Summary form only given. Fundamental processes in atoms, molecules, as well as condensed matter are triggered or mediated by the motion of electrons inside or between atoms. Electronic dynamics on atomic length scales tends to unfold within tens to thousands of attoseconds (1 attosecond [as] = 10-18 s). Recent breakthroughs in laser science are now opening the door to watching and controlling these hitherto inaccessible microscopic dynamics. The key to accessing the attosecond time domain is the control of the electric field of (visible) light, which varies its strength and direction within less than a femtosecond (1 femtosecond = 1000 attoseconds). Atoms exposed to a few oscillations cycles of intense laser light are able to emit a single extreme ultraviolet (XUV) burst lasting less than one femtosecond. Full control of the evolution of the electromagnetic field in laser pulses comprising a few wave cycles have recently allowed the reproducible generation and measurement of isolated sub-femtosecond XUV pulses, demonstrating the control of microscopic processes (electron motion and photon emission) on an attosecond time scale. These tools have enabled us to visualize the oscillating electric field of visible light with an attosecond "oscilloscope", to control single-electron and probe multi-electron dynamics in atoms, molecules and solids. Recent experiments hold promise for the development of an attosecond X-ray source, which may pave the way towards 4D electron imaging with sub-atomic resolution in space and time.

Attosecond Physics

The proteasome is an intricate molecular machine, which serves to degrade proteins following their conjugation to ubiquitin. Substrates dock onto the proteasome at its 19-subunit regulatory particle via a diverse set of ubiquitin receptors and are then translocated into an internal chamber within the 28-subunit proteolytic core particle (CP), where they are hydrolyzed. Substrate is threaded into the CP through a narrow gated channel, and thus translocation requires unfolding of the substrate. Six distinct ATPases in the regulatory particle appear to form a ring complex and to drive unfolding as well as translocation. ATP-dependent, degradation-coupled deubiquitination of the substrate is required both for efficient substrate degradation and for preventing the degradation of the ubiquitin tag. However, the proteasome also contains deubiquitinating enzymes (DUBs) that can remove ubiquitin before substrate degradation initiates, thus allowing some substrates to dissociate from the proteasome and escape degradation. Here we examine the key elements of this molecular machine and how they cooperate in the processing of proteolytic substrates.

Recognition and Processing of Ubiquitin-Protein Conjugates by the Proteasome

1.1. Uncharacterized Protein Segments Are a Source of Functional Novelty
Over the past decade, we have observed a massive increase in the amount of information describing protein sequences from a variety of organisms.1,2 While this may reflect the diversity in sequence space, and possibly also in function space,3 a large proportion of the sequences lacks any useful function annotation.4,5 Often these sequences are annotated as putative or hypothetical proteins, and for the majority their functions still remain unknown.6,7 Suggestions about potential protein function, primarily molecular function, often come from computational analysis of their sequences. For instance, homology detection allows for the transfer of information from well-characterized protein segments to those with similar sequences that lack annotation of molecular function.8−10 Other aspects of function, such as the biological processes proteins participate in, may come from genetic- and disease-association studies, expression and interaction network data, and comparative genomics approaches that investigate genomic context.11−17 Characterization of unannotated and uncharacterized protein segments is expected to lead to the discovery of novel functions as well as provide important insights into existing biological processes. In addition, it is likely to shed new light on molecular mechanisms of diseases that are not yet fully understood. Thus, uncharacterized protein segments are likely to be a large source of functional novelty relevant for discovering new biology.

/pdf/classification-of-intrinsically-disordered-regions-and-2mev7glgpx.pdf

Classification of intrinsically disordered regions and proteins.

Classification of Intrinsically Disordered Regions and Proteins

Small-angle scattering (SAS) of x-rays and neutrons is a fundamental tool in the study of biological macromolecules. The major advantage of the method lies in its ability to provide structural information about partially or completely disordered systems. SAS allows one to study the structure of native particles in near physiological environments and to analyse structural changes in response to variations in external conditions. In this review we concentrate on SAS studies of isotropic systems, in particular, solutions of biological macromolecules, an area where major progress has been achieved during the last decade. Solution scattering studies are especially important, given the challenge of the ‘post-genomic’ era with vast numbers of protein sequences becoming available. Numerous structural initiatives aim at large-scale expression and purification of proteins for subsequent structure determination using x-ray crystallography and NMR spectroscopy. Because of the requirement of good crystals for crystallography and the low molecular mass requirement of NMR, a significant fraction of proteins cannot be analysed using these two high-resolution methods. Progress in SAS instrumentation and novel analysis methods, which substantially improve the resolution and reliability of the structural models, makes the method an important complementary tool for these initiatives. The review covers the basics of x-ray and neutron SAS, instrumentation, mathematical methods used in data analysis and major modelling techniques. Examples of applications of SAS to different types of biomolecules (proteins, nucleic acids, macromolecular complexes, polyelectrolytes) are presented. A brief account of the new opportunities offered by third and fourth generation synchrotron radiation sources (time-resolved studies, coherent scattering and single molecule scattering) is also given.

/pdf/small-angle-scattering-studies-of-biological-macromolecules-3aateici8x.pdf

Small-angle scattering studies of biological macromolecules in solution

The geometric relationship between the two protein degradation signals of proteasome substrates, the polyubiquitin chain and the unfolded region, is dictated by the locations of their recognition sites on the proteasome.

Defining the geometry of the two-component proteasome degron

The proteasome controls the turnover of many cellular proteins Two structural features are typically required for proteins to be degraded: covalently attached ubiquitin polypeptides that allow binding to the proteasome and an unstructured region in the targeted protein that initiates proteolysis Here, we have tested the degradation of model proteins to further explore how the proteasome selects its substrates Using purified yeast proteasome and mammalian proteasome in cell lysate, we have demonstrated that the two structural features can act in trans when separated onto different proteins in a multisubunit complex In such complexes, the location of the unstructured initiation site and its chemical properties determine which subunit is degraded Thus, our findings reveal the molecular basis of subunit specificity in the degradation of protein complexes In addition, our data provide a plausible explanation for how adaptor proteins can bind to otherwise stable proteins and target them for degradation

Substrate selection by the proteasome during degradation of protein complexes

The proteasome controls the concentrations of most proteins in eukaryotic cells. It recognizes its protein substrates through ubiquitin tags and initiates degradation at disordered regions within the substrate. Here we show that the proteasome has pronounced preferences for the amino acid sequence of the regions at which it initiates degradation. Specifically, proteins in which the initiation regions have biased amino acid compositions show longer half-lives in yeast than proteins with unbiased sequences in the regions. The relationship is also observed on a genomic scale in mouse cells. These preferences affect the degradation rates of proteins in vitro, can explain the unexpected stability of natural proteins in yeast and may affect the accumulation of toxic proteins in disease. We propose that the proteasome's sequence preferences provide a second component to the degradation code and may fine-tune protein half-life in cells.

/pdf/sequence-composition-of-disordered-regions-fine-tunes-37geskv8el.pdf

Tomonao Inobe

Papers

Defining the geometry of the two-component proteasome degron

Substrate selection by the proteasome during degradation of protein complexes

Sequence composition of disordered regions fine-tunes protein half-life

Paradigms of protein degradation by the proteasome.

Fast Compaction of α-Lactalbumin During Folding Studied by Stopped-flow X-ray Scattering