718 research outputs found
The French in Vermont : some current views
Occasional paper (University of Vermont. Center for Research on Vermont) ; no. 6
Kinesin-1 captures RNA cargo in its adaptable coils
The prototypic and ubiquitous microtubule motor, kinesin-1, uses a variety of adaptor proteins to facilitate the selective transport of diverse cargo within the cell. These cargo adaptors bind to the motor complex through interactions with the kinesin light or heavy chains (KLCs or KHCs). In this issue of Genes & Development, Dimitrova-Paternoga et al. (pp. 976â991) present the first structural characterization of a KHCâcargo adaptor interface. They describe an antiparallel heterotrimeric coiled-coil complex between the carboxy tail of KHC and Tm1-I/C (aTm1), the atypical tropomyosin that is important for oskar mRNA transport in Drosophila oocytes. This interaction enhances direct binding between KHC and RNA. Their findings demonstrate the structural plasticity of the KHC tail as a platform for proteinâprotein interactions and reveal how a cargo adaptor protein can modify a motorâRNA interface to promote transport
Impact of ultrafast electronic damage in single particle x-ray imaging experiments
In single particle coherent x-ray diffraction imaging experiments, performed
at x-ray free-electron lasers (XFELs), samples are exposed to intense x-ray
pulses to obtain single-shot diffraction patterns. The high intensity induces
electronic dynamics on the femtosecond time scale in the system, which can
reduce the contrast of the obtained diffraction patterns and adds an isotropic
background. We quantify the degradation of the diffraction pattern from
ultrafast electronic damage by performing simulations on a biological sample
exposed to x-ray pulses with different parameters. We find that the contrast is
substantially reduced and the background is considerably strong only if almost
all electrons are removed from their parent atoms. This happens at fluences of
at least one order of magnitude larger than provided at currently available
XFEL sources.Comment: 15 pages, 3 figures submitted to PR
CCBuilder:An interactive web-based tool for building, designing and assessing coiled-coil protein assemblies
Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo . Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models.
Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures.
Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder
Interpretation of heart rate variability via detrended fluctuation analysis and alpha-beta filter
Detrended fluctuation analysis (DFA), suitable for the analysis of
nonstationary time series, has confirmed the existence of persistent long-range
correlations in healthy heart rate variability data. In this paper, we present
the incorporation of the alpha-beta filter to DFA to determine patterns in the
power-law behaviour that can be found in these correlations. Well-known
simulated scenarios and real data involving normal and pathological
circumstances were used to evaluate this process. The results presented here
suggest the existence of evolving patterns, not always following a uniform
power-law behaviour, that cannot be described by scaling exponents estimated
using a linear procedure over two predefined ranges. Instead, the power law is
observed to have a continuous variation with segment length. We also show that
the study of these patterns, avoiding initial assumptions about the nature of
the data, may confer advantages to DFA by revealing more clearly abnormal
physiological conditions detected in congestive heart failure patients related
to the existence of dominant characteristic scales.Comment: 18 pages, 14 figure
Spectral Simplicity of Apparent Complexity, Part I: The Nondiagonalizable Metadynamics of Prediction
Virtually all questions that one can ask about the behavioral and structural
complexity of a stochastic process reduce to a linear algebraic framing of a
time evolution governed by an appropriate hidden-Markov process generator. Each
type of question---correlation, predictability, predictive cost, observer
synchronization, and the like---induces a distinct generator class. Answers are
then functions of the class-appropriate transition dynamic. Unfortunately,
these dynamics are generically nonnormal, nondiagonalizable, singular, and so
on. Tractably analyzing these dynamics relies on adapting the recently
introduced meromorphic functional calculus, which specifies the spectral
decomposition of functions of nondiagonalizable linear operators, even when the
function poles and zeros coincide with the operator's spectrum. Along the way,
we establish special properties of the projection operators that demonstrate
how they capture the organization of subprocesses within a complex system.
Circumventing the spurious infinities of alternative calculi, this leads in the
sequel, Part II, to the first closed-form expressions for complexity measures,
couched either in terms of the Drazin inverse (negative-one power of a singular
operator) or the eigenvalues and projection operators of the appropriate
transition dynamic.Comment: 24 pages, 3 figures, 4 tables; current version always at
http://csc.ucdavis.edu/~cmg/compmech/pubs/sdscpt1.ht
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