Conformational changes of the chaperone SecB upon binding to a model substrate - bovine pancreatic trypsin inhibitor (BPTI)

SecB is a homotetrameric cytosolic chaperone that forms part of the protein translocation machinery in E. coli. Due to SecB, nascent polypeptides are maintained in an unfolded translocation-competent state devoid of tertiary structure and thus are guided to the translocon. In vitro SecB rapidly binds to a variety of ligands in a non-native state. We have previously investigated the bound state conformation of the model substrate bovine pancreatic trypsin inhibitor (BPTI) as well as the conformation of SecB itself by using proximity relationships based on site-directed spin labeling and pyrene fluorescence methods. It was shown that SecB undergoes a conformational change during the process of substrate binding. Here, we generated SecB mutants containing but a single cysteine per subunit or an exposed highly reactive new cysteine after removal of the nearby intrinsic cysteines. Quantitative spin labeling was achieved with the methanethiosulfonate spin label (MTS) at positions C97 or E90C, respectively. Highfield (W-band) electron paramagnetic resonance (EPR) measurements revealed that with BPTI present the spin labels are exposed to a more polar/hydrophilic environment. Nanoscale distance measurements with double electron-electron resonance (DEER) were in excellent agreement with distances obtained by molecular modeling. Binding of BPTI also led to a slight change in distances between labels at C97 but not at E90C. While the shorter distance in the tetramer increased, the larger diagonal distance decreased. These findings can be explained by a widening of the tetrameric structure upon substrate binding much like the opening of two pairs of scissors.

Novel Pentameric Structure of the Diarrhea-Inducing Region of the Rotavirus Enterotoxigenic Protein NSP4

A novel pentameric structure which differs from the previously reported tetrameric form of the diarrhea-inducing region of the rotavirus enterotoxin NSP4 is reported here. A significant feature of this pentameric form is the absence of the calcium ion located in the core region of the tetrameric structures. The lysis of cells, the crystallization of the region spanning residues 95 to 146 of NSP4 (NSP4(95-146)) of strain ST3 (ST3: NSP4(95-146)) at acidic pH, and comparative studies of the recombinant purified peptide under different conditions by size-exclusion chromatography (SEC) and of the crystal structures suggested pH-, Ca(2+)-, and protein concentration-dependent oligomeric transitions in the peptide. Since the NSP4(95-146) mutant lacks the N-terminal amphipathic domain (AD) and most of the C-terminal flexible region (FR), to demonstrate that the pentameric transition is not a consequence of the lack of the N- and C-terminal regions, glutaraldehyde cross-linking of the Delta N72 and Delta N94 mutant proteins, which contain or lack the AD, respectively, but possess the complete C-terminal FR, was carried out. The results indicate the presence of pentamers in preparations of these longer mutants. Detailed SEC analyses of Delta N94 prepared under different conditions, however, revealed protein concentration-dependent but metal ion-and pH-independent pentamer accumulation at high concentrations which dissociated into tetramers and lower oligomers at low protein concentrations. While calcium appeared to stabilize the tetramer, magnesium in particular stabilized the dimer. Delta N72 existed primarily in the multimeric form under all conditions. These findings of a calcium-free NSP4 pentamer and its concentration-dependent and largely calcium-independent oligomeric transitions open up a new dimension in an understanding of the structural basis of its multitude of functions.

X-ray structure of a galactose-specific lectin from Spatholobous parviflorous

A galactose-specific seed lectin from Spatholobous parviflorus (SPL) has been purified, crystallized and its X-ray structure solved. It is the first lectin purified and crystallized from the genus Spatholobus (family: Fabaceae). The crystals belong to the space group P1, with a = 60.792 angstrom, b = 60.998 angstrom, c = 78.179 angstrom, alpha = 78.68 degrees, beta = 88.62 degrees, gamma = 104.32 degrees. The data were collected at 2.04 angstrom resolution under cryocondition, on a MAR image-plate detector system, mounted on a rotating anode X-ray generator. The coordinates of Dolichos biflorus lectin (1lu1) were successfully used for the structure solution by molecular replacement method. The primary structure of the SPL was not known earlier and it was unambiguously visible in the electron density. S. parviflorus lectin is a hetero-dimeric-tetramer with two alpha and two beta chains of 251 and 239 residues respectively. SPL has two metal ions, Ca(2+) and Mn(2+), bound to a loop region of each chain. The SPL monomers are in jelly roll form. (C) 2011 Elsevier B.V. All rights reserved.

Quaternary association in beta-prism I fold plant lectins: Insights from X-ray crystallography, modelling and molecular dynamics

Dimeric banana lectin and calsepa, tetrameric artocarpin and octameric heltuba are mannose-specific beta-prism I fold lectins of nearly the same tertiary structure. MD simulations on individual subunits and the oligomers provide insights into the changes in the structure brought about in the protomers on oligomerization, including swapping of the N-terminal stretch in one instance. The regions that undergo changes also tend to exhibit dynamic flexibility during MD simulations. The internal symmetries of individual oligomers are substantially retained during the calculations. Energy minimization and simulations were also carried out on models using all possible oligomers by employing the four different protomers. The unique dimerization pattern observed in calsepa could be traced to unique substitutions in a peptide stretch involved in dimerization. The impossibility of a specific mode of oligomerization involving a particular protomer is often expressed in terms of unacceptable steric contacts or dissociation of the oligomer during simulations. The calculations also led to a rationale for the observation of a heltuba tetramer in solution although the lectin exists as an octamer in the crystal, in addition to providing insights into relations among evolution, oligomerization and ligand binding.

Crystallographic Study of Novel Transthyretin Ligands Exhibiting Negative-Cooperativity between Two Thyroxine Binding Sites

Background: Transthyretin (TTR) is a homotetrameric serum and cerebrospinal fluid protein that transports thyroxine (T4) and retinol by binding to retinol binding protein. Rate-limiting tetramer dissociation and rapid monomer misfolding and disassembly of TTR lead to amyloid fibril formation in different tissues causing various amyloid diseases. Based on the current understanding of the pathogenesis of TTR amyloidosis, it is considered that the inhibition of amyloid fibril formation by stabilization of TTR in native tetrameric form is a viable approach for the treatment of TTR amyloidosis. Methodology and Principal Findings: We have examined interactions of the wtTTR with a series of compounds containing various substitutions at biphenyl ether skeleton and a novel compound, previously evaluated for binding and inhibiting tetramer dissociation, by x-ray crystallographic approach. High resolution crystal structures of five ligands in complex with wtTTR provided snapshots of negatively cooperative binding of ligands in two T4 binding sites besides characterizing their binding orientations, conformations, and interactions with binding site residues. In all complexes, the ligand has better fit and more potent interactions in first T4 site i.e. (AC site) than the second T4 site (BD site). Together, these results suggest that AC site is a preferred ligand binding site and retention of ordered water molecules between the dimer interfaces further stabilizes the tetramer by bridging a hydrogen bond interaction between Ser117 and its symmetric copy. Conclusion: Novel biphenyl ether based compounds exhibit negative-cooperativity while binding to two T4 sites which suggests that binding of only single ligand molecule is sufficient to inhibit the TTR tetramer dissociation.

Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray cystallography

Crystal structure analysis of a galactose-specific lectin from a leguminous food crop Dolichos lablab (Indian lablab beans) has been carried out to obtain insights into its quaternary association and lectin-carbohydrate interactions. The analysis led to the identification of adenine binding sites at the dimeric interfaces of the heterotetrameric lectin. Structural details of similar adenine binding were reported in only one legume lectin, Dolichos biflorus, before this study. Here, we present the structure of the galactose-binding D. lablab lectin at different pH values in the native form and in complex with galactose and adenine. This first structure report on this lectin also provides a high resolution atomic view of legume lectin-adenine interactions. The tetramer has two canonical and two DB58-like interfaces. The binding of adenine, a non-carbohydrate ligand, is found to occur at four hydrophobic sites at the core of the tetramer at the DB58-like dimeric interfaces and does not interfere with the carbohydrate-binding site. To support the crystallographic observations, the adenine binding was further quantified by carrying out isothermal calorimetric titration. By this method, we not only estimated the affinity of the lectin to adenine but also showed that adenine binds with negative cooperativity in solution.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila

Cytosolic nucleotidase II (cN-II) from Legionellapneumophila (Lp) catalyzes the hydrolysis of GMP and dGMP displaying sigmoidal curves, whereas catalysis of IMP hydrolysis displayed a biphasic curve in the initial rate versus substrate concentration plots. Allosteric modulators of mammalian cN-II did not activate LpcN-II although GTP, GDP and the substrate GMP were specific activators. Crystal structures of the tetrameric LpcN-II revealed an activator-binding site at the dimer interface. A double mutation in this allosteric-binding site abolished activation, confirming the structural observations. The substrate GMP acting as an activator, partitioning between the allosteric and active site, is the basis for the sigmoidicity of the initial velocity versus GMP concentration plot. The LpcN-II tetramer showed differences in subunit organization upon activator binding that are absent in the activator-bound human cN-II structure. This is the first observation of a structural change induced by activator binding in cN-II that may be the molecular mechanism for enzyme activation. DatabaseThe coordinates and structure factors reported in this paper have been submitted to the Protein Data Bank under the accession numbers and . The accession number of GMP complexed LpcN-II is . Structured digital abstract andby() andby() Structured digital abstract was added on 5 March 2014 after original online publication]

Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance

In many organisms ``Universal Stress Proteins'' CUSPS) are induced in response to a variety of environmental stresses. Here we report the structures of two USPs, YnaF and YdaA from Salmonella typhimurium determined at 1.8 angstrom and 2.4 angstrom resolutions, respectively. YnaF consists of a single USP domain and forms a tetrameric organization stabilized by interactions mediated through chloride ions. YdaA is a larger protein consisting of two tandem USP domains. Two protomers of YdaA associate to form a structure similar to the YnaF tetramer. YdaA showed ATPase activity and an ATP binding motif G-2X-G-9X-G(S/T/N) was found in its C-terminal domain. The residues corresponding to this motif were not conserved in YnaF although YnaF could bind ATP. However, unlike YdaA, YnaF did not hydrolyse ATP in vitro. Disruption of interactions mediated through chloride ions by selected mutations converted YnaF into an ATPase. Residues that might be important for ATP hydrolysis could be identified by comparing the active sites of native and mutant structures. Only the C-terminal domain of YdaA appears to be involved in ATP hydrolysis. The structurally similar N-terminal domain was found to bind a zinc ion near the segment equivalent to the phosphate binding loop of the C-terminal domain. Mass spectrometric analysis showed that YdaA might bind a ligand of approximate molecular weight 800 daltons. Structural comparisons suggest that the ligand, probably related to an intermediate in lipid A biosynthesis, might bind at a site close to the zinc ion. Therefore, the N-terminal domain of YdaA binds zinc and might play a role in lipid metabolism. Thus, USPs appear to perform several distinct functions such as ATP hydrolysis, altering membrane properties and chloride sensing. (C) 2015 Elsevier Inc. All rights reserved.

Halogen bonds in some dihalogenated phenols: applications to crystal engineering

3,4-Dichlorophenol (1) crystallizes in the tetragonal space group I4(1)/a with a short axis of 3.7926 (9) angstrom. The structure is unique in that both type I and type II Cl.....Cl interactions are present, these contact types being distinguished by the angle ranges of the respective C-Cl....Cl angles. The present study shows that these two types of contacts are utterly different. The crystal structures of 4-bromo-3-chlorophenol (2) and 3-bromo-4-chlorophenol (3) have been determined. The crystal structure of (2) is isomorphous to that of (1) with the Br atom in the 4-position participating in a type II interaction. However, the monoclinic P2(1)/c packing of compound (3) is different; while the structure still has O-H....O hydrogen bonds, the tetramer O-H.....O synthon seen in (1) and (2) is not seen. Rather than a type I Br....Br interaction which would have been mandated if (3) were isomorphous to (1) and (2), Br forms a Br....O contact wherein its electrophilic character is clearly evident. Crystal structures of the related compounds 4-chloro-3-iodophenol (4) and 3,5-dibromophenol (5) were also determined. A computational survey of the structural landscape was undertaken for (1), (2) and (3), using a crystal structure prediction protocol in space groups P2(1)/c and I4(1)/a with the COMPASS26 force field. While both tetragonal and monoclinic structures are energetically reasonable for all compounds, the fact that (3) takes the latter structure indicates that Br prefers type II over type I contacts. In order to differentiate further between type I and type II halogen contacts, which being chemically distinct are expected to have different distance fall-off properties, a variable-temperature crystallography study was performed on compounds (1), (2) and (4). Length variations with temperature are greater for type II contacts compared with type I. The type II Br....Br interaction in (2) is stronger than the corresponding type II Cl....Cl interaction in (1), leading to elastic bending of the former upon application of mechanical stress, which contrasts with the plastic deformation of (1). The observation of elastic deformation in (2) is noteworthy; in that it finds an explanation based on the strengths of the respective halogen bonds, it could also be taken as a good starting model for future property design. Cl/Br isostructurality is studied with the Cambridge Structural Database and it is indicated that this isostructurality is based on shape and size similarity of Cl and Br, rather than arising from any chemical resemblance.

Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis

Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) from Mycobacterium smegmatis in apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domain via flexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The L alpha 1-covering loop-L alpha 2 region, together with the N beta 2-N alpha 2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.