23 research outputs found
HydrogenâDeuterium Exchange Mass Spectrometry Reveals Unique Conformational and Chemical Transformations Occurring upon [4Fe-4S] Cluster Binding in the Type 2 lâSerine Dehydratase from <i>Legionella pneumophila</i>
The
type 2 l-serine dehydratase from <i>Legionella
pneumophila</i> (<i>lp</i>LSD) contains a [4Fe-4S]<sup>2+</sup> cluster that acts as a Lewis acid to extract the hydroxyl
group of l-serine during the dehydration reaction. Surprisingly,
the crystal structure shows that all four of the iron atoms in the
cluster are coordinated with protein cysteinyl residues and that the
cluster is buried and not exposed to solvent. If the crystal structure
of <i>lp</i>LSD accurately reflects the structure in solution,
then substantial rearrangement at the active site is necessary for
the substrate to enter. Furthermore, repair of the oxidized protein
when the cluster has degraded would presumably entail exposure of
the buried cysteine ligands. Thus, the conformation required for the
substrate to enter may be similar to those required for a new cluster
to enter the active site. To address this, hydrogenâdeuterium
exchange combined with mass spectrometry (HDX MS) was used to probe
the conformational changes that occur upon oxidative degradation of
the FeâS cluster. The regions that show the most significant
differential HDX are adjacent to the cluster location in the holoenzyme
or connect regions that are adjacent to the cluster. The observed
decrease in flexibility upon cluster binding provides direct evidence
that the âtail-in-mouthâ conformation observed in the
crystal structure also occurs in solution and that the C-terminal
peptide is coordinated to the [4Fe-4S] cluster in a precatalytic conformation.
This observation is consistent with the requirement of an activation
step prior to catalysis and the unusually high level of resistance
to oxygen-induced cluster degradation. Furthermore, peptide mapping
of the apo form under nonreducing conditions revealed the formation
of disulfide bonds between C396 and C485 and possibly between C343
and C385. These observations provide a picture of how the cluster
loci are stabilized and poised to receive the cluster in the apo form
and the requirement for a reduction step during cluster formation
Conformational-Sensitive Fast Photochemical Oxidation of Proteins and Mass Spectrometry Characterize Amyloid Beta 1â42 Aggregation
Preventing
and treating Alzheimerâs disease require understanding
the aggregation of amyloid beta 1â42 (Aβ<sub>1â42</sub>) to give oligomers, protofibrils, and fibrils. Here we describe
footprinting of Aβ<sub>1â42</sub> by hydroxyl radical-based
fast photochemical oxidation of proteins (FPOP) and mass spectrometry
(MS) to monitor the time-course of Aβ<sub>1â42</sub> aggregation.
We resolved five distinct stages characterized by two sigmoidal behaviors,
showing the time-dependent transitions of monomers-paranuclei-protofibrils-fibrillar
aggregates. Kinetic modeling allows deciphering the amounts and interconversion
of the dominant Aβ<sub>1â42</sub> species. Moreover,
the irreversible footprinting probe provides insights into the kinetics
of oligomerization and subsequent fibrillar growth by allowing the
conformational changes of Aβ<sub>1â42</sub> at subregional
and even amino-acid-residue levels to be revealed. The middle domain
of Aβ<sub>1â42</sub> plays a major role in aggregation,
whereas the N-terminus retains most of its solvent-accessibility during
aggregation, and the hydrophobic C-terminus is involved to an intermediate
extent. This approach affords an in situ, real-time monitoring of
the solvent accessibility of Aβ<sub>1â42</sub> at various
stages of oligomerization, and provides new insights on site-specific
aggregation of Aβ<sub>1â42</sub> for a sample state beyond
the capabilities of most other biophysical methods
Fast Photochemical Oxidation of Proteins and Mass Spectrometry Follow Submillisecond Protein Folding at the Amino-Acid Level
We report a study of submillisecond protein folding with
amino-acid
residue resolution achieved with a two-laser pump/probe experiment
with analysis by mass spectrometry. The folding of a test protein,
barstar, can be triggered by a laser-induced temperature jump (T jump)
from âź0 °C to âźroom temperature. Subsequent reactions
via fast photochemical oxidation of proteins (FPOP) at various fractional
millisecond points after the T jump lead to oxidative modification
of solvent-accessible side chains whose âprotectionâ
changes with time and extent of folding. The modifications are identified
and quantified by LC-MS/MS following proteolysis. Among all the segments
that form secondary structure in the native state, helix<sub>1</sub> shows a decreasing trend of oxidative modification during the first
0.1â1 ms of folding while others do not change in this time
range. Residues I5, H17, L20, L24 and F74 are modified less in the
intermediate state than the denatured state, likely due to full or
partial protection of these residues as folding occurs. We propose
that in the early folding stage, barstar forms a partially solvent-accessible
hydrophobic core consisting of several residues that have long-range
interaction with other, more remote residues in the protein sequence.
Our data not only are consistent with the previous conclusion that
barstar fast folding follows the nucleation-condensation mechanism
with the nucleus centered on helix<sub>1</sub> formed in a folding
intermediate but also show the efficacy of this new approach to following
protein folding on the submillisecond time range
Primary and Higher Order Structure of the Reaction Center from the Purple Phototrophic Bacterium Blastochloris viridis: A Test for Native Mass Spectrometry
The reaction center
(RC) from the phototrophic bacterium Blastochloris
viridis was the first integral membrane
protein complex to have its structure determined by X-ray crystallography
and has been studied extensively since then. It is composed of four
protein subunits, H, M, L, and C, as well as cofactors, including
bacteriopheophytin (BPh), bacteriochlorophyll (BCh), menaquinone,
ubiquinone, heme, carotenoid, and Fe. In this study, we utilized mass
spectrometry-based proteomics to study this protein complex via bottom-up
sequencing, intact protein mass analysis, and native MS ligand-binding
analysis. Its primary structure shows a series of mutations, including
an unusual alteration and extension on the C-terminus of the M-subunit.
In terms of quaternary structure, proteins such as this containing
many cofactors serve to test the ability to introduce native-state
protein assemblies into the gas phase because the cofactors will not
be retained if the quaternary structure is seriously perturbed. Furthermore,
this specific RC, under native MS, exhibits a strong ability not only
to bind the special pair but also to preserve the two peripheral BChâs
HydrogenâDeuterium Exchange and Mass Spectrometry Reveal the pH-Dependent Conformational Changes of Diphtheria Toxin T Domain
The
translocation (T) domain of diphtheria toxin plays a critical
role in moving the catalytic domain across the endosomal membrane.
Translocation/insertion is triggered by a decrease in pH in the endosome
where conformational changes of T domain occur through several kinetic
intermediates to yield a final trans-membrane form. High-resolution
structural studies are only applicable to the static T-domain structure
at physiological pH, and studies of the T-domain translocation pathway
are hindered by the simultaneous presence of multiple conformations.
Here, we report the application of hydrogenâdeuterium exchange
mass spectrometry (HDX-MS) for the study of the pH-dependent conformational
changes of the T domain in solution. Effects of pH on intrinsic HDX
rates were deconvolved by converting the on-exchange times at low
pH into times under our âstandard conditionâ (pH 7.5).
pH-Dependent HDX kinetic analysis of T domain clearly reveals the
conformational transition from the native state (W-state) to a membrane-competent
state (W<sup>+</sup>-state). The initial transition occurs at pH 6
and includes the destabilization of N-terminal helices accompanied
by the separation between N- and C-terminal segments. The structural
rearrangements accompanying the formation of the membrane-competent
state expose a hydrophobic hairpin (TH8â9) to solvent, prepare
it to insert into the membrane. At pH 5.5, the transition is complete,
and the protein further unfolds, resulting in the exposure of its
C-terminal hydrophobic TH8â9, leading to subsequent aggregation
in the absence of membranes. This solution-based study complements
high resolution crystal structures and provides a detailed understanding
of the pH-dependent structural rearrangement and acid-induced oligomerization
of T domain
Peptide-Level Interactions between Proteins and Small-Molecule Drug Candidates by Two HydrogenâDeuterium Exchange MS-Based Methods: The Example of Apolipoprotein E3
We describe a platform
utilizing two methods based on hydrogenâdeuterium
exchange (HDX) coupled with mass spectrometry (MS) to characterize
interactions between a protein and a small-molecule ligand. The model
system is apolipoprotein E3 (apoE3) and a small-molecule drug candidate.
We extended PLIMSTEX (proteinâligand interactions by mass spectrometry,
titration, and H/D exchange) to the regional level by incorporating
enzymatic digestion to acquire binding information for peptides. In
a single experiment, we not only identified putative binding sites,
but also obtained affinities of 6.0, 6.8, and 10.6 ÎźM for the
three different regions, giving an overall binding affinity of 7.4
ÎźM. These values agree well with literature values determined
by accepted methods. Unlike those methods, PLIMSTEX provides <i>site-specific</i> binding information. The second approach,
modified SUPREX (stability of unpurified proteins from rates of H/D
exchange) coupled with electrospray ionization (ESI), allowed us to
obtain detailed understanding about apoE unfolding and its changes
upon ligand binding. Three binding regions, along with an additional
site, which may be important for lipid binding, show increased stability
(less unfolding) upon ligand binding. By employing a single parameter,
Î<i>C</i><sub>1/2</sub>%, we compared relative changes
of denaturation between peptides. This integrated platform provides
information orthogonal to commonly used HDX kinetics experiments,
providing a general and novel approach for studying proteinâligand
interactions
Continuous and Pulsed HydrogenâDeuterium Exchange and Mass Spectrometry Characterize CsgE Oligomerization
We report the use of hydrogenâdeuterium
amide exchange coupled
to mass spectrometry (HDX-MS) to study the interfaces of and conformational
changes accompanying CsgE oligomerization. This protein plays an important
role in enteric bacteria biofilm formation. Biofilms provide protection
for enteric bacteria from environmental extremes and raise concerns
about controlling bacteria and infectious disease. Their proteinaceous
components, called curli, are extracellular functional amyloids that
initiate surface contact and biofilm formation. The highly regulated
curli biogenesis involves a major subunit, CsgA, a minor subunit CsgB,
and a series of other accessory proteins. CsgE, possibly functioning
as oligomer, is a chaperonin-like protein that delivers CsgA to an
outer-membrane bound oligomeric CsgG complex. No higher-order structure,
or interfaces and dynamics of its oligomerization, however, are known.
In this work, we determined regions involved in CsgE self-association
by continuous HDX, and, on the basis of that, prepared a double mutant
W48A/F79A, derived from interface alanine scan, and verified that
it exists as monomer. Using pulsed HDX and MS, we suggest there is
a structural rearrangement occurring during the oligomerization of
CsgE
HydrogenâDeuterium Exchange Mass Spectrometry Reveals Calcium Binding Properties and Allosteric Regulation of Downstream Regulatory Element Antagonist Modulator (DREAM)
Downstream regulatory element antagonist
modulator (DREAM) is an
EF-hand Ca<sup>2+</sup>-binding protein that also binds to a specific
DNA sequence, downstream regulatory elements (DRE), and thereby regulates
transcription in a calcium-dependent fashion. DREAM binds to DRE in
the absence of Ca<sup>2+</sup> but detaches from DRE under Ca<sup>2+</sup> stimulation, allowing gene expression. The Ca<sup>2+</sup> binding properties of DREAM and the consequences of the binding
on protein structure are key to understanding the function of DREAM.
Here we describe the application of hydrogenâdeuterium exchange
mass spectrometry (HDX-MS) and site-directed mutagenesis to investigate
the Ca<sup>2+</sup> binding properties and the subsequent conformational
changes of full-length DREAM. We demonstrate that all EF-hands undergo
large conformation changes upon calcium binding even though the EF-1
hand is not capable of binding to Ca<sup>2+</sup>. Moreover, EF-2
is a lower-affinity site compared to EF-3 and -4 hands. Comparison
of HDX profiles between wild-type DREAM and two EF-1 mutated constructs
illustrates that the conformational changes in the EF-1 hand are induced
by long-range structural interactions. HDX analyses also reveal a
conformational change in an N-terminal leucine-charged residue-rich
domain (LCD) remote from Ca<sup>2+</sup>-binding EF-hands. This LCD
domain is responsible for the direct interaction between DREAM and
cAMP response element-binding protein (CREB) and regulates the recruitment
of the co-activator, CREB-binding protein. These long-range interactions
strongly suggest how conformational changes transmit the Ca<sup>2+</sup> signal to CREB-mediated gene transcription
Structural Analysis of Diheme Cytochrome <i>c</i> by HydrogenâDeuterium Exchange Mass Spectrometry and Homology Modeling
A lack
of X-ray or nuclear magnetic resonance structures of proteins
inhibits their further study and characterization, motivating the
development of new ways of analyzing structural information without
crystal structures. The combination of hydrogenâdeuterium exchange
mass spectrometry (HDX-MS) data in conjunction with homology modeling
can provide improved structure and mechanistic predictions. Here a
unique diheme cytochrome <i>c</i> (DHCC) protein from <i>Heliobacterium modesticaldum</i> is studied with both HDX and homology modeling to bring some definition of the structure of the
protein and its role. Specifically, HDX data were used to guide the
homology modeling to yield a more functionally relevant structural
model of DHCC