On chirality transfer in electron donor-acceptor complexes. A prediction for the sulfinimine···BF3 system

Stabilization energies of the electron donor-acceptor sulfinimine···BF(3) complexes calculated at either the B3LYP/aug-cc-pVTZ or the MP2/aug-cc-pVTZ level do not allow to judge, whether the N- or O-atom in sulfinimine is stronger electron-donor to BF(3) . The problem seems to be solvable because chirality transfer phenomenon between chiral sulfinimine and achiral BF(3) is expected to be vibrational circular dichroism (VCD) active. Moreover, the bands associated with the achiral BF(3) molecule are predicted to be the most intense in the entire spectrum. However, the VCD band robustness analyses show that most of the chirality transfer modes of BF(3) are unreliable. Conversely, variation of VCD intensity with change of intermolecular distance, angle, and selected dihedrals between the complex partners shows that to establish the robustness of chirality transfer mode. It is also necessary to determine the influence of the potential energy surface (PES) shape on the VCD intensity. At the moment, there is still no universal criterion for the chirality transfer mode robustness and the conclusions formulated based on one system cannot be directly transferred even to a quite similar one. However, it is certain that more attention should be focused on relation of PES shape and the VCD mode robustness problem.     

Competition and interplay between the lithium bonding and hydrogen bonding: R3C···HY···LiY and R3C···LiY···HY triads as a working model (R=H, CH3; Y=CN, NC)

UMP2 calculations with aug-cc-pVDZ basis set were used to analyze intermolecular interactions in R₃C···HY···LiY and R₃C···LiY···HY triads (R=H, CH₃; Y=CN, NC), which are connected via lithium and hydrogen bonds. To better understand the properties of these systems, the corresponding dyads were also studied. Molecular geometries and binding energies of dyads, and triads were investigated at the UMP2/aug-cc-pVDZ computational level. Particular attention was paid to parameters such as cooperative energies, and many-body interaction energies. All studied complexes, with the simultaneous presence of a lithium bond and a hydrogen bond, showed cooperativity with energy values ranging between ?1.71 and ?9.03 kJ mol^?1. The electronic properties of the complexes were analyzed using parameters derived from atoms in molecules (AIM) methodology. Energy decomposition analysis revealed that the electrostatic interactions are the major source of the attraction in the title complexes.     

Conformational activation of the EF-Tu·GTPase activity Stimulation of the 2′(3′)-O-l-phenylalanyladenosine-promoted EF-Tu·GTPase upon binding of the tRNAPhe lacking the terminal adenosine residue

The elongation factor Tu (EF-Tu) dependent GTPase (in the presence of aurodox) is stimulated by analogs of the aminoacyl tRNA 3′-terminus in the following order: A-Phe < C-A-Phe < C-C-A-Phe. The GTPase-promoting activity of A-Phe is strongly enhanced by tRNA-C-C (devoid of 3′-terminal adenosine residue) but not by intact tRNA-C-C-A. On the other hand, the activity of C-A-Phe as the EF-Tu·GTPase promoter is only slightly enhanced by tRNA-C-C.     

Effect of stepwise microhydration on the guanidinium···π interaction

Polychlorinated biphenyls (PCBs) are potentially hazardous to the environment because of their chemical stability and biological toxicity. In this study, we identified the binding mode of a representative PCB180 to human serum albumin (HSA) using fluorescence and molecular dynamics (MD) simulation methods. PCB180 bound exactly at subdomain IIIA of HSA based on the fluorescence study along with site marker displacement experiments. PCB180 also induced conformational changes that were governed mainly by hydrophobic forces. MD studies and free energy calculations also made important contributions to the understanding of the effects of an HSA-PCB180 system on conformational changes. The simulations on binding behavior proved that PCB180 was located only in subdomain IIIA. Hydrophobic interactions dominated the mode of binding behavior. The results obtained using the two methods correlated well with each other. Our findings provide a framework for elucidating the mechanisms of PCB180-HSA binding, and may also help in further research on the transportation, distribution, and toxicity effects of PCBs when introduced into human blood serum.     

Effect of stepwise microhydration on the methylammonium···phenol and ammonium···phenol interaction

A computational study has been performed for studying the characteristics of the interaction of phenol with ammonium and methylammonium cations. The effect of the presence of water molecules has also been considered by microhydrating the clusters with up to three water molecules. Clusters of phenol with ammonium and methylammonium cations present similar characteristics, though ammonium complexes have been found to be more stable than the methylammonium ones. The first water molecule included in the complexes interacts with a N-H group of ammoniun cations and simultaneously with the hydroxyl oxygen atom of phenol (or the aromatic ring). This first water molecule is more tightly bound in the complex, so the stability gain as more water molecules are included drops significantly by 2-3 kcal?mol^?1 with respect to the first one. As more water molecules are included, the differences between favorable coordination sites (the cation, the hydroxyl group or a previous water molecule) decrease. As a consequence, several of the most stable complexes located including three water molecules already exhibit hydrogen bonds between the hydroxyl group and one water molecule. The results indicate that a cyclic pattern formed by a series of hydrogen bonds: π···H-N-H···O-H···O-?, is characteristic of the most stable minima, being kept as more water molecules are included in the system. Therefore, this pattern can be expected to be crucial in ammonium cations···phenol interaction if exposed to the solvent to any degree.     

Structural model of the p14/SF3b155 · branch duplex complex

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14 · bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein-RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14 · duplex interaction must be disrupted before the first step of splicing.     

Assembly of the Non-Canonical Myo9a-RhoGAP and RhoA·GDP Transition State Complex in the Presence of MgF3−

The Protein Journal - Myo9a is an actin-based molecular motor with a RhoGAP domain in its C-terminal tail. It plays a role in a variety of biological processes, such as in regulating the immune...     

Regulation of the AGS3·Gαi Signaling Complex by a Seven-transmembrane Span Receptor

G-protein signaling modulators (GPSM) play diverse functional roles through their interaction with G-protein subunits. AGS3 (GPSM1) contains four G-protein regulatory motifs (GPR) that directly bind Gα_i free of Gβγ providing an unusual scaffold for the “G-switch” and signaling complexes, but the mechanism by which signals track into this scaffold are not well understood. We report the regulation of the AGS3·Gα_i signaling module by a cell surface, seven-transmembrane receptor. AGS3 and Gα_i1 tagged with Renilla luciferase or yellow fluorescent protein expressed in mammalian cells exhibited saturable, specific bioluminescence resonance energy transfer indicating complex formation in the cell. Activation of α₂-adrenergic receptors or μ-opioid receptors reduced AGS3-RLuc·Gα_i1-YFP energy transfer by over 30%. The agonist-mediated effects were inhibited by pertussis toxin and co-expression of RGS4, but were not altered by Gβγ sequestration with the carboxyl terminus of GRK2. Gα_i-dependent and agonist-sensitive bioluminescence resonance energy transfer was also observed between AGS3 and cell-surface receptors typically coupled to Gα_i and/or Gα_o indicating that AGS3 is part of a larger signaling complex. Upon receptor activation, AGS3 reversibly dissociates from this complex at the cell cortex. Receptor coupling to both Gαβγ and GPR-Gα_i offer additional flexibility for systems to respond and adapt to challenges and orchestrate complex behaviors.     

Crystal and molecular structure of the sulfhydryl protease calotropin DI at 3·2 Å resolution

The three-dimensional structure of the sulfhydryl protease calotropin DI from the madar plant, Calotropis gigantea, has been determined at 3·2 Å resolution using the multiple isomorphous replacement method with five heavy atom derivatives. A Fourier synthesis based on protein phases with a mean figure of merit of 0·857 was used for model building. The polypeptide backbone of calotropin DI is folded to form two distinct lobes, one of which is comprised mainly of α-helices, while the other is characterized by a system of all antiparallel pleated sheets. The overall molecular architecture closely resembles those found in the sulfhydryl proteases papain and actinidin.Despite the unknown amino acid sequence of calotropin DI a number of residues around its active center could be identified. These amino acid side-chains were found in a similar arrangement as the corresponding ones in papain and actinidin. The polypeptide chain between residues 1 and 18 of calotropin DI folds in a unique manner, providing a possible explanation for the unusual inability of calotropin DI to hydrolyze those synthetic substrates that papain and actinidin act upon.     

Studies on the BF3·Et2O catalyzed Baeyer-Villiger reaction of spiroketalic steroidal ketones

During reactions of 23-oxosapogenins and the corresponding isomeric 22-oxo-23-spiroketals with MCPBA in the presence of BF₃·Et₂O, equilibration occurs between the ketones. The Baeyer-Villiger type oxidation is followed by fragmentation to the dinorcholanic lactones and 3-methylbutyrolactone. The mechanistic aspects of these reactions in the 25R and 25S series are discussed.     

Strength of CH···π interactions in the C-terminal subdomain of villin headpiece

The relative free energies of the folded structures of the seven model peptides with PLX (X = W, Y, F, H, and A) and ALX (X = W and A) sequences to the corresponding extended structures are calculated using the density functional methods in water to evaluate the relative strengths of CH···π interactions, especially proline···aromatic interactions for the PLX motif of the C-terminal subdomain of villin headpiece. It has been found that the Pro···π contacts for the folded structures of the PLW, PLY, PLF, and PLH peptides have in common a geometric pattern having the edge of the Pro ring interacting with the face of the aromatic ring, as found for functionally important Pro residues in proteins. At the M06-2X/cc-pVTZ//SMD M06-2X/6-31+G(d) level of theory, the relative stabilities of the folded structures to the extended structures are obtained in the order PLW > ALW > PLA > PLH > PLY > ALA > PLF by the conformational Gibbs free energies in water, which is reasonably consistent with the observed results from the CD thermal analysis for wild-type and mutants of the C-terminal subdomains of villin headpieces. Although the interaction energies excluding the solvation free energies play a role in determining the relative stabilities of the PLX and ALX peptides, the solvation and entropic terms are found to be of consequence, too. In particular, it has been known that ～40% of the total interaction energy of the PLW peptide is ascribed to the CH···π interactions of the contacting side chains for Pro and Trp residues, in which the dispersion terms play a role.     

Free energy calculations on the stability of the 14-3-3ζ protein

Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.     

Does the γ subunit move to an abortive position for ATP hydrolysis when the F1·ADP·Mg complex isomerizes to the inactive F1*·ADP·Mg complex?

F₁-ATPases transiently entrap inhibitory MgADP in a catalytic site during turnover when noncatalytic sites are not saturated with ATP. An initial burst of ATP hydrolysis rapidly decelerates to a slow intermediate rate that gradually accelerates to a final steady-state rate. Transition from the intermediate to the final rate is caused by slow binding of ATP to noncatalytic sites which promotes dissociation of inhibitory MgADP from the affected catalytic site. Evidence from several laboratories suggests that the γ subunit rotates with respect to α/β subunit pairs of F₁-ATPases during ATP hydrolysis. The α₃β₃ and α₃β₃δ subcomplexes of the TF₁-ATPase do not entrap inhibitory MgADP in a catalytic site during turnover, suggesting involvement of the γ subunit in the entrapment process. From these observations, it is proposed that the γ subunit moves into an abortive position for ATP hydrolysis when inhibitory MgADP is entrapped in a catalytic site during ATP hydrolysis.     

Mutations in the 5’ NTR and the Non-Structural Protein 3A of the Coxsackievirus B3 Selectively Attenuate Myocarditogenicity

The 5’ non-translated region (NTR) is an important molecular determinant that controls replication and virulence of coxsackievirus B (CVB)3. Previous studies have reported many nucleotide (nt) sequence differences in the Nancy strain of the virus, including changes in the 5’ NTR with varying degrees of disease severity. In our studies of CVB3-induced myocarditis, we sought to generate an infectious clone of the virus for routine in vivo experimentation. By determining the viral nt sequence, we identified three new nt substitutions in the clone that differed from the parental virus strain: C97U in the 5’ NTR; a silent mutation, A4327G, in non-structural protein 2C; and C5088U (resulting in P1449L amino acid change) in non-structural protein 3A of the virus leading us to evaluate the role of these changes in the virulence properties of the virus. We noted that the disease-inducing ability of the infectious clone-derived virus in three mouse strains was restricted to pancreatitis alone, and the incidence and severity of myocarditis were significantly reduced. We then reversed the mutations by creating three new clones, representing 1) U97C; 2) G4327A and U5088C; and 3) their combination together in the third clone. The viral titers obtained from all the clones were comparable, but the virions derived from the third clone induced myocarditis comparable to that induced by wild type virus; however, the pancreatitis-inducing ability remained unaltered, suggesting that the mutations described above selectively influence myocarditogenicity. Because the accumulation of mutations during passages is a continuous process in RNA viruses, it is possible that CVB3 viruses containing such altered nts may evolve naturally, thus favoring their survival in the environment.     

Further studies on the copper(II) complexes of lysine: [Cu(II)(H3N·C5H10·CH·NH2·COO)2] [HgI3]2

Spontaneous resolution in the formation of the [HgI₃]⁻ salts of the copper complex of racemic lysine was previously reported. X-ray and IR studies were used to support this conclusion. Gas chromatographic studies using a chiral phase on the crystals originally studied, and on newly formed crystals using D,L-lysine, do not substantiate the suggestion that spontaneous resolution occurs.     

Structural Basis for the Recognition of Tyrosine-based Sorting Signals by the μ3A Subunit of the AP-3 Adaptor Complex

Tyrosine-based signals fitting the YXXØ motif mediate sorting of transmembrane proteins to endosomes, lysosomes, the basolateral plasma membrane of polarized epithelial cells, and the somatodendritic domain of neurons through interactions with the homologous μ1, μ2, μ3, and μ4 subunits of the corresponding AP-1, AP-2, AP-3, and AP-4 complexes. Previous x-ray crystallographic analyses identified distinct binding sites for YXXØ signals on μ2 and μ4, which were located on opposite faces of the proteins. To elucidate the mode of recognition of YXXØ signals by other members of the μ family, we solved the crystal structure at 1.85 Å resolution of the C-terminal domain of the μ3 subunit of AP-3 (isoform A) in complex with a peptide encoding a YXXØ signal (SDYQRL) from the trans-Golgi network protein TGN38. The μ3A C-terminal domain consists of an immunoglobulin-like β-sandwich organized into two subdomains, A and B. The YXXØ signal binds in an extended conformation to a site on μ3A subdomain A, at a location similar to the YXXØ-binding site on μ2 but not μ4. The binding sites on μ3A and μ2 exhibit similarities and differences that account for the ability of both proteins to bind distinct sets of YXXØ signals. Biochemical analyses confirm the identification of the μ3A site and show that this protein binds YXXØ signals with 14–19 μm affinity. The surface electrostatic potential of μ3A is less basic than that of μ2, in part explaining the association of AP-3 with intracellular membranes having less acidic phosphoinositides.     

Protein S3 in the human 80S ribosome adjoins mRNA 3′ of the A-site codon

The protein environment of mRNA 3′ of the A-site codon (the decoding site) in the human 80S ribosome was studied using a set of oligoribonucleotide derivatives bearing a UUU triplet at the 5′-end and a perfluoroarylazide group at one of the nucleotide residues 3′ of this triplet. Analogues of mRNA were phased into the ribosome using binding at the tRNA^Phe P-site, which recognizes the UUU codon. Mild UV irradiation of ribosome complexes with tRNA^Phe and mRNA analogues resulted in the predominant crosslinking of the analogues with the 40S subunit components, mainly with proteins and, to a lesser extent, with rRNA. Among the 40S subunit ribosomal proteins, the S3 protein was the main target for modification in all cases. In addition, minor crosslinking with the S2 protein was observed. The crosslinking with the S3 and S2 proteins occurred both in ternary complexes and in the absence of tRNA. Within ternary complexes, crosslinking with S15 protein was also found, its efficiency considerably falling when the modified nucleotide was moved from positions +5 to +12 relative to the first codon nucleotide in the P-site. In some cases, crosslinking with the S30 protein was observed; it was most efficient for the derivative containing a photoreactive group at the +7 adenosine residue. The results indicate that the S3 protein in the human ribosome plays a key role in the formation of the mRNA binding site 3′ of the codon in the decoding site.