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Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D.

Federico Forneris1, B Tom Burnley1, Piet Gros1

  • 1Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Acta Crystallographica. Section D, Biological Crystallography
|March 7, 2014
PubMed
Summary
This summary is machine-generated.

Human factor D (FD), a complement immune response protein, exhibits conformational dynamics similar to thrombin. Unlike thrombin, FD possesses a unique self-inhibitory loop that maintains its inactive state, crucial for immune regulation.

Keywords:
complement systemensemble refinementproteolysisstructural dynamics

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Immunology

Background:

  • Human factor D (FD) is a serine proteinase vital for the complement immune response.
  • FD's substrate interactions and exosite region are key to its function.
  • Protein dynamics and allosteric regulation, influenced by ions like Na+, are critical in related enzymes like thrombin.

Purpose of the Study:

  • To investigate the structural dynamics of Human Factor D (FD) and thrombin using ensemble refinement (ER).
  • To compare the conformational flexibility and dynamics of FD with thrombin.
  • To elucidate the mechanism of FD's self-inhibition and its role in immune response regulation.

Main Methods:

  • Ensemble refinement (ER) of X-ray crystal structures for FD and thrombin.
  • Comparative analysis of ER data with existing NMR data for thrombin.
  • Characterization of the R202A FD variant to assess activity and conformational changes.

Main Results:

  • ER revealed that FD, like thrombin, possesses conformational dynamics.
  • The R202A FD variant showed increased activity and displayed both active and inactive conformations.
  • FD's exosite loops were disordered in the variant, similar to thrombin without Na+.
  • FD utilizes a self-inhibitory loop to maintain an ordered, inactive state, distinct from thrombin's regulation.

Conclusions:

  • Human Factor D exhibits conformational dynamics comparable to thrombin.
  • FD has evolved a unique self-inhibitory mechanism involving its exosite and a self-inhibitory loop to regulate its activity.
  • Ensemble refinement of crystal structures offers a valuable method for studying protein dynamics, complementing spectroscopic techniques.