The results of the fifth blind test of crystal structure prediction, which show important success with more challenging large and flexible molecules, are presented and discussed.
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.
prediction; blind test; polymorph; crystal structure prediction
Increased frequency of cavum septum pellucidum (CSP) has been inconsistently observed in schizophrenia, and little is known about its functional implications. We investigated whether patients with schizophrenia were more likely than healthy controls to have CSP, and among patients assessed the relationship between CSP, psychiatric symptoms, and selected neuropsychological functions. Seventy-seven patients with diagnoses of DSM-IV schizophrenia spectrum disorders and 55 healthy controls were studied and completed a 1.5 T MRI scan. Two raters, blind to group membership, determined the presence, length and grade of the CSP. A subset of participants also underwent neuropsychological testing. A CSP of at least 1 mm in length was present in 68.8% of patients and 76.4% of controls, and the groups did not differ significantly with respect to presence or absence, length, overall size, or percent with an abnormally large CSP (≥ 6 mm). Patients with an abnormally large CSP demonstrated poorer performance on measures of verbal learning and memory than patients with smaller CSP. Among patients, CSP length was significantly correlated with negative symptoms, verbal learning, and sentence comprehension. Among patients with abnormally large CSP, CSP length was correlated with reaction time on two conditions of a Continuous Performance Test. CSP, while prevalent, was not more frequent in our sample of patients with schizophrenia, and had few associations with symptom severity or neuropsychological deficits.
Schizophrenia; MRI; Cavum Septum Pellucidum; Neuropsychology
The crystal structure of cold-shock protein E from S. typhimurium (StCspE) has been determined at 1.1 Å resolution.
In prokaryotic organisms, cold shock triggers the production of a small highly conserved family of cold-shock proteins (CSPs). CSPs have been well studied structurally and functionally in Escherichia coli and Bacillus subtilis, but Salmonella typhimurium CSPs remain relatively uncharacterized. In S. typhimurium, six homologous CSPs have been identified: StCspA–E and StCspH. The crystal structure of cold-shock protein E from S. typhimurium (StCspE) has been determined at 1.1 Å resolution and has an R factor of 0.203 after refinement. The three-dimensional structure is similar to those of previously determined CSPs and is composed of five antiparallel β-strands forming a classic OB fold/five-stranded β-barrel. This first structure of a CSP from S. typhimurium provides new insight into the cold-shock response of this bacterium.
cold-shock proteins; Salmonella typhimurium
This paper describes the application of our distributed computing framework for crystal structure prediction (CSP), Modified Genetic Algorithms for Crystal and Cluster Prediction (MGAC) to predict the crystal structure of flexible molecules using the General Amber Force Field (GAFF) and the CHARMM program. The MGAC distributed computing framework which includes a series of tightly integrated computer programs for generating the molecule’s force field, sampling crystal structures using a distributed parallel genetic algorithm, local energy minimization of the structures followed by the classifying, sorting and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential.
The title compound, C14H9N, is the second crystallographically characterized example of an ynamine with an H atom in the C-terminal position. There are two independent molecules (A and B) in the asymmetric unit. The structures of both molecules are essentially planar (r.m.s. deviation = 0.0312 and 0.0152 Å). The N—Csp bond lengths are 1.353 (4) and 1.350 (4) Å, and those of the acetylene bonds are 1.189 (4) and 1.190 (4) Å. The Csp—H bond lengths are 0.95 (5) and 0.97 (4) Å. These geometries are consistent with those of the previously reported ynamine characterized by crystallography. In the crystal, the molecules stack along the c axis, forming two kinds of columnar structures. The acetylene C atoms of molecule A have a short contact [3.341 (4) Å and 3.396 (4) Å] with an adjacent molecule A at the C—C bond of the fused part, which originates in π–π stacking interaction; no remarkable spatial contact is recognized within the stacking of molecule B.
The title molecule, C18H24O12, has crystallographic 2/m symmetry with two acetate group located on a mirror plane. The H—Csp
2 torsion angles characterizing orientation of the acetyl groups with respect to the cyclohexane ring are 0.0, 23.9 and −23.9°. The cyclohexane ring is in a chair conformation with all substituents in equatorial positions. In the crystal, molecules are connected through C—H⋯O hydrogen bonds into a chain extending along the c axis.
In the absence of three-dimensional (3D) structures of potential drug targets, ligand-based drug design is one of the popular approaches for drug discovery and lead optimization. 3D structure-activity relationships (3D QSAR) and pharmacophore modeling are the most important and widely used tools in ligand-based drug design that can provide crucial insights into the nature of the interactions between drug target and ligand molecule and provide predictive models suitable for lead compound optimization. This review article will briefly discuss the features and potential application of recent advances in ligand-based drug design, with emphasis on a detailed description of a novel 3D QSAR method based on the conformationally sample pharmacophore (CSP) approach (denoted CSP-SAR). In addition, data from a published study is used to compare the CSP-SAR approach to the Catalyst method, emphasizing the utility of the CSP approach for ligand-based model development.
CoMFA; computer-aided drug design; CoMSIA; CSP; drug discovery; lead optimization; pharmacophore
Intrinsically fluorescent glucose derived carbon nanospheres (CSP) efficiently enter mammalian cells and also cross the blood brain barrier (BBB). However, the mechanistic details of CSP entry inside mammalian cells and its specificity are not known.
In this report, the biochemical and cellular mechanism of CSP entry into the living cell have been investigated. By employing confocal imaging we show that CSP entry into the mammalian cells is an ATP-dependent clathrin mediated endocytosis process. Zeta potential studies suggest that it has a strong preference for cells which possess high levels of glucose transporters such as the glial cells, thereby enabling it to target individual organs/tissues such as the brain with increased specificity.
The endocytosis of Glucose derived CSP into mammalian cells is an ATP dependent process mediated by clathrin coated pits. CSPs utilize the surface functional groups to target cells containing glucose transporters on its membrane thereby implicating a potential application for specific targeting of the brain or cancer cells.
The title diphenylarsino compound, C30H32As2 or Ph2As(CH2)6AsPh2, lies about a crystallographic inversion centre located at the mid-point of the central Csp
3 bond of the methylene chain. The two benzene rings bonded to As are inclined to one another at a dihedral angle of 75.98 (8)°. In the crystal structure, weak intermolecular C—H⋯π interactions stack the molecules down the b axis.
The title compound, C72F36, is one of four isomers of C60(CF3)12 for which crystal structures have been obtained. The fullerene molecule has an idealized Ih C60 core with the 12 CF3 groups arranged in an asymmetric fashion on two ribbons of edge-sharing C6(CF3)2 hexagons, a para–meta–para–para–para–meta–para ribbon and a para–meta–para ribbon, giving an overall pmp
mp,pmp structure. There are no cage Csp
3 bonds. The F atoms of two CF3 groups are disordered over two positions; the site occupancy factors are 0.85/0.15 and 0.73/0.27. There are intramolecular F⋯F contacts between pairs of CF3 groups on the same hexagon that range from 2.521 (3) to 2.738 (4) Å.
Insect chemical communication and chemosensory systems rely on proteins coded by several gene families. Here, we have combined protein modeling with evolutionary analysis in order to study the evolution and structure of chemosensory proteins (CSPs) within arthropods and, more specifically, in ants by using the data available from sequenced genomes. Ants and other social insects are especially interesting model systems for the study of chemosensation, as they communicate in a highly complex social context and much of their communication relies on chemicals. Our ant protein models show how this complexity has shaped CSP evolution; the proteins are highly modifiable by their size, surface charge and binding pocket. Based on these findings, we divide ant CSPs into three groups: typical insect CSPs, an ancient 5-helical CSP and hymenopteran CSPs with a small binding pocket, and suggest that these groups likely serve different functions. The hymenopteran CSPs have duplicated repeatedly in individual ant lineages. In these CSPs, positive selection has driven surface charge changes, an observation which has possible implications for the interaction between CSPs and ligands or odorant receptors. Our phylogenetic analysis shows that within the Arthropoda the only highly conserved gene is the ancient 5-helical CSP, which is likely involved in an essential ubiquitous function rather than chemosensation. During insect evolution, the 6-helical CSPs have diverged and perform chemosensory functions among others. Our results contribute to the general knowledge of the structural differences between proteins underlying chemosensation and highlight those protein properties which have been affected by adaptive evolution.
In the title molecule, C10H11NO2, the benzene ring forms dihedral angles of 33.15 (2) and 6.20 (2)° with the mean planes of the amide and propenoxy groups, respectively. The amide –NH2 group is oriented toward the propenoxy substituent and forms a weak intramolecular N—H⋯O hydrogen bond to the propenoxy O atom. The conformation of the propenoxy group at the Csp
3 and Csp
3—O bonds is synperiplanar and antiperiplanar, respectively. In the crystal, N—H⋯O hydrogen bonds involving the amide groups generate C(4) and R
3(7) motifs that organize the molecules into tapes along the a-axis direction. There are C—H⋯π interactions between the propenoxy –CH2 group and the aromatic system of neighboring molecules within the tape. The mean planes of the aromatic ring and the propenoxy group belonging to molecules located on opposite sites of the tape form an angle of 83.16 (2)°.
The title compound, C33H34O4Si, is a dioxasilepine compound, an effective chiral dopant for the determination of high helical twisting powers in liquid crystals. Its structure consists of a five-membered dioxolo ring fused to a seven-membered dioxasilepine ring which contains two sets of phenyl rings in a twisted butterfly shape attached to the two Csp
3 atoms in the ring opposite each other. Two methyl groups are attached to the Si atom in the ring and two additional methyl groups are attached to the Csp
3 atom in the dioxolo ring (one of which is disordered) and which lies in an envelope pattern. The dihedral angles between the mean planes of the phenyl ring pairs are 85.9 (2) and 83.5 (1)°. The dihedral angles between the mean planes of the dioxolo ring and the two pairs of butterfly shaped phenyl rings are 46.2 (1), 67.7 (1), 35.6 (7) and 83.5 (1)°.
The title compound, C10H11NTe, is the first organyl ethynyl telluride, R—Te—C C—H, to be structurally characterized. In the L-shaped molecule, the aryl moiety, viz. Me2NC6H4Te, is almost perpendicular to the Te—C C—H fragment. The Te—Csp
2 bond [2.115 (3) Å] is significantly longer than the Te—Csp bond [2.041 (4) Å]. The Te—C C group is approximately linear [Te—C—C = 178.5 (4)° and C C = 1.161 (5) Å], while the coordination at the Te atom is angular [C—Te—C = 95.92 (14)°]. In the crystal structure, there are Csp—H⋯N hydrogen bonds which are perpendicular to the CNMe2 group; the N atom displays some degree of pyramidalization. Centrosymmetrically related pairs of molecules are linked by Te⋯π(aryl) interactions, with Te⋯Cg = 3.683 (4) Å and Csp—Te⋯Cg = 159.1 (2)° (Cg is the centroid of the benzene ring). These interactions lead to the formation of zigzag ribbons which run along c and are approximately parallel to (110).
In the title compound, C26H43N7O, each piperazine ring adopts a chair conformation. Two 1-methylpiperazine rings bond to one Csp
3 of the pyrrole ring via the piperazine N atoms, while the third one links to the N atom of the indolin-2-one unit through a flexible ethyl group with an almost syn conformation. In the crystal, molecules are connected through methylene–carbonyl C—H⋯O interactions into an infinite chain along the c axis. The almost parallel arrays are stacked, forming a three-dimensional framework.
Two cold shock genes, cspL and cspP, have been cloned from two Lactobacillus plantarum strains. These genes, which are nonallelic, were present in all strains tested. The genes encode 66-amino-acid polypeptides related to each other and to the cold shock Csp family. Transcription of cspP rendered a single mRNA, while two cspL mRNAs were found with common 5' ends. The amounts of these transcripts increased moderately upon exposure of the cultures to cold.
The purpose of this paper is to describe a clearly defined manual method for calculating cortical silent period (CSP) length that can be employed successfully and reliably by raters after minimal training in subjects with focal hand dystonia (FHD) and healthy subjects. A secondary purpose was to explore intra-subject variability of the CSP in subjects with FHD vs. healthy subjects.
Two raters previously naïve to CSP identification and one experienced rater independently analyzed 170 CSP measurements collected in six subjects with focal hand dystonia (FHD) and nine healthy subjects. Intraclass correlation coefficient (ICC) was calculated to quantify inter-rater reliability within the two groups of subjects. The relative variability of CSP in each group was calculated by coefficient of variation (CV). Relative variation between raters within repeated measures of individual subjects was also quantified by CV.
Reliability measures were as follows: mean of three raters: all subjects: ICC= 0.976; within healthy subjects: ICC=0.965; in subjects with FHD: ICC= 0.956. The median within-subject variability for the healthy group was CV=7.33% and in subjects with FHD: CV= 11.78%. The median variability of calculating individual subject CSP duration between raters was CV=10.23% in subjects with dystonia and CV=10.46% in healthy subjects.
Manual calculation of CSP results in excellent reliability between raters of varied levels of experience. Healthy subjects display less variability in CSP. Despite greater variability, the CSP in impaired subjects can be reliably calculated across raters.
cortical silent period; cortical excitability; focal hand dystonia; reliability; definition; methodology; transcranial magnetic stimulation
Members of the group of 7-kDa cold-shock proteins (CSPs) are the proteins with the highest level of induction upon cold shock in the lactic acid bacterium Lactococcus lactis MG1363. By using double-crossover recombination, two L. lactis strains were generated in which genes encoding CSPs are disrupted: L. lactis NZ9000ΔAB lacks the tandemly orientated cspA and cspB genes, and NZ9000ΔABE lacks cspA, cspB, and cspE. Both strains showed no differences in growth at normal and at low temperatures compared to that of the wild-type strain, L. lactis NZ9000. Two-dimensional gel electrophoresis showed that upon disruption of the cspAB genes, the production of remaining CspE at low temperature increased, and upon disruption of cspA, cspB, and cspE, the production of CspD at normal growth temperatures increased. Northern blot analysis showed that control is most likely at the transcriptional level. Furthermore, it was established by a proteomics approach that some (non-7-kDa) cold-induced proteins (CIPs) are not cold induced in the csp-lacking strains, among others the histon-like protein HslA and the signal transduction protein LlrC. This supports earlier observations (J. A. Wouters, M. Mailhes, F. M. Rombouts, W. M. De Vos, O. P. Kuipers, and T. Abee, Appl. Environ. Microbiol. 66:3756–3763, 2000). that the CSPs of L. lactis might be directly involved in the production of some CIPs upon low-temperature exposure. Remarkably, the adaptive response to freezing by prior exposure to 10°C was significantly reduced in strain NZ9000ΔABE but not in strain NZ9000ΔAB compared to results with wild-type strain NZ9000, indicating a notable involvement of CspE in cryoprotection.
Induction of competence for natural genetic transformation in Streptococcus pneumoniae depends on pheromone-mediated cell-cell communication and a signaling pathway consisting of the competence-stimulating peptide (CSP), its membrane-embedded histidine kinase receptor ComD, and the cognate response regulator ComE. Extensive screening of pneumococcal isolates has revealed that two major CSP variants, CSP1 and CSP2, are found in members of this species. Even though the primary structures of CSP1 and CSP2 are about 50% identical, they are highly specific for their respective receptors, ComD1 and ComD2. In the present work, we have investigated the structural basis of this specificity by determining the three-dimensional structure of CSP1 from nuclear magnetic resonance data and comparing the agonist activity of a number of CSP1/CSP2 hybrid peptides toward the ComD1 and ComD2 receptors. Our results show that upon exposure to membrane-mimicking environments, the 17-amino-acid CSP1 pheromone adopts an amphiphilic α-helical configuration stretching from residue 6 to residue 12. Furthermore, the pattern of agonist activity displayed by the various hybrid peptides revealed that hydrophobic amino acids, some of which are situated on the nonpolar side of the α-helix, strongly contribute to CSP specificity. Together, these data indicate that the identified α-helix is an important structural feature of CSP1 which is essential for effective receptor recognition under natural conditions.
Aging is associated with increased central aortic systolic pressure (CSP) and pulse pressure which are predictive of cardiovascular events. Mechanisms implicated for higher central pressures include a higher forward incident pressure wave (P1), higher augmented pressure (AP), and shorter reflected wave round trip travel time (Tr). African-Americans (AA) have more frequent and deleterious blood pressure elevation. Using applanation tonometry, we studied the association of age and CSP with P1 and AP in 900 AA subjects. Data showed that in subjects ≤50 years old, CSP was mediated by AP but not P1 or Tr, whereas in those >50, CSP was mediated by both AP and P1 and to a lesser extent by Tr. Predictive models were significant (R2 = 0.97) for both age groups. In conclusion, wave reflection is the primary determinant of CSP in younger AA, while in older subjects, CSP is mediated by both the magnitude and timing of wave reflection as well as aortic impedance.
The structure of the title compound, C13H14O2, a pentacycloundecane cage derivative, exhibits unusual Csp
3 single-bond lengths ranging from 1.505 (3) to 1.607 (2) Å and strained bond angles as small as 88.7 (1)° and as large as 121.0 (2)°. In this meso compound, an internal non-crystallographic mirror plane exists, bisecting the molecule. In the crystal, weak C—H⋯O hydrogen bonds link the molecules into an infinite spiral about a twofold screw axis along the  direction.
Escherichia coli contains nine members of the CspA family. CspA and some of its homologues play critical role in cold acclimation of cells by acting as RNA chaperones, destabilizing nucleicacid secondary structures. Disruption of nucleic acid melting activity of CspE led to loss of its transcription antitermination activity and consequently its cold acclimation activity. To date, the melting activity of Csp proteins was studied using partially double-stranded model nucleic acids substrates forming stem–loop structures. Here, we studied the mechanism of nucleic acid melting by CspE. We show that CspE melts the stem region in two directions, that CspE-induced melting does not require the continuity of the substrate's loop region, and CspE can efficiently melt model substrates with single-stranded overhangs as short as 4 nt. We further show that preferential binding of CspE at the stem–loop junction site initiates melting; binding of additional CspE molecules that fully cover the single-stranded region of a melting substrate leads to complete melting of the stem.
Some chemosensory proteins (CSPs) are expressed in insect sensory appendages and are thought to be involved in chemical signaling by ants. We identified fourteen unique CSP sequences in EST libraries of the red imported fire ant, Solenopsis invicta. One member of this group (Si-CSP1) is highly expressed in worker antennae, suggesting an olfactory function. A shotgun proteomic analysis of antennal proteins confirms the high level of Si-CSP1 expression, and also shows expression of another CSP and two odorant-binding proteins (OBPs). We cloned and expressed the coding sequence for Si-CSP1. We used cyclodextrins as solubilizers to investigate ligand binding. Fire ant cuticular lipids strongly inhibit Si-CSP1 binding to the fluorescent dye N-phenyl-naphthylamine, suggesting cuticular substances are ligands for Si-CSP1. Analysis of the cuticular lipids shows that the endogenous ligands of Si-CSP1 are not cuticular hydrocarbons.
chemosensory proteins; Solenopsis invicta; proteomics; cuticular lipids; cyclodextrin
In Streptococcus pneumoniae, competence and bacteriocin genes are controlled by two two-component systems, ComED and BlpRH, respectively. In Streptococcus mutans, both functions are controlled by the ComED system. Recent studies in S. mutans revealed a potential ComE binding site characterized by two 11 bp direct repeats shared by each of the bacteriocin genes responsive to the competence-stimulating peptide (CSP). Interestingly, this sequence was not found in the upstream region of the CSP structural gene comC. Since comC is suggested to be part of a CSP-responsive and ComE-dependent autoregulatory loop, it was of interest to determine how it was possible that the ComED system could simultaneously regulate bacteriocin expression and natural competence. Using the intergenic region IGS1499, shared by the CSP-responsive bacteriocin nlmC and comC, it was demonstrated that both genes are likely to be regulated by a bifunctional ComE. In a comE null mutant, comC gene expression was increased similarly to a fully induced wild-type. In contrast, nlmC gene expression was nearly abolished. Deletion of ComD exerted a similar effect on both genes to that observed with the comE null mutation. Electrophoretic mobility shift assays (EMSAs) with purified ComE revealed specific shift patterns dependent on the presence of one or both direct repeats in the nlmC–comC promoter region. The two direct repeats were also required for the promoter activity of both nlmC and comC. These results suggest that gene regulation of comC in S. mutans is fundamentally different from that reported for S. pneumoniae, which implicates a unique regulatory mechanism that allows the coordination of bacteriocin production with competence development.
The title compound, C18H17NO6 [systematic name: (2R,3R)-4-benzylamino-2-benzoyloxy-3-hydroxy-4-oxobutanoic acid], is the first structurally characterized unsymmetrical monoamide–monoacyl tartaric acid derivative. The molecule shows a staggered conformation around the tartramide Csp3—Csp3 bond with trans-oriented carboxyl and amide groups. The molecular conformation is stabilized by an intramolecular N—H⋯O hydrogen bond. In the crystal, molecules are linked by O—H⋯O hydrogen bonds between the carboxyl and amide carbonyl groups, forming translational chains along . Further O—H⋯O and N—H⋯O hydrogen bonds as well as weaker C—H⋯O and C—H⋯π intermolecular interactions extend the supramolecular assembly into a double-layer structure parallel to (100). There are no directional interactions between the double layers.