Description of peptide bond planarity from high-resolution neutron crystallography.

Biophys Physicobiol

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

Published: September 2023

Neutron crystallography is a highly effective method for visualizing hydrogen atoms in proteins. In our recent study, we successfully determined the high-resolution (1.2 Å) neutron structure of high-potential iron-sulfur protein, refining the coordinates of some amide protons without any geometric restraints. Interestingly, we observed that amide protons are deviated from the peptide plane due to electrostatic interactions. Moreover, the difference in the position of the amide proton of Cys75 between reduced and oxidized states is possibly attributed to the electron storage capacity of the iron-sulfur cluster. Additionally, we have discussed about the rigidity of the iron-sulfur cluster based on the results of the hydrogen-deuterium exchange. Our research underscores the significance of neutron crystallography in protein structure elucidation, enriching our understanding of protein functions at an atomic resolution.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728621PMC
http://dx.doi.org/10.2142/biophysico.bppb-v20.0035DOI Listing

Publication Analysis

Top Keywords

neutron crystallography
12
high-resolution neutron
8
amide protons
8
iron-sulfur cluster
8
description peptide
4
peptide bond
4
bond planarity
4
planarity high-resolution
4
neutron
4
crystallography neutron
4

Similar Publications

X-ray diffraction (XRD) has evolved significantly since its inception, becoming a crucial tool for material structure characterization. Advancements in theory, experimental techniques, diffractometers and detection technology have led to the acquisition of highly accurate diffraction patterns, surpassing previous expectations. Extracting comprehensive information from these patterns necessitates different models due to the influence of both electron density and thermal motion on diffracted beam intensity.

View Article and Find Full Text PDF

Integrated edge-to-exascale workflow for real-time steering in neutron scattering experiments.

Struct Dyn

November 2024

Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.

We introduce a computational framework that integrates artificial intelligence (AI), machine learning, and high-performance computing to enable real-time steering of neutron scattering experiments using an edge-to-exascale workflow. Focusing on time-of-flight neutron event data at the Spallation Neutron Source, our approach combines temporal processing of four-dimensional neutron event data with predictive modeling for multidimensional crystallography. At the core of this workflow is the Temporal Fusion Transformer model, which provides voxel-level precision in predicting 3D neutron scattering patterns.

View Article and Find Full Text PDF

Towards improved accuracy of Hirshfeld atom refinement with an alternative electron density partition.

IUCrJ

January 2025

Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland.

Hirshfeld atom refinement (HAR) is generally the chosen method for obtaining accurate hydrogen atom parameters from X-ray diffraction data. Still, determination can prove challenging, especially in the case of atomic displacement parameters (ADPs). We demonstrate that such a situation can occur when the ADP values of the bonding partner of the hydrogen atom are not determined accurately.

View Article and Find Full Text PDF

Quantifying Long-Time Hydrogen-Deuterium Exchange of Bovine Serum Albumin with Hydrogen-Deuterium Exchange Small-Angle Neutron Scattering.

J Phys Chem B

January 2025

Center for Neutron Science, Department of Chemical and Biomolecular Engineering, College of Engineering, University of Delaware, Newark, Delaware 19711, United States.

Hydrogen-deuterium exchange (HDX) measured by small-angle neutron scattering (HDX-SANS) is used to measure HDX in bovine serum albumin (BSA) under different temperatures and formulation conditions. HDX-SANS measurements are performed at 40, 50, and 60 °C in DO after storing proteins at 4 °C for 1 week to pre-exchange the readily accessible hydrogens. This enables us to probe the long-time HDX of protons at the core of the BSA proteins, which is more challenging for solvent molecules to access.

View Article and Find Full Text PDF

Histidine is a key amino-acid residues in proteins that can exist in three different protonation states: two different neutral tautomeric forms and a protonated, positively charged one. It can act as both donor and acceptor of hydrogen bonds, coordinate metal ions, and engage in acid/base catalysis. Human Carbonic Anhydrase II (HCA II) is a pivotal enzyme catalyzing the reversible hydration of carbon dioxide.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!