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Determined Structure (determine + structure)
Selected AbstractsThe Identity of European Law: Mapping Out the European Legal SpaceEUROPEAN LAW JOURNAL, Issue 2 2000Christopher Harding The main purpose of this discussion is to supply some content to the concept of the ,European legal space' at the turn of the twentieth century. The term ,legal space' is used in preference to ,legal system' or ,systems' in order to convey a sense of the complex, non-hierarchical, overlapping, interlocking and evolutionary character of contemporary European legal phenomena. A number of evident legal orders may be identified within the overall European space: those of the EC, the EU, the EEA, the Council of Europe and the OSCE, although to refer to some of these as ,orders' may be misleading, by implying too much in terms of a centrally determined structure. It is also possible to point to less evident legal ordering, such as the process of norm exportation contained in the Europe Agreements concluded between the EU and individual non-Member States, or the kind of order resulting from transatlantic co-operation in fields such as criminal justice (which also challenges the description of ,European'). In juristic terms, the argument here confronts the primacy traditionally accorded to the sovereign state in the field of law-making, and draws upon two non-juridical models of analysis: that of multi-level governance, as used by political scientists to indicate a shift away from the exclusive authority and legitimacy claimed by sovereign states; and the biological model of catalytic closure, used to indicate evolution through a process of spontaneous reactions within a body. Both models may be usefully employed to probe the dynamics of European legal ordering at the close of the Twentieth Century. [source] The crystal structure of a xyloglucan-specific endo-,-1,4-glucanase from Geotrichum sp.FEBS JOURNAL, Issue 18 2009M128 xyloglucanase reveals a key amino acid residue for substrate specificity Geotrichum sp. M128 possesses two xyloglucan-specific glycoside hydrolases belonging to family 74, xyloglucan-specific endo-,-1,4-glucanase (XEG) and oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH). Despite their similar amino acid sequences (48% identity), their modes of action and substrate specificities are distinct. XEG catalyzes the hydrolysis of xyloglucan polysaccharides in endo mode, while OXG-RCBH acts on xyloglucan oligosaccharides at the reducing end in exo mode. Here, we determined the crystal structure of XEG at 2.5 Å resolution, and compared it to a previously determined structure of OXG-RCBH. For the most part, the amino acid residues that interact with substrate are conserved between the two enzymes. However, there are notable differences at subsite positions ,1 and +2. OXG-RCBH has a loop around the +2 site that blocks one end of the active site cleft, which accounts for its exo mode of action. In contrast, XEG lacks a corresponding loop at this site, thereby allowing binding to the middle of the main chain of the substrate. At the ,1 site in OXG-RCBH, Asn488 interacts with the xylose side chain of the substrate, whereas the ,1 site is occupied by Tyr457 in XEG. To confirm the contribution of this residue to substrate specificity, Tyr457 was substituted by Gly in XEG. The wild-type XEG cleaved the oligoxyloglucan at a specific site; the Y457G variant cleaved the same substrate, but at various sites. Together, the absence of a loop in the cleft and the presence of bulky Tyr457 determine the substrate specificity of XEG. [source] Comparison of DNA Complex Formation Behaviour for Two Closely Related Lexitropsin AnaloguesHELVETICA CHIMICA ACTA, Issue 5 2009Abstract Two closely related lexitropsin analogues that differ only in the form of the ,headgroup' functionality (CHO (for 1) vs. Ac (for 2)) have been studied in their DNA-binding capacity for the sequence d(GCATATATGC) using 1H-NMR spectroscopy. DNA-Complex formation for the CHO derivative was apparent from the observation of new NMR signals on titration of DNA with ligand. Detailed investigation and assignment of the data for a ligand/DNA-duplex ratio of 2,:,1 clearly delineated the structure as one associated with the ,minor groove' class of DNA complexes. The structure of the complex was determined on the basis of the acquired NMR data. Features characteristic of typical 2,:,1 minor-groove complexes were apparent. In a similar experimental approach, the Ac analogue ligand,DNA binding response was investigated. Despite the close similarity in chemical structure to the CHO case, the Ac analogue was found to produce NMR data of a much poorer quality. This was attributed to more rapid on/off chemical exchange equilibrium between ligand and DNA. From close analysis and comparison of the NMR data for the ,Ac' and ,CHO' headgroup ligand,DNA complexes, it was possible to ascertain that the same type of complex formed in each case but with different relative binding constants. Consideration of the nature and form of these complexes has been made with reference to a previously determined structure from our laboratory for the related lexitropsin analogue thiazotropsin A. [source] A computational study of the crystal and electronic structure of the room temperature organometallic ferromagnet V(TCNE)2,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2008Anderi L. Tchougréeff Abstract We study numerically the crystal and electronic structure of the room temperature organometallic ferromagnet of general composition V(TCNE)x × y solvent with x , 2, starting from both the experimental structure of its iron analog which results from the EXAFS experiment as well as the theoretical model structure compatible with magnetic measurements on this type of compounds. The results of the numerical study performed at the density functional level of theory show that the experimentally determined structure complies with the magnetic measurements and thus can serve as a prototype structure for the entire family of the M(TCNE)2 organometallic magnets. Both the results of the numerical study and the magnetic experiments are interpreted using a proposed model Hamiltonian. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Minimum sequence requirements for selective RNA-ligand binding: A molecular mechanics algorithm using molecular dynamics and free-energy techniquesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2006Peter C. Anderson Abstract In vitro evolution techniques allow RNA molecules with unique functions to be developed. However, these techniques do not necessarily identify the simplest RNA structures for performing their functions. Determining the simplest RNA that binds to a particular ligand is currently limited to experimental protocols. Here, we introduce a molecular-mechanics based algorithm employing molecular dynamics simulations and free-energy methods to predict the minimum sequence requirements for selective ligand binding to RNA. The algorithm involves iteratively deleting nucleotides from an experimentally determined structure of an RNA-ligand complex, performing energy minimizations and molecular dynamics on each truncated structure, and assessing which truncations do not prohibit RNA binding to the ligand. The algorithm allows prediction of the effects of sequence modifications on RNA structural stability and ligand-binding energy. We have implemented the algorithm in the AMBER suite of programs, but it could be implemented in any molecular mechanics force field parameterized for nucleic acids. Test cases are presented to show the utility and accuracy of the methodology. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source] The structure of receptor-associated protein (RAP)PROTEIN SCIENCE, Issue 8 2007Donghan Lee Abstract The receptor-associated protein (RAP) is a molecular chaperone that binds tightly to certain newly synthesized LDL receptor family members in the endoplasmic reticulum (ER) and facilitates their delivery to the Golgi. We have adopted a divide-and-conquer strategy to solve the structures of the individual domains of RAP using NMR spectroscopy. We present here the newly determined structure of domain 2. Based on this structure and the structures of domains 1 and 3, which were solved previously, we utilized experimental small-angle neutron scattering (SANS) data and a novel simulated annealing protocol to characterize the overall structure of RAP. The results reveal that RAP adopts a unique structural architecture consisting of three independent three-helix bundles that are connected by long and flexible linkers. The flexible linkers and the quasi-repetitive structural architecture may allow RAP to adopt various possible conformations when interacting with the LDL receptors, which are also made of repetitive substructure units. [source] High resolution structure of the HDGF PWWP domain: A potential DNA binding domainPROTEIN SCIENCE, Issue 2 2006Stephen M. Lukasik Abstract Hepatoma Derived Growth Factor (HDGF) is an endogenous nuclear-targeted mitogen that is linked with human disease. HDGF is a member of the weakly conserved PWWP domain family. This 70,amino acid motif, originally identified from the WHSC1 gene, has been found in more than 60 eukaryotic proteins. In addition to the PWWP domain, many proteins in this class contain known chromatin remodeling domains, suggesting a role for HDGF in chromatin remodeling. We have determined the NMR structure of the HDGF PWWP domain to high resolution using a combination of NOEs, J-couplings, and dipolar couplings. Comparison of this structure to a previously determined structure of the HDGF PWWP domain shows a significant difference in the C-terminal region. Comparison to structures of other PWWP domains shows a high degree of similarity to the PWWP domain structures from Dnmt3b and mHRP. The results of selected and amplified binding assay and NMR titrations with DNA suggest that the HDGF PWWP domain may function as a nonspecific DNA-binding domain. Based on the NMR titrations, we propose a model of the interaction of the PWWP domain with DNA. [source] Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domainPROTEIN SCIENCE, Issue 8 2005Charmaine Hoang Abstract The pseudouridine synthase TruB is responsible for the universally conserved post-transcriptional modification of residue 55 of elongator tRNAs. In addition to the active site, the "thumb," a peripheral domain unique to the TruB family of enzymes, makes extensive interactions with the substrate. To coordinate RNA binding and release with catalysis, the thumb may be able to sense progress of the reaction in the active site. To establish whether there is a structural correlate of communication between the active site and the RNA-sequestering thumb, we have solved the structure of a catalytically inactive point mutant of TruB in complex with a substrate RNA, and compared it to the previously determined structure of an active TruB bound to a reaction product. Superposition of the two structures shows that they are extremely similar, except in the active site and, intriguingly, in the relative position of the thumb. Because the two structures were solved using isomorphous crystals, and because the thumb is very well ordered in both structures, the displacement of the thumb we observe likely reflects preferential propagation of active site perturbations to this RNA-binding domain. One of the interactions between the active site and the thumb involves an active site residue whose hydrogen-bonding status changes during the reaction. This may allow the peripheral RNA-binding domain to monitor progress of the pseudouridylation reaction. [source] Induced fit in guanidino kinases,comparison of substrate-free and transition state analog structures of arginine kinasePROTEIN SCIENCE, Issue 1 2003Mohammad S. Yousef Abstract Arginine kinase (AK) is a member of the guanidino kinase family that plays an important role in buffering ATP concentration in cells with high and fluctuating energy demands. The AK specifically catalyzes the reversible phosphoryl transfer between ATP and arginine. We have determined the crystal structure of AK from the horseshoe crab (Limulus polyphemus) in its open (substrate-free) form. The final model has been refined at 2.35 Å with a final R of 22.3% (Rfree = 23.7%). The structure of the open form is compared to the previously determined structure of the transition state analog complex in the closed form. Classically, the protein would be considered two domain, but dynamic domain (DynDom) analysis shows that most of the differences between the two structures can be considered as the motion between four rigid groups of nonsequential residues. ATP binds near a cluster of positively charged residues of a fixed dynamic domain. The other three dynamic domains close the active site with separate hinge rotations relative to the fixed domain. Several residues of key importance for the induced motion are conserved within the phosphagen kinase family, including creatine kinase. Substantial conformational changes are induced in different parts of the enzyme as intimate interactions are formed with both substrates. Thus, although induced fit occurs in a number of phosphoryl transfer enzymes, the conformational changes in phosphagen kinases appear to be more complicated than in prior examples. [source] Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2010Jeremy D. Wilbur Huntingtin-interacting protein 1 (HIP1) is an important link between the actin cytoskeleton and clathrin-mediated endocytosis machinery. HIP1 has also been implicated in the pathogenesis of Huntington's disease. The binding of HIP1 to actin is regulated through an interaction with clathrin light chain. Clathrin light chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. To understand the mechanism of this conformational regulation, a high-resolution crystal structure of a stable fragment from the HIP1 coiled-coil domain was determined. The flexibility of the HIP1 coiled-coil region was evident from its variation from a previously determined structure of a similar region. A hydrogen-bond network and changes in coiled-coil monomer interaction suggest that the HIP1 coiled-coil domain is uniquely suited to allow conformational flexibility. [source] Heterogeneity and dynamics in villin headpiece crystal structuresACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2009Jianmin Meng The villin headpiece domain (HP67) is the C-terminal F-actin-binding motif that confers F-actin-bundling activity to villin, a component of the actin bundles that support the brush-border microvilli. It has been investigated extensively by both experimental and theoretical measurements. Our laboratory, for example, has determined both its NMR and its crystal structures. This study presents the structures of HP67 and its pH-stabilized mutant (H41Y) in a different crystal form and space group. For both constructs, two molecules are found in each asymmetric unit in the new space group P61. While one of the two structures (Mol A) is structurally similar to our previously determined structure (Mol X), the other (Mol B) has significant deviations, especially in the N-terminal subdomain, where lattice contacts do not appear to contribute to the difference. In addition, the structurally most different crystal structure, Mol B, is actually closer to the averaged NMR structure. Harmonic motions, as suggested by the B -factor profiles, differ between these crystal structures; crystal structures from the same space group share a similar pattern. Thus, heterogeneity and dynamics are observed in different crystal structures of the same protein even for a protein as small as villin headpiece. [source] Structural studies of glucose-6-phosphate and NADP+ binding to human glucose-6-phosphate dehydrogenaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2005Sheila Gover Human glucose-6-phosphate dehydrogenase (G6PD) is NADP+ -dependent and catalyses the first and rate-limiting step of the pentose phosphate shunt. Binary complexes of the human deletion mutant, ,G6PD, with glucose-6-phosphate and NADP+ have been crystallized and their structures solved to 2.9 and 2.5,Å, respectively. The structures are compared with the previously determined structure of the Canton variant of human G6PD (G6PDCanton) in which NADP+ is bound at the structural site. Substrate binding in ,G6PD is shown to be very similar to that described previously in Leuconostoc mesenteroides G6PD. NADP+ binding at the coenzyme site is seen to be comparable to NADP+ binding in L. mesenteroides G6PD, although some differences arise as a result of sequence changes. The tetramer interface varies slightly among the human G6PD complexes, suggesting flexibility in the predominantly hydrophilic dimer,dimer interactions. In both complexes, Pro172 of the conserved peptide EKPxG is in the cis conformation; it is seen to be crucial for close approach of the substrate and coenzyme during the enzymatic reaction. Structural NADP+ binds in a very similar way in the ,G6PD,NADP+ complex and in G6PDCanton, while in the substrate complex the structural NADP+ has low occupancy and the C-terminal tail at the structural NADP+ site is disordered. The implications of possible interaction between the structural NADP+ and G6P are considered. [source] The 1.4,Å resolution structure of Paracoccus pantotrophus pseudoazurinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010Shabir Najmudin Pseudoazurins are small type 1 copper proteins that are involved in the flow of electrons between various electron donors and acceptors in the bacterial periplasm, mostly under denitrifying conditions. The previously determined structure of Paracoccus pantotrophus pseudoazurin in the oxidized form was improved to a nominal resolution of 1.4,Å, with R and Rfree values of 0.188 and 0.206, respectively. This high-resolution structure makes it possible to analyze the interactions between the monomers and the solvent structure in detail. Analysis of the high-resolution structure revealed the structural regions that are responsible for monomer,monomer recognition during dimer formation and for protein,protein interaction and that are important for partner recognition. The pseudoazurin structure was compared with other structures of various type 1 copper proteins and these were grouped into families according to similarities in their secondary structure; this may be useful in the annotation of copper proteins in newly sequenced genomes and in the identification of novel copper proteins. [source] Structures of the Reactive Intermediates in Organocatalysis with Diarylprolinol EthersHELVETICA CHIMICA ACTA, Issue 7 2009Abstract Structures of the reactive intermediates (enamines and iminium ions) of organocatalysis with diarylprolinol derivatives have been determined. To this end, diarylprolinol methyl and silyl ethers, 1, and aldehydes, PhCH2CHO, tBuCH2CHO, PhCH=CHCHO, are condensed to the corresponding enamines, A and 3 (Scheme,2), and cinnamoylidene iminium salts, B and 4 (Scheme,3). These are isolated and fully characterized by melting/decomposition points, [,]D, elemental analysis, IR and NMR spectroscopy, and high-resolution mass spectrometry (HR-MS). Salts with BF4, PF6, SbF6, and the weakly coordinating Al[OC(CF3)3]4 anion were prepared. X-Ray crystal structures of an enamine and of six iminium salts have been obtained and are described herein (Figs.,2 and 4,8, and Tables,2 and 7) and in a previous preliminary communication (Helv. Chim. Acta2008, 91, 1999). According to the NMR spectra (in CDCl3, (D6)DMSO, (D6)acetone, or CD3OD; Table,1), the major isomers 4 of the iminium salts have (E)-configuration of the exocyclic NC(1,) bond, but there are up to 11% of the (Z)-isomer present in these solutions (Fig.,1). In all crystal structures, the iminium ions have (E)-configuration, and the conformation around the exocyclic N-CC-O bond is synclinal-exo (cf.C and L), with one of the phenyl groups over the pyrrolidine ring, and the RO group over the , -system. One of the meta -substituents (Me in 4b, CF3 in 4c and 4e) on a 3,5-disubstituted phenyl group is also located in the space above the , -system. DFT Calculations at various levels of theory (Tables,3,6) confirm that the experimentally determined structures (cf. Fig.,10) are by far (up to 8.3,kcal/mol) the most stable ones. Implications of the results with respect to the mechanism of organocatalysis by diarylprolinol derivatives are discussed. [source] Practical modeling of molecular systems with symmetriesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2010Sergei Grudinin Abstract A new method for efficient modeling of macromolecular systems with symmetries is presented. The method is based on a hierarchical representation of the molecular system and a novel fast binary tree-based neighbor list construction algorithm. The method supports all types of molecular symmetry, including crystallographic symmetry. Testing the proposed neighbor list construction algorithm on a number of different macromolecular systems containing up to about 200,000 of atoms shows that (1) the current binary tree-based neighbor list construction algorithm scales linearly in the number of atoms for the central subunit, and sublinearly for its replicas, (2) the overall computational overhead of the method for a system with symmetry with respect to the same system without symmetry scales linearly with the cutoff value and does not exceed 50% for all but one tested macromolecules at the cutoff distance of 12 Å. (3) the method may help produce optimized molecular structures that are much closer to experimentally determined structures when compared with the optimization without symmetry, (4) the method can be applied to models of macromolecules with still unknown detailed structure. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] The plasma von Willebrand factor O -glycome comprises a surprising variety of structures including ABH antigens and disialosyl motifsJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 1 2010K. CANIS Summary.,Background: von Willebrand factor (VWF) is a key component for maintenance of normal hemostasis. Its glycan moieties, accounting for about 20% of its molecular weight, have been shown to affect many of its properties. Previous studies reported correlations between VWF secretion, half-life and the nature or presence of its N -glycans, and more importantly between VWF plasma level and the type of N -linked ABH antigens. Despite the presence of 10 predicted O -glycosylation sites, the O -glycome remains poorly characterized, impairing the complete elucidation of its influence on VWF functions. So far only a single glycan structure, a disialyl core 1 glycan, has been identified. Objectives: To define an exhaustive profile of the VWF O -glycan structures to help the understanding of their role in VWF regulation and properties. Methods: Plasma-derived VWF O -linked sugars were isolated and analyzed using state-of-the-art mass spectrometry methodologies. Results and conclusions: We provide here a detailed analysis of the human plasma-derived VWF O -glycome. Eighteen O -glycan structures including both core 1 and core 2 structures are now demonstrated to be present on VWF. Amongst the newly determined structures are unusual tetra-sialylated core 1 O -glycans and ABH antigen-containing core 2 O -glycans. In conjunction with current models explaining VWF activity, knowledge of the complete O -glycome will facilitate research aimed at providing a better understanding of the influence of glycosylation on VWF functions. [source] How well can the accuracy of comparative protein structure models be predicted?PROTEIN SCIENCE, Issue 11 2008David Eramian Comparative structure models are available for two orders of magnitude more protein sequences than are experimentally determined structures. These models, however, suffer from two limitations that experimentally determined structures do not: They frequently contain significant errors, and their accuracy cannot be readily assessed. We have addressed the latter limitation by developing a protocol optimized specifically for predicting the C, root-mean-squared deviation (RMSD) and native overlap (NO3.5Å) errors of a model in the absence of its native structure. In contrast to most traditional assessment scores that merely predict one model is more accurate than others, this approach quantifies the error in an absolute sense, thus helping to determine whether or not the model is suitable for intended applications. The assessment relies on a model-specific scoring function constructed by a support vector machine. This regression optimizes the weights of up to nine features, including various sequence similarity measures and statistical potentials, extracted from a tailored training set of models unique to the model being assessed: If possible, we use similarly sized models with the same fold; otherwise, we use similarly sized models with the same secondary structure composition. This protocol predicts the RMSD and NO3.5Å errors for a diverse set of 580,317 comparative models of 6174 sequences with correlation coefficients (r) of 0.84 and 0.86, respectively, to the actual errors. This scoring function achieves the best correlation compared to 13 other tested assessment criteria that achieved correlations ranging from 0.35 to 0.71. [source] Free energy determinants of tertiary structure and the evaluation of protein modelsPROTEIN SCIENCE, Issue 11 2000Donald Petrey Abstract We develop a protocol for estimating the free energy difference between different conformations of the same polypeptide chain. The conformational free energy evaluation combines the CHARMM force field with a continuum treatment of the solvent. In almost all cases studied, experimentally determined structures are predicted to be more stable than misfolded "decoys." This is due in part to the fact that the Coulomb energy of the native protein is consistently lower than that of the decoys. The solvation free energy generally favors the decoys, although the total electrostatic free energy (sum of Coulomb and solvation terms) favors the native structure. The behavior of the solvation free energy is somewhat counterintuitive and, surprisingly, is not correlated with differences in the burial of polar area between native structures and decoys. Rather, the effect is due to a more favorable charge distribution in the native protein, which, as is discussed, will tend to decrease its interaction with the solvent. Our results thus suggest, in keeping with a number of recent studies, that electrostatic interactions may play an important role in determining the native topology of a folded protein. On this basis, a simplified scoring function is derived that combines a Coulomb term with a hydrophobic contact term. This function performs as well as the more complete free energy evaluation in distinguishing the native structure from misfolded decoys. Its computational efficiency suggests that it can be used in protein structure prediction applications, and that it provides a physically well-defined alternative to statistically derived scoring functions. [source] Dynamics of the Hck-SH3 domain: Comparison of experiment with multiple molecular dynamics simulationsPROTEIN SCIENCE, Issue 1 2000David A. Horita Abstract Molecular dynamics calculations provide a method by which the dynamic properties of molecules can be explored over timescales and at a level of detail that cannot be obtained experimentally from NMR or X-ray analyses. Recent work (Philippopoulos M, Mandel AM, Palmer AG III, Lim C, 1997, Proteins 28:481,493) has indicated that the accuracy of these simulations is high, as measured by the correspondence of parameters extracted from these calculations to those determined through experimental means. Here, we investigate the dynamic behavior of the Src homology 3 (SH3) domain of hematopoietic cell kinase (Hck) via 15N backbone relaxation NMR studies and a set of four independent 4 ns solvated molecular dynamics calculations. We also find that molecular dynamics simulations accurately reproduce fast motion dynamics as estimated from generalized order parameter (S2) analysis for regions of the protein that have experimentally well-defined coordinates (i.e., stable secondary structural elements). However, for regions where the coordinates are not well defined, as indicated by high local root-mean-square deviations among NMR-determined structural family members or high B -factors/low electron density in X-ray crystallography determined structures, the parameters calculated from a short to moderate length (less than 5,10 ns) molecular dynamics trajectory are dependent on the particular coordinates chosen as a starting point for the simulation. [source] Prediction of the crystal structures of perovskites using the software program SPuDSACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2001Michael W. Lufaso The software program SPuDS has been developed to predict the crystal structures of perovskites, including those distorted by tilting of the octahedra. The user inputs the composition and SPuDS calculates the optimal structure in ten different Glazer tilt systems. This is performed by distorting the structure to minimize the global instability index, while maintaining rigid octahedra. The location of the A -site cation is chosen so as to maximize the symmetry of its coordination environment. In its current form SPuDS can handle up to four different A -site cations in the same structure, but only one octahedral ion. Structures predicted by SPuDS are compared with a number of previously determined structures to illustrate the accuracy of this approach. SPuDS is also used to examine the prospects for synthesizing new compounds in tilt systems with multiple A -site coordination geometries (a+a+a+, a0b+b+, a0b,c+). [source] ,-Peroxo-bis[trans -chloro(1,4,8,11-tetraazacyclotetradecane)cobalt(III)] bis(tetraphenylborate) diacetone solvateACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2001Gareth R. Lewis The title complex, [Co2Cl2(,-O2)(cyclam)2](C24H20B)2·2Me2CO, was obtained when [Co(cyclam)Cl2](BPh4)2 was crystallized from acetone in air; cyclam is 1,4,8,11-tetraazacyclotetradecane, C10H24N4. The peroxo O,O moiety straddles a crystallographic centre of inversion (the two octahedral Co atoms are symmetrically bridged by the O2 moiety), hence only half of the complex cation is in the asymmetric unit. A comparison of the O,O [1.483,(3),Å], Co,Cl [2.2647,(8),Å] and Co,O [1.894,(2),Å] bond lengths with similar bonds in previously determined structures indicates the oxidation of CoII to CoIII during the crystallization process. In the crystal lattice, cation dimers are encapsulated by six [BPh4], anions, with C,H,, hydrogen bonds between the cyclam methylene groups and the phenyl rings of the anion. [source] Protein flexibility: coordinate uncertainties and interpretation of structural differencesACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2009Alexander A. Rashin Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent `noise', showing that some previous interpretations of protein coordinate changes attributed to external conditions or mutations may be doubtful or erroneous. The use of uncertainty thresholds, DDMs, the newly introduced CDDMs (contact distance difference matrices) and a novel simple rotation algorithm allows a more meaningful classification and description of protein motions, distinguishing between various rigid-fragment motions and nonrigid conformational deformations. It is also shown that half of 75 pairs of identical molecules, each from the same asymmetric crystallographic cell, exhibit coordinate differences that range from just outside the coordinate uncertainty threshold to the full magnitude of large functional movements. Thus, crystallization might often induce protein conformational changes that are comparable to those related to or induced by the protein function. [source] Structure of the nucleotide-binding domain of Plasmodium falciparum Rab6 in the GDP-bound formACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2000Debasish Chattopadhyay Rab proteins are small Ras-like GTPases which play important roles in regulating intracellular vesicle trafficking. The nucleotide-binding domain of Rab6 from the malaria parasite Plasmodium falciparum was crystallized with GDP bound to the active site. The MAD phasing technique was used to determine the crystal structure to 2.3,Å resolution. Comparisons of the structure of GDP-bound PfRab6 with the recently determined structures of Rab3A in complex with either a GTP analog or with GTP and Rabphillin present structural evidence supporting the traditional model for the molecular GTP/GDP switch in Rab proteins. PfRab6 residues homologous to those distinguishing human Rab6 isoforms, which differ in binding to Rabkinesin-6 in human cells, are located next to the recognized complementarity-determining region (CDR) and constitute a conceptual broadening of that domain. Despite significant observable differences in Golgi ultrastructure, the Rab6 core structure and switch mechanism appear highly conserved when compared with murine Rab3a structures. A significant difference between the PfRab6 and higher eukaryotic Rabs may be the lack of CDR features that allow binding interactions with Rabkinesin-type effectors. [source] Structures and Vibrational Spectra of the Sulfur-Rich Oxides SnO (n = 4,9): The Importance of ,*,,* InteractionsCHEMISTRY - A EUROPEAN JOURNAL, Issue 2 2007Wah Wong Prof. Abstract The structures of a large number of isomers of the sulfur oxides SnO with n = 4,9 have been calculated at the G3X(MP2) level of theory. In most cases, homocyclic molecules with exocyclic oxygen atoms in an axial position are the global minimum structures. Perfect agreement is obtained with experimentally determined structures of S7O and S8O. The most stable S4O isomer as well as some less stable isomers of S5O and S6O are characterized by a strong ,*,,* interaction between SO and SS groups, which results in relatively long SS bonds with internuclear distances of 244,262,pm. Heterocyclic isomers are less stable than the global minimum structures, and this energy difference approximately increases with the ring size: 17 (S4O), 40 (S5O), 32 (S6O), 28 (S7O), 45 (S8O), and 54,kJ,mol,1 (S9O). Owing to a favorable ,*,,* interaction, preference for an axial (or endo) conformation is calculated for the global energy minima of S7O, S8O, and S9O. Vapor-phase decomposition of SnO molecules to SO2 and S8 is strongly exothermic, whereas the formation of S2O and S8 is exothermic if n<7, but slightly endothermic for S7O, S8O, and S9O. The calculated vibrational spectra of the most stable isomers of S6O, S7O, and S8O are in excellent agreement with the observed data. [source] | |||||||||||||||||||||||||