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Related Concept Videos

Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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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.
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Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
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Related Experiment Video

Updated: Jan 10, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
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Exploration of questionable backbone conformations in crystallographic structure models using a structural alphabet.

Clémence Sarrau1, Marine Baillif1, Lucas Mantel1

  • 1Université Paris Cité, Unité de Biologie Fonctionnelle et Adaptative (BFA) CNRS UMR 8251 - In Silico Pharmacological Profiling (IsPP) INSERM U1133, F-75205 Paris CEDEX 13, France.

Acta Crystallographica. Section D, Structural Biology
|November 24, 2025
PubMed
Summary

Researchers developed a method to identify questionable protein backbone conformations in X-ray models. Over 18% of residues showed such conformations, potentially impacting structural data interpretation and biological relevance.

Keywords:
crystallographic structuresquestionable conformationsstructural alphabetstructural deformation

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • X-ray crystallography is crucial for protein structure determination, contributing over 80% of Protein Data Bank models.
  • Crystallographic models, even high-resolution ones, can contain artifacts and errors from crystallization, modeling, and refinement.
  • These limitations can lead to inaccurate atomic positions, causing local or global structural distortions.

Purpose of the Study:

  • To develop a reliable protocol for identifying residues with questionable backbone conformations in X-ray protein structure models.
  • To quantify the prevalence of these conformations and analyze their characteristics.
  • To investigate the impact of questionable conformations on specific protein structures and their biological relevance.

Main Methods:

  • A set of 826 nonredundant X-ray protein structure models was used.
  • Each model underwent energy minimization to relax atomic geometry.
  • Residues showing conformational differences between the X-ray and minimized models were identified using the HMM-SA structural alphabet.

Main Results:

  • Over 18% of residues across the analyzed set exhibited questionable backbone conformations.
  • These conformations were independent of model resolution, deposition date, or crystal system.
  • A correlation was observed between questionable conformations and secondary structures, with an overrepresentation in alpha-helices.
  • Analysis of HIV-2 protease (1hsi) revealed that questionable conformations may affect functionally important regions like the binding site flaps.

Conclusions:

  • A novel protocol effectively quantifies and localizes questionable backbone conformations in X-ray models.
  • These identified conformations can be structural outliers or sparsely sampled states, potentially affecting biological interpretation.
  • The findings highlight the need for careful evaluation of protein models derived from X-ray crystallography.