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PubMed1997

Analysis of the in vitro secondary structure of cucumber mosaic virus satellite RNA.

The solution conformation of two variants of cucumber mosaic virus satellite RNA (CMV satRNA) was analyzed using several enzymatic and chemical probes. Ribonuclease T1 and nuclease S1 were used to map unpaired nucleotides, and nuclease V1 was used to detect double-stranded, or stacked, bases. Chemical probing with dimethylsulphate and diethylpyrocarbonate also identified unpaired and unstacked nucleotides, respectively. Modified or cleaved positions were identified by direct gel electrophoresis of radioactively labeled RNA, or by analysis of DNA sequence patterns generated by primer-extension with reverse transcriptase. Additional information was obtained by a gel-fractionation method under nondenaturing conditions for the identification of base paired fragments. On these data, a model for the in vitro secondary structure of CMV satRNA is proposed. Results support the existence of a complex structure with 51% of nucleotides involved in base pairs (40 G:C, 28 G:U, and 18 A:U pairs). Several structural elements, numbered I-VI, were defined, and interactions between separate domains are suggested. Comparisons of experimental data and a formerly reported secondary structure model for CMV satRNA support the validity of the structure we propose.

Base Composition↗
PubMed2002

Structure of a complex of the human alpha/beta T cell receptor (TCR) HA1.7, influenza hemagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity.

The alpha/beta T cell receptor (TCR) HA1.7 specific for the hemagglutinin (HA) antigen peptide from influenza A virus is HLA-DR1 restricted but cross-reactive for the HA peptide presented by the allo-major histocompatibility complex (MHC) class II molecule HLA-DR4. We report here the structure of the HA1.7/DR4/HA complex, determined by X-ray crystallography at a resolution of 2.4 A. The overall structure of this complex is very similar to the previously reported structure of the HA1.7/DR1/HA complex. Amino acid sequence differences between DR1 and DR4, which are located deep in the peptide binding groove and out of reach for direct contact by the TCR, are able to indirectly influence the antigenicity of the pMHC surface by changing the conformation of HA peptide residues at position P5 and P6. Although TCR HA1.7 is cross-reactive for HA presented by DR1 and DR4 and tolerates these conformational differences, other HA-specific TCRs are sensitive to these changes. We also find a dependence of the width of the MHC class II peptide-binding groove on the sequence of the bound peptide by comparing the HA1.7/DR4/HA complex with the structure of DR4 presenting a collagen peptide. This structural study of TCR cross-reactivity emphasizes how MHC sequence differences can affect TCR binding indirectly by moving peptide atoms.

Alleles↗
PubMed1999

Structural changes of the active site tunnel of Humicola insolens cellobiohydrolase, Cel6A, upon oligosaccharide binding.

The mechanisms of crystalline cellulose degradation by cellulases are of paramount importance for the exploitation of these enzymes in applied processes, such as biomass conversion. Cellulases have traditionally been classified into cellobiohydrolases, which are effective in the degradation of crystalline materials, and endoglucanases, which appear to act on "soluble" regions of the substrate. Humicola insolensCel6A (CBH II) is a cellobiohydrolase from glycoside hydrolase family 6 whose native structure has been determined at 1.9 A resolution [Varrot, A., Hastrup, S., Schülein, M., and Davies, G. J. (1999) Biochem. J. 337, 297-304]. Here we present the structure of the catalytic core domain of Humicola insolens cellobiohydrolase II Cel6A in complex with glucose/cellotetraose at 1.7 A resolution. Crystals of Cel6A, grown in the presence of cellobiose, reveal six binding subsites, with a single glucose moiety bound in the -2 subsite and cellotetraose in the +1 to +4 subsites. The complex structure is strongly supportive of the assignment of Asp 226 as the catalytic acid and consistent with proposals that Asp 405 acts as the catalytic base. The structure undergoes several conformational changes upon substrate binding, the most significant of which is a closing of the two active site loops (residues 174-196 and 397-435) with main-chain movements of up to 4.5 A observed. This complex not only defines the polysaccharide-enzyme interactions but also provides the first three-dimensional demonstration of conformational change in this class of enzymes.

Binding Sites↗
PubMed1999

Electron crystal structure of an RNA polymerase II transcription elongation complex.

The structure of an actively transcribing complex, containing yeast RNA polymerase II with associated template DNA and product RNA, was determined by electron crystallography. Nucleic acid, in all likelihood the "transcription bubble" at the active center of the enzyme, occupies a previously noted 25 A channel in the protein structure. Details are indicative of a roughly 90 degrees bend of the DNA between upstream and downstream regions. The DNA apparently lies entirely on one face of the polymerase, rather than passing through a hole to the opposite side, as previously suggested.

Crystallography↗
PubMed1991

Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes.

The structures of NADP+ and magnesium isocitrate bound to the NADP(+)-dependent isocitrate dehydrogenase of Escherichia coli have been determined and refined at 2.5-A resolution. NADP+ is bound by the large domain of isocitrate dehydrogenase, a structure that has little similarity to the supersecondary structure of the nucleotide-binding domain of the lactate dehydrogenase-like family of nucleotide-binding proteins. The coenzyme-binding site confirms the fundamentally different evolution of the isocitrate dehydrogenase-like and the lactate dehydrogenase-like classes of nucleotide-binding proteins. In the magnesium-isocitrate complex, magnesium is coordinated to the alpha-carboxylate and alpha-hydroxyl oxygen of isocitrate in a manner suitable for stabilization of a negative charge on the hydroxyl oxygen during both the dehydrogenation and decarboxylation steps of the conversion of isocitrate to alpha-ketoglutarate. The metal ion is also coordinated by aspartate side chains 283' (of the second subunit of the dimer) and 307 and two water molecules in a roughly octahedral arrangement. On the basis of the geometry of the active site, the base functioning in the dehydrogenation step is most likely aspartate 283'. E. coli isocitrate dehydrogenase transfers a hydride stereospecifically to the A-side of NADP+, and models for a reactive ternary complex consistent with this stereospecificity are discussed.

Binding Sites↗
PubMed1989

Structure of the complex of Streptomyces griseus proteinase B and polypeptide chymotrypsin inhibitor-1 from Russet Burbank potato tubers at 2.1 A resolution.

A low molecular weight protein inhibitor of serine proteinases from Russet Burbank potato tubers, polypeptide chymotrypsin inhibitor-1 (PCI-1), has been crystallized in complex with Streptomyces griseus proteinase B (SGPB). The three-dimensional structure of the complex has been solved at 2.1 A resolution by the molecular replacement method and has been refined to a final R-factor (= sigma[[Fo[-[Fc[[/sigma[Fo[) of 0.142 (8.0 to 2.1 A resolution data). The reactive site bond of PCI-1 (Leu38I to Asn39I) is intact in the complex, and there is no significant distortion of the peptide from planarity. The distance between the active site serine O gamma of SGPB and the carbonyl carbon of the scissile bond of PCI-1 is 2.8 A (1 A = 0.1 nm). The inhibitor has little secondary structure, having a three-stranded antiparallel beta-sheet on the side opposite the reactive site and four beta-turns. PCI-1 has four disulphide bridges; these presumably take the place of extensive secondary structure in keeping the reactive site conformationally constrained. The pairing of the cystine residues, which had not been characterized chemically, is as follows: Cys3I to Cys40I, Cys6I to Cys24I, Cys7I to Cys36I, and Cys13I to Cys49I. The molecular structure of SGPB in the PCI-1 complex agrees closely with the structure of SGPB complexed with the third domain of the turkey ovomucoid inhibitor (OMTKY3). A least-squares overlap of all atoms in SGPB gives a root-mean-square difference of 0.37 A. One of the loops of SGPB (Ser35 to Gly40) differs in conformation in the two complexes by more than 2.0 A root-mean-square for the main-chain atoms. Thr39 displays the largest differences with the carbonyl carbon atom deviating by 3.6 A. This conformational alternative is a result of the differences in the molecular structures of the P'4 residues following the reactive site bonds of the two inhibitors. This displacement avoids a close contact (1.3 A) between the carbonyl oxygen of Ser38 of SGPB and Pro42I C beta of PCI-1. The solvent structure of the PCI-1-SGPB complex includes 179 waters, two sulphate or phosphate ions, and one calcium or potassium ion, which appears to play a role in crystal formation. The molecular structure of PCI-1 determined here has allowed the proposal of a model for the structure of a two-domain inhibitor from potatoes and tomatoes, inhibitor II.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2003

A structural basis for the mechanism of aspartate-beta-semialdehyde dehydrogenase from Vibrio cholerae.

L-Aspartate-beta-semialdehyde dehydrogenase (ASADH) catalyzes the reductive dephosphorylation of beta-aspartyl phosphate to L-aspartate-beta-semialdehyde in the aspartate biosynthetic pathway of plants and micro-organisms. The aspartate pathway produces fully one-quarter of the naturally occurring amino acids, but is not found in humans or other eukaryotic organisms, making ASADH an attractive target for the development of new antibacterial, fungicidal, or herbicidal compounds. We have determined the structure of ASADH from Vibrio cholerae in two states; the apoenzyme and a complex with NADP, and a covalently bound active site inhibitor, S-methyl-L-cysteine sulfoxide. Upon binding the inhibitor undergoes an enzyme-catalyzed reductive demethylation leading to a covalently bound cysteine that is observed in the complex structure. The enzyme is a functional homodimer, with extensive intersubunit contacts and a symmetrical 4-amino acid bridge linking the active site residues in adjacent subunits that could serve as a communication channel. The active site is essentially preformed, with minimal differences in active site conformation in the apoenzyme relative to the ternary inhibitor complex. The conformational changes that do occur result primarily from NADP binding, and are localized to the repositioning of two surface loops located on the rim at opposite sides of the NADP cleft.

Apoenzymes↗
PubMed2000

Synthesis and characterization of square planar nickel(II)-arylthiolate complexes with the biphenyl-2,2'-dithiolate ligand.

Two new NiIIS4 complexes with the biphenyl-2,2'-dithiolate ligand (L) are reported. The dinuclear complex 1, [Ni2L3]2-, was formed in the reaction of 2-3 equiv of Na2L and [NiCl4]2- and the mononuclear complex [NiL2]2- (2) by using 4-10 equiv of Na2L. Complexes 1 and 2 have been crystallographically characterized. (Et4N)2[1].0.5S2Ph2, CH3CN: C60H71N3Ni2S7, triclinic, P1, a = 13.806(2) A, b = 14.267(2) A, c = 16.873(2) A, alpha = 69.263(10) degrees, beta = 69.267(8) degrees, gamma = 83.117(10) degrees, Z = 2, R1 = 0.0752 (wR2 = 0.2011). (Et4N)(Na.CH3CN)[2]: C34H39N2NaNiS4, triclinic, P1, a = 9.9570(10) A, b = 13.2670(10) A, c = 13.9560(10) A, alpha = 108.489(7) degrees, beta = 90.396(6) degrees, gamma = 103.570(4) degrees, Z = 2, R1 = 0.0390 (wR2 = 0.0995). Both complexes are square planar about the nickel ion in the solid state as well as in solution. Most Ni(II)-thiolate complexes are square planar except the tetrahedral mononuclear complexes with monodentate arylthiolate ligands that cannot force a square planar geometry. The ligand (L) has some flexibility to change its bite angle via the phenyl-phenyl bond and should not force a planar geometry on its complexes either. Therefore, it is interesting that 2 has adopted a square planar structure. Complex 2 readily converts to 1 in solution when not in the presence of excess L in a process that is presumably similar to that known for other mononuclear, bidentate ligated Ni(II) complexes. Both complexes, at least in the solid state, appear to have an inclination to bind another metal ion on one face of the complex (Ni2+ in 1, Na+ in 2). We hope to take advantage of this in future work to synthesize relevant model complexes for the active sites of the nickel-iron hydrogenases after suitable modifications are made to L.

Binding Sites↗
PubMed1993

Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: crystal structures of the complexed and peptide-free forms.

The crystal structure of the Src SH2 domain complexed with a high affinity 11-residue phosphopeptide has been determined at 2.7 A resolution by X-ray diffraction. The peptide binds in an extended conformation and makes primary interactions with the SH2 domain at six central residues: PQ(pY)EEI. The phosphotyrosine and the isoleucine are tightly bound by two well-defined pockets on the protein surface, resulting in a complex that resembles a two-pronged plug engaging a two-holed socket. The glutamate residues are in solvent-exposed environments in the vicinity of basic side chains of the SH2 domain, and the two N-terminal residues cap the phosphotyrosine-binding site. The crystal structure of Src SH2 in the absence of peptide has been determined at 2.5 A resolution, and comparison with the structure of the high affinity complex reveals only localized and relatively small changes.

Amino Acid Sequence↗
PubMed2025

Complex de novo structural variants are an underestimated cause of rare disorders.

Complex de novo structural variants (dnSVs) are crucial genetic factors in rare disorders, yet their prevalence and characteristics in rare disorders remain poorly understood. Here, we conduct a comprehensive analysis of whole-genome sequencing data of 12,568 families, including 13,698 offspring with rare diseases, obtained as part of the UK 100,000 Genomes Project. We identify 1,870 dnSVs, constituting the largest dnSV dataset reported to date. Complex dnSVs (n = 158; 8.4%) emerge as the third most common type of SV, following simple deletions and duplications. We classify 65% of these complex dnSVs into 11 subtypes. Among probands with dnSVs (n = 1,696), 9% exhibit exon-disrupting pathogenic dnSVs associated with the probands' phenotype. Notably, 12% of exon-disrupting pathogenic dnSVs and 22% of de novo deletions or duplications previously identified by array-based or whole-exome sequencing methods are found to be complex dnSVs. We also find distinct genomic properties of de novo deletions depending on the parent of origin. This study highlights the importance of complex dnSVs in the cause of rare disorders and demonstrates the necessity of specific genomic analysis to avoid overlooking these variants.

Humans↗
PubMed2005

The crystal structure of Escherichia coli ketopantoate reductase with NADP+ bound.

The NADPH-dependent reduction of ketopantoate to pantoate, catalyzed by ketopantoate reductase (KPR; EC 1.1.1.169), is essential for the biosynthesis of pantothenate (vitamin B(5)). Here we present the crystal structure of Escherichia coli KPR with NADP(+) bound, solved to 2.1 A resolution. The cofactor is bound in the active site cleft between the N-terminal Rossmann-fold domain and the C-terminal alpha-helical domain. The thermodynamics of cofactor and substrate binding were characterized by isothermal titration calorimetry. The dissociation constant for NADP(+) was found to be 6.5 muM, 20-fold larger than that for NADPH (0.34 muM). The difference is primarily due to the entropic term, suggesting favorable hydrophobic interactions of the more lipophilic nicotinamide ring in NADPH. Comparison of this binary complex structure with the previously studied apoenzyme reveals no evidence for large domain movements on cofactor binding. This observation is further supported both by molecular dynamics and by calorimetric analysis. A model of the ternary complex, based on the structure presented here, provides novel insights into the molecular mechanism of enzyme catalysis. We propose a conformational switch of the essential Lys176 from the "resting" state observed in our structure to an "active" state, to bind ketopantoate. Additionally, we identify the importance of Asn98 for substrate binding and enzyme catalysis.

Alcohol Oxidoreductases↗
PubMed1998

Localizing components of a complex task: sentence processing and working memory.

Three areas of the left hemisphere play different roles in sentence comprehension. An area of posterior middle and superior temporal gyrus shows activation correlated with the structural complexity of a sentence, suggesting that this area supports processing of sentence structure. The lateral anterior temporal gyrus is more activated bilaterally by all sentence conditions than by word lists; thus the function of the area probably does not directly support processing of structure but rather processing of words specific to a sentence context. Left inferior frontal cortex also shows activation related to sentence complexity but is also more activated in word list processing than in simple sentences; this region may thus support a form of verbal working memory which maintains sentence structural information as well as lexical items.

Adult↗
PubMed2006

Structure-toxicity relationships for different types of dinuclear platinum complexes.

Nine structurally distinct dinuclear platinum complexes have been evaluated in a novel model system for the investigation of renal epithelial toxicity of platinum drugs. The results showed that these compounds are toxic when applied at the basolateral side of renal epithelia, whereas their toxic effects on the apical side are negligible. Such a difference in toxicity of the complexes has been found to result from their poor uptake through the apical membrane, as compared to the basolateral membrane. Toxicity of the compounds on the basolateral side varies depending on their structure. Structure-toxicity relationships for the group of complexes with rigid ligands and for the group of complexes with flexible ligands are discussed. Among the dinuclear complexes with rigid ligands, sterically hindered complexes are less toxic, due to their poor uptake and low reactivity towards glutathione. Within the group of complexes with flexible ligands, cis-configured isomers are more toxic than their trans-counterparts.

Animals↗
PubMed1986

Cognitive structure changes with psychotherapy in neurosis.

This study investigated the relationship between improvement in psychotherapy and changes in cognitive complexity (structural organization and differentiation). Before undergoing 30 sessions of psychoanalytically oriented psychotherapy, 27 psychoneurotic subjects specified the target (major) complaints, described 15 figures (including themselves) and completed the repertory grid. After psychotherapy, subjects rated their improvement on the target complaints and again described the 15 figures and completed the repertory grid. The results showed that improvement in psychotherapy was associated with increased complexity in the patients' cognitive organization of the psychosocial world, but not with increased cognitive differentiation in interpersonal perception. Implications for the theory of neurosis and evaluation of change in the process of psychotherapy are discussed.

Adult↗
PubMed1983

Down's syndrome in the male. Reproductive pathology and meiotic studies.

Studies on testicular histology and meiosis were carried out by the use of light and electron microscopy in an 18-year-old Down's syndrome male in an attempt to follow the fate of the extra chromosome 21 and to evaluate the effects of this condition on spermatogenesis and the reproductive functions. The histological changes in the testes corresponded to spermatogenic arrest. Electron microscopic whole-mount spreadings of meiotic cells in the pachytene stage showed that in most nuclei an extra chromosome 21 was not detectable. Only in a small number of nuclei, univalents or trivalents with segmental pairing structures of an extra chromosome could be discovered. In contrast, the great majority of (C-banded) diakinesis figures showed the presence of a supernumerary G (no. 21) chromosome. The absence of a traceable extra chromosome 21 in most pachytene cells is explained by the assumption that it is intimately connected with and hidden in the sex vesicle, whose complex structure does not allow the identification of single elements. Strong support for this assumption is seen (a) in the general tendency of narrow spatial association of unpaired segments with the XY complex and (b) in close structural similarities occurring between univalents or nonsynapsed segments of trivalents and the nonpaired segments of the sex chromosomes. It is suggested that the association or connection of an extra chromosome with the XY complex during pachytene interferes with the phenomenon of X inactivation. In animal systems such abnormal interference is related with spermatogenic breakdown and, in a general way, with male hybrid type sterility. So far, the range of sterility vs. fertility in cases of male Down's syndrome is not yet fully clear, but it appears that impairment of fertility, and sterility are most frequent. If so, it is proposed that the effect of the trisomy 21 condition on spermatogenesis (and fertility) is a consequence of the behavior of the extra chromosome in the meiotic prophase.

Adolescent↗
PubMed2005

Deletion of the glucosidase II gene in Trypanosoma brucei reveals novel N-glycosylation mechanisms in the biosynthesis of variant surface glycoprotein.

The trypanosomatids are generally aberrant in their protein N-glycosylation pathways. However, protein N-glycosylation in the African trypanosome Trypanosoma brucei, etiological agent of human African sleeping sickness, is not well understood. Here, we describe the creation of a bloodstream-form T. brucei mutant that is deficient in the endoplasmic reticulum enzyme glucosidase II. Characterization of the variant surface glycoprotein, the main glycoprotein synthesized by the parasite with two N-glycosylation sites, revealed unexpected changes in the N-glycosylation of this molecule. Structural characterization by mass spectrometry, nuclear magnetic resonance spectroscopy, and chemical and enzymatic treatments revealed that one of the two glycosylation sites was occupied by conventional oligomannose structures, whereas the other accumulated unusual structures in the form of Glcalpha1-3Manalpha1-2Manalpha1-2Manalpha1-3(Manalpha1-6)Manbeta1-4GlcNAcbeta1-4GlcNAc, Glcalpha1-3Manalpha1-2Manalpha1-2Manalpha1-3(GlcNAcbeta1-2Manalpha1-6)Manbeta1-4GlcNAcbeta1-4GlcNAc, and Glcalpha1-3Manalpha1-2Manalpha1-2Manalpha1-3(Galbeta1-4GlcNAcbeta1-2Manalpha1-6)Manbeta1-4GlcNAcbeta1-4GlcNAc. The possibility that these structures might arise from Glc1Man9GlcNAc2 by unusually rapid alpha-mannosidase processing was ruled out using a mixture of alpha-mannosidase inhibitors. The results suggest that bloodstream-form T. brucei can transfer both Man9GlcNAc2 and Man5GlcNAc2 to the variant surface glycoprotein in a site-specific manner and that, unlike organisms that transfer exclusively Glc3Man9GlcNAc2, the T. brucei UDP-Glc: glycoprotein glucosyltransferase and glucosidase II enzymes can use Man5GlcNAc2 and Glc1Man5GlcNAc2, respectively, as their substrates. The ability to transfer Man5GlcNAc2 structures to N-glycosylation sites destined to become Man(4-3)GlcNAc2 or complex structures may have evolved as a mechanism to conserve dolichol-phosphate-mannose donors for glycosylphosphatidylinositol anchor biosynthesis and points to fundamental differences in the specificities of host and parasite glycosyltransferases that initiate the synthesis of complex N-glycans.

Animals↗
PubMed1997

The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate.

The three-dimensional structure of the complex of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco; EC 4.1.1.39) from spinach with its natural substrate ribulose 1,5-bisphosphate (RuBP) has been determined both under activating and non-activating conditions by X-ray crystallography to a resolution of 2.1 A and 2.4 A, respectively. Under activating conditions, the use of calcium instead of magnesium as the activator metal ion enabled us to trap the substrate in a stable complex for crystallographic analysis. Comparison of the structure of the activated and the non-activated RuBP complexes shows a tighter binding for the substrate in the non-activated form of the enzyme, in line with previous solution studies. In the non-activated complex, the substrate triggers isolation of the active site by inducing movements of flexible loop regions of the catalytic subunits. In contrast, in the activated complex the active site remains partly open, probably awaiting the binding of the gaseous substrate. By inspection of the structures and by comparison with other complexes of the enzyme we were able to identify a network of hydrogen bonds that stabilise a closed active site structure during crucial steps in the reaction. The present structure underlines the central role of the carbamylated lysine 201 in both activation and catalysis, and completes available structural information for our proposal on the mechanism of the enzyme.

Calcium↗
PubMed2006

Large gas-solid structural differences in complexes of haloacetonitriles with boron trifluoride.

The structural properties of the singly halogenated derivatives of CH(3)CN-BF(3) (X-CH(2)CN-BF(3): X = F, Cl, Br, I) have been investigated via single-crystal X-ray crystallography, solid-state infrared spectroscopy, and correlated electronic-structure theory. Taken together, these data illustrate large differences between the gas-phase and solid-state structures of these systems. Calculated gas-phase structures (B3PW91/aug-cc-pVTZ) of FCH(2)CN-BF(3), ClCH(2)CN-BF(3), and BrCH(2)CN-BF(3) indicate that the B-N dative bonds in these systems are quite weak, with distances of 2.422, 2.374, and 2.341 A, respectively. However, these distances, as well as other calculated structural parameters and normal-mode vibrational frequencies, indicate that the dative interactions do become slightly stronger in proceeding from F- to Br-CH(2)CN-BF(3). In contrast, solid-state structures for FCH(2)CN-BF(3), ClCH(2)CN-BF(3), and ICH(2)CN-BF(3) from X-ray crystallography all have B-N distances that are quite short, about 1.65 A. Thus, the B-N distances of the F- and Cl-containing derivatives contract by over 0.7 A upon crystallization. Large shifts in the vibrational modes involving motions of the BF(3) subunit parallel these structural changes. An X-ray crystal structure could not be determined for BrCH(2)CN-BF(3)(s), but the solid-state IR spectrum is consistent with those obtained previously for related complexes and suggests that the solid-state structure resembles those of the others, and in turn, implicates a large gas-solid structural difference for this species as well.

Journal Article↗