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At least 1,603 records · Page 89Linked to original sources
PubMed2001

CD81 extracellular domain 3D structure: insight into the tetraspanin superfamily structural motifs.

Human CD81, a known receptor for hepatitis C virus envelope E2 glycoprotein, is a transmembrane protein belonging to the tetraspanin family. The crystal structure of human CD81 large extracellular domain is reported here at 1.6 A resolution. Each subunit within the homodimeric protein displays a mushroom-like structure, composed of five alpha-helices arranged in 'stalk' and 'head' subdomains. Residues known to be involved in virus binding can be mapped onto the head subdomain, providing a basis for the design of antiviral drugs and vaccines. Sequence analysis of 160 tetraspanins indicates that key structural features and the new protein fold observed in the CD81 large extracellular domain are conserved within the family. On these bases, it is proposed that tetraspanins may assemble at the cell surface into homo- and/or hetero-dimers through a conserved hydrophobic interface located in the stalk subdomain, while interacting with other liganding proteins, including hepatitis C virus E2, through the head subdomain. The topology of such interactions provides a rationale for the assembly of the so-called tetraspan-web.

Amino Acid Sequence↗
PubMed2005

A structure-based analysis of huntingtin mutant polyglutamine aggregation and toxicity: evidence for a compact beta-sheet structure.

Huntington's disease (HD) arises from an expanded polyglutamine (polyQ) in the N-terminus of the huntingtin (htt) protein. Neuronal degeneration and inclusions containing N-terminal fragments of mutant htt are present in the cortex and striatum of HD brain. Recently, a model of polyQ aggregate structure has been proposed on the basis of studies with synthetic polyQ peptides and includes an alternating beta-strand/beta-turn structure with seven glutamine residues per beta-strand. We tested this model in the context of the htt exon-1 N-terminal fragment in both mammalian cell culture and cultured primary cortical neurons. We found our data support this model in the htt protein and provide a better understanding of the structural basis of polyQ aggregation in toxicity in HD.

Animals↗
PubMed1994

Structure-activity and structure-side-effect relationships for the quinolone antibacterials.

The fluoroquinolones represent a major class of antibacterials with great therapeutic potential. Over the years, several structure-activity and side-effect relationships have been developed, covering thousands of analogues, in an effort to improve overall antimicrobial efficacy while reducing undesirable side-effects. In this review, the various structural features of the quinolones which govern antibacterial efficacy and influence the side-effect profile are delineated and summarized at the molecular level. Those features which most remarkably enhance antimicrobial effectiveness are: a halogen (F or Cl) at the 8-position which improves oral absorption and activity against anaerobes; an alkylated pyrrolidine or piperazine at C7 which increases serum half-life and potency vs Gram-positive bacteria; and a cyclopropyl group at N1 and an amino substituent at C5, both of which improve overall potency. Some side-effects of the quinolones are class effects, and cannot be modulated by molecular variation. These include gastrointestinal irritation and arthropathy. Several other potential side-effects are directly influenced by structural modification. For example, CNS effects and drug interactions with theophylline and NSAIDs are strongly influenced by the C7 substituent with simple pyrrolidines and piperazines the worst actors. Increasing steric bulk through alkylation ameliorates these effects. Phototoxicity is determined by the nature of the 8-position substituent with halogen causing the greatest photo reaction while hydrogen and methoxy show little light induced toxicity. Genetic toxicity is controlled in additive fashion by the choice of groups at the 1, 7 and 8 positions. From the analysis, those groups which mutually improve efficacy while reducing side-effects are identified. In addition, preclinical models for determining potential side-effects are discussed.

4-Quinolones↗
PubMed2002

Crystal structure of 9-amino-N-[2-(4-morpholinyl)ethyl]-4-acridinecarboxamide bound to d(CGTACG)2: implications for structure-activity relationships of acridinecarboxamide topoisomerase poisons.

The structure of the complex formed between d(CGTACG)2 and 9-amino-N-[2-(4-morpholinyl)ethyl]-4-acridinecarboxamide, an inactive derivative of the antitumour agents N-[2-(dimethylamino)ethyl]acridine-4-carboxamide (DACA) and 9-amino-DACA, has been solved to a resolution of 1.8 A using X-ray crystallography. The complex crystallises in the space group P6(4 )and the final structure has an overall R factor of 21.9%. A drug molecule intercalates between each of the CpG dinucleotide steps with its side chain lying in the major groove, and its protonated morpholino nitrogen partially occupying positions close to the N7 and O6 atoms of guanine G2. The morpholino group is disordered, the major conformer adopting a twisted boat conformation that makes van der Waals contact with the O4 oxygen of thymine T3. A water molecule forms bridging hydrogen bonds between the 4-carboxamide NH and the phosphate group of guanine G2. Sugar rings are found in alternating C3'-exo/C2'-endo conformations except for cytosine C1 which is C3'-endo. Intercalation perturbs helix winding throughout the hexanucleotide compared with B-DNA, steps 1 and 2 being unwound by 10 and 8 degrees, respectively, while the central TpA step is overwound by 11 degrees. An additional drug molecule lies at the end of each DNA helix linking it to the next duplex to form a continuously stacked structure. The protonated morpholino nitrogen of this 'end-stacked' drug hydrogen bonds to the N7 atom of guanine G6, and its conformationally disordered morpholino ring forms a C-H...O hydrogen bond with the guanine O6 oxygen. In both drug molecules the 4-carboxamide group is internally hydrogen bonded to the protonated N10 atom of the acridine ring. We discuss our findings with respect to the potential role played by the interaction of the drug side chain and the topoisomerase II protein in the poisoning of topoisomerase activity by the acridinecarboxamides.

Aminoacridines↗
PubMed1981

Comparative structural analysis of cytidine, ethenocytidine, and their protonated salts. I. Crystal and molecular structure of ethenocytidine.

The X-ray crystal and molecular structure of 3,N4-ethenocytidine (comes from Cyd) has been solved and refined on counter data to R = 0.038. A detailed discussion of the base electronic structure, molecular conformation and intermolecular interactions is the starting point for a comparative analysis of the series: Cyd, epsilon Cyd, Cyd . HCll and epsilon Cyd . HCl. Protonation changes the base electronic structure and results in a completely different molecular conformation and intermolecular interactions. Etheno-bridging does not alter the molecular conformation but it also changes the intermolecular interactions.

Cytidine↗
PubMed2003

NMR structure of an alpha-L-LNA:RNA hybrid: structural implications for RNase H recognition.

Alpha-L-LNA (alpha-L-ribo configured locked nucleic acid) is a nucleotide analogue that raises the thermostability of nucleic acid duplexes by up to approximately 4 degrees C per inclusion. We have determined the NMR structure of a nonamer alpha-L-LNA:RNA hybrid with three alpha-L-LNA modifications. The geometry of this hybrid is intermediate between A- and B-type, all nucleobases partake in Watson-Crick base pairing and base stacking, and the global structure is very similar to that of the corresponding unmodified hybrid. The sugar-phosphate backbone is rearranged in the vicinity of the modified nucleotides. As a consequence, the phosphate groups following the modified nucleotides are rotated into the minor groove. It is interesting that the alpha-L-LNA:RNA hybrid, which has an elevation in melting temperature of 17 degrees C relative to the corresponding DNA:RNA hybrid, retains the global structure of this hybrid. To our knowledge, this is the first example of such a substantial increase in melting temperature of a nucleic acid analogue that does not act as an N-type (RNA) mimic. alpha-L-LNA:RNA hybrids are recognised by RNase H with subsequent cleavage of the RNA strand, albeit with slow rates. We attempt to rationalise this impaired enzyme activity from the rearrangement of the sugar-phosphate backbone of the alpha-L-LNA:RNA hybrid.

Base Sequence↗
PubMed2004

SA-Search: a web tool for protein structure mining based on a Structural Alphabet.

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.

Amino Acid Sequence↗
PubMed2000

Structural characterization of protein-denaturant interactions: crystal structures of hen egg-white lysozyme in complex with DMSO and guanidinium chloride.

A variety of physico-chemical methods employ chemical denaturants to unfold proteins, and study different biophysical processes involved therein. Chemical denaturants are believed to induce unfolding by stabilizing the unfolded state of proteins over the folded state, either macroscopically or through specific interactions. In order to characterize the nature of specific interactions between proteins and denaturants, we have solved crystal structures of hen egg-white lysozyme complexed with denaturants, and report here dimethyl sulfoxide and guanidinium chloride complexes. The dimethyl sulfoxide molecules and guanidinium ions were seen to bind the protein at specific sites and were involved in characteristic interactions. They share a major binding site between them, the C site in the sugar binding cleft of the enzyme. Although the overall conformations of the complexes were very similar to the native structure, spectacular conformational changes were seen to occur locally. Temperature factors were also seen to drop dramatically in the local regions close to the denaturant binding sites. An interesting observation of the present study was the generation of a sodium ion binding site in hen egg-white lysozyme in the presence of denaturants, which was hitherto unknown in any of the other lysozyme structures solved so far. Loss of some of the crucial side chain-main chain interactions may form the initial events in lysozyme unfolding.

Animals↗
PubMed1996

What function for human lithostathine?: structural investigations by three-dimensional structure modeling and high-resolution NMR spectroscopy.

Human lithostathine is a 144-residue protein, expressed in various organs and pathologies. Several biological functions have been proposed for this protein. Among others, inhibition of nucleation and growth of CaCO3 crystals in the pancreas and bacterial aggregation has retained attention, because lithostathine presents high sequence similarities with calcium-dependent (or C-type) lectins. To study its structure-function relationship and compare it with that of C-type lectins, we have built a model for lithostathine. This model is derived from the only two C-type lectins of known structures: rat mannose binding protein and human E-selectin. An original strategy, inspired by that proposed by Havel and Snow, was designed for model building. We have undertaken NMR studies on the natural protein. Although complete structure determination has not yet been achieved, the NMR studies did confirm the main characteristics of the model. From analysis of the proposed model, we concluded that lithostathine is not expected to present sugar- or calcium-binding properties. Therefore, the mechanisms of bacterial aggregation and inhibition of CaCO3 nucleation and growth have not yet been elucidated.

Amino Acid Sequence↗
PubMed1994

Differential transcription, without replication, of non-structural and structural genes of human parvovirus B19 in the UT7/EPO cell as demonstrated by in situ hybridization.

Erythroid progenitor cells are the main target for B19 parvovirus infection. The UT7 cell line demonstrates a marked erythroid differentiation on induction by erythropoietin (EPO) (UT7/EPO cells) and therefore appears to be a potential target for B19 parvovirus. We aimed to evaluate the presence and localization of B19 nucleic acids in UT7/EPO cells by in situ hybridization. Three digoxigenin-labelled probes were used: two recognized specifically the non-structural region of the B19 genome and one probe was structural region-specific. In our experiment UT7/EPO cells were not permissive to B19 infection. Transcription led to nonstructural and structural gene transcripts without DNA replication or capsid protein synthesis.

Base Sequence↗
PubMed2004

Computed energetics of nucleotides in spatial ribozyme structures: an accurate identification of functional regions from structure.

Ribozymes are functionally diverse RNA molecules with intrinsic catalytic activity. Multiple structural and biochemical studies are required to establish which nucleotide bases are involved in the catalysis. The relative energetic properties of the nucleotide bases have been analyzed in a set of the known ribozyme structures. It was found that many of the known catalytic nucleotides can be identified using only the structure without any additional biochemical data. The results of the calculations compare well with the available biochemical data on RNA stability. Extensive in silico mutagenesis suggests that most of the nucleotides in ribozymes stabilize the RNA. The calculations show that relative contribution of the catalytic bases to RNA stability observably differs from contributions of the noncatalytic bases. Distinction between the concepts of "relative stability" and "mutational stability" is suggested. As results of prediction for several models of ribozymes appear to be in agreement with the published data on the potential active site regions, the method can potentially be used for prediction of functional nucleotides from nucleic sequence.

Catalytic Domain↗
PubMed2005

Structural basis of eukaryotic nitrate reduction: crystal structures of the nitrate reductase active site.

Nitrate assimilation in autotrophs provides most of the reduced nitrogen on earth. In eukaryotes, reduction of nitrate to nitrite is catalyzed by the molybdenum-containing NAD(P)H:nitrate reductase (NR; EC 1.7.1.1-3). In addition to the molybdenum center, NR contains iron-heme and flavin adenine dinucleotide as redox cofactors involved in an internal electron transport chain from NAD(P)H to nitrate. Recombinant, catalytically active Pichia angusta nitrate-reducing, molybdenum-containing fragment (NR-Mo) was expressed in P. pastoris and purified. Crystal structures for NR-Mo were determined at 1.7 and 2.6 angstroms. These structures revealed a unique slot for binding nitrate in the active site and identified key Arg and Trp residues potentially involved in nitrate binding. Dimeric NR-Mo is similar in overall structure to sulfite oxidases, with significant differences in the active site. Sulfate bound in the active site caused conformational changes, as compared with the unbound enzyme. Four ordered water molecules located in close proximity to Mo define a nitrate binding site, a penta-coordinated reaction intermediate, and product release. Because yeast NAD(P)H:NR is representative of the family of eukaryotic NR, we propose a general mechanism for nitrate reduction catalysis.

Animals↗
PubMed2006

Invarioms for improved absolute structure determination of light-atom crystal structures.

The determination of molecular absolute configuration from an X-ray analysis for structures that contain only light elements is challenging owing to the weak anomalous dispersion signal. The achievable precision of the Flack x parameter for such structures is therefore limited, especially when the independent-atom model is employed. Invariom modelling can improve this situation. Invarioms are theoretically predicted pseudoatoms within the Hansen & Coppens multipole formalism. They are transferable from one molecule to another and provide generalized aspherical atomic form factors. It is shown that, by application of the invariom approach, the precision and standard uncertainty of the Flack x parameter and therefore the reliability of deducing molecular chirality in an absolute structure determination can be improved.

Crystallography, X-Ray↗
PubMed2001

Avian haemoglobins and structural basis of high affinity for oxygen: structure of bar-headed goose aquomet haemoglobin.

Haemoglobin from the bar-headed goose (Anser indicus) has higher oxygen affinity than that from its lowland relatives such as greylag goose (A. anser). The crystal structure of bar-headed goose aquomet haemoglobin was determined at 2.3 A resolution and compared with the structures of the goose oxy, human, horse and other avian haemoglobins and the sequences of other avian haemoglobins. Four amino-acid residues differ between greylag goose and bar-headed goose haemoglobins, among which Alaalpha119 and Aspbeta125 in bar-headed goose haemoglobin reduces the contacts between the alpha(1) and beta(1) subunits compared with Pro and Glu, respectively, and therefore may increase the oxygen affinity by loosening the alpha(1)beta(1) interface. Compared with human oxy haemoglobin, the relative orientation of two alphabeta dimers in the bar-headed goose aquomet and oxy Hbs are rotated by about 4 degrees, indicating a unique quaternary structural difference from the typical R state. This new 'R(H)' state is probably correlated with the higher oxygen affinity of bar-headed goose haemoglobin.

Animals↗
PubMed2002

Structures of V45E and V45Y mutants and structure comparison of a variety of cytochrome b5 mutants.

Val45 is a highly conserved residue and a component of the heme-pocket wall of cytochrome b(5). The crystal structures of cytochrome b(5) mutants V45E and V45Y have been determined at high resolution. Their overall structures were very similar to that of the wild-type protein. However, Val45 of the wild-type protein points towards the heme, but the large side chains of both Glu45 and Tyr45 of the mutants point towards the solvent. A channel is thus opened and the hydrophobicity of the heme pocket is decreased. The rotation of the porphyrin ring and the conformational change of the axial ligand His39 in the V45Y mutant indicate that the microenvironment of the heme is disturbed because of the mutation. The binding constants and the electron-transfer rates between cytochrome b(5) and cytochrome c decrease owing to the mutation, which can be accounted for by molecular modeling: the inter-iron distances increase in order to eliminate the unreasonably close contacts resulting from the large volumes of the mutated side chains. The influence of the mutations on the redox potentials and protein stability is also discussed. The structures of seven mutants of cytochrome b(5) are compared with each other and the effects of these mutations on the protein properties and functions are summarized.

Binding Sites↗
PubMed2004

Structure of potato calmodulin PCM6: the first report of the three-dimensional structure of a plant calmodulin.

The crystal structure of a potato calmodulin (PCM6) was solved by molecular replacement and refined to a crystallographic R factor of 22.8% (R(free) = 25.0%) using X-ray diffraction data in the resolution range 8.0-2.0 A. This is the first report of the three-dimensional structure of a plant Ca(2+)-calmodulin. PCM6 crystallizes in a crystal form that belongs to space group P2(1)2(1)2(1), which is different to that of most other calmodulin crystals. The main structural difference between PCM6 and the other calmodulins is in the central helix region and appears to be caused by crystal packing. The surface properties of PCM6 molecules were compared with those of animal calmodulins, which provided an explanation for the unique crystal-packing state of PCM6.

Amino Acid Sequence↗
PubMed2004

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.

The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms. The SSM results are compared with those obtained from other protein comparison servers, and the advantages and disadvantages of different scores that are used for structure recognition are discussed. A new score, balancing the r.m.s.d. and alignment length Nalign, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and Nalign.

Algorithms↗
PubMed2005

Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.

In order to understand the induced fit and the thermostabilization mechanisms of ATP-dependent phosphoenolpyruvate carboxykinase, the crystal structure of the enzyme from the extreme thermophile Thermus thermophilus HB8 (TtPEPCK) was determined and compared with those of orthologues of known structure from two mesophilic organisms. The protomer structures in these orthologues, which exhibit open/closed interdomain conformations, are similar. Isomorphous crystals of unliganded and ATP-bound TtPEPCK were obtained. The asymmetric units of both crystal forms contain two protomers A and B with closed and open conformations, respectively. ATP was only observed in the interdomain cleft of the closed protomer, suggesting that the induced fit of TtPEPCK agrees with the so-called ;conformational selection' mechanism where ligand binding is not essential for domain closure although its binding leads to the stabilization of the closed state. A bound calcium observed in the N-terminal domain of TtPEPCK probably contributes to the thermal stability. A combination of hydrophobic effects, ion pairs and entropic effects might also contribute to the thermostability of TtPEPCK.

Amino Acid Sequence↗