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X-ray Crystallography02:18

X-ray Crystallography

The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Determination of Crystal Structures01:29

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

Updated: Jul 19, 2026

Essential Metal Uptake in Gram-negative Bacteria: X-ray Fluorescence, Radioisotopes, and Cell Fractionation
10:34

Essential Metal Uptake in Gram-negative Bacteria: X-ray Fluorescence, Radioisotopes, and Cell Fractionation

Published on: February 1, 2018

Ab initio self-consistent x-ray absorption fine structure analysis for metalloproteins.

Nicholas Dimakis1, Grant Bunker

  • 1University of Texas-Pan American, Edinburg, TX, USA. dimakis@utpa.edu

Biophysical Journal
|October 3, 2006
PubMed
Summary

This study presents an automated method for determining metalloprotein active site structures using X-ray absorption fine structure (XAFS). The new technique combines advanced simulations and algorithms, reducing the need for prior assumptions about protein vibrations.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Biochemistry

Background:

  • X-ray absorption fine structure (XAFS) is crucial for analyzing metalloprotein structures.
  • Accurate analysis of XAFS data has been hindered by the need for assumptions regarding vibrational properties of coordinating residues.

Purpose of the Study:

  • To develop an automated procedure for precise structural determination of metalloprotein active sites.
  • To overcome limitations in current XAFS data analysis by minimizing ad hoc assumptions.

Main Methods:

  • Direct multiple-scattering simulation of XAFS spectra.
  • Integration of electron multiple-scattering calculations with density functional theory (DFT) for vibrational modes.
  • Application of the genetic algorithm 'differential evolution' for global parameter optimization.

Main Results:

  • Successful automated structural determination of metalloprotein active sites.
  • The procedure requires only minimal initial information for self-consistent iterative refinement.
  • Eliminates the need for ad hoc assumptions on vibrational properties.

Conclusions:

  • The presented automated method significantly advances structural analysis of metalloproteins using XAFS.
  • This approach offers a more robust and accurate way to probe metal sites in various biological environments.
  • Facilitates deeper understanding of metalloprotein function through precise structural insights.