4.4 Article

Direct evidence that all three histidine residues coordinate to Cu(II) in amyloid-β1-16

期刊

BIOCHEMISTRY
卷 47, 期 35, 页码 9117-9123

出版社

AMER CHEMICAL SOC
DOI: 10.1021/bi801014x

关键词

-

资金

  1. National Science Foundation CAREER [MCB 0346898]

向作者/读者索取更多资源

We provide direct evidence that all three histidine residues in amyloid-beta(1-16) (A beta(1-16)) coordinate to Cu(II). In our approach, we generate A beta(1-16) analogues, in each of which a selected histidine residue is isotopically enriched with (15)N. Pulsed electron spin resonance (ESR) experiments such as electron spin echo envelope modulation (ESEEM) and hyperfine sublevel correlation (HYSCORE) spectroscopy clearly show that all three histidine imidazole rings at positions 6, 13 and 14 in A beta(1-16) bind to Cu(II). The method employed here does not require either chemical side chain modification or amino acid residue. replacement, each of which is traditionally used to determine whether an amino acid residue in a protein binds to a metal ion. We find that the histidine coordination in the A beta(1-16) peptide is independent of the Cu(II)-to-peptide ratio, which is in contrast to the A beta(1-40) peptide. The ESR results also suggest tight binding between the histidine residues and the Cu(II) ion, which is likely the reason for the high binding affinity of the A beta peptide for Cu(II).

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.4
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Review Chemistry, Multidisciplinary

Going the dHis-tance: Site-Directed Cu2+ Labeling of Proteins and Nucleic Acids

Austin Gamble Jarvi, Xiaowei Bogetti, Kevin Singewald, Shreya Ghosh, Sunil Saxena

Summary: This Account showcases the use of site-directed Cu2+ labeling in proteins and DNA for measuring biomolecular structure and dynamics with electron paramagnetic resonance (EPR) spectroscopy. The labeling scheme provides a straightforward method for obtaining biophysical information that is not accessible using traditional EPR labels. The integration of molecular dynamics (MD) simulations with EPR distance information is expected to advance our understanding of protein and DNA conformational changes and interactions.

ACCOUNTS OF CHEMICAL RESEARCH (2021)

Article Chemistry, Physical

Cleavage-Resistant Protein Labeling With Hydrophilic Trityl Enables Distance Measurements In-Cell

Zikri Hasanbasri, Kevin Singewald, Teresa D. Gluth, Benoit Driesschaert, Sunil Saxena

Summary: Sensitive in-cell distance measurements in proteins can be achieved using deuterated OX063 with a maleimide linker (mOX063-d(24)), enabling high protein labeling and more sensitive measurements at 150K compared to 80K. The signal intensity of mOX063-d(24) remains appreciable even in the crowded environment of cells.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

Article Chemistry, Multidisciplinary

Cu(ii)-based DNA labeling identifies the structural link between transcriptional activation and termination in a metalloregulator

Joshua Casto, Alysia Mandato, Lukas Hofmann, Idan Yakobov, Shreya Ghosh, Sharon Ruthstein, Sunil Saxena

Summary: Understanding the structural and mechanistic details of protein-DNA interactions can lead to new ways of combating the virulence of pathogenic bacteria. The study on the Copper Efflux Regulator (CueR) protein reveals that it can bend DNA at high protein concentrations, and this bending enables the coordination with RNA polymerase.

CHEMICAL SCIENCE (2022)

Article Multidisciplinary Sciences

Structures of highly flexible intracellular domain of human α7 nicotinic acetylcholine receptor

Vasyl Bondarenko, Marta M. Wells, Qiang Chen, Tommy S. Tillman, Kevin Singewald, Matthew J. Lawless, Joel Caporoso, Nicole Brandon, Jonathan A. Coleman, Sunil Saxena, Erik Lindahl, Yan Xu, Pei Tang

Summary: In this study, using a combination of experiments and computational methods, the full-length intracellular domain (ICD) structure of the human alpha 7 nicotinic acetylcholine receptor in a resting state was determined. It was found that a significant portion of the ICD residues are located in highly flexible regions, with a large loop (loop L) contributing to its stability by anchoring onto the MA helix. Known motifs for cytoplasmic binding, regulation, and signaling were observed in both helices and disordered flexible regions, highlighting the important role of ICD conformational plasticity in orchestrating various biological processes.

NATURE COMMUNICATIONS (2022)

Article Biochemistry & Molecular Biology

Allostery-driven changes in dynamics regulate the activation of bacterial copper transcription factor

Idan Yakobov, Alysia Mandato, Lukas Hofmann, Kevin Singewald, Yulia Shenberger, Lada Gevorkyan-Airapetov, Sunil Saxena, Sharon Ruthstein

Summary: In this study, the dynamical changes of Escherichia coli CueR as a function of copper and DNA binding are measured using EPR spectroscopy. The results show that copper controls the activation of the transcription processes by initiating a series of dynamical changes over the protein.

PROTEIN SCIENCE (2022)

Article Biochemistry & Molecular Biology

Beyond structure: Deciphering site-specific dynamics in proteins from double histidine-based EPR measurements

Kevin Singewald, James A. Wilkinson, Zikri Hasanbasri, Sunil Saxena

Summary: The dynamics of site-specific proteins play a crucial role in protein function. This study utilized EPR spectroscopy to measure the dynamics of specific sites on a protein surface, and validated the results using molecular dynamics simulations. Additionally, small variations were observed at different sites, potentially due to local geometry and electrostatics. This work expands the utility of Cu(II)NTA-based EPR measurements.

PROTEIN SCIENCE (2022)

Article Chemistry, Multidisciplinary

Synthesis of Square Planar Cu4 Clusters

Manasseh Kusi Osei, Saber Mirzaei, Xiaowei Bogetti, Edison Castro, Mohammad Azizur Rahman, Sunil Saxena, Raul Hernandez Sanchez

Summary: Template-assisted synthesis of [M-4] clusters was achieved using a tetraamine scaffold L-R(NH2)(4) to direct the formation of C-4-symmetric L-R(NH)(4)Cu-4 clusters. The study showed the importance of metal-metal direct interactions in cluster formation. Computational and experimental analysis indicated the presence of a delocalized electronic structure in the clusters.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2022)

Review Biophysics

The use of EPR spectroscopy to study transcription mechanisms

L. Hofmann, A. Mandato, S. Saxena, S. Ruthstein

Summary: Electron paramagnetic resonance (EPR) spectroscopy is a promising structural biology tool to unravel complex and dynamic biological mechanisms. In this article, the advantages of continuous wave (CW) and pulsed EPR distance measurements in resolving transcription processes and protein-DNA interaction are discussed.

BIOPHYSICAL REVIEWS (2022)

Article Biochemical Research Methods

Store-bought is fine: Sensitivity considerations using shaped pulses for DEER measurements on Cu(II) labels

Joshua Casto, Xiaowei Bogetti, Hannah R. Hunter, Zikri Hasanbasri, Sunil Saxena

Summary: The narrow excitation bandwidth of monochromic pulses limits the sensitivity of pulsed dipolar spectroscopy on Cu(II)-based measurements. To overcome this limitation, frequency-swept pulses with large excitation bandwidths have been used. In this study, we demonstrate the effectiveness of chirp pulses on commercial instrumentation for Cu(II) distance measurements, and discuss the sensitivity considerations for robust distance measurements using Cu(II) labels in proteins. We show that a sweeping bandwidth chirp pulse can significantly improve the sensitivity of long-range distance measurements, while the sensitivity of short-range distances only slightly increases due to specific considerations for the chirp pulse duration.

JOURNAL OF MAGNETIC RESONANCE (2023)

Article Chemistry, Physical

Double Quantum Coherence ESR at Q-Band Enhances the Sensitivity of Distance Measurements at Submicromolar Concentrations

Alysia Mandato, Zikri Hasanbasri, Sunil Saxena

Summary: There have been significant improvements in pulsed ESR sensitivity, making it more applicable for the measurement of biological distance constraints at physiological concentrations and in complex systems. This work demonstrates the power of double quantum coherence (DQC) experiments at Q-band frequencies, enabling rapid and reliable measurements of spin distances at nanomolar concentrations. These nanomolar concentration measurements can lead to further advancements in the use of ESR, especially in cellular contexts.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2023)

Article Biochemistry & Molecular Biology

Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation

Xiaowei Bogetti, Anthony Bogetti, Joshua Casto, Gordon Rule, Lillian Chong, Sunil Saxena

Summary: The catalytic activity of hGSTA1-1 depends on the conformational dynamics of its C-terminal helix a9. The structure of the ligand-free state of the hGSTA1-1 homodimer was determined using EPR distance measurements and WE simulations. Negative cooperativity between the monomers of hGSTA1-1 was observed in the simulations, which suggests its importance in interacting with various toxic substrates.

PROTEIN SCIENCE (2023)

Review Chemistry, Multidisciplinary

Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics

Xiaowei Bogetti, Sunil Saxena

Summary: This Review discusses computational modeling techniques that enhance the interpretation of Electron Paramagnetic Resonance (EPR) measurements of biomolecules. Molecular dynamics simulations and enhanced sampling strategies are utilized to predict EPR spectra and sample stable conformations of biomolecules and their spin labels. The integration of de novo predictions, EPR measurements, and MD simulations is proposed for efficient sampling of alternate protein conformations. The importance of coupling EPR with modeling tools to investigate protein dynamics and structure is highlighted.

CHEMPLUSCHEM (2023)

Article Chemistry, Physical

Efficient sampling of molecular orientations for Cu(ii)-based DEER on protein labels

Zikri Hasanbasri, Nicholas A. Moriglioni, Sunil Saxena

Summary: Combining rigid Cu(ii) labels and pulsed-EPR techniques allows for precise investigation of protein structure and dynamics through distance constraint measurements. The unknown relative orientation of spins in a bilabeled protein poses a challenge due to the orientational selectivity effect. This study dissects the orientational selectivity phenomenon using in silico samples to optimize acquisition schemes and demonstrates the efficiency of rectangular pulses in double electron-electron resonance experiments.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2023)

Review Chemistry, Analytical

Measurement of Protein Dynamics from Site Directed Cu(II) Labeling

Kevin Singewald, Hannah Hunter, Timothy F. Cunningham, Sharon Ruthstein, Sunil Saxena

Summary: This review focuses on the use of Electron Paramagnetic Resonance (EPR) to measure residue-specific dynamics in proteins, with a specific emphasis on Cu(II)-based spin labels. It discusses the limitations of nitroxide-based spin labels and showcases the use of new Cu(II)-based protein labels, which improve rigidity and expand the spin-labeling toolkit. The review also describes how EPR measurements of the Cu(II) label reflect protein backbone motion and fluctuations, and provides insights into the measurement of site-specific dynamics at both alpha-helices and beta-sheets using the dHis motif. The review concludes by outlining the limitations of the dHis method and suggesting future developments.

ANALYSIS & SENSING (2023)

Article Chemistry, Physical

An optimal acquisition scheme for Q-band EPR distance measurements using Cu2+-based protein labels

Xiaowei Bogetti, Zikri Hasanbasri, Hannah R. Hunter, Sunil Saxena

Summary: Recent advances in site-directed Cu2+ labeling of proteins and nucleic acids have provided a new methodology for measuring the structure-function relationship in biomolecules. However, accessing the higher sensitivity of Q-band DEER has been challenging for Cu2+ labels designed for proteins. In this study, the orientational effects of the label are analyzed through simulations, and it is shown that three strategically selected magnetic field DEER measurements are generally sufficient for obtaining an orientational-averaged DEER time trace at Q-band.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)

暂无数据