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The Domain Of Images, Chapter 1, In Portuguese, James Elkins

James Elkins

This is the opening chapter of the book "Domain of Images" (Cornell University Press), in Portuguese.

Crystallographic, Molecular Dynamics, And Enzymatic Studies Of Multi-Drug Resistant Hiv-1 Protease And Implications For Structure Based Drug Design (Project 1); Crystallographic Studies Of Human Myelin Protein Zero (Project 2), Zhigang Liu

Wayne State University Dissertations

Under drug selection pressure, emerging mutations render HIV-1 protease drug resistance, leading to the therapy failure in anti-HIV treatment.Tthe multidrug-resistant 769 (MDR) HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) is selected for the present study to understand drug resistance issue.

Ten additional mutations are introduced to MDR769 HIV-1 protease to study the structural influences brought by these mutations. We get crystal structures of four variants (I10V, A82F, A82S and A82T) of MDR769 HIV-1 protease. All these mutations fail to further open the flaps and expand the active site cavity of MDR769 …

Surface Entropy Reduction To Increase The Crystallizability Of The Fab-Rna Complex, Priyadarshini Palaniandy Ravindran

Electronic Theses and Dissertations

Crystallizing RNA has been an imperative facet and a challenging task in the world of RNA research. Assistive methods such as Chaperone Assisted RNA Crystallography (CARC), employing monoclonal antibody fragments (Fabs) as crystallization chaperones have enabled us to obtain RNA crystal structures by increasing the crystal contacts and providing initial phasing information. Using this technology the crystal structure of [delta]C209 P4-P6 RNA (an independent folding domain of the self-splicing Tetrahymena group I intron) complexed to Fab2 (high affinity binding Fab) has been resolved to 1.95 Å (1). Although the complexed class I ligase ribozyme has also been crystallized using CARC …

A Kinesin Motor In A Force-Producing Conformation, Elisabeth Heuston, C. Eric Bronner, F Jon Kull, Sharyn A. Endow

Dartmouth Scholarship

Kinesin motors hydrolyze ATP to produce force and move along microtubules, converting chemical energy into work by a mechanism that is only poorly understood. Key transitions and intermediate states in the process are still structurally uncharacterized, and remain outstanding questions in the field. Perturbing the motor by introducing point mutations could stabilize transitional or unstable states, providing critical information about these rarer states.

Lipid-Protein Interactions Probed By Electron Crystallography, Steve L. Reichow, Tamir Gonen

Chemistry Faculty Publications and Presentations

Electron crystallography is arguably the only electron cryomicroscopy (cryoEM) technique able to deliver an atomic-resolution structure of membrane proteins embedded in the lipid-bilayer. In the electron crystallographic structures of the light driven ion pump, bacteriorhodopsin, and the water channel, aquaporin-0, sufficiently high resolution was obtained and both lipid and protein were visualized, modeled and described in detail. An extensive network of lipid-protein interactions mimicking native membranes is established and maintained in two-dimensional (2D) crystalline vesicles used for structural analysis by electron crystallography. Lipids are tightly integrated into the protein's architecture where they can affect the function, structure, quaternary assembly and …

Capturing Hammerhead Ribozyme Structures In Action By Modulating General Base Catalysis, Young-In Chi, Monika Martick, Monica Lares, Rosalind Kim, William G. Scott, Sung-Hou Kim

Center for Structural Biology Faculty Publications

We have obtained precatalytic (enzyme-substrate complex) and postcatalytic (enzyme-product complex) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation …

Electron Crystallography Of Aquaporins, Simeon Andrews, Steve Reichow, Tamir Gonen

Chemistry Faculty Publications and Presentations

Aquaporins are a family of ubiquitous membrane proteins that form a pore for the permeation of water. Both electron and X-ray crystallography played major roles in determining the atomic structures of a number of aquaporins. This review focuses on electron crystallography, and its contribution to the field of aquaporin biology. We briefly discuss electron crystallography and the two-dimensional crystallization process. We describe features of aquaporins common to both electron and X-ray crystallographic structures; as well as some structural insights unique to electron crystallography, including aquaporin junction formation and lipid-protein interactions.

Crystal Structure Of The Vibrio Cholerae Quorum-Sensing Regulatory Protein Hapr, Rukman S. De Silva, Gabriela Kovacikova, Wei Lin, Ronald K. Taylor, Karen Skorupski, F. Jon Kull

Dartmouth Scholarship

Quorum sensing in Vibrio cholerae involves signaling between two-component sensor protein kinases and the response regulator LuxO to control the expression of the master regulator HapR. HapR, in turn, plays a central role in regulating a number of important processes, such as virulence gene expression and biofilm formation. We have determined the crystal structure of HapR to 2.2-Å resolution. Its structure reveals a dimeric, two-domain molecule with an all-helical structure that is strongly conserved with members of the TetR family of transcriptional regulators. The N-terminal DNA-binding domain contains a helix-turn-helix DNA-binding motif and alteration of certain residues in this domain …

Anisotropic Atomic Motions In High-Resolution Protein Crystallography Molecular Dynamics Simulations, Conrad J. Burden, Aaron J. Oakley

Faculty of Science - Papers (Archive)

Molecular dynamics (MD) simulations using empirical force fields are popular for the study of proteins. In this work, we compare anisotropic atomic fluctuations in nanosecond-timescale MD simulations with those observed in an ultra-high-resolution crystal structure of crambin. In order to make our comparisons, we have developed a compact graphical technique for assessing agreement between spatial atomic distributions determined by MD simulations and observed anisotropic temperature factors.

Crystal Structure Of The Gtpase Domain Of Rat Dynamin 1, Thomas F. Reubold, Susanne Eschenburg, Andreas Becker, Marilyn Leonard, Sandra L. Schmid, Richard B. Vallee, F. Jon Kull, Dietmar J. Manstein

Dartmouth Scholarship

Here, we present the 1.9-A crystal structure of the nucleotide-free GTPase domain of dynamin 1 from Rattus norvegicus. The structure corresponds to an extended form of the canonical GTPase fold observed in Ras proteins. Both nucleotide-binding switch motifs are well resolved, adopting conformations that closely resemble a GTP-bound state not previously observed for nucleotide-free GTPases. Two highly conserved arginines, Arg-66 and Arg-67, greatly restrict the mobility of switch I and are ideally positioned to relay information about the nucleotide state to other parts of the protein. Our results support a model in which switch I residue Arg-59 gates GTP binding …

A Subgroup Algorithm To Identify Cross-Rotation Peaks Consistent With Non-Crystallographic Symmetry, Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald

Dartmouth Scholarship

Molecular replacement (MR) often plays a prominent role in determining initial phase angles for structure determination by X-ray crystallography. In this paper, an efficient quaternion-based algorithm is presented for analyzing peaks from a cross-rotation function in order to identify model orientations consistent with proper non-crystallographic symmetry (NCS) and to generate proper NCS-consistent orientations missing from the list of cross-rotation peaks. The algorithm, CRANS, analyzes the rotation differences between each pair of cross-rotation peaks to identify finite subgroups. Sets of rotation differences satisfying the subgroup axioms correspond to orientations compatible with the correct proper NCS. The CRANS algorithm was first …

Crystal Structure Of The Sars Protein From Staphylococcus Aureus, Ronggui Li, Adhar C. Manna, Shaodong Dai, Ambrose L. Cheung, Gongyi Zhang

Dartmouth Scholarship

The expression of virulence determinants in Staphylococcus aureus is controlled by global regulatory loci (e.g., sarA and agr). One of these determinants, protein A (spa), is activated by sarS, which encodes a 250-residue DNA-binding protein. Genetic analysis indicated that the agr locus likely mediates spa repression by suppressing the transcription of sarS. Contrary to SarA and SarR, which require homodimer formation for proper function, SarS is unusual within the SarA protein family in that it contains two homologous halves, with each half sharing sequence similarity to SarA and SarR. Here we report the 2.2 Å …

Time-Averaging Crystallographic Refinement, Celia Schiffer

Celia A. Schiffer

In: Wilfred F. van Gunsteren and Paul K. Weiner, Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications (Volume 3 of Computer Simulation of Biomolecular Systems), Springer, 1997, p. 265-269. ISBN 9072199251, 9789072199256.

Full text of chapter is available through Google Book Search limited preview: Google Book Search description

Divergent-Beam X-Ray Diffraction In The Scanning Electron Microscopy And Its Use For The Study Of The Semiconductor Epitaxial Layers, J. Hejna

Scanning Electron Microscopy

Among the X-ray techniques belonging to the family of Kassel methods the divergent-beam diffraction method gives the best contrast for semiconductor specimens.

The technique has been accomplished in the scanning electron microscope (SEM) in a back reflection configuration. Epitaxial layers of GaAsSb and GaAsSbP on GaAs [100] oriented substrates were investigated. The diffraction lines from lattice planes giving only high Bragg angles were used. For the purpose of the layer strain analysis, the diffraction experiments were carried out for specimens placed horizontally (the lines {711} type recorded) and for tilted 45° (the lines {551) type recorded). A Cu foil was …