Tetramer Model Research Articles

Comparative modeling of the quaternary structure for the human TRPM8 channel and analysis of its binding features

The aim of this study was to generate a reliable model for the homotetrameric structure of the human TRPM8 cation channel, a temperature sensor involved in innocuous cold perceptions. The described model was generated using a fragmental strategy and its interaction capacities were explored by docking a representative set of ligands. The analysis of the quaternary structure suggests that the N-terminus possesses a solenoidal topology which could be involved in tetramerization due to its electrostatic characteristics. Again, the tetramer model unveils a precise fitting between the segments of neighbouring monomers affording attractive suggestions for the multifaceted mechanism of channel gating. Docking results are in convincing agreement with mutational analyses and confirm that S4 and S4–S5 linker play a key role in channel activation. Overall, the proposed model could find fertile applications to further investigate the gating mechanism and to design truly selective ligands able to clarify the pathophysiological roles of the TRPM8 channel.

Structure of Amantadine-Bound M2 Transmembrane Peptide of Influenza A in Lipid Bilayers from Magic-Angle-Spinning Solid-State NMR: The Role of Ser31 in Amantadine Binding

The M2 proton channel of influenza A is the target of the antiviral drugs amantadine and rimantadine, whose effectiveness has been abolished by a single-site mutation of Ser31 to Asn in the transmembrane domain of the protein. Recent high-resolution structures of the M2 transmembrane domain obtained from detergent-solubilized protein in solution and crystal environments gave conflicting drug binding sites. We present magic-angle-spinning solid-state NMR results of Ser31 and a number of other residues in the M2 transmembrane peptide (M2TMP) bound to lipid bilayers. Comparison of the spectra of the membrane-bound apo and complexed M2TMP indicates that Ser31 is the site of the largest chemical shift perturbation by amantadine. The chemical shift constraints lead to a monomer structure with a small kink of the helical axis at Gly34. A tetramer model is then constructed using the helix tilt angle and several interhelical distances previously measured on unoriented bilayer samples. This tetramer model differs from the solution and crystal structures in terms of the openness of the N-terminus of the channel, the constriction at Ser31, and the side-chain conformations of Trp41, a residue important for channel gating. Moreover, the tetramer model suggests that Ser31 may interact with amantadine amine via hydrogen bonding. While the apo and drug-bound M2TMP have similar average structures, the complexed peptide has much narrower linewidths at physiological temperature, indicating drug-induced changes of the protein dynamics in the membrane. Further, at low temperature, several residues show narrower lines in the complexed peptide than the apo peptide, indicating that amantadine binding reduces the conformational heterogeneity of specific residues. The differences of the current solid-state NMR structure of the bilayer-bound M2TMP from the detergent-based M2 structures suggest that the M2 conformation is sensitive to the environment, and care must be taken when interpreting structural findings from non-bilayer samples.

Defining the DNA Substrate Binding Sites on HIV-1 Integrase

A tetramer model for human immunodeficiency virus type 1 (HIV-1) integrase (IN) with DNA representing long terminal repeat (LTR) termini was previously assembled to predict the IN residues that interact with the LTR termini; these predictions were experimentally verified for nine amino acid residues [Chen, A., Weber, I. T., Harrison, R. W. & Leis, J. (2006). Identification of amino acids in HIV-1 and avian sarcoma virus integrase subsites required for specific recognition of the long terminal repeat ends. J. Biol. Chem., 281, 4173–4182]. In a similar strategy, the unique amino acids found in avian sarcoma virus IN, rather than HIV-1 or Mason–Pfizer monkey virus IN, were substituted into the structurally related positions of HIV-1 IN. Substitutions of six additional residues (Q44, L68, E69, D229, S230, and D253) showed changes in the 3′ processing specificity of the enzyme, verifying their predicted interaction with the LTR DNA. The newly identified residues extend interactions along a 16-bp length of the LTR termini and are consistent with known LTR DNA/HIV-1 IN cross-links. The tetramer model for HIV-1 IN with LTR termini was modified to include two IN binding domains for lens-epithelium-derived growth factor/p75. The target DNA was predicted to bind in a surface trench perpendicular to the plane of the LTR DNA binding sites of HIV-1 IN and extending alongside lens-epithelium-derived growth factor. This hypothesis is supported by the in vitro activity phenotype of HIV-1 IN mutant, with a K219S substitution showing loss in strand transfer activity while maintaining 3′ processing on an HIV-1 substrate. Mutations at seven other residues reported in the literature have the same phenotype, and all eight residues align along the length of the putative target DNA binding trench.

Molecular Modeling of Vasopressin V2 Receptor Tetramer in Hydrated Lipid Membrane

Based on accessible experimental data we have constructed a model of Vasopressin V2 Receptor (V2R) tetramer in fully hydrated lipid membrane. To the best of our knowledge, this is the first Molecular Dynamics (MD) simulation of the tetramer model of a GPCR other than rhodopsin. The model consists of three inactive and one active V2R monomers. The activated unit is stabilized by Gsα (Ile382-Leu394) fragment and includes its natural ligand – vasopressin (AVP) docked. The pairs of neighboring protomers form contact dimers with the interface created by transmembrane helices TM3, TM4 of one partner and TM7, TM6 of the other. The between-dimers interface is composed by TM5 and TM4 of all monomers. Since experimental studies of GPCR oligomerization are not generally possible, there is a strong interest in using theoretical methods to predict their structure. Herein the NAnoscale Molecular Dynamics (NAMD) 2.6 package and CHARMm force field were used to conduct unconstrained MD calculations in periodic conditions. The optimal adjusting of monomers in lipid membrane surrounding was the purpose of simulation. Residues responsible for the oligomer stabilization were suggested and a compatibility of the whole model with available experimental data was discussed.

Topologically novel copper molybdate phases based on 3,4′-dipyridylketone: Hydrothermal synthesis, structural characterization, and magnetic properties

Hydrothermal treatment of CuCl 2·2H 2O, MoO 3, and 3,4′-dipyridylketone (3,4′-dpk) in 1:1:2 mole ratio afforded the new mixed metal oxide phases [Cu 2(MoO 4) 2(3,4′-dpk)(H 2O)] ( 1) or [Cu 4(3,4′-dpk) 4(Mo 8O 26)] ( 2), depending on the pH of the initial reaction mixture. Compound 1 possesses unique one-dimensional (1-D) [Cu 2(MoO 4) 2(H 2O)] n ribbons constructed from the linkage of {Cu II 4O 6} tetrameric units through isolated [MoO 4] 2– tetrahedra. These ribbons in turn are connected into a two-dimensional (2–D) coordination polymer structure by tethering 3,4′-dpk ligands. Compound 2, containing monovalent copper ions, manifests an unprecedented “X-rail” 1-D extended structure with (6 28) 4(6 6) topology formed from the bracketing of discrete [ β–Mo 8O 26] 4– anions by four [ Cu I ( 3 , 4 ′ ‐ dpk ) ] n n + chains. The variable temperature magnetic susceptibility behavior of 1 was fit to a linear tetramer model, with g=2.03(3), J 1=25.8(7) cm –1 and J 2=−46(1) cm –1. Antiferromagnetic inter-tetramer interactions ( zJ′=−0.21(3) cm –1) were also evident. Crystallographic data: 1 monoclinic, P2 1/ c, a=10.3911(11) Å, b=6.9502(6) Å, c=22.958(2) Å, β=100.658(7)°, V=1629.5(3) Å 3, R 1=0.1256, and w R 2=0.2038; 2 triclinic, P 1 ¯ , a=10.9000(3) Å, b=11.7912(4) Å, c=13.5584(4) Å, α=102.482(2)°, β=102.482(2)°, γ=117.481(2)°, V=1450.98(8) Å 3, R 1=0.0428, and w R 2=0.0630.

Dynamics of the Acetylcholinesterase Tetramer

Acetylcholinesterase rapidly hydrolyzes the neurotransmitter acetylcholine in cholinergic synapses, including the neuromuscular junction. The tetramer is the most important functional form of the enzyme. Two low-resolution crystal structures have been solved. One is compact with two of its four peripheral anionic sites (PAS) sterically blocked by complementary subunits. The other is a loose tetramer with all four subunits accessible to solvent. These structures lacked the C-terminal amphipathic t-peptide (WAT domain) that interacts with the proline-rich attachment domain (PRAD). A complete tetramer model (AChEt) was built based on the structure of the PRAD/WAT complex and the compact tetramer. Normal mode analysis suggested that AChEt could exist in several conformations with subunits fluctuating relative to one another. Here, a multiscale simulation involving all-atom molecular dynamics and C α-based coarse-grained Brownian dynamics simulations was carried out to investigate the large-scale intersubunit dynamics in AChEt. We sampled the ns- μs timescale motions and found that the tetramer indeed constitutes a dynamic assembly of monomers. The intersubunit fluctuation is correlated with the occlusion of the PAS. Such motions of the subunits “gate” ligand-protein association. The gates are open more than 80% of the time on average, which suggests a small reduction in ligand-protein binding. Despite the limitations in the starting model and approximations inherent in coarse graining, these results are consistent with experiments which suggest that binding of a substrate to the PAS is only somewhat hindered by the association of the subunits.

The Structure of Molten Lithium Carbonate Calculated by DFT and MD Simulations

The structures having the minimum interaction energy of the Li2CO3 monomer, dimer, trimer and tetramer were derived using the density functional theory (DFT). These structures were optimized. The structures of the monomer and the dimer agreed with the ab initio molecular orbital calculation results at a Hartree - Fock level. The structures of the trimer and the tetramer model were C3h and C2 symmetry, respectively. Then we carried out the harmonic frequency analysis of these geometries. The tetramer model showed the best agreement among these results with the Raman spectrum of the liquid state. On the other hand, we calculated the total structure factor S(Q) of the trimer and tetramer geometries considered from the DFT calculation to examine the local structure of molten Li2CO3. The calculation result corresponding to the tetramer model reproduced satisfactorily the position and the height of the S(Q) peaks.

Loop202-208in Avian Sarcoma Virus Integrase Mediates Tetramer Assembly and Processing Activity

Integrase (IN) catalyzes insertion of the retroviral genome into the host via two sequential reactions. The processing activity cleaves the 3'-dinucleotides from the two ends of the viral DNA which are then inserted into the host DNA. Tetramers are required for the joining step. While dimers have been shown to catalyze processing, they do so inefficiently, and the oligomeric requirement for processing is unknown. We have replaced loop202-208 at the putative dimer-dimer interface of the avian sarcoma virus IN with its analogue, loop188-194, from human immunodeficiency virus IN. The mutation abolished disintegration activity and a 2 x 10(-2) s-1 fast phase during single-turnover processing. A 3 x 10(-4) s-1 slow processing phase was unaffected. Preincubation with a DNA substrate known to promote tetramerization increased products formed during the fast phase by 2.5-fold only for wild-type IN, correlating the fast and slow phases with processing by tetramers and dimers, respectively. We propose a novel tetramer model for coupling processing and integration based on efficient processing by the tetramer. We provide for the first time direct evidence of the functional relevance of a structural element, loop202-208, which appears to be required for mediating the interaction between dimer halves of the active tetramer.

Structural characterization of dimeric murine aminoacylase III

Aminoacylase III (AAIII) plays an important role in deacetylation of acetylated amino acids and N-acetylated S-cysteine conjugates of halogenated alkenes and alkanes. AAIII, recently cloned from mouse kidney and partially characterized, is a mixture of tetramers and dimers. In the present work, AAIII dimers were purified and shown to be enzymatically active. Limited trypsinolysis showed two domains of ∼9 and 25 kDa. The three-dimensional structure of the dimer was studied by electron microscopy of negative stained samples and by single-particle reconstruction. A 16 Å resolution model of the AAIII dimer was created. It has an unusual, cage-like, structure. A realistic AAIII tetramer model was built from two dimers.

Structural Basis for p53 Binding-induced DNA Bending

Specific p53 binding-induced DNA bending has important biological implications such as transcription activation. However, the detailed structures of the bent DNA and the p53-DNA complex are still unavailable, hampering our understanding of the mechanism for p53-induced DNA bending and its consequent biological significance. To gain insight into the p53 binding-induced DNA bending, we performed molecular dynamics simulations on DNA segments with the consensus sequence for p53-specific binding, half site DNA-p53 complexes, and full site DNA-p53 complexes. We show that each DNA-bound p53 core domain caused a local DNA conformational change within the quarter site; upon the binding of the p53 dimer, there was an apparent DNA bending at the center of the half site; when bound with two p53 dimers, the full site DNAs with two different sequences bent 20 and 35 degrees, respectively. These results are in agreement with experimental observations. Our simulations demonstrate that the two p53 dimers favored a staggered conformation in which they make favorable interactions at the interface. This dimer-dimer interface organization necessitated conformational changes in the DNA, leading to the bending at the center of the full site, which in turn is dependent on the DNA sequence. Overall, our results provide the detailed atomic model for the DNA-p53 tetramer complex and delineate the roles of DNA-p53, p53 dimer-dimer interactions, and DNA sequence in specific p53 binding-induced DNA conformational changes.

The C–H···O Hydrogen Bonding Effects on the 17O Electric Field Gradient and Chemical Shielding Tensors in Crystalline 1-Methyluracil: A DFT Study

A density functional study was carried out to investigate the C-H···O hydrogen bonding effects on the 17O electric field gradient and chemical shielding tensors in crystalline 1-methyluracil. Since the structural coordinates were obtained from a neutron diffraction study, no geometry optimization was needed in performing the calculations. It is demonstrated that C-H···O hydrogen bonding has different influences on O2 and O4 EFG and CS tensors. In the tetramer model of 1-methyluracil, which is much closer to the real crystalline phase, the influence of C-H···O on the O4 EFG and CS tensors is significant, whereas this influence is negligible for O2.

Identification of Amino Acids in HIV-1 and Avian Sarcoma Virus Integrase Subsites Required for Specific Recognition of the Long Terminal Repeat Ends

A tetramer model for HIV-1 integrase (IN) with DNA representing 20 bp of the U3 and U5 long terminal repeats (LTR) termini was assembled using structural and biochemical data and molecular dynamics simulations. It predicted amino acid residues on the enzyme surface that can interact with the LTR termini. A separate structural alignment of HIV-1, simian sarcoma virus (SIV), and avian sarcoma virus (ASV) INs predicted which of these residues were unique. To determine whether these residues were responsible for specific recognition of the LTR termini, the amino acids from ASV IN were substituted into the structurally equivalent positions of HIV-1 IN, and the ability of the chimeras to 3 ' process U5 HIV-1 or ASV duplex oligos was determined. This analysis demonstrated that there are multiple amino acid contacts with the LTRs and that substitution of ASV IN amino acids at many of the analogous positions in HIV-1 IN conferred partial ability to cleave ASV substrates with a concomitant loss in the ability to cleave the homologous HIV-1 substrate. HIV-1 IN residues that changed specificity include Val(72), Ser(153), Lys(160)-Ile(161), Gly(163)-Val(165), and His(171)-Leu(172). Because a chimera that combines several of these substitutions showed a specificity of cleavage of the U5 ASV substrate closer to wild type ASV IN compared with chimeras with individual amino acid substitutions, it appears that the sum of the IN interactions with the LTRs determines the specificity. Finally, residues Ser(153) and Val(72) in HIV-1 IN are among those that change in enzymes that develop resistance to naphthyridine carboxamide- and diketo acid-related inhibitors in cells. Thus, amino acid residues involved in recognition of the LTRs are among these positions that change in development of drug resistance.

Paramagnetic Semiconductors: Hybrid Molecular Materials Based on Ethyl- and Methyl-pyridinium-Substituted Verdazyl Radical Cations and the Ni(dmit)2 Anion (dmit = 1,3-Dithiol-2-thione-4,5-dithiolate)

Abstract Four kinds of 1:1 salts of 3-(4- and 3-alkyl-pyridinium)-1,5-diphenylverdazyl (alkyl = ethyl and methyl) radical cations with the Ni(dmit)2 anion ([p-EtPyDV]+[Ni(dmit)2]− (1), [m-EtPyDV]+[Ni(dmit)2]− (2), [p-MePyDV]+[Ni(dmit)2]− (3), and [m-MePyDV]+[Ni(dmit)2]− (4)) have been prepared. The magnetic properties of salts 1–4 were discussed based on the results obtained by magnetic susceptibility and ESR measurements of 1–4 and the crystal structure analysis of 1. The results of the crystal structure analysis of salt 1 indicate the dimer formation in Ni(dmit)2 anion molecules, and the dimers are sandwiched between two verdazyl cations [p-EtPyDV]+, indicating the formation of a magnetic linear tetramer in 1. The magnetic susceptibility data for salt 1 have been fitted to a four-spin linear tetramer model using an end exchange interaction of 2J1/kB = −780 K and a central interaction of 2J2/kB = −200 K. The conductivity (σ) of salts 1, 2, 3, and 4 at room temperature was σ = 2.3 × 10−5, 1.8 × 10−4, 1.4 × 10−5, and 5.4 × 10−6 S cm−1 with an activation energy of EA = 0.28, 0.52, 0.21, and 0.33 eV, respectively. The 1:1 salts 1–4 are new molecular paramagnetic semiconductors.

Functionally Important Substructures of Circadian Clock Protein KaiB in a Unique Tetramer Complex

KaiB is a component of the circadian clock molecular machinery in cyanobacteria, which are the simplest organisms that exhibit circadian rhythms. Here we report the x-ray crystal structure of KaiB from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. The KaiB crystal diffracts at a resolution of 2.6 A and includes four subunits organized as a dimer of dimers, each composed of two non-equivalent subunits. The overall shape of the tetramer is an elongated hexagonal plate, with a single positively charged cleft flanked by two negatively charged ridges whose surfaces includes several terminal chains. Site-directed mutagenesis of Synechococcus KaiB confirmed that alanine substitution of residues Lys-11 or Lys-43 in the cleft, or deletion of C-terminal residues 95-108, which forms part of the ridges, strongly weakens in vivo circadian rhythms. Characteristics of KaiB deduced from the x-ray crystal structure were also confirmed by physicochemical measurements of KaiB in solution. These data suggest that the positively charged cleft and flanking negatively charged ridges in KaiB are essential for the biological function of KaiB in the circadian molecular machinery in cyanobacteria.

The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis

Acetylcholinesterase (AChE) rapidly hydrolyzes acetylcholine in the neuromuscular junctions and other cholinergic synapses to terminate the neuronal signal. In physiological conditions, AChE exists as tetramers associated with the proline-rich attachment domain (PRAD) of either collagen-like Q subunit (ColQ) or proline-rich membrane-anchoring protein. Crystallographic studies have revealed that different tetramer forms may be present, and it is not clear whether one or both are relevant under physiological conditions. Recently, the crystal structure of the tryptophan amphiphilic tetramerization (WAT) domain of AChE associated with PRAD ([WAT]4PRAD), which mimics the interface between ColQ and AChE tetramer, became available. In this study we built a complete tetrameric mouse [AChET]4–ColQ atomic structure model, based on the crystal structure of the [WAT]4PRAD complex. The structure was optimized using energy minimization. Block normal mode analysis was done to investigate the low-frequency motions of the complex and to correlate the structure model with the two known crystal structures of AChE tetramer. Significant low-frequency motions among the catalytic domains of the four AChE subunits were observed, while the [WAT]4PRAD part held the complex together. Normal mode involvement analysis revealed that the two lowest frequency modes were primarily involved in the conformational changes leading to the two crystal structures. The first 30 normal modes can account for more than 75% of the conformational changes in both cases. The evidence further supports the idea of a flexible tetramer model for AChE. This model can be used to study the implications of the association of AChE with ColQ.

Scanning Tunneling Microscopy and Surface Simulation of Zinc-Blende GaN(001) Intrinsic4×Reconstruction: Linear Gallium Tetramers?

Scanning tunneling microscopy images confirm electron diffraction studies that the zinc-blende GaN(001)-4x reconstruction consists of rows aligned along [110] with a spacing along [110] of 4a. Dual-bias imaging shows a 180 degree shift of the corrugation maximum position between the profiles of empty and occupied states, in agreement with surface simulations based on the 4 x 1 linear tetramer model of Neugebauer et al. [Phys. Rev. Lett. 80, 3097 (1998)]. Electronic structure calculations predict a surface band gap of 1.1 eV, close to the measured value of 1.14 eV and the previously predicted value (1.2 eV). Despite the successes of this model, high-resolution images reveal an unexpected 3x periodicity (not seen in diffraction) along the [110] row direction, indicating the need for a 4 x 3 model, and putting into question the existence of linear Ga tetramers.

Constructing HIV-1 integrase tetramer and exploring influences of metal ions on forming integrase–DNA complex

HIV-1 integrase (IN) is essential for the replication of HIV-1 in human cells. At present, the complete structure of complex IN–DNA has not been resolved. In this paper, a HIV-1 IN tetramer model was built with homology modeling and molecular dynamics simulation approach, in which two Mg 2+ ions were reasonably located in each catalytic core domain. Moreover, it was found that the AB and CD chains of HIV-1 IN tetramer were different in the structures and metal ions of HIV-1 IN tetramer might have great influences on DNA locating on IN. These findings may provide a more complete structural basis for guiding drug discovery and revealing integration mechanism.

Magnetic semiconductors: Molecular materials based on alkyl-pyridinium-substituted verdazyl radical cations and Ni(dmit)2 anion

Abstract Five kinds of (1:1) and (1:3) salts of 3-(4- and 3-alkyl-pyridinium)-1,5-diphenylverdazyl (alkyl = ethyl and methyl) radical cations with Ni(dmit)2 anion ([p-EtPyDV]+[Ni(dmit)2]− (1), [m-EtPyDV]+[Ni(dmit)2]− (2), [p-MePyDV]+[Ni(dmit)2]− (3), [m-MePyDV]+[Ni(dmit)2]− (4), and [ p - MePyDV ] + [ Ni ( dmit ) 2 ] 3 - ( 5 ) ) (dmit = 1,3-dithiol-2-thione-4,5-dithiolate) have been prepared, and the magnetic susceptibilities (χM’s) have been measured between 1.8 and 300 K. The χM of salt 1 can be well explained by a four-spin linear tetramer model ([p-EtPyDV]+–[Ni(dmit)2]−–[Ni(dmit)2]−–[p-EtPyDV]+) with an end exchange interaction 2J1/kB = −780 K and a central interaction 2J2/kB = −200 K. The formation of magnetic tetramer in salt 1 has been ascertained by the crystal structure analysis of 1. The χM of salt 2 was explained by the sum of the contributions from: (i) a dimer system (2J/kB = −320 K) due to Ni(dmit)2 anions and (ii) the one-dimensional (1D) Heisenberg ferromagnetic linear-chain system (2J kB = +2.5 K) due to verdazyl cations. The χM of salt 3 is similar to that of salt 1, suggesting a formation of magnetic tetramer in salt 3. The χM of salt 4 shows a broad maximum at Tmax = 100 ± 2 K, and can be explained by a 1D Heisenberg antiferromagnetic alternating-chain model with 2J1/kB = −165 K (alternation parameter α = J2/J1 = 0.6). The conductivity (σ) of salts 1, 2, 3 and 4 at 293 K was σ = 2.3 × 10−5, 1.1 × 10−3, 1.4 × 10−5 and 5.4 × 10−6 S cm−1 with an activation energy of EA = 0.28, 0.52, 0.21 and 0.33 eV, respectively. The (1:3) salt 5 (σ = 1.0 S cm−1, EA = 0.048 eV) showed three to five orders of magnitude higher conductivity than those of the (1:1) salts 1–4 at room temperature. All the (1:1) and (1:3) salts 1–5 are new molecular paramagnetic semiconductors.

Tetrameric Mouse Acetylcholinesterase: Continuum Diffusion Rate Calculations by Solving the Steady-State Smoluchowski Equation Using Finite Element Methods

The tetramer is the most important form for acetylcholinesterase in physiological conditions, i.e., in the neuromuscular junction and the nervous system. It is important to study the diffusion of acetylcholine to the active sites of the tetrameric enzyme to understand the overall signal transduction process in these cellular components. Crystallographic studies revealed two different forms of tetramers, suggesting a flexible tetramer model for acetylcholinesterase. Using a recently developed finite element solver for the steady-state Smoluchowski equation, we have calculated the reaction rate for three mouse acetylcholinesterase tetramers using these two crystal structures and an intermediate structure as templates. Our results show that the reaction rates differ for different individual active sites in the compact tetramer crystal structure, and the rates are similar for different individual active sites in the other crystal structure and the intermediate structure. In the limit of zero salt, the reaction rates per active site for the tetramers are the same as that for the monomer, whereas at higher ionic strength, the rates per active site for the tetramers are ∼67%–75% of the rate for the monomer. By analyzing the effect of electrostatic forces on ACh diffusion, we find that electrostatic forces play an even more important role for the tetramers than for the monomer. This study also shows that the finite element solver is well suited for solving the diffusion problem within complicated geometries.

The Structure of DC-SIGNR with a Portion of its Repeat Domain Lends Insights to Modeling of the Receptor Tetramer

The dendritic cell-specific ICAM-3 non-integrin (DC-SIGN) and its close relative DC-SIGNR recognize various glycoproteins, both pathogenic and cellular, through the receptor lectin domain-mediated carbohydrate recognition. While the carbohydrate-recognition domains (CRD) exist as monomers and bind individual carbohydrates with low affinity and are permissive in nature, the full-length receptors form tetramers through their repeat domain and recognize specific ligands with high affinity. To understand the tetramer-based ligand binding avidity, we determined the crystal structure of DC-SIGNR with its last repeat region. Compared to the carbohydrate-bound CRD structure, the structure revealed conformational changes in the calcium and carbohydrate coordination loops of CRD, an additional disulfide bond between the N and the C termini of the CRD, and a helical conformation for the last repeat. On the basis of the current crystal structure and other published structures with sequence homology to the repeat domain, we generated a tetramer model for DC-SIGN/R using homology modeling and propose a ligand-recognition index to identify potential receptor ligands.