Homodimeric Complex Research Articles

Peroxisome proliferator-activated receptor gamma (PPARγ) has multiple binding points that accommodate ligands in various conformations: Structurally similar PPARγ partial agonists bind to PPARγ LBD in different conformations.

In the course of studies directed toward the creation of human peroxisome proliferator-activated receptor gamma (hPPARγ) partial agonists, we designed and synthesized benzylsulfonylaminocarbonyl derivative (3) by structural modification of our reported hPPARγ partial agonist 2. Co-crystallization of 3 with the hPPARγ ligand-binding domain (LBD) afforded a homodimeric complex in which one of the LBDs adopts a fully active structure without bound 3, while the other LBD exhibits a non-fully active structure containing one molecule of bound 3. Interestingly, 2 and 3 are structurally similar, but bind to hPPARγ LBD in distinct conformations, that is, the sulfonylaminocarbonyl moiety of bound 3 is directed at 180° away from that of bound 2. These results support our previous proposal that the hPPARγ LBD has multiple binding points that can be utilized to accommodate structurally flexible hPPAR ligands.

Different structures of the two peroxisome proliferator-activated receptor gamma (PPARγ) ligand-binding domains in homodimeric complex with partial agonist, but not full agonist.

We designed and synthesized acylsulfonamide derivative (3) as a human peroxisome proliferator-activated receptor gamma (hPPARγ) partial agonist by structural modification of hPPARγ full agonist 1. Co-crystallization of 3 with hPPARγ LBD afforded a homodimeric complex, and X-ray crystallographic analysis at 2.1Å resolution showed that one of the LBDs adopts a fully active structure identical with that in the complex of rosiglitazone, a full agonist; however, the other LBD in the complex of 3 exhibits a different (non-fully active) structure. Interestingly, the apo-homodimer contained similar LBD structures. Intrigued by these results, we surveyed reported X-ray crystal structures of partial agonists complexed with hPPARγ LBD homodimer, and identified several types of LBD structures distinct from the fully active structure. In contrast, both LBDs in the rosiglitazone complex have the fully active structure. These results suggest hPPARγ partial agonists lack the ability to induce fully active LBD. The presence of at least one non-fully active LBD in the agonist complex may be a useful criterion to distinguish hPPARγ partial agonists from full agonists.

The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA.

The pentatricopeptide repeat (PPR) protein family is a large family of RNA-binding proteins that is characterized by tandem arrays of a degenerate 35-amino-acid motif which form an α-solenoid structure. PPR proteins influence the editing, splicing, translation and stability of specific RNAs in mitochondria and chloroplasts. Zea mays PPR10 is amongst the best studied PPR proteins, where sequence-specific binding to two RNA transcripts, atpH and psaJ, has been demonstrated to follow a recognition code where the identity of two amino acids per repeat determines the base-specificity. A recently solved ZmPPR10:psaJ complex crystal structure suggested a homodimeric complex with considerably fewer sequence-specific protein–RNA contacts than inferred previously. Here we describe the solution structure of the ZmPPR10:atpH complex using size-exclusion chromatography-coupled synchrotron small-angle X-ray scattering (SEC-SY-SAXS). Our results support prior evidence that PPR10 binds RNA as a monomer, and that it does so in a manner that is commensurate with a canonical and predictable RNA-binding mode across much of the RNA–protein interface.

Structural analysis of the EGFR/HER3 heterodimer reveals the molecular basis for activating HER3 mutations.

The human epidermal growth factor receptor (HER) tyrosine kinases homo- and heterodimerize to activate downstream signaling pathways. HER3 is a catalytically impaired member of the HER family that contributes to the development of several human malignancies and is mutated in a subset of cancers. HER3 signaling depends on heterodimerization with a catalytically active partner, in particular epidermal growth factor receptor (EGFR) (the founding family member, also known as HER1) or HER2. The activity of homodimeric complexes of catalytically active HER family members depends on allosteric activation between the two kinase domains. To determine the structural basis for HER3 signaling through heterodimerization with a catalytically active HER family member, we solved the crystal structure of the heterodimeric complex formed by the isolated kinase domains of EGFR and HER3. The structure showed HER3 as an allosteric activator of EGFR and revealed a conserved role of the allosteric mechanism in activation of HER family members through heterodimerization. To understand the effects of cancer-associated HER3 mutations at the molecular level, we solved the structures of two kinase domains of HER3 mutants, each in a heterodimeric complex with the kinase domain of EGFR. These structures, combined with biochemical analysis and molecular dynamics simulations, indicated that the cancer-associated HER3 mutations enhanced the allosteric activator function of HER3 by redesigning local interactions at the dimerization interface.

Native structure of photosystem II at 1.95Å resolution viewed by femtosecond X-ray pulses.

Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation, and slight differences were found in the Mn-Mn distances determined by XRD, EXAFS and theoretical studies. Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.

Highly thermostable carbonic anhydrase from Persephonella marina EX-H1: Its expression and characterization for CO2-sequestration applications

The codon-optimized carbonic anhydrase gene of Persephonella marina EX-H1 (PMCA) was expressed and characterized. The gene with the signal peptide removed, PMCA(sp−), resulted in the production of approximately five times more purified protein than from the intact gene PMCA using an Escherichia coli expression system. PMCA(sp−) is formed as homo-dimer complex. PMCA(sp−) has a wide pH tolerance (optimum pH 7.5) and a high thermostability even at 100°C (88min of thermal deactivation half-life). The melting temperature for PMCA(sp−) was 84.5°C. The apparent kcat and Km values for CO2 hydration were 3.2×105s−1 and 10.8mM. The activity of the PMCA(sp−) enzyme was enhanced by Zn2+, Co2+, and Mg2+, but was strongly inhibited by Cu2+, Fe3+, Al3+, Pb2+, Ag+, and Hg2+. PMCA(sp−) readily catalyzed the hydration of CO2, precipitating CaCO3 as calcite in the presence of Ca2+.

Abstract SY06-04: Regulation of cancer cell proliferation and survival by NF-κB

Abstract SY06-04: Regulation of cancer cell proliferation and survival by NF-κB

Structural analysis of the homodimeric reaction center complex from the photosynthetic green sulfur bacterium Chlorobaculum tepidum.

The reaction center (RC) complex of the green sulfur bacterium Chlorobaculum tepidum is composed of the Fenna–Matthews–Olson antenna protein (FMO) and the reaction center core (RCC) complex. The RCC complex has four subunits: PscA, PscB, PscC, and PscD. We studied the FMO/RCC complex by chemically cross-linking the purified sample followed by biochemical and spectroscopic analysis. Blue-native gels showed that there were two types of FMO/RCC complexes, which are consistent with complexes with one copy of FMO per RCC and two copies of FMO per RCC. Sodium dodecyl sulfate–polyacrylamide gel electrophoresis analysis of the samples after cross-linking showed that all five subunits of the RC can be linked by three different cross-linkers: bissulfosuccinimidyl suberate, disuccinimidyl suberate, and 3,3-dithiobis-sulfosuccinimidyl propionate. The interaction sites of the cross-linked complex were also studied using liquid chromatography coupled to tandem mass spectrometry. The results indicated that FMO, PscB, PscD, and part of PscA are exposed on the cytoplasmic side of the membrane. PscD helps stabilize FMO to the reaction center and may facilitate transfer of the electron from the RC to ferredoxin. The soluble domain of the heme-containing cytochrome subunit PscC and part of the core subunit PscA are located on the periplasmic side of the membrane. There is a close relationship between the periplasmic portions of PscA and PscC, which is needed for the efficient transfer of the electron between PscC and P840.

Virtual issue: structure characterization of biomolecules.

The structural diversity of biomolecules is quite simply enormous. Although many polymeric biomolecules such as proteins, and ribonucleic (RNA) and deoxyribonucleic (DNA) acids have complex but rather well-defined lowest-energy structures, it became increasingly apparent in recent years that many of them have not. Especially for proteins, but also for RNA, it has been shown that they can instead feature a number of significantly different yet similarly stable structures, or even generally lack defined structure at all, which led to the idea that a static view of single, rigid structures may not be sufficient for understanding the properties and function of biomolecules. This fundamental insight into the dynamic nature of biomolecules, and its highly important implications in folding and binding, only became possible with the use of newly developed or refined experimental approaches. This virtual issue in ChemistryOpen on the “Structure Characterization of Biomolecules” highlights the fruitful interplay between chemical synthesis and advanced techniques for biomolecular characterization in solution and in the gas phase, among them, nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), ion mobility spectrometry (IMS), microscale thermophoresis (MST), and kinetic capillary electrophoresis (KCE). Berezovski and co-workers (DOI: 10.1002/open.201400002) used KCE in combination with MS and IMS to study fast conformational dynamics of DNA G-quadruplexes, and demonstrate that rate and equilibrium constants for DNA folding and metal binding can be determined by KCE-MS. They further show that both drift and migration times in IMS and KCE are different for unfolded and folded, metal-bound DNA. Also concerned with DNA binding is the contribution by Diederichsen and co-workers (DOI: 10.1002/open.201400001), who have synthesized two new compounds, each of which comprises four nucleobase recognition units on a rigid template that is based on a cyclopeptide backbone. Binding of these triostin A analogues was studied by MST, temperature-dependent UV spectroscopy, and MS, which showed evidence for self-aggregation of the TTTT but not the ATTA sequence, and specific binding of the ATTA motif to DNA. The work by Konrat and co-workers (DOI: 10.1002/open.201402008) focuses on magnetic resonance based experimental techniques for the structural characterization of weak and transient protein/protein and protein/RNA complexes. They use sophisticated relaxation dispersion experiments to study lowly populated states of the Escherichia coli cold shock protein CspA complexed to RNA, with detection of either protein or RNA signals, and of the homodimeric complex of an oncogenic protein. Moreover, they introduce a new approach that combines NMR with electron paramagnetic resonance (EPR) spectroscopy to obtain structural information on substates of intrinsically disordered proteins that previously escaped detection by conventional techniques. Sharon and co-workers (DOI: 10.1002/open.201402002) have developed an improved rapid mixing device for time-resolved electrospray ionization (ESI) MS measurements to monitor protein folding, unfolding, and enzymatic reactions. Using cytochrome C as a model system, they demonstrate increased signal-to-noise ratio in ESI mass spectra, and a threefold decrease in experimental repeat error compared to previous capillary mixing devices. This virtual issue in ChemistryOpen on the “Structure Characterization of Biomolecules” highlights the fruitful interplay between chemical synthesis and advanced techniques for biomolecular characterization in solution and in the gas phase… Overall, the contributions in this virtual issue beautifully illustrate the value of combining experimental approaches and techniques for the structural characterization of biomolecules to obtain deeper insight into the dynamic nature and function of proteins, nucleic acids, and their complexes. Priv.-Doz. Dr. Kathrin Breuker Guest Editor Editorial Advisory Board Member ChemistryOpen

Structural mapping of semiquinone catalytic intermediates at the quinol binding site of the nitrate reductase A from Escherichia coli by selective 15N labeling and pulsed EPR

Respiratory supercomplexes have been extensively studied in mitochondria, but much less concerned in prokaryotes. Here we present the detailed characterization work on a supercomplex III/IV isolated from native membranes of eubacterium Aquifex aeolicus. This supercomplex III/IV survives fromdetergent solubilization and ismonodispersed in both ion-exchange and size-exclusion chromatography. It consists of cytochrome b, cytochrome c1 and Rieske protein from the cytochrome bc1 complex and subunits I, II and IIa from the cytochrome oxidase. Major subunits are clearly visible on SDS-PAGE and later on identified by MALDI-MS. Activity assay showed that this supercomplex has higher turnover numbers than the purified cytochrome oxidase, which was called “Cox2” in our former work [1]. The stoichiometry of the supercomplex has been characterized as a homo-dimeric bc1 complex and a monomeric oxidase based on heme ratios, protein amounts and metal contents. Functional analysis on the supercomplex III2IV indicates potential interaction between the cytochrome bc1 complex and the cytochrome oxidase. In order to investigate the potential interaction, crosslinking work of the supercomplex has been performed, antibodies against protein subunits have been produced, and mass spectrometry has been applied. Further functional analysis of the supercomplex would be done as soon as possible aiming to get a picture of the supercomplex functional organization.

On the electrostatic properties of homodimeric proteins.

A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology, 9(2), e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily in an electrostatic funnel. It is demonstrated that the electrostatic dipole moment of the dimer is predominantly perpendicular to the axis connecting the centers of the mass of the monomers. In addition, the surface points with highest potential are located in the proximity of the interfacial plane of the homodimeric complexes. These findings indicate that frequently homodimerization provides specific electrostatic features needed for the function of proteins.

Mass spectroscopy locates the extrinsic proteins of photosystem II

The photosynthetic oxidation of water is catalyzed by photosystem II (PSII), a multisubunit pigment-protein embedded in the thylakoid membranes of cyanobacteria, algae, and plants. This remarkable photoenzyme is capable of generating the highly oxidizing chemical species required to extract four tightly bound electrons of two substrate water-molecules, yielding biosynthetically useful reductant and by-product O2. PSII is a large homodimeric complex in vivo, with a combined mass of ∼700 kDa. Each PSII monomer comprises more than 20 different proteins collectively coordinating ∼60 cofactors, including 35 chlorophylls, 2 pheophytins, 2 plastoquinone molecules, and the Mn4Ca cluster, responsible for H2O-oxidation (1, 2). Despite much progress, including the 1.9 A crystal structure of cyanobacterial PSII (1, 3), crucial structural information is missing. This lack includes extrinsic proteins affecting the Mn4Ca cluster, not observed in the PSII crystal structure because they are lost during the purification and crystallization process. In PNAS, Liu et al. use complementary technical approaches to construct a model for the binding of one of the lost extrinsic proteins, PsbQ, to the PSII, complex, and in doing so provide an example for the solution of the more general structural problem of defining the 3D structure of separately crystallized proteins that assemble into larger macromolecular complexes (4).

Regulation of Acetate Kinase Isozymes and Its Importance for Mixed-Acid Fermentation in Lactococcus lactis

Acetate kinase (ACK) converts acetyl phosphate to acetate along with the generation of ATP in the pathway for mixed-acid fermentation in Lactococcus lactis. The reverse reaction yields acetyl phosphate for assimilation purposes. Remarkably, L. lactis has two ACK isozymes, and the corresponding genes are present in an operon. We purified both enzymes (AckA1 and AckA2) from L. lactis MG1363 and determined their oligomeric state, specific activities, and allosteric regulation. Both proteins form homodimeric complexes, as shown by size exclusion chromatography and static light-scattering measurements. The turnover number of AckA1 is about an order of magnitude higher than that of AckA2 for the reaction in either direction. The Km values for acetyl phosphate, ATP, and ADP are similar for both enzymes. However, AckA2 has a higher affinity for acetate than does AckA1, suggesting an important role under acetate-limiting conditions despite the lower activity. Fructose-1,6-bisphosphate, glyceraldehyde-3-phosphate, and phospho-enol-pyruvate inhibit the activities of AckA1 and AckA2 to different extents. The allosteric regulation of AckA1 and AckA2 and the pool sizes of the glycolytic intermediates are consistent with a switch from homolactic to mixed-acid fermentation upon slowing of the growth rate.

Recent advances in the structural molecular biology of Ets transcription factors: interactions, interfaces and inhibition

The Ets family of eukaryotic transcription factors is based around the conserved Ets DNA-binding domain. Although their DNA-binding selectivity is biochemically and structurally well characterized, structures of homodimeric and ternary complexes point to Ets domains functioning as versatile protein-interaction modules. In the present paper, we review the progress made over the last decade to elucidate the structural mechanisms involved in modulation of DNA binding and protein partner selection during dimerization. We see that Ets domains, although conserved around a core architecture, have evolved to utilize a variety of interaction surfaces and binding mechanisms, reflecting Ets domains as dynamic interfaces for both DNA and protein interaction. Furthermore, we discuss recent advances in drug development for inhibition of Ets factors, and the roles structural biology can play in their future.

Functional and Structural Study of the Dimeric Inner Membrane Protein SbmA

SbmA protein has been proposed as a dimeric secondary transporter. The protein is involved in the transport of microcins B17 and J25, bleomycin, proline-rich antimicrobial peptides, antisense peptide phosphorodiamidate morpholino oligomers, and peptide nucleic acids into the Escherichia coli cytoplasm. The sbmA homologue is found in a variety of bacteria, though the physiological role of the protein is hitherto unknown. In this work, we carried out a functional and structural analysis to determine which amino acids are critical for the transport properties of SbmA. We created a set of 15 site-directed sbmA mutants in which single conserved amino acids were replaced by glycine residues. Our work demonstrated that strains carrying the site-directed mutants V102G, F219G, and E276G had a null phenotype for SbmA transport functions. In contrast, strains carrying the single point mutants W19G, W53G, F60G, S69G, N155G, R190, L233G, A344G, T255G, N308G, and R385G showed transport capacities indistinguishable from those of strains harboring a wild-type sbmA. The strain carrying the Y116G mutant exhibited mixed phenotypic characteristics. We also demonstrated that those sbmA mutants with severely impaired transport capacity showed a dominant negative phenotype. Electron microscopy data and in silico three-dimensional (3D) homology modeling support the idea that SbmA forms a homodimeric complex, closely resembling the membrane-spanning region of the ATP-binding cassette transporter family. Direct mapping of the sbmA single point mutants on the protein surface allowed us to explain the observed phenotypic differences in transport ability.

Fusion of an Fc chain to a VHH boosts the accumulation levels in Arabidopsis seeds

Nanobodies® (VHHs) provide powerful tools in therapeutic and biotechnological applications. Nevertheless, for some applications, bivalent antibodies perform much better, and for this, an Fc chain can be fused to the VHH domain, resulting in a bivalent homodimeric VHH-Fc complex. However, the production of bivalent antibodies in Escherichia coli is rather inefficient. Therefore, we compared the production of VHH7 and VHH7-Fc as antibodies of interest in Arabidopsis seeds for detecting prostate-specific antigen (PSA), a well-known biomarker for prostate cancer in the early stages of tumour development. The influence of the signal sequence (camel versus plant) and that of the Fc chain origin (human, mouse or pig) were evaluated. The accumulation levels of VHHs were very low, with a maximum of 0.13% VHH of total soluble protein (TSP) in homozygous T3 seeds, while VHH-Fc accumulation levels were at least 10- to 100-fold higher, with a maximum of 16.25% VHH-Fc of TSP. Both the camel and plant signal peptides were efficiently cleaved off and did not affect the accumulation levels. However, the Fc chain origin strongly affected the degree of proteolysis, but only had a slight influence on the accumulation level. Analysis of the mRNA levels suggested that the low amount of VHHs produced in Arabidopsis seeds was not due to a failure in transcription, but rather to translation inefficiency, protein instability and/or degradation. Most importantly, the plant-produced VHH7 and VHH7-Fc antibodies were functional in detecting PSA and could thus be used for diagnostic applications.

The Significance of Quantum Chemical Interactions for Medicinal Science and Design of β-Secretase Inhibitors

This review discusses the importance of quantum chemical interactions in biomolecules for medicinal science and their relevance to the author's β-secretase (BACE1) inhibitor drug discovery research. Although molecular mechanics/dynamics (MM/MD) methods are available in many in silico design tools used for drug discovery, they cannot accurately evaluate quantum effects between biomolecules and drugs. The key roles of biomolecular quantum chemical interactions in drug discovery are discussed using the arginine side chain as an example. Arginine is recognized as a charged amino acid in commonly used drug design software, unlike other amino acids with π-electron orbitals, such as phenylalanine, tyrosine, and tryptophan. Quantum chemical interactions via the arginine side chain are crucial for molecular recognition, and are found in many X-ray crystal structures, such as protein-protein, protein homodimer, RNA aptamer-protein, and enzyme-inhibitor complexes. This review describes the essential role of quantum chemical interactions via the arginine side chain in the mechanism of BACE1 inhibition, and proposes an "electron donor/acceptor bioisostere" concept for medicinal science based on quantum chemical interactions. Several potent BACE1 inhibitors, as well as the first peptides with BACE1 inhibiting activity were designed and synthesized based on studies of quantum chemical interactions via arginine side chain and the "electron donor bioisostere" concept.

Erythropoietin: multiple targets, actions, and modifying influences for biological and clinical consideration

Erythropoietin (EPO), a humoral regulator of erythropoiesis and replacement therapy for selected red blood cell disorders in EPO-deficient patients, has been implicated in a wide range of activities on diverse cell, tissue, and organ types. EPO signals via two receptors, one comprising EPO receptor (EPOR) homodimers and the other a heterodimer of EPOR and CD131-the common β chain component of the GM-CSF, interleukin (IL)-3, and IL-5 receptors. Ligation of EPORs triggers various signaling pathways, including the JAK2-STAT5 and MAPK-NF-κB pathways, depending both on the receptor and the target cell type. A new study in this issue reveals a novel EPO-triggered pathway involving a Spi2A serpin-lysosome-cathepsin cascade that is initiated through the homodimeric EPOR complex and is required for the survival of erythroid progenitors. A full understanding of EPO's effects on various cell types and their potential clinical relevance requires more work on the signaling events initiated through both EPORs, the effects of other cytokines and growth factors that modulate EPO's actions, and a comparison of the effects of full-length versus truncated forms of EPO.

RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.

Novel homodimer model of the β-adrenergic receptor in complex with free fatty acids and cholesterol: first-principles calculation studies.

We propose a theoretical novel homodimer model of the β- adrenergic receptor (βAR) in complex with a heterogeneous mixture of free fatty acids (FFAs) and cholesterol based on first-principles calculations. We used the density-functional-based tight binding with dispersion (DFTB-D) method, which accurately evaluates van der Waals interactions between FFAs and amino acid residues in the receptor. The calculations suggest that a stable homodimer of bAR can form a complex with FFAs and cholesterol by extensive van der Waals interactions in the cell membrane, and that the heterogeneous composition of the FFAs is important for the stability of the homodimer complex. The stable van der Waals interactions propagate from one of the bAR to the other through the cholesterol and FFAs in the homodimer complex. The energy propagation in the complex has the potential to enhance molecular signaling in adipocytes, because the stability of the complex can influence anti-adiposity effects after oral treatment of the FFA components.