Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Optimizing pKa computation in proteins with pH adapted conformations.

Gernot Kieseritzky1, Ernst-Walter Knapp

  • 1Fachbereich Biologie, Chemie, Pharmazie/Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.

Proteins
|December 7, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Quantification of Local Electric Field Changes at the Active Site of Cytochrome <i>c</i> Oxidase by Fourier Transform Infrared Spectroelectrochemical Titrations.

Frontiers in chemistry·2021
Same author

Retraction: The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation.

Physical chemistry chemical physics : PCCP·2017
Same author

The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation.

Physical chemistry chemical physics : PCCP·2017
Same author

Influence of Heterogeneity on the Ultrafast Photoisomerization Dynamics of Pfr in Cph1 Phytochrome.

Photochemistry and photobiology·2017
Same author

Structural and Vibrational Characterization of the Chromophore Binding Site of Bacterial Phytochrome Agp1.

Photochemistry and photobiology·2017
Same author

Merging Structural Information from X-ray Crystallography, Quantum Chemistry, and EXAFS Spectra: The Oxygen-Evolving Complex in PSII.

The journal of physical chemistry. B·2016

This study introduces a novel method for calculating protein pK(A) values using optimized conformations and self-consistent electrostatics. The approach accurately predicts experimental values, offering insights into pH-dependent protein behavior.

Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Chemistry

Background:

  • Accurate prediction of protein pK(A) values is crucial for understanding protein function and interactions.
  • Existing methods often struggle with the conformational flexibility and surface salt bridge dynamics of proteins.

Purpose of the Study:

  • To develop a robust computational method for determining protein pK(A) values.
  • To improve the accuracy of pK(A) predictions by incorporating optimized protein conformations and self-consistent electrostatics.

Main Methods:

  • Utilized electrostatic energy computations on a limited set of optimized protein conformations derived from crystal structures.
  • Self-consistently determined hydrogen positions and salt bridge geometries at varying pH levels (low, ambient, high).

Related Experiment Videos

Main Results:

  • Achieved a Root Mean Square Deviation (RMSD) of 1.12 for 185 experimental pK(A) values across 15 proteins, comparable to existing methods.
  • Demonstrated that considering salt bridge conformational changes at the protein surface is critical for accurate pK(A) prediction.
  • The method showed improved accuracy for strongly shifted experimental pK(A) values compared to other approaches.

Conclusions:

  • The developed method provides accurate pK(A) predictions without needing empirical corrections for conformational flexibility.
  • The approach allows for the interpretation of computed pK(A) values in relation to pH-dependent hydrogen bonding and salt bridge structures.
  • A web service is available for performing these pK(A) computations.