5 research outputs found
Human Hsp70 Substrate-Binding Domains Recognize Distinct Client Proteins
The 13 Hsp70 proteins in humans act on unique sets of
substrates
with diversity often being attributed to J-domain-containing protein
(Hsp40 or JDP) cofactors. We were therefore surprised to find drastically
different binding affinities for Hsp70-peptide substrates, leading
us to probe substrate specificity among the 8 canonical Hsp70s from
humans. We used peptide arrays to characterize Hsp70 binding and then
mined these data using machine learning to develop an algorithm for
isoform-specific prediction of Hsp70 binding sequences. The results
of this algorithm revealed recognition patterns not predicted based
on local sequence alignments. We then showed that none of the human
isoforms can complement heat-shocked DnaK knockout Escherichia coli cells. However, chimeric Hsp70s
consisting of the human nucleotide-binding domain and the substrate-binding
domain of DnaK complement during heat shock, providing further evidence
in vivo of the divergent function of the Hsp70 substrate-binding domains.
We also demonstrated that the differences in heat shock complementation
among the chimeras are not due to loss of DnaJ binding. Although we
do not exclude JDPs as additional specificity factors, our data demonstrate
substrate specificity among the Hsp70s, which has important implications
for inhibitor development in cancer and neurodegeneration
Human Hsp70 Substrate-Binding Domains Recognize Distinct Client Proteins
The 13 Hsp70 proteins in humans act on unique sets of
substrates
with diversity often being attributed to J-domain-containing protein
(Hsp40 or JDP) cofactors. We were therefore surprised to find drastically
different binding affinities for Hsp70-peptide substrates, leading
us to probe substrate specificity among the 8 canonical Hsp70s from
humans. We used peptide arrays to characterize Hsp70 binding and then
mined these data using machine learning to develop an algorithm for
isoform-specific prediction of Hsp70 binding sequences. The results
of this algorithm revealed recognition patterns not predicted based
on local sequence alignments. We then showed that none of the human
isoforms can complement heat-shocked DnaK knockout Escherichia coli cells. However, chimeric Hsp70s
consisting of the human nucleotide-binding domain and the substrate-binding
domain of DnaK complement during heat shock, providing further evidence
in vivo of the divergent function of the Hsp70 substrate-binding domains.
We also demonstrated that the differences in heat shock complementation
among the chimeras are not due to loss of DnaJ binding. Although we
do not exclude JDPs as additional specificity factors, our data demonstrate
substrate specificity among the Hsp70s, which has important implications
for inhibitor development in cancer and neurodegeneration
Human Hsp70 Substrate-Binding Domains Recognize Distinct Client Proteins
The 13 Hsp70 proteins in humans act on unique sets of
substrates
with diversity often being attributed to J-domain-containing protein
(Hsp40 or JDP) cofactors. We were therefore surprised to find drastically
different binding affinities for Hsp70-peptide substrates, leading
us to probe substrate specificity among the 8 canonical Hsp70s from
humans. We used peptide arrays to characterize Hsp70 binding and then
mined these data using machine learning to develop an algorithm for
isoform-specific prediction of Hsp70 binding sequences. The results
of this algorithm revealed recognition patterns not predicted based
on local sequence alignments. We then showed that none of the human
isoforms can complement heat-shocked DnaK knockout Escherichia coli cells. However, chimeric Hsp70s
consisting of the human nucleotide-binding domain and the substrate-binding
domain of DnaK complement during heat shock, providing further evidence
in vivo of the divergent function of the Hsp70 substrate-binding domains.
We also demonstrated that the differences in heat shock complementation
among the chimeras are not due to loss of DnaJ binding. Although we
do not exclude JDPs as additional specificity factors, our data demonstrate
substrate specificity among the Hsp70s, which has important implications
for inhibitor development in cancer and neurodegeneration
Data Streaming for Metabolomics: Accelerating Data Processing and Analysis from Days to Minutes
The speed and throughput
of analytical platforms has been a driving
force in recent years in the “omics” technologies and
while great strides have been accomplished in both chromatography
and mass spectrometry, data analysis times have not benefited at the
same pace. Even though personal computers have become more powerful,
data transfer times still represent a bottleneck in data processing
because of the increasingly complex data files and studies with a
greater number of samples. To meet the demand of analyzing hundreds
to thousands of samples within a given experiment, we have developed
a data streaming platform, XCMS Stream, which capitalizes on the acquisition
time to compress and stream recently acquired data files to data processing
servers, mimicking just-in-time production strategies from the manufacturing
industry. The utility of this XCMS Online-based technology is demonstrated
here in the analysis of T cell metabolism and other large-scale metabolomic
studies. A large scale example on a 1000 sample data set demonstrated
a 10 000-fold time savings, reducing data analysis time from
days to minutes. Further, XCMS Stream has the capability to increase
the efficiency of downstream biochemical dependent data acquisition
(BDDA) analysis by initiating data conversion and data processing
on subsets of data acquired, expanding its application beyond data
transfer to smart preliminary data decision-making prior to full acquisition
Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses
Active data screening is an integral
part of many scientific activities,
and mobile technologies have greatly facilitated this process by minimizing
the reliance on large hardware instrumentation. In order to meet with
the increasingly growing field of metabolomics and heavy workload
of data processing, we designed the first remote metabolomic data
screening platform for mobile devices. Two mobile applications (apps),
XCMS Mobile and METLIN Mobile, facilitate access to XCMS and METLIN,
which are the most important components in the computer-based XCMS
Online platforms. These mobile apps allow for the visualization and
analysis of metabolic data throughout the entire analytical process.
Specifically, XCMS Mobile and METLIN Mobile provide the capabilities
for remote monitoring of data processing, real time notifications
for the data processing, visualization and interactive analysis of
processed data (e.g., cloud plots, principle component analysis, box-plots,
extracted ion chromatograms, and hierarchical cluster analysis), and
database searching for metabolite identification. These apps, available
on Apple iOS and Google Android operating systems, allow for the migration
of metabolomic research onto mobile devices for better accessibility
beyond direct instrument operation. The utility of XCMS Mobile and
METLIN Mobile functionalities was developed and is demonstrated here
through the metabolomic LC-MS analyses of stem cells, colon cancer,
aging, and bacterial metabolism