Dan McElheny

The dynamic energy landscape of dihydrofolate reductase catalysis.

We used nuclear magnetic resonance relaxation dispersion to characterize higher energy conformational substates of Escherichia coli dihydrofolate reductase. Each intermediate in the catalytic cycle samples low-lying excited states whose conformations resemble the ground-state structures of preceding and following intermediates. Substrate and cofactor exchange occurs through these excited substates. The maximum hydride transfer and steady-state turnover rates are governed by the dynamics of transitions between ground and excited states of the intermediates. Thus, the modulation of the energy landscape by the bound ligands funnels the enzyme through its reaction cycle along a preferred kinetic path.

Aβ(1–42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease

Increasing evidence has suggested that formation and propagation of misfolded aggregates of 42-residue human amyloid β (Aβ(1–42)), rather than of the more abundant Aβ(1–40), provokes the Alzheimers disease cascade. However, structural details of misfolded Aβ(1–42) have remained elusive. Here we present the atomic model of an Aβ(1–42) amyloid fibril, from solid-state NMR (ssNMR) data. It displays triple parallel-β-sheet segments that differ from reported structures of Aβ(1–40) fibrils. Remarkably, Aβ(1–40) is incompatible with the triple-β-motif, because seeding with Aβ(1–42) fibrils does not promote conversion of monomeric Aβ(1–40) into fibrils via cross-replication. ssNMR experiments suggest that C-terminal Ala42, absent in Aβ(1–40), forms a salt bridge with Lys28 to create a self-recognition molecular switch that excludes Aβ(1–40). The results provide insight into the Aβ(1–42)-selective self-replicating amyloid-propagation machinery in early-stage Alzheimers disease.

Molecular-Level Examination of Cu2+ Binding Structure for Amyloid Fibrils of 40-Residue Alzheimer's β by Solid-State NMR Spectroscopy

Cu(2+) binding to Alzheimers β (Aβ) peptides in amyloid fibrils has attracted broad attention, as it was shown that Cu ion concentration elevates in Alzheimers senile plaque and such association of Aβ with Cu(2+) triggers the production of neurotoxic reactive oxygen species (ROS) such as H(2)O(2). However, detailed binding sites and binding structures of Cu(2+) to Aβ are still largely unknown for Aβ fibrils or other aggregates of Aβ. In this work, we examined molecular details of Cu(2+) binding to amyloid fibrils by detecting paramagnetic signal quenching in 1D and 2D high-resolution (13)C solid-state NMR (SSNMR) for full-length 40-residue Aβ(1-40). Selective quenching observed in (13)C SSNMR of Cu(2+)-bound Aβ(1-40) suggested that primary Cu(2+) binding sites in Aβ(1-40) fibrils include N(ε) in His-13 and His-14 and carboxyl groups in Val-40 as well as in Glu sidechains (Glu-3, Glu-11, and/or Glu-22). (13)C chemical shift analysis demonstrated no major structural changes upon Cu(2+) binding in the hydrophobic core regions (residues 18-25 and 30-36). Although the ROS production via oxidization of Met-35 in the presence of Cu(2+) has been long suspected, our SSNMR analysis of (13)C(ε)H(3)-S- in M35 showed little changes after Cu(2+) binding, excluding the possibility of Met-35 oxidization by Cu(2+) alone. Preliminary molecular dynamics (MD) simulations on Cu(2+)-Aβ complex in amyloid fibrils confirmed binding sites suggested by the SSNMR results and the stabilities of such bindings. The MD simulations also indicate the coexistence of a variety of Cu(2+)-binding modes unique in Aβ fibril, which are realized by both intra- and intermolecular contacts and highly concentrated coordination sites due to the in-register parallel β-sheet arrangements.

Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands

Enzyme catalysis can be described as progress over a multi-dimensional energy landscape where ensembles of interconverting conformational substates channel the enzyme through its catalytic cycle. We applied NMR relaxation dispersion to investigate the role of bound ligands in modulating the dynamics and energy landscape of Escherichia coli dihydrofolate reductase to obtain insights into the mechanism by which the enzyme efficiently samples functional conformations as it traverses its reaction pathway. Although the structural differences between the occluded substrate binary complexes and product ternary complexes are very small, there are substantial differences in protein dynamics. Backbone fluctuations on the μs-ms timescale in the cofactor binding cleft are similar for the substrate and product binary complexes, but fluctuations on this timescale in the active site loops are observed only for complexes with substrate or substrate analog and are not observed for the binary product complex. The dynamics in the substrate and product binary complexes are governed by quite different kinetic and thermodynamic parameters. Analogous dynamic differences in the E:THF:NADPH and E:THF:NADP+ product ternary complexes are difficult to rationalize from ground-state structures. For both of these complexes, the nicotinamide ring resides outside the active site pocket in the ground state. However, they differ in the structure, energetics, and dynamics of accessible higher energy substates where the nicotinamide ring transiently occupies the active site. Overall, our results suggest that dynamics in dihydrofolate reductase are exquisitely “tuned” for every intermediate in the catalytic cycle; structural fluctuations efficiently channel the enzyme through functionally relevant conformational space.

Geometry and Efficacy of Cross-Strand Trp/Trp, Trp/Tyr, and Tyr/Tyr Aromatic Interaction in a β-Hairpin Peptide

The Trpzip2 peptide (WTWENGKWTWK-NH(2)), designed by Cochran and co-workers, contains two pairs of Trps having cross-strand interaction and forms a stable antiparallel beta-hairpin. In order to study the geometries and effects on the structure and stability of different aromatic interactions, selected tryptophan residues were substituted with Tyr to get three Trpzip2 mutants with different Trp/Trp, Trp/Tyr, and Tyr/Tyr interacting pairs. Their native-state structures were determined using two-dimensional (2D) NMR and shown to have the same cross-strand edge-to-face Trp/Trp interaction as that in Trpzip2 for the Trp/Trp pair. The analogous Trp/Tyr and Tyr/Tyr pairs also tended to have an edge-to-face geometry. The effects of specific Trp/Trp, Trp/Tyr, and Tyr/Tyr interactions on hairpin stability were studied by varying temperature and monitoring structure with electronic circular dichroism (CD) and infrared (IR) absorption spectra. IR and CD temperature variations were fit to a two-state model that yielded lower T(m) values for Tyr containing mutants, indicating that Trp/Tyr and Tyr/Tyr interactions have less contribution to hairpin stability than the Trp/Trp interaction. Trp/Tyr interactions can provide significant stabilization, much greater than the Trp/aliphatic interaction, but Tyr/Tyr interactions are not as significant. Cross-strand interacting residues involving Trp with an edge-to-face orientation with Trp or Tyr had the strongest impact on hairpin stability.

A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase.

Correlated networks of amino acids have been proposed to play a fundamental role in allostery and enzyme catalysis. These networks of amino acids can be traced from surface-exposed residues all the way into the active site, and disruption of these networks can decrease enzyme activity. Substitution of the distal Gly121 residue in Escherichia coli dihydrofolate reductase results in an up to 200-fold decrease in the hydride transfer rate despite the fact that the residue is located 15 Å from the active-site center. In this study, nuclear magnetic resonance relaxation experiments are used to demonstrate that dynamics on the picosecond to nanosecond and microsecond to millisecond time scales are changed significantly in the G121V mutant of dihydrofolate reductase. In particular, picosecond to nanosecond time scale dynamics are decreased in the FG loop (containing the mutated residue at position 121) and the neighboring active-site loop (the Met20 loop) in the mutant compared to those of the wild-type enzyme, suggesting that these loops are dynamically coupled. Changes in methyl order parameters reveal a pathway by which dynamic perturbations can be propagated more than 25 Å across the protein from the site of mutation. All of the enzyme complexes, including the model Michaelis complex with folate and nicotinamide adenine dinucleotide phosphate bound, assume an occluded ground-state conformation, and we do not observe sampling of a higher-energy closed conformation by (15)N R2 relaxation dispersion experiments. This is highly significant, because it is only in the closed conformation that the cofactor and substrate reactive centers are positioned for reaction. The mutation also impairs microsecond to millisecond time scale fluctuations that have been implicated in the release of product from the wild-type enzyme. Our results are consistent with an important role for Gly121 in controlling protein dynamics critical for enzyme function and further validate the dynamic energy landscape hypothesis of enzyme catalysis.

Atomic structures of peptide self-assembly mimics

Although the β-rich self-assemblies are a major structural class for polypeptides and the focus of intense research, little is known about their atomic structures and dynamics due to their insoluble and noncrystalline nature. We developed a protein engineering strategy that captures a self-assembly segment in a water-soluble molecule. A predefined number of self-assembling peptide units are linked, and the β-sheet ends are capped to prevent aggregation, which yields a mono-dispersed soluble protein. We tested this strategy by using Borrelia outer surface protein (OspA) whose single-layer β-sheet located between two globular domains consists of two β-hairpin units and thus can be considered as a prototype of self-assembly. We constructed self-assembly mimics of different sizes and determined their atomic structures using x-ray crystallography and NMR spectroscopy. Highly regular β-sheet geometries were maintained in these structures, and peptide units had a nearly identical conformation, supporting the concept that a peptide in the regular β-geometry is primed for self-assembly. However, we found small but significant differences in the relative orientation between adjacent peptide units in terms of β-sheet twist and bend, suggesting their inherent flexibility. Modeling shows how this conformational diversity, when propagated over a large number of peptide units, can lead to a substantial degree of nanoscale polymorphism of self-assemblies.

Raf Kinase Inhibitory Protein Function Is Regulated via a Flexible Pocket and Novel Phosphorylation-Dependent Mechanism

ABSTRACT Raf kinase inhibitory protein (RKIP/PEBP1), a member of the phosphatidylethanolamine binding protein family that possesses a conserved ligand-binding pocket, negatively regulates the mammalian mitogen-activated protein kinase (MAPK) signaling cascade. Mutation of a conserved site (P74L) within the pocket leads to a loss or switch in the function of yeast or plant RKIP homologues. However, the mechanism by which the pocket influences RKIP function is unknown. Here we show that the pocket integrates two regulatory signals, phosphorylation and ligand binding, to control RKIP inhibition of Raf-1. RKIP association with Raf-1 is prevented by RKIP phosphorylation at S153. The P74L mutation increases kinase interaction and RKIP phosphorylation, enhancing Raf-1/MAPK signaling. Conversely, ligand binding to the RKIP pocket inhibits kinase interaction and RKIP phosphorylation by a noncompetitive mechanism. Additionally, ligand binding blocks RKIP association with Raf-1. Nuclear magnetic resonance studies reveal that the pocket is highly dynamic, rationalizing its capacity to interact with distinct partners and be involved in allosteric regulation. Our results show that RKIP uses a flexible pocket to integrate ligand binding- and phosphorylation-dependent interactions and to modulate the MAPK signaling pathway. This mechanism is an example of an emerging theme involving the regulation of signaling proteins and their interaction with effectors at the level of protein dynamics.

Capturing a Reactive State of Amyloid Aggregates NMR-BASED CHARACTERIZATION OF COPPER-BOUND ALZHEIMER DISEASE AMYLOID β-FIBRILS IN A REDOX CYCLE

Background: Association of redox-active Cu2+ with aggregated Aβ in amyloid plaques has been linked with ROS and oxidative stress in AD. Results: Cu2+/Cu+-bound Aβ fibrils undergo a redox cycle reaction with ascorbate and oxygen to produce H2O2. Conclusion: Cu2+/Cu+ ions bound to histidines of Aβ fibril offer enzyme-like reaction centers. Significance: The first site-specific structural evidence is presented on Cu+-bound Aβ fibrils that generate ROS. The interaction of redox-active copper ions with misfolded amyloid β (Aβ) is linked to production of reactive oxygen species (ROS), which has been associated with oxidative stress and neuronal damages in Alzheimer disease. Despite intensive studies, it is still not conclusive how the interaction of Cu+/Cu2+ with Aβ aggregates leads to ROS production even at the in vitro level. In this study, we examined the interaction between Cu+/Cu2+ and Aβ fibrils by solid-state NMR (SSNMR) and other spectroscopic methods. Our photometric studies confirmed the production of ∼60 μm hydrogen peroxide (H2O2) from a solution of 20 μm Cu2+ ions in complex with Aβ(1–40) in fibrils ([Cu2+]/[Aβ] = 0.4) within 2 h of incubation after addition of biological reducing agent ascorbate at the physiological concentration (∼1 mm). Furthermore, SSNMR 1H T1 measurements demonstrated that during ROS production the conversion of paramagnetic Cu2+ into diamagnetic Cu+ occurs while the reactive Cu+ ions remain bound to the amyloid fibrils. The results also suggest that O2 is required for rapid recycling of Cu+ bound to Aβ back to Cu2+, which allows for continuous production of H2O2. Both 13C and 15N SSNMR results show that Cu+ coordinates to Aβ(1–40) fibrils primarily through the side chain Nδ of both His-13 and His-14, suggesting major rearrangements from the Cu2+ coordination via Nϵ in the redox cycle. 13C SSNMR chemical shift analysis suggests that the overall Aβ conformations are largely unaffected by Cu+ binding. These results present crucial site-specific evidence of how the full-length Aβ in amyloid fibrils offers catalytic Cu+ centers.

Role of different β-turns in β-hairpin conformation and stability studied by optical spectroscopy

Model β‐hairpin peptides based on variations in the turn sequence of Cochrans tryptophan zipper peptide, SWTWENGKWTWK, were studied using electronic circular dichroism (ECD), fluorescence, and infrared (IR) spectroscopies. The trpzip2 Asn–Gly turn sequence was substituted with Thr–Gly, Aib–Gly, DPro–Gly, and Gly–Asn (trpzip1) to study the impact of turn stability on β‐hairpin formation. Stability and conformational changes of these hairpins were monitored by thermodynamic analyses of the temperature variation of both FTIR (amide I′) and ECD spectral intensities. These changes were fit to a two‐state model which yielded different Tm values, representing the folding/unfolding process, for hairpins with different β‐turns. Different β‐turns show systematic contributions to hairpin structure formation, and their inclusion in hairpin design can modify the folding pathways. Aib–Gly or DPro–Gly sequences stabilize the turn resulting in residual Trp–Trp interaction at high temperatures, but at the same time the β‐structure (cross strand H‐bonds) can become less stable due to constraints of the turn, as seen for DPro–Gly. The structure of the Aib–Gly turn containing hairpin was determined by NMR and was shown to be like trpzip2 (Asn–Gly turn) as regards turn and strand geometries, but to differ from trpzip1 (Gly–Asn turn). The Munoz and Eaton statistical mechanically derived multistate model, tested as an alternate point of view, represented contributions from H‐bonds and hydrophobic interactions as well as conformational change as interdependent. Use of different spectral methods that vary in dependence on these physical interactions along with the structural variations provided insight to the complex folding pathways of these small, well‐folded peptides. Proteins 2012.