17 research outputs found
Conditional ambiguity of oneâdimensional crystal structures determined from a minimum of diffraction intensity data
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113118/1/S0108767311007616.pd
Diffusion dependent cell behavior in microenvironments
Understanding the interaction between soluble factors and cells in the cellular microenvironment is critical to understanding a wide range of diseases. Microchannel culture systems provide a tool for separating diffusion and convection based transport making possible controlled studies of the effects of soluble factors in the cellular microenvironment. In this paper we compare the proliferation kinetics of cells in traditional culture flasks to those in microfluidic channels, and explore the relationship between microchannel geometry and cell proliferation. PDMS (polydimethylsiloxane) microfluidic channels were fabricated using micromolding methods. Fall armyworm ovarian cells (Sf9) were homogeneously seeded in a series of different sized microchannels and cultured under a no flow condition. The proliferation rates of Sf9 cells in all of the microchannels were slower than in the flask culture over the first 24 h of culture. The proliferation rates in the microchannels then continuously decreased reaching 5% of that in the flasks over the next 48 h and maintained this level for 5 days. This growth inhibition was reversible and influenced only by the cell seeding density and the channel height but not the channel length or width. One possible explanation for the observed dimension-dependent cell proliferation is the accumulation of different functional molecules in the diffusion dominant microchannel environment. This study provides insights into the potential effects of the diffusion of soluble factors and related effects on cell behavior in microenvironments relevant to the emerging use of microchannel culture systems
Contributions of Coulombic and Hofmeister Effects to the Osmotic Activation of <i>Escherichia coli</i> Transporter ProP
Osmosensing transporters mediate
osmolyte accumulation to forestall
cellular dehydration as the extracellular osmolality increases. ProP
is a bacterial osmolyte-H<sup>+</sup> symporter, a major facilitator
superfamily member, and a paradigm for osmosensing. ProP activity
is a sigmoid function of the osmolality. It is determined by the osmolality,
not the magnitude or direction of the osmotic shift, in cells and
salt-loaded proteoliposomes. The activation threshold varies directly
with the proportion of anionic phospholipid in cells and proteoliposomes.
The osmosensory mechanism was probed by varying the salt composition
and concentration outside and inside proteoliposomes. Data analysis
was based on the hypothesis that the fraction of maximal transporter
activity at a particular luminal salt concentration reflects the proportion
of ProP molecules in an active conformation. ProP attained the same
activity at the same osmolality when diverse, membrane-impermeant
salts were added to the external medium. Contributions of Coulombic
and/or Hofmeister salt effects to ProP activation were examined by
varying the luminal salt cation (K<sup>+</sup> and Na<sup>+</sup>)
and anion (chloride, phosphate, and sulfate) composition and then
systematically increasing the luminal salt concentration by increasing
the external osmolality. ProP activity increased with the sixth power
of the univalent cation concentration, independent of the type of
anion. This indicates that salt activation of ProP is a Coulombic,
cation effect resulting from salt cation accumulation and not site-specific
cation binding. Possible origins of this Coulombic effect include
folding or assembly of anionic cytoplasmic ProP domains, an increase
in local membrane surface charge density, and/or the juxtaposition
of anionic protein and membrane surfaces during activation
Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coliâż â
Facile diffusion of globular proteins within a cytoplasm that is dense with biopolymers is essential to normal cellular biochemical activity and growth. Remarkably, Escherichia coli grows in minimal medium over a wide range of external osmolalities (0.03 to 1.8 osmol). The mean cytoplasmic biopolymer volume fraction (â©ÏâȘ) for such adapted cells ranges from 0.16 at 0.10 osmol to 0.36 at 1.45 osmol. For cells grown at 0.28 osmol, a similar â©ÏâȘ range is obtained by plasmolysis (sudden osmotic upshift) using NaCl or sucrose as the external osmolyte, after which the only available cellular response is passive loss of cytoplasmic water. Here we measure the effective axial diffusion coefficient of green fluorescent protein (DGFP) in the cytoplasm of E. coli cells as a function of â©ÏâȘ for both plasmolyzed and adapted cells. For plasmolyzed cells, the median DGFP (\documentclass[10pt]{article}
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\begin{equation*}D_{GFP}^{m}\end{equation*}\end{document}) decreases by a factor of 70 as â©ÏâȘ increases from 0.16 to 0.33. In sharp contrast, for adapted cells, \documentclass[10pt]{article}
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\begin{equation*}D_{GFP}^{m}\end{equation*}\end{document} decreases only by a factor of 2.1 as â©ÏâȘ increases from 0.16 to 0.36. Clearly, GFP diffusion is not determined by â©ÏâȘ alone. By comparison with quantitative models, we show that the data cannot be explained by crowding theory. We suggest possible underlying causes of this surprising effect and further experiments that will help choose among competing hypotheses. Recovery of the ability of proteins to diffuse in the cytoplasm after plasmolysis may well be a key determinant of the time scale of the recovery of growth
Quantifying Interactions of Nucleobase Atoms with Model Compounds for the Peptide Backbone and Glutamine and Asparagine Side Chains in Water
Alkylureas
display hydrocarbon and amide groups, the primary functional
groups of proteins. To obtain the thermodynamic information that is
needed to analyze interactions of amides and proteins with nucleobases
and nucleic acids, we quantify preferential interactions of alkylureas
with nucleobases differing in the amount and composition of water-accessible
surface area (ASA) by solubility assays. Using an established additive
ASA-based analysis, we interpret these thermodynamic results to determine
interactions of each alkylurea with five types of nucleobase unified
atoms (carbonyl sp<sup>2</sup>O, amino sp<sup>3</sup>N, ring sp<sup>2</sup>N, methyl sp<sup>3</sup>C, and ring sp<sup>2</sup>C). All
alkylureas interact favorably with nucleobase sp<sup>2</sup>C and
sp<sup>3</sup>C atoms; these interactions become more favorable with
an increasing level of alkylation of urea. Interactions with nucleobase
sp<sup>2</sup>O are most favorable for urea, less favorable for methylurea
and ethylurea, and unfavorable for dialkylated ureas. Contributions
to overall alkylureaânucleobase interactions
from interactions with each nucleobase atom type are proportional
to the ASA of that atom type with proportionality constant (interaction
strength) α, as observed previously for urea. Trends in α-values
for interactions of alkylureas with nucleobase atom types parallel
those for corresponding amide compound atom types, offset because
nucleobase α-values are more favorable. Comparisons between
ethylated and methylated ureas show interactions of amide compound
sp<sup>3</sup>C with nucleobase sp<sup>2</sup>C, sp<sup>3</sup>C,
sp<sup>2</sup>N, and sp<sup>3</sup>N atoms are favorable while amide
sp<sup>3</sup>Cânucleobase sp<sup>2</sup>O interactions are
unfavorable. Strongly favorable interactions of urea with nucleobase
sp<sup>2</sup>O but weakly favorable interactions with nucleobase
sp<sup>3</sup>N indicate that amide
sp<sup>2</sup>Nânucleobase sp<sup>2</sup>O and nucleobase sp<sup>3</sup>Nâamide sp<sup>2</sup>O hydrogen bonding (NH···Oî»C)
interactions are favorable while amide sp<sup>2</sup>Nânucleobase
sp<sup>3</sup>N interactions are unfavorable. These favorable amideânucleobase
hydrogen bonding interactions are prevalent in specific proteinânucleotide
complexes
Experimental Atom-by-Atom Dissection of AmideâAmide and AmideâHydrocarbon Interactions in H<sub>2</sub>O
Quantitative information about amide
interactions in water is needed
to understand their contributions to protein folding and amide effects
on aqueous processes and to compare with computer simulations. Here
we quantify interactions of urea, alkylated ureas, and other amides
by osmometry and amideâaromatic hydrocarbon interactions by
solubility. Analysis of these data yields strengths of interaction
of ureas and naphthalene with amide sp<sup>2</sup>O, amide sp<sup>2</sup>N, aliphatic sp<sup>3</sup>C, and amide and aromatic sp<sup>2</sup>C unified atoms in water. Interactions of amide sp<sup>2</sup>O with urea and naphthalene are favorable, while amide sp<sup>2</sup>Oâalkylurea interactions are unfavorable, becoming more unfavorable
with increasing alkylation. Hence, amide sp<sup>2</sup>Oâamide
sp<sup>2</sup>N interactions (proposed nâÏ* hydrogen
bond) and amide sp<sup>2</sup>Oâaromatic sp<sup>2</sup>C (proposed
nâÏ*) interactions are favorable in water, while amide
sp<sup>2</sup>Oâsp<sup>3</sup>C interactions are unfavorable.
Interactions of all ureas with sp<sup>3</sup>C and amide sp<sup>2</sup>N are favorable and increase in strength with increasing alkylation,
indicating favorable sp<sup>3</sup>Câamide sp<sup>2</sup>N
and sp<sup>3</sup>Câsp<sup>3</sup>C interactions. Naphthalene
results show that aromatic sp<sup>2</sup>Câamide sp<sup>2</sup>N interactions in water are unfavorable while sp<sup>2</sup>Câsp<sup>3</sup>C interactions are favorable. These results allow interactions
of amide and hydrocarbon moieties and effects of urea and alkylureas
on aqueous processes to be predicted or interpreted in terms of structural
information. We predict strengths of favorable ureaâbenzene
and <i>N</i>-methylacetamide interactions from experimental
information to compare with simulations and indicate how amounts of
hydrocarbon and amide surfaces buried in protein folding and other
biopolymer processes and transition states can be determined from
analysis of urea and diethylurea effects on equilibrium and rate constants