15 research outputs found
Fluorotryptophan Incorporation Modulates the Structure and Stability of Transthyretin in a Site-Specific Manner
Abnormal deposition
of aggregated wild-type (WT) human transthyretin
(TTR) and its pathogenic variants is responsible for cardiomyopathy
and neuropathy related to TTR amyloidosis. The tryptophan (Trp) fluorescence
measurements typically used to study structural changes of TTR do
not yield site-specific information on the two Trp residues per TTR
protomer. To obtain such information, tryptophan labeled with fluorine
at the 5 and 6 positions (5FW and 6FW) was incorporated into TTR.
Fluorescence of 5FW and 6FW-labeled WT-TTR (WT-5FW and WT-6FW) and
a single-Trp mutant W41Y showed that the photophysics of incorporated
fluoro-Trp is consistent with site-specific solvation of the indole
ring of W41 and W79. <sup>19</sup>F-NMR showed that solvent accessibility
depends on both the location of the Trp and the position of the fluorine
substituent in the indole ring. Unexpectedly, differences were observed
in the rates of aggregation, with WT-6FW aggregating more rapidly
than WT-5FW or WT-TTR. Real-time <sup>19</sup>F-NMR urea unfolding
experiments revealed that WT-5FW is kinetically more stable than WT-6FW,
consistent with the aggregation assay. In addition, structural perturbations
of residues distant from either Trp site are more extensive in WT-6FW.
Notably, residues in the dimer interfaces are perturbed by 6FW at
residue 79; pathogenic mutations in these regions are associated with
reduced tetramer stability and amyloidogenesis. The differences in
behavior that arise from the replacement of a fluorine at the 5-position
of a tryptophan with one at the adjacent 6-position emphasize the
delicate balance of stability in the TTR tetramer
Side-Chain Conformational Heterogeneity of Intermediates in the <i>Escherichia coli</i> Dihydrofolate Reductase Catalytic Cycle
<i>Escherichia coli</i> dihydrofolate reductase (DHFR)
provides a paradigm for the integrated study of the role of protein
dynamics in enzyme function. Previous studies of backbone and side
chain dynamics have yielded unprecedented insights into the mechanism
by which DHFR progresses through the structural changes that occur
during its catalytic cycle. Here we report a comprehensive study of
the χ<sub>1</sub> rotamer populations of the aromatic and γ-methyl
containing residues for complexes of the catalytic cycle, based on
NMR measurement of <sup>3</sup><i>J</i><sub>CγCO</sub> and <sup>3</sup><i>J</i><sub>CγN</sub> coupling
constants. We report conformational and dynamic information for eight
distinct complexes, where transitions between rotamer wells may occur
on a broad picosecond to millisecond time scale. This large volume
of <sup>3</sup><i>J</i> data has allowed us to fit new Karplus
parameterizations for aromatic side chains and to select the best
available of previously determined parameters for Ile, Thr, and Val.
The <sup>3</sup><i>J</i><sub>CγCO</sub> and <sup>3</sup><i>J</i><sub>CγN</sub> coupling constants are found
to be extremely sensitive measures of side chain χ<sub>1</sub> rotamers and to give important insights into the extent of conformational
averaging. For a subset of residues in DHFR, the extent of rotamer
averaging is invariant to the nature of the bound ligand, while for
other residues the rotamer averaging differs in one or more complexes
of the enzymatic cycle. These variable-averaging residues are generally
located near the active site, but the phenomenon extends into the
adenosine binding domain. For several residues, the rotamer populations
in different DHFR complexes appear to depend on whether the complex
is in the closed or occluded state, and some residues are exquisitely
sensitive to small changes in the nature of the bound ligand
Side Chain Conformational Averaging in Human Dihydrofolate Reductase
The three-dimensional structures
of the dihydrofolate reductase
enzymes from <i>Escherichia coli</i> (ecDHFR or ecE) and <i>Homo sapiens</i> (hDHFR or hE) are very similar, despite a rather
low level of sequence identity. Whereas the active site loops of ecDHFR
undergo major conformational rearrangements during progression through
the reaction cycle, hDHFR remains fixed in a closed loop conformation
in all of its catalytic intermediates. To elucidate the structural
and dynamic differences between the human and <i>E. coli</i> enzymes, we conducted a comprehensive analysis of side chain flexibility
and dynamics in complexes of hDHFR that represent intermediates in
the major catalytic cycle. Nuclear magnetic resonance relaxation dispersion
experiments show that, in marked contrast to the functionally important
motions that feature prominently in the catalytic intermediates of
ecDHFR, millisecond time scale fluctuations cannot be detected for
hDHFR side chains. Ligand flux in hDHFR is thought to be mediated
by conformational changes between a hinge-open state when the substrate/product-binding
pocket is vacant and a hinge-closed state when this pocket is occupied.
Comparison of X-ray structures of hinge-open and hinge-closed states
shows that helix αF changes position by sliding between the
two states. Analysis of χ<sub>1</sub> rotamer populations derived
from measurements of <sup>3</sup><i>J</i><sub>CγCO</sub> and <sup>3</sup><i>J</i><sub>CγN</sub> couplings
indicates that many of the side chains that contact helix αF
exhibit rotamer averaging that may facilitate the conformational change.
The χ<sub>1</sub> rotamer adopted by the Phe31 side chain depends
upon whether the active site contains the substrate or product. In
the holoenzyme (the binary complex of hDHFR with reduced nicotinamide
adenine dinucleotide phosphate), a combination of hinge opening and
a change in the Phe31 χ<sub>1</sub> rotamer opens the active
site to facilitate entry of the substrate. Overall, the data suggest
that, unlike ecDHFR, hDHFR requires minimal backbone conformational
rearrangement as it proceeds through its enzymatic cycle, but that
ligand flux is brokered by more subtle conformational changes that
depend on the side chain motions of critical residues
Probing the Non-Native H Helix Translocation in Apomyoglobin Folding Intermediates
Apomyoglobin folds via sequential
helical intermediates that are
formed by rapid collapse of the A, B, G, and H helix regions. An equilibrium
molten globule with a similar structure is formed near pH 4. Previous
studies suggested that the folding intermediates are kinetically trapped
states in which folding is impeded by non-native packing of the G
and H helices. Fluorescence spectra of mutant proteins in which cysteine
residues were introduced at several positions in the G and H helices
show differential quenching of W14 fluorescence, providing direct
evidence of translocation of the H helix relative to helices A and
G in both the kinetic and equilibrium intermediates. Förster
resonance energy transfer measurements show that a 5-({2-[(acetyl)Âamino]Âethyl}Âamino)Ânaphthalene-1-sulfonic
acid acceptor coupled to K140C (helix H) is closer to Trp14 (helix
A) in the equilibrium molten globule than in the native state, by
a distance that is consistent with sliding of the H helix in an N-terminal
direction by approximately one helical turn. Formation of an S108C–L135C
disulfide prevents H helix translocation in the equilibrium molten
globule by locking the G and H helices into their native register.
By enforcing nativelike packing of the A, G, and H helices, the disulfide
resolves local energetic frustration and facilitates transient docking
of the E helix region onto the hydrophobic core but has only a small
effect on the refolding rate. The apomyoglobin folding landscape is
highly rugged, with several energetic bottlenecks that frustrate folding;
relief of any one of the major identified bottlenecks is insufficient
to speed progression to the transition state
Slow Dynamics of Tryptophan–Water Networks in Proteins
Water has a profound effect on the
dynamics of biomolecules and
governs many biological processes, leading to the concept that function
is slaved to solvent dynamics within and surrounding the biomolecule.
Protein conformational changes on μs–ms time scales are
frequently associated with protein function, but little is known about
the behavior of protein-bound water on these time scales. Here we
have used NMR relaxation dispersion measurements to probe the tryptophan
indoles in the enzyme dihydrofolate reductase (DHFR). We find that
during structural changes on the μs–ms time scale, large
chemical shift changes are often observed for the NH proton on the
indole ring, while relatively smaller chemical shift changes are observed
for the ring nitrogen atom. Comparison with experimental chemical
shifts and density functional theory-based chemical shift predictions
show that during the structural change the tryptophan indole NHs remain
bound to water, but the geometry of the protein-bound water networks
changes. These results establish that relaxation dispersion measurements
can indirectly probe water dynamics and indicate that water can influence,
or be influenced by, protein conformational changes on the μs–ms
time scale. Our data show that structurally conserved bound water
molecules can play a critical role in transmitting information between
functionally important regions of the protein and provide evidence
that internal protein motions can be coupled through the mediation
of hydrogen-bonded water bound in the protein structure
Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway
The
enzyme dihydrofolate reductase (DHFR, E) from Escherichia
coli is a paradigm for the role of protein
dynamics in enzyme catalysis. Previous studies have shown that the
enzyme progresses through the kinetic cycle by modulating the dynamic
conformational landscape in the presence of substrate dihydrofolate
(DHF), product tetrahydrofolate (THF), and cofactor (NADPH or NADP<sup>+</sup>). This study focuses on the quantitative description of the
relationship between protein fluctuations and product release, the
rate-limiting step of DHFR catalysis. NMR relaxation dispersion measurements
of millisecond time scale motions for the E:THF:NADP<sup>+</sup> and
E:THF:NADPH complexes of wild-type and the Leu28Phe (L28F) point mutant
reveal conformational exchange between an occluded ground state and
a low population of a closed state. The backbone structures of the
occluded ground states of the wild-type and mutant proteins are very
similar, but the rates of exchange with the closed excited states
are very different. Integrated analysis of relaxation dispersion data
and THF dissociation rates measured by stopped-flow spectroscopy shows
that product release can occur by two pathways. The intrinsic pathway
consists of spontaneous product dissociation and occurs for all THF-bound
complexes of DHFR. The allosteric pathway features cofactor-assisted
product release from the closed excited state and is utilized only
in the E:THF:NADPH complexes. The L28F mutation alters the partitioning
between the pathways and results in increased flux through the intrinsic
pathway relative to the wild-type enzyme. This repartitioning could
represent a general mechanism to explain changes in product release
rates in other E. coli DHFR mutants
Structural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and Nucleic Acids
The interactions of the human double-stranded
RNA-binding zinc
finger protein JAZ with RNA or DNA were investigated using electrophoretic
mobility-shift assays, isothermal calorimetry, and nuclear magnetic
resonance spectroscopy. Consistent with previous reports, JAZ has
very low affinity for duplex DNA or single-stranded RNA, but it binds
preferentially to double-stranded RNA (dsRNA) with no detectable sequence
specificity. The affinity of JAZ for dsRNA is unaffected by local
structural features such as loops, overhangs, and bulges, provided
a sufficient length of reasonably well-structured A-form RNA (about
18 bp for a single zinc finger) is present. Full-length JAZ contains
four Cys<sub>2</sub>His<sub>2</sub> zinc fingers (ZF1–4) and
has the highest apparent affinity for dsRNA; two-finger constructs
ZF12 and ZF23 have lower affinity, and ZF34 binds even more weakly.
The fourth zinc finger, ZF4, has no measurable RNA-binding affinity.
Single zinc finger constructs ZF1, ZF2, and ZF3 show evidence for
multiple-site binding on the minimal RNA. Fitting of quantitative
NMR titration and isothermal calorimetry data to a two-site binding
model gave <i>K</i><sub>d1</sub> ∼ 10 μM and <i>K</i><sub>d2</sub> ∼ 100 μM. Models of JAZ–RNA
complexes were generated using the high-ambiguity-driven biomolecular
docking (HADDOCK) program. Single zinc fingers bind to the RNA backbone
without sequence specificity, forming complexes with contacts between
the RNA minor groove and residues in the N-terminal β strands
and between the major groove and residues in the helix–kink–helix
motif. We propose that the non-sequence-specific interaction between
the zinc fingers of JAZ with dsRNA is dependent only on the overall
shape of the A-form RNA
Mapping Interactions of the Intrinsically Disordered C‑Terminal Regions of Tetrameric p53 by Segmental Isotope Labeling and NMR
The C-terminal region of the tumor suppressor protein
p53 contains
three domains, nuclear localization signal (NLS), tetramerization
domain (TET), and C-terminal regulatory domain (CTD), which are essential
for p53 function. Characterization of the structure and interactions
of these domains within full-length p53 has been limited by the overall
size and flexibility of the p53 tetramer. Using trans-intein splicing, we have generated full-length p53 constructs in
which the C-terminal region is isotopically labeled with 15N for NMR analysis, allowing us to obtain atomic-level information
on the C-terminal domains in the context of the full-length protein.
Resonances of NLS and CTD residues have narrow linewidths, showing
that these regions are largely solvent-exposed and dynamically disordered,
whereas resonances from the folded TET are broadened beyond detection.
Two regions of the CTD, spanning residues 369–374 and 381–388
and with high lysine content, make dynamic and sequence-independent
interactions with DNA in regions that flank the p53 recognition element.
The population of DNA-bound states increases as the length of the
flanking regions is extended up to approximately 20 base pairs on
either side of the recognition element. Acetylation of K372, K373,
and K382, using a construct of the transcriptional coactivator CBP
containing the TAZ2 and acetyltransferase domains, inhibits interaction
of the CTD with DNA. This work provides high-resolution insights into
the behavior of the intrinsically disordered C-terminal regions of
p53 within the full-length tetramer and the molecular basis by which
the CTD mediates DNA binding and specificity
Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway
The
enzyme dihydrofolate reductase (DHFR, E) from Escherichia
coli is a paradigm for the role of protein
dynamics in enzyme catalysis. Previous studies have shown that the
enzyme progresses through the kinetic cycle by modulating the dynamic
conformational landscape in the presence of substrate dihydrofolate
(DHF), product tetrahydrofolate (THF), and cofactor (NADPH or NADP<sup>+</sup>). This study focuses on the quantitative description of the
relationship between protein fluctuations and product release, the
rate-limiting step of DHFR catalysis. NMR relaxation dispersion measurements
of millisecond time scale motions for the E:THF:NADP<sup>+</sup> and
E:THF:NADPH complexes of wild-type and the Leu28Phe (L28F) point mutant
reveal conformational exchange between an occluded ground state and
a low population of a closed state. The backbone structures of the
occluded ground states of the wild-type and mutant proteins are very
similar, but the rates of exchange with the closed excited states
are very different. Integrated analysis of relaxation dispersion data
and THF dissociation rates measured by stopped-flow spectroscopy shows
that product release can occur by two pathways. The intrinsic pathway
consists of spontaneous product dissociation and occurs for all THF-bound
complexes of DHFR. The allosteric pathway features cofactor-assisted
product release from the closed excited state and is utilized only
in the E:THF:NADPH complexes. The L28F mutation alters the partitioning
between the pathways and results in increased flux through the intrinsic
pathway relative to the wild-type enzyme. This repartitioning could
represent a general mechanism to explain changes in product release
rates in other E. coli DHFR mutants
Structural Basis for Interaction of the Tandem Zinc Finger Domains of Human Muscleblind with Cognate RNA from Human Cardiac Troponin T
The human muscleblind-like
proteins (MBNL) regulate tissue-specific
splicing by targeting cardiac troponin T and other pre-mRNAs; aberrant
targeting of CUG and CCUG repeat expansions frequently accompanies
the neuromuscular disease myotonic dystrophy. We show, using biolayer
interferometry (Octet) and NMR spectroscopy, that the zinc finger
domains of MBNL isoform 1 (MBNL1) are necessary and sufficient for
binding CGCU sequences within the pre-mRNA of human cardiac troponin
T. Protein constructs containing zinc fingers 1 and 2 (zf12) and zinc
fingers 3 and 4 (zf34) of MBNL1 each fold into a compact globular
tandem zinc finger structure that participates in RNA binding. NMR
spectra show that the stoichiometry of the interaction between zf12
or zf34 and the CGCU sequence is 1:1, and that the RNA is single-stranded
in the complex. The individual zinc fingers within zf12 or zf34 are
nonequivalent: the primary RNA binding surface is formed in each pair
by the second zinc finger (zf2 or zf4), which interacts with the CGCU
RNA sequence. The NMR structure of the complex between zf12 and a
15-base RNA of sequence <sub>95</sub>GUCÂU<u>CGÂCU</u>UÂUÂUÂCÂCCC<sub>109</sub>, containing a single
CGCU element, shows the single-stranded RNA wrapped around zf2 and
extending to bind to the C-terminal helix. Bases C101, U102, and U103
make well-defined and highly ordered contacts with the protein, whereas
neighboring bases are less well-ordered in the complex. Binding of
the MBNL zinc fingers to cardiac troponin T pre-mRNA is specific and
relatively simple, unlike the complex multiple dimer–trimer
stoichiometries postulated in some previous studies