Structural study of a small molecule receptor bound to dimethyllysine in lysozyme

Lysine is a ubiquitous residue on protein surfaces. Post translational modifications of lysine, including methylation to the mono-, di- or trimethylated amine result in chemical and structural alterations that have major consequences for protein interactions and signalling pathways. Small molecules that bind to methylated lysines are potential tools to modify such pathways. To make progress in this direction, detailed structural data of ligands in complex with methylated lysine is required. Here, we report a crystal structure of p-sulfonatocalix[4]arene (sclx₄) bound to methylated lysozyme in which the lysine residues were chemically modified from Lys-NH₃ ⁺ to Lys-NH(Me₂)⁺. Of the six possible dimethyllysine sites, sclx₄ selected Lys116-Me₂ and the dimethylamino substituent was deeply buried in the calixarene cavity. This complex confirms the tendency for Lys-Me₂ residues to form cation–π interactions, which have been shown to be important in protein recognition of histone tails bearing methylated lysines. Supporting data from NMR spectroscopy and MD simulations confirm the selectivity for Lys116-Me₂ in solution. The structure presented here may serve as a stepping stone to the development of new biochemical reagents that target methylated lysines.     

Tuning the Protein‐Induced Absorption Shifts of Retinal in Engineered Rhodopsin Mimics

Rational design of light‐capturing properties requires understanding the molecular and electronic structure of chromophores in their native chemical or biological environment. We employ here large‐scale quantum chemical calculations to study the light‐capturing properties of retinal in recently designed human cellular retinol binding protein II (hCRBPII) variants (Wang et al. Science, 2012 , 338, 1340–1343). Our calculations show that these proteins absorb across a large part of the visible spectrum by combined polarization and electrostatic effects. These effects stabilize the ground or excited state energy levels of the retinal by perturbing the Schiff‐base or β‐ionone moieties of the chromophore, which in turn modulates the amount of charge transfer within the molecule. Based on the predicted tuning principles, we design putative in silico mutations that further shift the absorption properties of retinal in hCRBPII towards the ultraviolet and infrared regions of the spectrum.     

Proteomics analysis of in vitro protein methylation during Src-induced transformation

Src, a nonreceptor tyrosine kinase, was the first oncogene identified from an oncogenic virus. Mechanistic studies of Src-induced transformations aid in understanding the pathologic processes underlying tumorigenesis and may provide new strategies for cancer therapy. Although several pathways and protein modifications are reportedly involved in Src-induced transformation, the detailed mechanisms of their regulation remain unclear. Protein methylation is an important PTM that is widely involved in cellular physiology. In this study, we determined if protein methylation was involved in Src activation and which methylated proteins were associated with this activity. Using in vitro methylation and 2-DE analysis of viral Src (v-Src)-transformed rat kidney epithelial cells (RK3E), several known and novel methylated proteins were identified based on their changes in methylation signal intensity upon transformation. Among these, elongation factor 2 (EF-2), heterogeneous nuclear ribonucleoprotein K (hnRNP K), and β-tubulin protein expressions remained unchanged, indicating that their altered methylation levels were due to Src activation. In addition, the altered expression of β-actin, vimentin, and protein phosphatase 2, catalytic subunit (PPP2C) as well as protein phosphatase 2, catalytic subunit methylation were also confirmed in RK3E cells transformed with a human oncogenic Src mutant (Src531), supporting their association with Src-induced transformation in human cancer. Together, we showed putative involvement of protein methylation in Src activation and our identification of methylated proteins provides important targets for extensively studying Src-induced transformations.     

Attraction between electrophilic caps: A counterintuitive case of noncovalent interactions

Intermolecular attractive interaction between electrophilic sites is a counterintuitive phenomenon, as the electrostatic interaction therein is repulsive and destabilizing. Here, we confirm this phenomenon in four representative complexes, using state-of-the-art quantum mechanical methods. By employing the block-localized wavefunction (BLW) method, which can turn off intermolecular charge transfer interactions, we profoundly demonstrated the significance of charge transfer interactions in these seemingly counterintuitive complexes. Indeed, after being “turned off” the intermolecular charge transfer interaction in, for example, the FNSi···BrF complex, the originally attractive intermolecular interaction turns to be repulsive. The energy decomposition approach based on the BLW method (BLW-ED) can partition the overall stability gained on the formation of intermolecular noncovalent interaction into several physically meaningful components. According to the BLW-ED analysis, the electrostatic repulsion in these counterintuitive cases is overwhelmed by the stabilizing polarization, dispersion interaction, and most importantly, the charge transfer interaction, resulting in the eventual counterintuitive overall attraction. The present study suggests that, predicting bonding sites of noncovalent interactions using only the “hole” concept may be not universally sufficient, because other significant stabilizing factors will contribute to the stability and sometimes, play even bigger roles than the electrostatic interaction and consequently govern the complex structures. © 2018 Wiley Periodicals, Inc.     

Interplay between cation-pi, anion-pi and pi-pi interactions.

The interplay between three important noncovalent interactions involving aromatic rings is studied by means of high level ab initio calculations. They demonstrate that very strong synergic effects are present in complexes where either cation–π or anion–π and π‐‐π interactions coexist. These strong synergic effects have been studied using the “atoms in molecules” theory and the physical nature of the interactions investigated by means of the molecular interaction potential with polarization (MIPp).     

Site-specific mapping and time-resolved monitoring of lysine methylation by high-resolution NMR spectroscopy

Methylation and acetylation of protein lysine residues constitute abundant post-translational modifications (PTMs) that regulate a plethora of biological processes. In eukaryotic proteins, lysines are often mono-, di-, or trimethylated, which may signal different biological outcomes. Deconvoluting these different PTM types and PTM states is not easily accomplished with existing analytical tools. Here, we demonstrate the unique ability of NMR spectroscopy to discriminate between lysine acetylation and mono-, di-, or trimethylation in a site-specific and quantitative manner. This enables mapping and monitoring of lysine acetylation and methylation reactions in a nondisruptive and continuous fashion. Time-resolved NMR measurements of different methylation events in complex environments including cell extracts contribute to our understanding of how these PTMs are established in vitro and in vivo.     

The effect of cation size on ion pairing of methyl orange dye with tetraalkylammonium and benzyltrialkylammonium ions in aqueous solution

Formation constants have been measured by a solvent distribution method for the ion pairing of an arene sulfonate, methyl orange dye, with two series of quaternary ammonium ions: R₄N⁺(R=Et,n-Pr,n-Bu, andn-Pent) and C₆H₅CH₂R₃N⁺ (R=Me, Et,n-Pr,n-Bu,n-Pent, andn-Hex). Ion pairing increases dramatically as the length of the R group increases beyond butyl. Using a hard-sphere model for contact ion pairs, it is estimated that coulombic attraction contributes about –kT to the binding free energy and decreases slightly with increasing size of R₄N⁺. Other factors related to solvation effects, of which cosphere overlap predominates, contribute from –2kT to –7kT of binding energy. Plots of logK for association as a function of cation size show an inflection with decreasing slope between R=propyl and R=butyl. Possible causes for the inflection are considered.     

Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins

Protein structure and function is dependent on myriad noncovalent interactions. Direct detection and characterization of these weak interactions in large biomolecules, such as proteins, is experimentally challenging. Herein, we report the first observation and measurement of long‐range “through‐space” scalar couplings between methyl and backbone carbonyl groups in proteins. These J couplings are indicative of the presence of noncovalent C−H⋅⋅⋅π hydrogen‐bond‐like interactions involving the amide π network. Experimentally detected scalar couplings were corroborated by a natural bond orbital analysis, which revealed the orbital nature of the interaction and the origins of the through‐space J couplings. The experimental observation of this type of CH⋅⋅⋅π interaction adds a new dimension to the study of protein structure, function, and dynamics by NMR spectroscopy.     

Mobility Tuning of Polyrotaxane Surfaces to Stimulate Myocyte Differentiation

Polyrotaxanes, consisting of poly(ethylene glycol) and α‐cyclodextrins, are mechanically interlocked supermolecules. The structure allows α‐cyclodextrins to move along the polymer, referred to as molecular mobility. Here, polyrotaxane‐based triblock copolymers, composed of polyrotaxanes with different degrees of methylation and poly(benzyl methacrylate) at both terminals, are coated on culture surfaces to fabricate dynamic biointerfaces for myocyte differentiation. The molecular mobility increases with the degree of methylation and the contact angle hysteresis of water droplets and air bubbles. When the mouse myoblast cell line C2C12 is cultured on methylated polyrotaxane surfaces, the expression levels of myogenesis‐related genes, myogenin (Myog) and myosin heavy chain (Myhc) are altered by the degree of methylation. Polyrotaxane surfaces with intermediate degrees of methylation promote the highest expression levels among all the surfaces. The polyrotaxane surface provides an appropriate environment for myocyte differentiation by accurately adjusting the degrees of methylation.     

Biological soft materials

With one or two exceptions, biological materials are "soft", meaning that they combine viscous and elastic elements. This mechanical behavior results from self-assembled supramolecular structures that are stabilized by noncovalent interactions. It is an ongoing and profound challenge to understand the self-organization of biological materials. In many cases, concepts can be imported from soft-matter physics and chemistry, which have traditionally focused on materials such as colloids, polymers, surfactants, and liquid crystals. Using these ideas, it is possible to gain a new perspective on phenomena as diverse as DNA condensation, protein and peptide fibrillization, lipid partitioning in rafts, vesicle fusion and budding, and others, as discussed in this selective review of recent highlights from the literature.     

Computation of the binding affinities of catechol‐O‐methyltransferase inhibitors: Multisubstate relative free energy calculations

Alchemical free energy simulations are amongst the most accurate techniques for the computation of the free energy changes associated with noncovalent protein–ligand interactions. A procedure is presented to estimate the relative binding free energies of several ligands to the same protein target where multiple, low‐energy configurational substates might coexist, as opposed to one unique structure. The contributions of all individual substates were estimated, explicitly, with the free energy perturbation method, and combined in a rigorous fashion to compute the overall relative binding free energies and dissociation constants. It is shown that, unless the most stable bound forms are known a priori, inaccurate results may be obtained if the contributions of multiple substates are ignored. The method was applied to study the complex formed between human catechol‐O‐methyltransferase and BIA 9‐1067, a newly developed tight‐binding inhibitor that is currently under clinical evaluation for the therapy of Parkinson's disease. Our results reveal an exceptionally high‐binding affinity (K_d in subpicomolar range) and provide insightful clues on the interactions and mechanism of inhibition. The inhibitor is, itself, a slowly reacting substrate of the target enzyme and is released from the complex in the form of O‐methylated product. By comparing the experimental catalytic rate (k_cat) and the estimated dissociation rate (k_off) constants of the enzyme‐inhibitor complex, one can conclude that the observed inhibition potency (K_i) is primarily dependent on the catalytic rate constant of the inhibitor's O‐methylation, rather than the rate constant of dissociation of the complex. © 2012 Wiley Periodicals, Inc.     

EXCITED-STATE PROPERTIES OF DNA METHYLATED AT THE NV7 POSITION OF GUANINE AND ITS FREE FLUOROPHORE AT ROOM TEMPERATURE

The room-temperature optical properties of calf thymus DNA, with about 75% of its guanine residues methylated at position N-7, are compared with those of 7-methyl GMP which has the same fluorophore. The fluorescence spectrum of the methylated guanine residues depends strongly on the excitation wavelength, shifting to the blue as the wavelength increases. The fluorescence quantum yield, corrected for the contribution to absorption by the other virtually nonfluorescent residues, exhibits a pronounced drop at long excitation wavelengths relative to that for excitation at 265 nm. The degree of fluorescence polarization exhibits a weak dependence on the excitation and emission wavelengths. For 7-methyl GMP, the fluorescence spectrum is very weakly dependent on the excitation wavelength and its fluorescence quantum yield shows a moderate increase at long wavelengths. The degree of fluorescence polarization increases with increasing excitation wavelength particularly when monitoring the emission in the short wavelength region of the fluorescence spectrum. A pronounced drop of unknown origin is observed when exciting at 265 nm, which is not observed for methylated DNA. The methylated DNA data are interpreted in terms of a combination of (i) a heterogeneous environment of the methylated guanine residues, which results from sequence-dependent stacking interactions, and (ii) transfer of excitation energy from the other residues to the fluorescing methylated guanine residues. From the values of the quantum yields and those of the decay times, which we have recently reported (Georghiou et al., 1985), the following values are obtained for the radiative, k_t, and the sum of the nonradiative, σk₁, rate constants for deexcitation of the excited states of methylated DNA and its free fluorophore: 1.6 × 10⁸ s^-1 7 × 10⁷ s^-1 and 5 × 10¹⁰ s^-lvs 6 × 10⁹ s^-1. Because of energy transfer from the other residues. the k_f value for the methylated guanine residues is overestimated but their σk₁, value is not affected significantly and is by about an order of magnitude larger than that for 7-methyl GMP, apparently because of stacking interactions.     

Dynamics simulation on the flexibility and backbone motions of HP1 chromodomain bound to free and lysine 9‐methylated histone H3 tails

Histone methylation has emerged as a central epigenetic modification with both activating and repressive roles in eukaryotic chromatin. Drosophila HP1 (heterochromatin‐associated protein 1) is one of the chromodomain proteins that contain the essential aromatic residues as the recognition pocket for lysine methylated histone H3 tail. The aromatic cage indicates that the complex of chromodomain protein binding lysine methylated histone H3 tail can be seen as a typical host–guest system between protein and protein. About 10‐ns molecular dynamics simulations have been carried out in this study to examine how the presence of mono‐, trimethylated lysine 9 histone H3 tail (Me1K9, Me3K9 H3) influences the motions of HP1 protein receptor. The study shows that the conformation of HP1 protein free of H3 tail easily changes, whereas that of HP1 protein bound to methylated H3 tail does not. But the conformation of inserted Me1K9 H3 changes obviously as the Me1K recognition makes hydrogen‐bonded interactions associated with the aromatic cage even more unstable than those in free HP1 protein. The conformational change of Me1K9 H3 is correlated with the motions of HP1 protein. As the recognition factor going from Me1K to Me3K produces a more favorable interaction for aromatic ring, hydrogen‐bonded interactions associated with aromatic cage in Me3K9 H3‐HP1 complex were observed to be much more stable than those in Me1K9 H3‐HP1 complex and free HP1. Because of correlation, the flexibility of Me3K9 H3 decreases. The simulations indicate that both the MeK and the surrounding histone tail sequence are necessary features of recognition which significantly affect the flexibility and backbone motions of HP1 chromodomain. These findings confirm a regulatory mechanism of protein–protein interactions through a trimethylated post‐translational modification. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins

Protein structure and function is dependent on myriad noncovalent interactions. Direct detection and characterization of these weak interactions in large biomolecules, such as proteins, is experimentally challenging. Herein, we report the first observation and measurement of long-range “through-space” scalar couplings between methyl and backbone carbonyl groups in proteins. These J couplings are indicative of the presence of noncovalent C−H⋅⋅⋅π hydrogen-bond-like interactions involving the amide π network. Experimentally detected scalar couplings were corroborated by a natural bond orbital analysis, which revealed the orbital nature of the interaction and the origins of the through-space J couplings. The experimental observation of this type of CH⋅⋅⋅π interaction adds a new dimension to the study of protein structure, function, and dynamics by NMR spectroscopy.     

Solid‐Phase Synthesis of a Combinatorial Methylated (±)‐Epigallocatechin Gallate Library and the Growth‐Inhibitory Effects of these Compounds on Melanoma B16 Cells

We report on the solid‐phase synthesis of a combinatorial methylated (±)‐epigallocatechin gallate (EGCG) library and its biological evaluation. Epigallocatechin gallate (EGCG) and its methylated derivatives, which are members of the catechin family, exhibit various anti‐cancer effects. The solid‐phase synthesis of methylated EGCG involves the preparation of the α‐acyloxyketone by the coupling of a solid‐supported aldehyde with a ketone and an acid. The subsequent release and reductive etherification reaction of the solid‐supported α‐acyloxyketone provide the protected EGCG in good total yields. Sixty‐four methylated EGCGs were successfully prepared. The growth‐inhibitory effects of the methylated EGCG library were also examined. Although methylation of EGCG generally causes reduced growth inhibition, the growth‐inhibitory effect of 7‐OMe EGCGs was comparable to that of EGCG. The 7‐OMe EGCGs are attractive drug candidates because of their enhanced bioavailability.     

High-accuracy quantum mechanical studies of pi-pi interactions in benzene dimers

Although supramolecular chemistry and noncovalent interactions are playing an increasingly important role in modern chemical research, a detailed understanding of prototype noncovalent interactions remains lacking. In particular, pi-pi interactions, which are ubiquitous in biological systems, are not fully understood in terms of their strength, geometrical dependence, substituent effects, or fundamental physical nature. However, state-of-the-art quantum chemical methods are beginning to provide answers to these questions. Coupled-cluster theory through perturbative triple excitations in conjunction with large basis sets and extrapolations to the complete basis set limit have provided definitive results for the binding energy of several configurations of the benzene dimer, and benchmark-quality ab initio potential curves are being used to calibrate new density functional and force-field models for pi-pi interactions. Studies of substituted benzene dimers indicate flaws in the conventional wisdom about substituent effects in pi-pi interactions. Three-body and four-body interactions in benzene clusters have also been examined.     

Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and drbitrap mass spectrometry

Protein arginine (Arg) methylation serves an important functional role in eucaryotic cells, and typically occurs in domains consisting of multiple Arg in close proximity. Localization of methylarginine (MA) within Arg-rich domains poses a challenge for mass spectrometry (MS)-based methods; the peptides are highly charged under electrospray ionization (ESI), which limits the number of sequence-informative products produced by collision induced dissociation (CID), and loss of the labile methylation moieties during CID precludes effective fragmentation of the peptide backbone. Here the fragmentation behavior of Arg-rich peptides was investigated comprehensively using electron-transfer dissociation (ETD) and CID for both methylated and unmodified glycine-/Arg-rich peptides (GAR), derived from residues 679–695 of human nucleolin, which contains methylation motifs that are widely-represented in biological systems. ETD produced abundant information for sequencing and MA localization, whereas CID failed to provide credible identification for any available charge state (z=2–4). Nevertheless, CID produced characteristic neutral losses that can be employed to distinguish among different types of MA, as suggested by previous works and confirmed here with product ion scans of high accuracy/resolution by an LTQ/Orbitrap. To analyze MA-peptides in relatively complex mixtures, a method was developed that employs nano-LC coupled to alternating CID/ETD for peptide sequencing and MA localization/characterization, and an Orbitrap for accurate precursor measurement and relative quantification of MA-peptide stoichiometries. As proof of concept, GAR-peptides methylated in vitro by protein arginine N-methyltransferases PRMT1 and PRMT7 were analyzed. It was observed that PRMT1 generated a number of monomethylated (MMA) and asymmetric-dimethylated peptides, while PRMT7 produced predominantly MMA peptides and some symmetric-dimethylated peptides. This approach and the results may advance understanding of the actions of PRMTs and the functional significance of Arg methylation patterns.     

Chemical agents for binding post-translationally methylated lysines and arginines

Post-translational methylation, discovered more than half a century ago, encodes information in the form of a structural modification on a peptide or protein. The addition of a CH₃ group is one of the most subtle covalent modifications that exist in biology. In spite of this, recent years have revealed the many profound functional effects that arise from protein methylation in the cell. In an effort to open the doors to new assays and detection methods that would enable new basic and applied research into methylation pathways, chemical agents that can recognise and bind to methylated sites are now being pursued. In this review, we describe the supramolecular approaches to the recognition of methylated amino acids, peptides and proteins that have arisen in the last few years.