Dimer Conformation Research Articles

Charge transport modeling in bisphenazine derivative dimers as discotic liquid crystals: a TDDFT study

A theoretical study was conducted on bisphenazine derivatives which behave as discotic liquid crystals (DLCs). Different cofacial dimeric conformations were studied in order to model the packing in a column, which is the main arrangement found in a DLC. The intermolecular charge transport process was assessed employing the charge transfer integral “J” in the context of Marcus theory. This parameter was obtained via the TD-Split method with the M06L functional and a basis set containing diffuse and polarization functions. The resulting systems display a charge displacement from one molecule to the other. Furthermore, a bonding interaction is observed in the frontier molecular orbitals; this suggests that the best geometries for effective electron transfer are those in which the molecules are rotated, and not eclipsed or widely displaced geometries. Additionally, computations of the monomer were performed to study the electronic structure and the electronic excitations. This methodology provided new insights into one-dimensional migration of charges in DLC compounds by employing TDDFT.

Highly Enhanced Conformational Sampling of the Transmembrane Domain of Egf Receptor Sheds Light on the Activation Mechanism

The epidermal growth factor (EGF) receptor plays critical roles in regulating proliferation, survival and migration of cells. The activation of this receptor tyrosine kinase involves the dimerization of alpha helices in the transmembrane (TM) domain. Single point mutations in this region can modulate efficiency of helix dimerization and abnormal activation leads to human cancers. Therefore, it is crucial to determine modes and affinities of association in functional receptors and oncogenic forms. Various experimental and computational techniques have been recently used in this respect, which have provided substantial results. The emergence of innovative approaches might strongly contribute to improve our understanding of the activation mechanisms.Here, we develop a new computational method that combines coarse-grained molecular dynamics and metadynamics to investigate the dimerization of TM helices of EGF receptor. We perform simulations above the millisecond timescale to explore multiple events of association and dissociation. Our enhanced sampling protocol enables reconstruction of the multidimensional free energy landscape of the TM domain in its lipid bilayer environment. The results reveal complex free energy surfaces on which pathways of dimerization are clearly located. Then, cluster analyses enable identification of dimer conformations with N-terminal contacts of marginally higher stability than conformations displaying C-terminal contacts. Overall, the results suggest a mechanism in which the TM domain is a soft pivot and the dynamics of both ectodomain and juxta-membrane domain would drive the conformational change from inactive to active states of EGF receptor dimers. Application of the method to the homolog receptor Her2 will be also discussed to illustrate potential differences in the mechanisms of activation.

A Lys–Trp Cation−π Interaction Mediates the Dimerization and Function of the Chloride Intracellular Channel Protein 1 Transmembrane Domain

Chloride intracellular channel protein 1 (CLIC1) is a dual-state protein that can exist either as a soluble monomer or in an integral membrane form. The oligomerization of the transmembrane domain (TMD) remains speculative despite it being implicated in pore formation. The extent to which electrostatic and van der Waals interactions drive folding and association of the dimorphic TMD is unknown and is complicated by the requirement of interactions favorable in both aqueous and membrane environments. Here we report a putative Lys37-Trp35 cation-π interaction and show that it stabilizes the dimeric form of the CLIC1 TMD in membranes. A synthetic 30-mer peptide comprising a K37M TMD mutant was examined in 2,2,2-trifluoroethanol, sodium dodecyl sulfate micelles, and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine liposomes using far-ultraviolet (UV) circular dichroism, fluorescence, and UV absorbance spectroscopy. Our data suggest that Lys37 is not implicated in the folding, stability, or membrane insertion of the TMD peptide. However, removal of this residue impairs the formation of dimers and higher-order oligomers. This is accompanied by a 30-fold loss of chloride influx activity, suggesting that dimerization modulates the rate of chloride conductance. We propose that, within membranes, individual TMD helices associate via a Lys37-mediated cation-π interaction to form active dimers. The latter findings are also supported by results of modeling a putative TMD dimer conformation in which Lys37 and Trp35 form cation-π pairs at the dimer interface. Dimeric helix bundles may then associate to form fully active ion channels. Thus, within a membrane-like environment, aromatic interactions involving a polar lysine side chain provide a thermodynamic driving force for helix-helix association.

FT-IR, FT-Raman, NMR, UV and quantum chemical studies on monomeric and dimeric conformations of 3,5-dimethyl-4-methoxybenzoic acid

Extensive spectroscopic investigations along with theoretical quantum chemical studies on 3,5-dimethyl-4-methoxybenzoic acid (DMMBA) have been consummated. The fundamental vibrational transitions were addressed by experimental FT-IR (4000–400cm−1) and FT-Raman (4000–10cm−1) techniques and density functional calculations at B3LYP/6-311++G(d,p) and B3LYP/6-311++G(df,pd) levels of theory. The 1H, 13C and DEPT 135 NMR spectra of studied compound were recorded in deuterated dimethylsulfoxide (DMSO−d6), and compared with computed data obtained by using gauge including atomic orbital (GIAO) method. The electronic absorption spectra in methanol and ethanol solution were evaluated in the range of 200–400nm, and TD-DFT method was chosen for computational study. The spectroscopic and theoretical results were compared to the corresponding properties for monomer and dimer structures for the most stable conformer. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Moreover, the thermodynamic and nonlinear optical (NLO) properties were evaluated.

Conformers of dimers of carboxylic acids in the gas phase: A rotational study of difluoroacetic acid–formic acid

The rotational spectra of two conformers of the difluoroacetic acid–formic acid complex have been identified by pulsed jet Fourier transform microwave spectroscopy. They differ from each other depending on the trans or gauche arrangement of the terminal CHF2 group. The gauche form displays a doubling of the rotational transitions, from which the internal rotation barrier hindering the two equivalent gauche forms has been estimated to be 101.8(3)cm−1. The increase of the distance between the two monomers upon OH→OD deuteration (Ubbelohde effect) has been determined.

Packing interface energetics in different crystal forms of the λ Cro dimer

Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ∼5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures.

The maturation of HIV-1 protease precursor studied by discrete molecular dynamics

The equilibrium properties of a HIV-1-protease precursor are studied by means of an efficient molecular dynamics scheme, which allows for the simulation of the folding of the protein monomers and their dimerization into an active form and compare them with those of the mature protein. The results of the model provide, with atomic detail, an overall account of several experimental findings, including the NMR conformation of the mature dimer, the calorimetric properties of the system, the effects of the precursor tail on the dimerization constant, the secondary chemical shifts of the monomer, and the paramagnetic relaxation enhancement data associated with the conformations of the precursor. It is found that although the mature protein can dimerize in a unique, single way, the precursor populates several dimeric conformations in which monomers are always native-like, but their binding can be non-native.

PREDDIMER: a web server for prediction of transmembrane helical dimers

Here we present PREDDIMER, a web tool for prediction of dimer structure of transmembrane (TM) helices. PREDDIMER allows (i) reconstruction of a number of dimer structures for given sequence(s) of TM protein fragments, (ii) ranking and filtering of predicted structures according to respective values of a scoring function, (iii) visualization of predicted 3D dimer structures and (iv) visualization of surface hydrophobicity of TM helices and their contacting (interface) regions represented as 2D maps. We implemented online the original PREDDIMER algorithm and benchmarked the server on 11 TM sequences, whose 3D dimer conformations were obtained previously by nuclear magnetic resonance spectroscopy. In the most of tested cases backbone root-mean-square deviations of closest predicted conformations from the experimental reference are below 3 Å. A randomization test displays good anticorrelation (-0.82) between values of the scoring function and statistical significance of the prediction 'by chance'. Going beyond a single dimer conformation, our web tool predicts an ensemble of possible conformations, which may be useful for explanation of a functioning of bitopic membrane proteins, e.g. receptor tyrosine kinases. PREDDIMER can be accessed for free on the web at http://model.nmr.ru/preddimer/ newant@gmail.com Supplementary data are available at Bioinformatics online.

A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms

Tryptophan is an essential amino acid, and understanding the conformational preferences of monomer and dimer is a subject of outstanding relevance in biological systems. An exhaustive first principles investigation of tryptophan (W) and its ionized counterparts cations (WC), anions (WA), and zwitterions (WZ) has been carried out. A comprehensive and systematic study of tryptophan dimer (WD) conformations resulted in about 62 distinct minima on the potential energy surface. The hydrogen bonds and a variety of noncovalent interactions such as OH-π, NH-π, CH-π, CH-O, and π-π interactions stabilized different forms of tryptophan and its dimers. Over all in monomeric conformers which have NH-O, hydrogen bonds showed higher stability than other conformers. A cursory analysis reveal that the most stable dimers stabilized by hydrogen bonding interactions while the less stable dimers showed aromatic side chain interactions. Protein Data Bank analysis of tryptophan dimers reveals that at a larger distance greater than 5 Å, T-shaped orientations (CH-π interactions) are more prevalent, while stacked orientations (π-π interactions) are predominant at a smaller distance.

The common hereditary elliptocytosis-associated α-spectrin L260P mutation perturbs erythrocyte membranes by stabilizing spectrin in the closed dimer conformation

AbstractHereditary elliptocytosis (HE) and hereditary pyropoikilocytosis (HPP) are common disorders of erythrocyte shape primarily because of mutations in spectrin. The most common HE/HPP mutations are located distant from the critical αβ-spectrin tetramerization site, yet still interfere with formation of spectrin tetramers and destabilize the membrane by unknown mechanisms. To address this question, we studied the common HE-associated mutation, αL260P, in the context of a fully functional mini-spectrin. The mutation exhibited wild-type tetramer binding in univalent binding assays, but reduced binding affinity in bivalent-binding assays. Biophysical analyses demonstrated the mutation-containing domain was only modestly structurally destabilized and helical content was not significantly changed. Gel filtration analysis of the αL260P mini-spectrin indicated more compact structures for dimers and tetramers compared with wild-type. Chemical crosslinking showed structural changes in the mutant mini-spectrin dimer were primarily restricted to the vicinity of the αL260P mutation and indicated large conformational rearrangements of this region. These data indicate the mutation increased the stability of the closed dimer state, thereby reducing tetramer assembly and resulting in membrane destabilization. These results reveal a novel mechanism of erythrocyte membrane destabilization that could contribute to development of therapeutic interventions for mutations in membrane proteins containing spectrin-type domains associated with inherited disease.

Importance of indole N[sbnd]H hydrogen bonding in the organization and dynamics of gramicidin channels

The linear ion channel peptide gramicidin represents an excellent model for exploring the principles underlying membrane protein structure and function, especially with respect to tryptophan residues. The tryptophan residues in gramicidin channels are crucial for the structure and function of the channel. In order to test the importance of indole hydrogen bonding for the biophysical properties of gramicidin channels, we monitored the effect of N-methylation of gramicidin tryptophans, using a combination of steady state and time-resolved fluorescence approaches along with circular dichroism spectroscopy. We show here that in the absence of the hydrogen bonding ability of tryptophans, tetramethyltryptophan gramicidin (TM-gramicidin) is unable to maintain the single stranded, head-to-head dimeric channel conformation in membranes. Our results show that TM-gramicidin displays a red-shifted fluorescence emission maximum, lower red edge excitation shift (REES), and higher fluorescence intensity and lifetime, consistent with its nonchannel conformation. This is in agreement with the measured location (average depth) of the 1-methyltryptophans in TM-gramicidin using the parallax method. These results bring out the usefulness of 1-methyltryptophan as a fluorescent tool to examine the hydrogen bonding ability of tryptophans in proteins and peptides. We conclude that changes in the hydrogen bonding ability of tryptophans, along with coupled changes in peptide backbone structure induce the loss of single stranded β6.3 helical dimer conformation. These results agree with earlier results from size-exclusion chromatography and single-channel measurements for TM-gramicidin, and confirm the importance of indole hydrogen bonding for the conformation and function of ion channels and membrane proteins.

Novel Interaction of Ornithine Decarboxylase with Sepiapterin Reductase Regulates Neuroblastoma Cell Proliferation

Ornithine decarboxylase (ODC) is the sentinel enzyme in polyamine biosynthesis. Both ODC and polyamines regulate cell division, proliferation, and apoptosis. Sepiapterin reductase (SPR) catalyzes the last step in the biosynthesis of tetrahydrobiopterin (BH4), an essential cofactor of nitric oxide synthase, and has been implicated in neurological diseases but not yet in cancer. In this study, we present compelling evidence that native ODC and SPR physically interact, and we defined the individual amino acid residues involved in both enzymes using in silico protein–protein docking simulations. The resulting heterocomplex is a surprisingly compact structure, featuring two energetically and structurally equivalent binding modes both in monomer and in dimer conformations. The novel interaction between ODC and SPR proteins was confirmed under physiological conditions by co-immunoprecipitation and co-localization in neuroblastoma (NB) cells. Importantly, we showed that siRNA (small interfering RNA)-mediated knockdown of SPR expression significantly reduced endogenous ODC enzyme activity in NB cells, thus demonstrating the biological relevance of the ODC–SPR interaction. Finally, in a cohort of 88 human NB tumors, we found that high SPR mRNA expression correlated significantly with poor survival prognosis using a Kaplan–Meier analysis (log-rank test, P=5×10−4), suggesting an oncogenic role for SPR in NB tumorigenesis. In conclusion, we showed that ODC binds SPR and thus propose a new concept in which two well-characterized biochemical pathways converge via the interaction of two enzymes. We identified SPR as a novel regulator of ODC enzyme activity and, based on clinical evidence, present a model in which SPR drives ODC-mediated malignant progression in NB.

Interaction investigations of HipA binding to HipB dimer and HipB dimer + DNA complex: a molecular dynamics simulation study

We carried out molecular dynamics simulations and free energy calculations for a series of ternary and diplex models for the HipA protein, HipB dimer, and DNA molecule to address the mechanism of HipA sequestration and the binding order of events from apo HipB/HipA to 2HipA + HipB dimer + DNA complex. The results revealed that the combination of DNA with the HipB dimer is energetically favorable for the combination of HipB dimer with HipA protein. The binding of DNA to HipB dimer induces a long-range allosteric communication from the HipB2 -DNA interface to the HipA-HipB2 interface, which involves the closeness of α1 helices of HipB dimer to HipA protein and formations of extra hydrogen bonds in the HipA-HipB2 interface through the extension of α2/3 helices in the HipB dimer. These simulated results suggested that the DNA molecule, as a regulative media, modulates the HipB dimer conformation, consequently increasing the interactions of HipB dimer with the HipA proteins, which explains the mechanism of HipA sequestration reported by the previous experiment. Simultaneously, these simulations also explored that the thermodynamic binding order in a simulated physiological environment, that is, the HipB dimer first bind to DNA to form HipB dimer + DNA complex, then capturing strongly the HipA proteins to form a ternary complex, 2HipA + HipB dimer + DNA, for sequestrating HipA in the nucleoid.

Structure of the Toll/interleukin 1 receptor (TIR) domain of the immunosuppressive Brucella effector BtpA/Btp1/TcpB

BtpA/Btp1/TcpB is a virulence factor produced by Brucella species that possesses a Toll interleukin-1 receptor (TIR) domain. Once delivered into the host cell, BtpA interacts with MyD88 to interfere with TLR signalling and modulates microtubule dynamics. Here the crystal structure of the BtpA TIR domain at 3.15Å is presented. The structure shows a dimeric arrangement of a canonical TIR domain, similar to the Paracoccus denitrificans Tir protein but secured by a unique long N-terminal α-tail that packs against the TIR:TIR dimer. Structure-based mutations and multi-angle light scattering experiments characterized the BtpA dimer conformation in solution. The structure of BtpA will help with studies to understand the mechanisms involved in its interactions with MyD88 and with microtubules.

Naphthalene dimer and naphthalene dimer with Ar: calibration calculations and the effect of Ar on the stability and vibrational frequencies

The harmonic vibrational frequencies of naphthalene and its dimers are computed using density functional theory including an empirical correction for dispersion. The C–H out-of-plane bending modes in the naphthalene dimers show a red or a blue shift depending on the relative orientation of the two naphthalene molecules. The addition of Ar atoms does not significantly affect the vibrational frequencies, but changes the energy separation between the two dimer conformations.

The crystal structure of the orphan nuclear receptor NR2E3/PNR ligand binding domain reveals a dimeric auto-repressed conformation.

Photoreceptor-specific nuclear receptor (PNR, NR2E3) is a key transcriptional regulator of human photoreceptor differentiation and maintenance. Mutations in the NR2E3-encoding gene cause various retinal degenerations, including Enhanced S-cone syndrome, retinitis pigmentosa, and Goldman-Favre disease. Although physiological ligands have not been identified, it is believed that binding of small molecule agonists, receptor desumoylation, and receptor heterodimerization may switch NR2E3 from a transcriptional repressor to an activator. While these features make NR2E3 a potential therapeutic target for the treatment of retinal diseases, there has been a clear lack of structural information for the receptor. Here, we report the crystal structure of the apo NR2E3 ligand binding domain (LBD) at 2.8 Å resolution. Apo NR2E3 functions as transcriptional repressor in cells and the structure of its LBD is in a dimeric auto-repressed conformation. In this conformation, the putative ligand binding pocket is filled with bulky hydrophobic residues and the activation-function-2 (AF2) helix occupies the canonical cofactor binding site. Mutations designed to disrupt either the AF2/cofactor-binding site interface or the dimer interface compromised the transcriptional repressor activity of this receptor. Together, these results reveal several conserved structural features shared by related orphan nuclear receptors, suggest that most disease-causing mutations affect the receptor’s structural integrity, and allowed us to model a putative active conformation that can accommodate small ligands in its pocket.

Inverse correlation between Thr‐669 and constitutive tyrosine phosphorylation in the asymmetric epidermal growth factor receptor dimer conformation

We have recently identified tumor necrosis factor (TNF)-α-induced phosphorylation of epidermal growth factor receptor (EGFR) at Thr-669 and Ser-1046/1047 via ERK and p38 pathways, respectively. In the present study, we investigated the roles of ligand-induced phosphorylation of serine and threonine residues in EGFR-overexpressing MDA-MB-468 breast cancer cells. Epidermal growth factor and heregulin, an ErbB3 ligand, induced the phosphorylation of Thr-669 and Ser-1046/1047. Inversely, constitutive tyrosine phosphorylation of the C-terminal domain, including Tyr-1068, was significantly downregulated on ligand stimulation. Inhibition of the ERK pathway by U0126 blocked ligand-induced Thr-669 phosphorylation as well as Tyr-1068 dephosphorylation. Downregulation of constitutive tyrosine phosphorylation of EGFR in HEK293 cells stably expressing the wild type was abolished by substitution of Thr-669 for Ala. In an asymmetric EGFR homodimer structure, one Thr-669 in the receiver kinase of the dimer was involved in downregulation. Similarly, Thr-669 in an EGFR-ErbB3 heterodimer also participated in tyrosine dephosphorylation. These results indicate that ERK-mediated Thr-669 phosphorylation suppresses constitutive tyrosine phosphosphorylation in the homo- and heterodimer asymmetric conformations of the EGFR.

P73 – constitutively open for business

p73 – constitutively open for business

Synthesis, characterisation, mesomorphic investigation and temperature-dependent Raman study of a novel calamitic liquid crystal: methyl 4-(4′-n-alkoxybenzylideneamino)benzoate

A new series of Schiff base calamitic liquid crystal; methyl 4-(4′-n-alkoxybenzylideneamino)benzoate (MABAB), H2n+1C n OC6H4C(H)=NC6H4COOCH3 (n = 6, 8, 10, 12, 14, 16) has been synthesised and characterised by elemental analyses, Fourier transform infrared spectroscopy (FT-IR), 1H and 13C Nuclear Magnetic Resonance (NMR) spectroscopy. The mesomorphic properties of these compounds were studied by differential scanning calorimetry (DSC) and polarising optical microscopy (POM). All members of the series exhibit enantiotropic smectic A (SmA) mesophase. Temperature-dependent micro-Raman study of one of the members, MABAB-10 has been employed to identify phase transitions and the molecular rearrangement therein. Analysis of Raman marker bands; C–H in-plane bending, C–C stretching of phenyl rings and –C(H)=N– linking group of core confirms the transitions clearly as observed through DSC and POM. An in situ Raman measurement of C–H in-plane bending mode has also been performed to visualise the molecular changes more clearly. The Raman study gives an evidence of induced co-planarity of rings at Cr→SmA phase transition. The density functional theoretical (DFT) optimisation of monomer, dimer and rotational conformer of MABAB-10 also support the induced co-planarity at Cr→SmA phase transition.

Efficient Methods for the Quantum Chemical Treatment of Protein Structures: The Effects of London-Dispersion and Basis-Set Incompleteness on Peptide and Water-Cluster Geometries.

We demonstrate how quantum chemical Hartree-Fock (HF) or density functional theory (DFT) optimizations with small basis sets of peptide and water cluster structures are decisively improved if London-dispersion effects, the basis-set-superposition error (BSSE), and other basis-set incompleteness errors are addressed. We concentrate on three empirical corrections to these problems advanced by Grimme and co-workers that lead to computational strategies that are both accurate and efficient. Our analysis encompasses a reoptimized version of Hobza's P26 set of tripeptide structures, a new test set of conformers of cysteine dimers, and isomers of the water hexamer. These systems reflect features commonly found in protein crystal structures. In all cases, we recommend Grimme's DFT-D3 correction for London-dispersion. We recommend usage of large basis sets such as cc-pVTZ whenever possible to reduce any BSSE effects and, if this is not possible, to use Grimme's gCP correction to account for BSSE when small basis sets are used. We demonstrate that S-S and C-S bond lengths are very prone to basis-set incompleteness and that polarization functions should always be used on S atoms. At the double-ζ level, the PW6B95-D3-gCP DFT method combined with the SVP and 6-31G* basis sets yields accurate results. Alternatively, the HF-D3-gCP/SV method is recommended, with inclusion of polarization functions for S atoms only. Minimal basis sets offer an intriguing route to highly efficient calculations, but due to significant basis-set incompleteness effects, calculated bond lengths are seriously overestimated, making applications to large proteins very difficult, but we show that Grimme's newest HF-3c correction overcomes this problem and so makes this computational strategy very attractive. Our results provide a useful guideline for future applications to the optimization, quantum refinement, and dynamics of large proteins.