study protein–ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first‐encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide–protein complex. The peptide adopts several low‐population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated. © 2015 Wiley Periodicals, Inc.     

β-Cyclodextrin Inclusion Complexes with Catechol-Containing Antioxidants Protocatechuic Aldehyde and Protocatechuic Acid—An Atomistic Perspective on Structural and Thermodynamic Stabilities

Protocatechuic aldehyde (PCAL) and protocatechuic acid (PCAC) are catechol derivatives and have broad therapeutic effects associated with their antiradical activity. Their pharmacological and physicochemical properties have been improved via the cyclodextrin (CD) encapsulation. Because the characteristics of β-CD inclusion complexes with PCAL (1) and PCAC (2) are still equivocal, we get to the bottom of the inclusion complexation by an integrated study of single-crystal X-ray diffraction and DFT full-geometry optimization. X-ray analysis unveiled that PCAL and PCAC are nearly totally shielded in the β-CD wall. Their aromatic rings are vertically aligned in the β-CD cavity such that the functional groups on the opposite side of the ring (3,4-di(OH) and 1-CHO/1-COOH groups) are placed nearby the O6–H and O2–H/O3–H rims, respectively. The preferred inclusion modes in 1 and 2 help to establish crystal contacts of OH⋅⋅⋅O H-bonds with the adjacent β-CD OH groups and water molecules. By contrast, the DFT-optimized structures of both complexes in the gas phase are thermodynamically stable via the four newly formed host–guest OH⋯O H-bonds. The intermolecular OH⋅⋅⋅O H-bonds between PCAL/PCAC 3,4-di(OH) and β-CD O6–H groups, and the shielding of OH groups in the β-CD wall help to stabilize these antioxidants in the β-CD cavity, as observed in our earlier studies. Moreover, PCAL and PCAC in distinct lattice environments are compared for insights into their structural flexibility.     

Aromatic Rings as Molecular Determinants for the Molecular Recognition of Protein Kinase Inhibitors

Protein kinases are key enzymes in many signal transduction pathways, and play a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. However, aberrant function of kinases has been associated with cancers and many other diseases. Consequently, competitive inhibition of the ATP binding site of protein kinases has emerged as an effective means of curing these diseases. Over the past three decades, thousands of protein kinase inhibitors (PKIs) with varying molecular frames have been developed. Large-scale data mining of the Protein Data Bank resulted in a database of 2139 non-redundant high-resolution X-ray crystal structures of PKIs bound to protein kinases. This provided us with a unique opportunity to study molecular determinants for the molecular recognition of PKIs. A chemoinformatic analysis of 2139 PKIs resulted in findings that PKIs are “flat” molecules with high aromatic ring counts and low fractions of sp³ carbon. All but one PKI possessed one or more aromatic rings. More importantly, it was found that the average weighted hydrogen bond count is inversely proportional to the number of aromatic rings. Based on this linear relationship, we put forward the exchange rule of hydrogen bonding interactions and non-bonded π-interactions. Specifically, a loss of binding affinity caused by a decrease in hydrogen bonding interactions is compensated by a gain in binding affinity acquired by an increase in aromatic ring-originated non-bonded interactions (i.e., π–π stacking interactions, CH–π interactions, cation–π interactions, etc.), and vice versa. The very existence of this inverse relationship strongly suggests that both hydrogen bonding and aromatic ring-originated non-bonded interactions are responsible for the molecular recognition of PKIs. As an illustration, two representative PKI–kinase complexes were employed to examine the relative importance of different modes of non-bonded interactions for the molecular recognition of PKIs. For this purpose, two FDA-approved PKI drugs, ibrutinib and lenvatinib, were chosen. The binding pockets of both PKIs were thoroughly examined to identify all non-bonded intermolecular interactions. Subsequently, the strengths of interaction energies between ibrutinib and its interacting residues in tyrosine kinase BTK were quantified by means of the double hybrid DFT method B2PLYP. The resulting energetics for the binding of ibrutinib in tyrosine kinase BTK showed that CH–π interactions and π–π stacking interactions between aromatic rings of the drug and hydrophobic residues in its binding pocket dominate the binding interactions. Thus, this work establishes that, in addition to hydrogen bonding, aromatic rings function as important molecular determinants for the molecular recognition of PKIs. In conclusion, our findings support the following pharmacophore model for ATP-competitive kinase inhibitors: a small molecule features a scaffold of one or more aromatic rings which is linked with one or more hydrophilic functional groups. The former has the structural role of acting as a scaffold and the functional role of participating in aromatic ring-originated non-bonded interactions with multiple hydrophobic regions in the ATP binding pocket of kinases. The latter ensure water solubility and form hydrogen bonds with the hinge region and other hydrophilic residues of the ATP binding pocket.     

Exploiting Complex Fluorophore Interactions to Monitor Virus Capsid Disassembly

Supramolecular protein complexes are the corner stone of biological processes; they are essential for many biological functions. Unraveling the interactions responsible for the (dis)assembly of these complexes is required to understand nature and to exploit such systems in future applications. Virus capsids are well-defined assemblies of hundreds of proteins and form the outer shell of non-enveloped viruses. Due to their potential as a drug carriers or nano-reactors and the need for virus inactivation strategies, assessing the intactness of virus capsids is of great interest. Current methods to evaluate the (dis)assembly of these protein assemblies are experimentally demanding in terms of instrumentation, expertise and time. Here we investigate a new strategy to monitor the disassembly of fluorescently labeled virus capsids. To monitor surfactant-induced capsid disassembly, we exploit the complex photophysical interplay between multiple fluorophores conjugated to capsid proteins. The disassembly of the capsid changes the photophysical interactions between the fluorophores, and this can be spectrally monitored. The presented data show that this low complexity method can be used to study and monitor the disassembly of supramolecular protein complexes like virus capsids. However, the range of labeling densities that is suitable for this assay is surprisingly narrow.     

金属卟啉对杂环及DNA分子识别研究进展

介绍了近几年国内外关于组装金属卟啉对杂环分子、DNA碱基以及RNA的分子识别的研究进展, 并简述了本课题组对金属卟啉与杂环及药物分子复合物的理论研究工作. 金属卟啉广泛存在于自然界和生物体中, 此识别过程对研究和模拟生命体中各种细胞之间的相互作用具有重要意义. 组装后的金属卟啉可通过轴向配位、氢键及π-π堆积作用等识别杂环分子. 金属卟啉对DNA的识别主要有四种作用方式, 而金属卟啉对DNA以及RNA分子的识别主要靠疏水作用力、静电力以及自堆叠作用. 卟啉阳离子与DNA的结合位点受主体侧链取代基的空间结构影响. 金属卟啉对药物分子的识别靠配位键和氢键进行, 以配位键结合的复合物通常具有更高的结合能.