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Related Experiment Video

Updated: Sep 26, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures.

Mirko Schmitz1,2, Anne Schultze1,2, Raimonds Vanags3

  • 1Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany.

Nucleic Acids Research
|April 19, 2022
PubMed
Summary
This summary is machine-generated.

patcHwork is a new web server for analyzing protein pH sensitivity. It identifies pH-sensitive residues and their affected noncovalent bonds, aiding in understanding protein function changes.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Protein function is modulated by pH through alterations in amino acid residue charges.
  • Existing tools analyze charge distribution but not changes in noncovalent bonds between two pH values.
  • Understanding pH-dependent protein behavior is crucial for various biological processes.

Purpose of the Study:

  • To develop a user-friendly web server, patcHwork, for accessible protein pH sensitivity analysis.
  • To identify amino acids with charge shifts and affected noncovalent bonds at two distinct pH values.
  • To introduce the concept of 'patches' of nearby pH-sensitive residues impacting protein function.

Main Methods:

  • Utilized the Henderson-Hasselbalch equation for sequence-level pH-sensitive residue identification.
  • Integrated PDB2PQR and PROPKA tools with noncovalent bond algorithms for structure-based analysis.
  • Developed a graphical interface for visualizing pH-sensitive residues and interactions like salt bridges and hydrogen bonds.

Main Results:

  • patcHwork successfully identifies pH-sensitive residues and maps changes in salt bridges, hydrogen bonds, and aromatic interactions.
  • The server enables visualization of these changes, providing mechanistic insights into pH effects.
  • Demonstrated the utility of patcHwork on known pH-sensitive proteins.

Conclusions:

  • patcHwork enhances the accessibility of protein pH sensitivity analysis.
  • The tool aids in understanding how pH influences protein structure and function through noncovalent bond dynamics.
  • The concept of 'patches' offers a novel perspective on localized pH-mediated functional regulation.