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Quantitative Detection of Protein Electrostatic Environment via Intrinsic pKa Calculations

Title: Quantitative Detection of Protein Electrostatic Environment via Intrinsic pKa Calculations.
Name(s): Stribling, Dan, author
Department of Chemistry and Biochemistry
Type of Resource: text
Genre: Text
Issuance: serial
Date Issued: 2014
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: One of the primary contributors to protein structure and functioning in biological systems is the electrostatic environment experienced by the protein. This environment is caused by charged and polar chemical interactions, with the acidic protein residues ASP and GLU often acting as a significant source of charged interactions in protein systems. Knowledge of the charged states of these residues is given by the determination of their pKa values and provides a significant source of information on the electrostatic character of protein environments. This knowledge provides insight into a diverse array of biological processes such as enzymatic function, membrane transport, and immunological activity. Simulation study has recently arisen as a cost-effective method to determine the pKa value of acidic protein residues. This study has successfully used molecular dynamics simulation with the Orthogonal Space Tempering method to determine the pKa values of the acidic ASP and GLU residues on the reduced form of the Human Thioredoxin Protein, an enzyme responsible for combatting oxidative stress in the human body. The study achieved an unprecedented accuracy in the computational determination of the pKa values of these residues with an overall RSMD of 0.71 units. Notably, the pKa value of the buried ASP residue was obtained to a before-unseen accuracy with a deviation of the pKa value from the experimental values by 0.6 units. This study demonstrates the utility of the OST computational method and its major potential for use in the prediction of pKa values of acidic residues in protein systems.
Identifier: FSU_migr_uhm-0344 (IID)
Keywords: Chemistry, Computational Chemistry, Human Thioredoxin, Orthogonal Space Tempering, pKa
Submitted Note: A Thesis submitted to the Department of Chemistry & Biochemistry In partial fulfillment of the requirements for graduation with Honors in the Major.
Degree Awarded: Spring Semester, 2015.
Date of Defense: April 10, 2014.
Subject(s): Biochemistry
Molecular biology
Chemistry, Physical and theoretical
Persistent Link to This Record:
Owner Institution: FSU
Is Part of Series: Honors Theses.

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Stribling, D. (2014). Quantitative Detection of Protein Electrostatic Environment via Intrinsic pKa Calculations. Retrieved from