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Domain Movements (domain + movement)
Selected Abstracts2.9 Å crystal structure of ligand-free tryptophanyl-tRNA synthetase: Domain movements fragment the adenine nucleotide binding sitePROTEIN SCIENCE, Issue 2 2000Valentin A. Ilyin Abstract The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS) was solved at 2.9 Å using a combination of molecular replacement and maximum-entropy map/phase improvement. The dimeric structure (R = 23.7, Rfree = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl-5,AMP complex (TAM; Doublie S, Bricogne G, Gilmore CJ, Carter CW Jr, 1995, Structure 3:17,31). In agreement with small-angle solution X-ray scattering experiments, unliganded TrpRS has a conformation in which both monomers open, leaving only the tryptophan-binding regions of their active sites intact. The amino terminal ,A-helix, TIGN, and KMSKS signature sequences, and the distal helical domain rotate as a single rigid body away from the dinucleotide-binding fold domain, opening the AMP binding site, seen in the TAM complex, into two halves. Comparison of side-chain packing in ligand-free TrpRS and the TAM complex, using identification of nonpolar nuclei (Ilyin VA, 1994, Protein Eng 7:1189,1195), shows that significant repacking occurs between three relatively stable core regions, one of which acts as a bearing between the other two. These domain rearrangements provide a new structural paradigm that is consistent in detail with the"induced-fit" mechanism proposed for TyrRS by Fersht et al. (Fersht AR, Knill-Jones JW, Beduelle H, Winter G, 1988, Biochemistry 27:1581,1587). Coupling of ATP binding determinants associated with the two catalytic signature sequences to the helical domain containing the presumptive anticodon-binding site provides a mechanism to coordinate active-site chemistry with relocation of the major tRNA binding determinants. [source] High-resolution wide-angle X-ray scattering of protein solutions: effect of beam dose on protein integrityJOURNAL OF SYNCHROTRON RADIATION, Issue 5 2003Robert F. Fischetti Wide-angle X-ray scattering patterns from proteins in solution contain information relevant to the determination of protein fold. At relevant scattering angles, however, these data are weak, and the degree to which they might be used to categorize the fold of a protein is unknown. Preliminary work has been performed at the BioCAT insertion-device beamline at the Advanced Photon Source which demonstrates that one can collect X-ray scattering data from proteins in solution to spacings of at least 2.2,Å (q = 2.8,Å,1). These data are sensitive to protein conformational states, and are in good agreement with the scattering predicted by the program CRYSOL using the known three-dimensional atomic coordinates of the protein. An important issue in the exploitation of this technique as a tool for structural genomics is the extent to which the high intensity of X-rays available at third-generation synchrotron sources chemically or structurally damage proteins. Various data-collection protocols have been investigated demonstrating conditions under which structural degradation of even sensitive proteins can be minimized, making this technique a viable tool for protein fold categorization, the study of protein folding, unfolding, protein,ligand interactions and domain movement. [source] The high-resolution structure of pig heart succinyl-CoA:3-oxoacid coenzyme A transferaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Shu-Fen Coker The enzyme succinyl-CoA:3-oxoacid coenzyme A transferase (SCOT) participates in the metabolism of ketone bodies in extrahepatic tissues. It catalyses the transfer of coenzyme A (CoA) from succinyl-CoA to acetoacetate with a classical ping-pong mechanism. There is biochemical evidence that the enzyme undergoes conformational changes during the reaction, but no domain movements have been reported in the available crystal structures. Here, a structure of pig heart SCOT refined at 1.5,Å resolution is presented, showing that one of the four enzyme subunits in the crystallographic asymmetric unit has a molecule of glycerol bound in the active site; the glycerol molecule is hydrogen bonded to the conserved catalytic glutamate residue and is likely to occupy the cosubstrate-binding site. The binding of glycerol is associated with a substantial relative movement (a 13° rotation) of two previously undefined domains that close around the substrate-binding site. The binding orientation of one of the cosubstrates, acetoacetate, is suggested based on the glycerol binding and the possibility that this dynamic domain movement is of functional importance is discussed. [source] Hydrogen-deuterium exchange in membrane proteins monitored by IR spectroscopy: A new tool to resolve protein structure and dynamicsBIOPOLYMERS, Issue 1-2 2004C. Vigano Abstract As more and more high-resolution structures of proteins become available, the new challenge is the understanding of these small conformational changes that are responsible for protein activity. Specialized difference Fourier transform infrared (FTIR) techniques allow the recording of side-chain modifications or minute secondary structure changes. Yet, large domain movements remain usually unnoticed. FTIR spectroscopy provides a unique opportunity to record 1H/2H exchange kinetics at the level of the amide proton. This approach is extremely sensitive to tertiary structure changes and yields quantitative data on domain/domain interactions. An experimental setup designed for attenuated total reflection and a specific approach for the analysis of the results is described. The study of one membrane protein, the gastric H+,K+ -ATPase, demonstrates the usefulness of 1H/2H exchange kinetics for the understanding of the molecular movement related to the catalytic activity. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004 [source] Structure of Staphylococcus aureus guanylate monophosphate kinaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2006Kamel El Omari Nucleotide monophosphate kinases (NMPKs) are potential antimicrobial drug targets owing to their role in supplying DNA and RNA precursors. The present work reports the crystal structure of Staphylococcus aureus guanylate monophosphate kinase (SaGMK) at 1.9,Å resolution. The structure shows that unlike most GMKs SaGMK is dimeric, confirming the role of the extended C-terminus in dimer formation as first observed for Escherichia coli GMK (EcGMK). One of the two SaGMK dimers within the crystal asymmetric unit has two monomers in different conformations: an open form with a bound sulfate ion (mimicking the ,-phosphate of ATP) and a closed form with bound GMP and sulfate ion. GMP-induced domain movements in SaGMK can thus be defined by comparison of these conformational states. Like other GMKs, the binding of GMP firstly triggers a partial closure of the enzyme, diminishing the distance between the GMP-binding and ATP-binding sites. In addition, the closed structure shows the presence of a potassium ion in contact with the guanine ring of GMP. The potassium ion appears to form an integral part of the GMP-binding site, as the Tyr36 side chain has significantly moved to form a metal ion,ligand coordination involving the lone pair of the side-chain O atom. The potassium-binding site might also be exploited in the design of novel inhibitors. [source] Using virtual topologies to manage inter-domain QoS in next-generation networksINTERNATIONAL JOURNAL OF NETWORK MANAGEMENT, Issue 3 2010Ricardo B. Freitas Recently, several computer fields have turned to virtualization as a way to simplify complex problems. In this context, the Virtual Topology Service (VTS) was created to manage the advertisement and acquisition of virtual topologies (abstractions of the network status of a domain) and their use in inter-domain resource reservation to provide end-to-end quality of service (QoS). As an effort to create new network architectures which could attend current requirements like mobility and context-aware applications and support autonomous, heterogeneous and mobile domains next-generation networks (NGNs) emerged, with Ambient Networks (AN) as one of its instances. With an ever increasing multitude of online applications, end-to-end QoS has become increasingly important, especially for media and real-time uses. In this context, in order to better manage inter-domain QoS in these new networks, better coping with mobile nodes and domains, this work presents a new design and implementation of the VTS, adapted to the AN environment. The new VTS stores resource reservation information to enable the reuse of these reservations when re-establishing QoS after a node/domain movement. This implementation was tested on a real NGN prototype and showed considerable time saving when compared to QoS re-establishment without reusing the reservations. Copyright © 2009 John Wiley & Sons, Ltd. [source] | ||||||||||