Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Globular and Fibrous Proteins

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

Conservation of Protein Domains

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Polyprotic Acids

Polyprotic Acids

Acids are classified by the number of protons per molecule that they can give up in a reaction. Acids such as HCl, HNO3, and HCN that contain one ionizable hydrogen atom in each molecule are called monoprotic acids. Their reactions with water are:

Molecular Shape and Polarity

Molecular Shape and Polarity

Dipole Moment of a Molecule

You might also read

Related Articles

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

Sort by

Same author

Ancestral sequence reconstruction dissects structural and functional differences among eosinophil ribonucleases.

The Journal of biological chemistry·2024

Same author

Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1.

Nature communications·2022

Same author

Structure-mechanics statistical learning uncovers mechanical relay in proteins.

Chemical science·2022

Same author

Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.

Computational and structural biotechnology journal·2021

Same author

PKA17-A Coarse-Grain Grid-Based Methodology and Web-Based Software for Predicting Protein pK <sub>a</sub> Shifts.

Journal of computational chemistry·2019

Same author

Binding of Copper and Cisplatin to Atox1 Is Mediated by Glutathione through the Formation of Metal-Sulfur Clusters.

Biochemistry·2017

Search research articles

Related Experiment Video

Updated: Jun 23, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

Reproducing basic pKa values for turkey ovomucoid third domain using a polarizable force field.

Timothy H Click¹, George A Kaminski

¹Department of Chemistry, Central Michigan University, Mt. Pleasant, Michigan 48859, USA.

The Journal of Physical Chemistry. B

|May 13, 2009

Summary

This study accurately calculates protein pKa values for basic residues using a polarizable force field and Poisson-Boltzmann solvation. The advanced method shows high agreement with experimental data, improving protein residue pKa prediction.

More Related Videos

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase

PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase

Published on: September 26, 2020

Related Experiment Videos

Last Updated: Jun 23, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase

PCR Mutagenesis, Cloning, Expression, Fast Protein Purification Protocols and Crystallization of the Wild Type and Mutant Forms of Tryptophan Synthase

Published on: September 26, 2020

Area of Science:

Biophysics
Computational Chemistry
Protein Science

Background:

Previous studies focused on acidic residues in turkey ovomucoid third domain protein (OMTKY3).
Accurate calculation of ionization constants (pKa) is crucial for understanding protein function and behavior.

Purpose of the Study:

To determine the relative pKa values for basic residues in OMTKY3.
To evaluate the performance of different computational methods, including polarizable force fields (PFF) and continuum solvation models, for pKa calculations.

Main Methods:

Employed a polarizable force field (PFF) and compared it with a nonpolarizable OPLS-AA force field.
Utilized Poisson-Boltzmann (PBF) and surface generalized Born (SGB) models for solvation.
Calculated pKa by comparing energies of solvated protonated and deprotonated protein forms.

Main Results:

The PFF combined with the PBF solvation model yielded pKa values in close agreement with experimental data (average error of 0.7 pH units).
Considering only nearby (hydrogen-bonded) residues is sufficient for accurate pKa calculations.
The PBF solvation model outperformed the SGB model for these calculations.

Conclusions:

The PFF/PBF methodology provides accurate pKa shifts for basic protein residues.
This computational approach is suitable for assessing pKa values of both acidic and basic protein residues.
Advanced nonpolar energy calculation schemes further enhance the accuracy of the results.