35,411 research outputs found
Fiber depolymerization
Depolymerization is, by definition, a crucial process in the reversible assembly of various biopolymers. It may also be an important factor in the pathology of sickle cell disease. If sickle hemoglobin fibers fail to depolymerize fully during passage through the lungs then they will reintroduce aggregates into the systemic circulation and eliminate or shorten the protective delay (nucleation) time for the subsequent growth of fibers. We study how depolymerization depends on the rates of end- and side-depolymerization, kend and kside, which are, respectively, the rates at which fiber length is lost at each end and the rate at which new breaks appear per unit fiber length. We present both an analytic mean field theory and supporting simulations showing that the characteristic fiber depolymerization time View the MathML source depends on both rates, but not on the fiber length L, in a large intermediate regime 1 much less-than ksideL2/kend much less-than (L/d)2, with d the fiber diameter. We present new experimental data which confirms that both mechanisms are important and shows how the rate of side depolymerization depends strongly on the concentration of CO, acting as a proxy for oxygen. Our theory remains rather general and could be applied to the depolymerization of an entire class of linear aggregates, not just sickle hemoglobin fibers
Microtubule depolymerization by the kinesin-8 motor Kip3p: a mathematical model
Proteins from the kinesin-8 family promote microtubule (MT) depolymerization,
a process thought to be important for the control of microtubule length in
living cells. In addition to this MT shortening activity, kinesin 8s are motors
that show plus-end directed motility on MTs. Here we describe a simple model
that incorporates directional motion and destabilization of the MT plus end by
kinesin 8. Our model quantitatively reproduces the key features of
length-vs-time traces for stabilized MTs in the presence of purified kinesin 8,
including length-dependent depolymerization. Comparison of model predictions
with experiments suggests that kinesin 8 depolymerizes processively, i.e., one
motor can remove multiple tubulin dimers from a stabilized MT. Fluctuations in
MT length as a function of time are related to depolymerization processivity.
We have also determined the parameter regime in which the rate of MT
depolymerization is length dependent: length-dependent depolymerization occurs
only when MTs are sufficiently short; this crossover is sensitive to the bulk
motor concentration.Comment: 34 pages, 11 figure
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Analysis of gas chromatography/mass spectrometry data for catalytic lignin depolymerization using positive matrix factorization
Various catalytic technologies are being developed to efficiently convert lignin into renewable chemicals. However, due to its complexity, catalytic lignin depolymerization often generates a wide and complex distribution of product compounds. Gas chromatography/mass spectrometry (GC-MS) is a common analytical technique to profile the compounds that comprise lignin depolymerization products. GC-MS is applied not only to determine the product composition, but also to develop an understanding of the catalytic reaction pathways and of the relationships among catalyst structure, reaction conditions, and the resulting compounds generated. Although a very useful tool, the analysis of lignin depolymerization products with GC-MS is limited by the quality and scope of the available mass spectral libraries and the ability to correlate changes in GC-MS chromatograms to changes in lignin structure, catalyst structure, and other reaction conditions. In this study, the GC-MS data of the depolymerization products generated from organosolv hybrid poplar lignin using a copper-doped porous metal oxide catalyst and a methanol/dimethyl carbonate co-solvent was analyzed by applying a factor analysis technique, positive matrix factorization (PMF). Several different solutions for the PMF model were explored. A 13-factor solution sufficiently explains the chemical changes occurring to lignin depolymerization products as a function of lignin, reaction time, catalyst, and solvent. Overall, seven factors were found to represent aromatic compounds, while one factor was defined by aliphatic compounds
Simultaneous quantification of depolymerization and mineralization rates by a novel 15N tracing model
The depolymerization of soil organic matter, such as proteins and (oligo-)peptides, into monomers (e.g. amino acids) is currently considered to be the rate-limiting step for nitrogen (N) availability in terrestrial ecosystems. The mineralization of free amino acids (FAAs), liberated by the depolymerization of peptides, is an important fraction of the total mineralization of organic N. Hence, the accurate assessment of peptide depolymerization and FAA mineralization rates is important in order to gain a better process-based understanding of the soil N cycle. In this paper, we present an extended numerical 15N tracing model Ntrace, which incorporates the FAA pool and related N processes in order to provide a more robust and simultaneous quantification of depolymerization and gross mineralization rates of FAAs and soil organic N. We discuss analytical and numerical approaches for two forest soils, suggest improvements of the experimental work for future studies, and conclude that (i) when about half of all depolymerized peptide N is directly mineralized, FAA mineralization can be as important a rate-limiting step for total gross N mineralization as peptide depolymerization rate; (ii) gross FAA mineralization and FAA immobilization rates can be used to develop FAA use efficiency (NUEFAA), which can reveal microbial N or carbon (C) limitation
Long-time asymptotics for polymerization models
This study is devoted to the long-term behavior of nucleation, growth and
fragmentation equations, modeling the spontaneous formation and kinetics of
large polymers in a spatially homogeneous and closed environment. Such models
are, for instance, commonly used in the biophysical community in order to model
in vitro experiments of fibrillation. We investigate the interplay between four
processes: nucleation, polymeriza-tion, depolymerization and fragmentation. We
first revisit the well-known Lifshitz-Slyozov model, which takes into account
only polymerization and depolymerization, and we show that, when nucleation is
included, the system goes to a trivial equilibrium: all polymers fragmentize,
going back to very small polymers. Taking into account only polymerization and
fragmentation, modeled by the classical growth-fragmentation equation, also
leads the system to the same trivial equilibrium, whether or not nucleation is
considered. However, also taking into account a depolymer-ization reaction term
may surprisingly stabilize the system, since a steady size-distribution of
polymers may then emerge, as soon as polymeriza-tion dominates depolymerization
for large sizes whereas depolymerization dominates polymerization for smaller
ones-a case which fits the classical assumptions for the Lifshitz-Slyozov
equations, but complemented with fragmentation so that " Ostwald ripening "
does not happen.Comment: https://link.springer.com/article/10.1007/s00220-018-3218-
Direct Depolymerization Coupled to Liquid Extraction Surface Analysis-High-Resolution Mass Spectrometry for the Characterization of the Surface of Plant Tissues
The cuticle, the outermost layer covering the epidermis of most aerial organs of land plants, can have a heterogeneous composition even on the surface of the same organ. The main cuticle component is the polymer cutin which, depending on its chemical composition and structure, can have different biophysical properties. In this study, we introduce a new on-surface depolymerization method coupled to liquid extraction surface analysis (LESA) high-resolution mass spectrometry (HRMS) for a fast and spatially resolved chemical characterization of the cuticle of plant tissues. The method is composed of an on-surface saponification, followed by extraction with LESA using a chloroform-acetonitrile-water (49:49:2) mixture and direct HRMS detection. The method is also compared with LESA-HRMS without prior depolymerization for the analysis of the surface of the petals of Hibiscus richardsonii flowers, which have a ridged cuticle in the proximal region and a smooth cuticle in the distal region. We found that on-surface saponification is effective enough to depolymerize the cutin into its monomeric constituents thus allowing detection of compounds that were not otherwise accessible without a depolymerization step. The effect of the depolymerization procedure was more pronounced for the ridged/proximal cuticle, which is thicker and richer in epicuticular waxes compared with the cuticle in the smooth/distal region of the petal
Growth and dissolution of macromolecular Markov chains
The kinetics and thermodynamics of free living copolymerization are studied
for processes with rates depending on k monomeric units of the macromolecular
chain behind the unit that is attached or detached. In this case, the sequence
of monomeric units in the growing copolymer is a kth-order Markov chain. In the
regime of steady growth, the statistical properties of the sequence are
determined analytically in terms of the attachment and detachment rates. In
this way, the mean growth velocity as well as the thermodynamic entropy
production and the sequence disorder can be calculated systematically. These
different properties are also investigated in the regime of depolymerization
where the macromolecular chain is dissolved by the surrounding solution. In
this regime, the entropy production is shown to satisfy Landauer's principle
Kinetics and thermodynamics of first-order Markov chain copolymerization
We report a theoretical study of stochastic processes modeling the growth of
first-order Markov copolymers, as well as the reversed reaction of
depolymerization. These processes are ruled by kinetic equations describing
both the attachment and detachment of monomers. Exact solutions are obtained
for these kinetic equations in the steady regimes of multicomponent
copolymerization and depolymerization. Thermodynamic equilibrium is identified
as the state at which the growth velocity is vanishing on average and where
detailed balance is satisfied. Away from equilibrium, the analytical expression
of the thermodynamic entropy production is deduced in terms of the Shannon
disorder per monomer in the copolymer sequence. The Mayo-Lewis equation is
recovered in the fully irreversible growth regime. The theory also applies to
Bernoullian chains in the case where the attachment and detachment rates only
depend on the reacting monomer
Distribution of lifetimes of kinetochore-microtubule attachments: interplay of energy landscape, molecular motors and microtubule (de-)polymerization
Before a cell divides into two daughter cells, chromosomes are replicated
resulting in two sister chromosomes embracing each other. Each sister
chromosome is bound to a separate proteinous structure, called kinetochore
(kt), that captures the tip of a filamentous protein, called microtubule (MT).
Two oppositely oriented MTs pull the two kts attached to two sister chromosomes
thereby pulling the two sisters away from each other. Here we theoretically
study an even simpler system, namely an isolated kt coupled to a single MT;
this system mimics an {\it in-vitro} experiment where a single kt-MT attachment
is reconstituted using purified extracts from budding yeast. Our models not
only account for the experimentally observed "catch-bond-like" behavior of the
kt-MT coupling, but also make new predictions on the probability distribution
of the lifetimes of the attachments. In principle, our new predictions can be
tested by analyzing the data collected in the {\it in-vitro} experiments
provided the experiment is repeated sufficiently large number of times. Our
theory provides a deep insight into the effects of (a) size, (b) energetics,
and (c) stochastic kinetics of the kt-MT coupling on the distribution of the
lifetimes of these attachments.Comment: This is an author-created, un-copyedited version of an article
accepted for publication in "Physical Biology" (IOP). IOP Publishing Ltd is
not responsible for any errors or omissions in this version of the manuscript
or any version derived from i
Length control of microtubules by depolymerizing motor proteins
In many intracellular processes, the length distribution of microtubules is
controlled by depolymerizing motor proteins. Experiments have shown that,
following non-specific binding to the surface of a microtubule, depolymerizers
are transported to the microtubule tip(s) by diffusion or directed walk and,
then, depolymerize the microtubule from the tip(s) after accumulating there. We
develop a quantitative model to study the depolymerizing action of such a
generic motor protein, and its possible effects on the length distribution of
microtubules. We show that, when the motor protein concentration in solution
exceeds a critical value, a steady state is reached where the length
distribution is, in general, non-monotonic with a single peak. However, for
highly processive motors and large motor densities, this distribution
effectively becomes an exponential decay. Our findings suggest that such motor
proteins may be selectively used by the cell to ensure precise control of MT
lengths. The model is also used to analyze experimental observations of
motor-induced depolymerization.Comment: Added section with figures and significantly expanded text, current
version to appear in Europhys. Let
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