D I Svergun

..The SAXS data revealed that IRp60 is monomeric in solution with a molecular shape characteristic of the immunoglobulin-like structures. A homology model of IRp60 was built and validated experimentally against the SAXS data...

..The results support a model of activation that is consistent with most of the biochemical observations...

..The present study pinpoints loop II of NGF to be an important structural determinant for NGF biological activity mediated by TrkA receptor...

..The efficiency of these methods is illustrated by recent applications to biological macromolecules and nanocomposite particles...

..The new method substantially improves the resolution and reliability of models derived from scattering data and makes solution scattering a useful technique in large-scale structural characterization of proteins...

..The solution structure of the long ncd construct (MC1) including complete N-terminal coiled-coil and motor domains is modeled by adding a straight coiled-coil section to the model of MC5...

..Substantial progress has also been made in the quantitative analysis and modelling of assembly and folding processes, and intermolecular interactions...

..The protein-rRNA map enlarges the basis for the models of the rRNA folding and can further help to localize proteins in high-resolution crystallographic density maps...

..Possibilities of synergistic use of the method with other techniques are considered...

..58 and 1.53 nm, respectively) were required. A clear correlation was observed between the magnitude of the distortions induced by the crystal environment and the interfacial area between subunits...

..Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data...

..Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces...

..Implications of the combined use of synchrotron-based circular dichroism spectropolarimetry and X-ray scattering in structural biology and proteomics are discussed...

..Potential DNA binding surfaces of sigma54 are also predicted by comparison with the sigma54 core binding fragment...

..The constructed models of these assemblies provided support for a model of vertex assembly onto the virion. Although similar in overall architecture, clear differences between PRD1 and adenovirus spike assemblies have been revealed...

..This flexibility may be important for biological activity and for the formation of alphaB-crystallin complexes of variable sizes and compositions...

..2 nm for the recombinant protein, indicating a more extended structure in solution than that derived from the recent NMR data [Peterson, C.W., Narula, S.S. & Armitage, I.A. (1996) FEBS Lett. 379, 85-93]...

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..After validation in simulated examples, the methods have been applied to add missing loops or domains to several proteins where partial structures were available...

..14 nm away from the molecular center along this axis...

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..Thermostability of the hexameric form of the nitrite reductase is characterized in terms of thermoinactivation and thermodenaturation...

..One major difference is the tendency of Balf2DeltaC to dimerize on different surfaces to that used for oligomerization when binding to ssDNA, and this may have implications for the mechanism of replication initiation...

..Examples of the application of the various methods are given...

..These results suggest that the extended structure of Pex5p may play a role in interactions with other substrates such as lipids and membrane proteins during the formation of functional multiprotein complexes...

..The efficiency of the methods is demonstrated in model examples, and potential sources of ambiguity are discussed...

..In the latter case, EOM is able to distinguish between rigid and flexible proteins and to directly assess the interdomain contacts...

..However, the relative arrangement of the EG and C subunits in solution is more open than that in the holoenzyme, suggesting a conformational change of EGC during regulatory assembly and disassembly...

..Domains 3 and 4 were found to be in close contact, whereas domains 2 and especially 1 had loose contacts with the rest of the protein...

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..The methods described are implemented in publicly available computer programs running on major hardware platforms...

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..The holoenzyme model allows for independent catalytic activity of the alpha beta protomers, which is consistent with the available biochemical evidence...

..2-3.4 nm between their axes. The ULF appears to be a dynamic and a relatively loosely packed structure with a roughly even mass distribution over its cross-section...

..These results suggest a possible role of telethonin in linking titin filaments at the Z-disk periphery...

..Notably, the UBA domain has the same unusual conformation as in MARK2, and it binds at the same site. Remarkable differences occur in the catalytic domain at helix C, the catalytic loop, and the activation segment...

..The proposed methodology for assessment of low-resolution structures and interactions is a powerful means for rational design of PEGylated therapeutic agents...

..The dimer in solution differs from the active form observed in the crystal, resembling instead the model of the inactive full-length response regulator PhoB...

..Consequently, at the elevated protein concentrations in the crowded environment inside the cell the observed tetramer may constitute the biologically relevant functional unit of the enzyme...

..This finding suggests that Rd behaves as an independent domain and is freely available to participate in redox reactions with protein partners...

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..Our results suggest that glucoamylase functions via transient dimer formation during hydrolysis of insoluble substrates and address the question of the cooperative effect of starch binding and hydrolysis...

..Simulations show that C c samples about half of the surface area of adrenodoxin. It is concluded that the complex of Adx/C c is entirely dynamic and can be considered as a pure encounter complex...

..These data, together with the low-resolution structures of a full-length form and a truncated form of HBHA obtained by small-angle X-ray scattering, have unambiguously indicated that HBHA has a dimeric structure with an elongated shape...

..We propose a possible mechanism for H(C) oligomerisation and discuss how this may relate to toxicity...

..The regulation model emerging from this study, including at least three different conformational states, allows the tight regulation of the enzyme without compromising fast response in the presence of natural targets...

..This study of Gfa1p focuses on the features that distinguish it from the prokaryotic homologue in terms of quaternary structure, control of the enzymatic activity and details of the isomerase active site...

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..Our findings support a shared pattern of assembly across DMPK, ROCKs, and MRCK members of this family...

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..Taken together, our results indicate that, contrary to Src and Abl, Btk might not require an assembled conformation for the regulation of its activity...

..A fundamental consequence of this result is that two Fd molecules bind consecutively to Fd-GltS to yield the reduced FMN cofactor during catalysis...

..Chem.16, 1207-1216] and comparison with indole-3-pyruvic acid conversion by pyruvate decarboxylases from Saccharomyces cerevisiae and Zymomonas mobilis provided some insight into the catalytic mechanism of indolepyruvate decarboxylase...

..Bernocco, S., Font, B., Moali, C., Eichenberger, D., Farjanel, J., Burchardt, E. R., van der Rest, M., Kessler, E., and Hulmes, D. J. S. (2002) J. Biol. Chem. 277, 33864-33869) for the mechanism of action of PCPE...

..Vma5p is an elongated boot-shaped particle consisting of two distinct domains. Co-reconstitution of Vma5p to V1 without C from Manduca sexta resulted in a V1-Vma5p hybrid complex and a 20% increase in ATPase hydrolysis activity...

..These conclusions obviate the need for assuming large conformational changes in RFs during termination...

..The core domains enveloped the response element in the center of the molecule, with the Taz2-bound TADs projecting outward from the core...

..However, several of these techniques indicate that it is not fully extended, but becomes significantly more extended under denaturing conditions...

..Hints on the probable conformations are also obtained. This experimental finding opens new perspectives for the often hypothesized active role of the hemopexin-like domain in the enzymatic activity of MMPs...

..The transmission path of the nucleotide effect toward the main hinge of PGK is described for the first time at the level of interactions existing in the tertiary structure...

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..This study represents the first attempt to understand the multifunctional properties of this important parasite-derived molecule by studying its structure...

..Our results demonstrate that, beyond catalytic activity, the three-copper cluster at the N-terminal-C-terminal interface plays a crucial role in the structural stability of human ceruloplasmin...

..Within the decoupling approximation, the experimental data can be fitted using an effective interparticle interaction potential involving short-range attraction and long-range repulsion...

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..These NK1 variants have no detectable agonistic activity on, behave as bona fide receptor antagonists by blocking cell migration and DNA synthesis in target cells and have strong prospects as therapeutics for human cancer...

..The data show that multiple assembly forms are a general feature of lumazine synthases...

..Based on the high precision of our refined structure, we show that Josephin contains an open cleft which could be directly implicated in the interaction with polyubiquitin chains and other partners...

..thermophilus and E. coli. Thermodynamic analyses and the X-ray scattering results for T. thermophilus RF2 in solution suggest that the compact conformation of RF2 resembles a physiological state in absence of the ribosome...

..This model reveals that nearly spherical micellar cores of about 10 nm in diameter (filled with Pt nanoparticles) aggregate forming slightly oblate hollow bodies with an outer diameter of about 40 nm...

..The distinct helical oligomer described in this study defines a conceptually new basis of structure-based drug design against amyloid diseases...

..Finally, we suggest that a specific pair of glycine residues in the linker might act as a major conformational switch...

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..Results allow the comparative analysis of PRT and pyrimidine NP families and expose related structural motifs involved in nucleotide/nucleoside recognition by these enzyme families...

..We also describe the high-resolution crystal structure of the catalytic domain alone, and we show that, in solution, it binds ATP. The conformational flexibility of this domain is discussed and related to other structural information...

..It can be expected that this principle is generally applicable to all Ig-tandems from I-band titin...

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..We propose a mechanistic model based on freely jointed rigid segments that rationalizes the response to stretch of titin Ig-tandems according to molecular features...

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..Moreover, small angle x-ray scattering measurements for tricorn and inhibited F1 have been interpreted as formation of transient and substrate-induced complexes...

..These new insights into the structure and RNA binding properties of PTB suggest revised models of its mechanism of action...

..Notably, the interface of Dcp1 and Dcp2 is not fully conserved, explaining why the Dcp1-Dcp2 interaction in higher eukaryotes requires an additional factor...