The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

/pdf/ucsf-chimera-a-visualization-system-for-exploratory-research-59xu54fhxg.pdf

UCSF Chimera--a visualization system for exploratory research and analysis.

Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

/pdf/phaser-crystallographic-software-2ceb03fha6.pdf

Phaser crystallographic software

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Living in an oxygenated environment has required the evolution of effective cellular strategies to detect and detoxify metabolites of molecular oxygen known as reactive oxygen species. Here we review evidence that the appropriate and inappropriate production of oxidants, together with the ability of organisms to respond to oxidative stress, is intricately connected to ageing and life span.

Oxidants, oxidative stress and the biology of ageing.

Diabetes-specific microvascular disease is a leading cause of blindness, renal failure and nerve damage, and diabetes-accelerated atherosclerosis leads to increased risk of myocardial infarction, stroke and limb amputation. Four main molecular mechanisms have been implicated in glucose-mediated vascular damage. All seem to reflect a single hyperglycaemia-induced process of overproduction of superoxide by the mitochondrial electron-transport chain. This integrating paradigm provides a new conceptual framework for future research and drug discovery.

http://www.chem.uwec.edu/Chem454/BiochemDiabetes.pdf

Biochemistry and molecular cell biology of diabetic complications

/pdf/complement-convertase-formation-based-on-the-structures-of-54gomgif9v.pdf

Complement convertase formation based on the structures of C3b in complex with factors B and D

Crystal structure of leech anti-platelet protein

C1 assembly is revealed by mass spectrometry and electron microscopy

The Crystallography & NMR System (CNS) is described.


Keywords:

CNS;
Crystallography & NMR System;
structure determination

CNS, a program system for structure‐determination and refinement

To enhance our understanding of how recognition and specificity for different ligands can be accomplished by related antibodies, we are studying the evolution of ligand binding properties by site-directedmutagenesis. Themost active catalytic Diels-Alder antibody known to date, 1E9, and the steroid binding antibody, DB3, derive from the same polyspecific germ line sequences and share 85% sequence identity. In spite of their close relationship, they fulfill very different specific tasks with high efficiency. Through sequential amino acid exchanges, we changed the specificity of 1E9 to that of DB3. Binding studies reveal that just a few residues are predominantly responsible for achieving either an efficient catalysis of the Diels-Alder reaction or, when mutated, convert the 1E9 Fab into a strong steroid binder. We determined the structures of the 1E9 mutants as apo-proteins, as well as in complex with different steroids. The structures highlight that only two residues in the substrate binding site are necessary and sufficient for discriminating structurally diverse ligands. Additionally, the structures reveal that despite strong binding (nM Kds) several distinct binding modes are employed promiscuously in order to accommodate structurally different steroids in the engineered ligand binding sites. The potential of antibodies as biocatalysts and the clinical utility of diagnostic and therapeutic antibodies have been the impetus behind the rapid development of antibody engineering. Our studies contribute to the advancement of this field by demonstrating how relativelyminor changes can be rationally employed to modify antibody specificity and function.

/pdf/formation-of-amyloid-fibres-followed-by-x-ray-diffraction-in-13gtw7wjnq.pdf

Formation of amyloid fibres followed by X-ray diffraction in real time. Implications for the identity of bio-active species in conformational diseases like Alzheimer's disease

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