Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment

The Journal of Physical Chemistry. B
Joanna MakowskaHarold A Scheraga

Abstract

We compared the ability of two theoretical methods of pH-dependent conformational calculations to reproduce experimental potentiometric titration curves of two models of peptides: Ac-K5-NHMe in 95% methanol (MeOH)/5% water mixture and Ac-XX(A)7OO-NH2 (XAO) (where X is diaminobutyric acid, A is alanine, and O is ornithine) in water, methanol (MeOH), and dimethyl sulfoxide (DMSO), respectively. The titration curve of the former was taken from the literature, and the curve of the latter was determined in this work. The first theoretical method involves a conformational search using the electrostatically driven Monte Carlo (EDMC) method with a low-cost energy function (ECEPP/3 plus the SRFOPT surface-solvation model, assumming that all titratable groups are uncharged) and subsequent reevaluation of the free energy at a given pH with the Poisson-Boltzmann equation, considering variable protonation states. In the second procedure, molecular dynamics (MD) simulations are run with the AMBER force field and the generalized Born model of electrostatic solvation, and the protonation states are sampled during constant-pH MD runs. In all three solvents, the first pKa of XAO is strongly downshifted compared to the value for the reference com...Continue Reading

References

Dec 26, 1989·Biochemistry·K SomanR Fletterick
Jan 1, 1988·Proteins·M K Gilson, B H Honig
Feb 1, 1997·Protein Science : a Publication of the Protein Society·S T WlodekJ A McCammon
Jul 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Zhengshuang ShiNeville R Kallenbach
Jan 7, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Aleksandra M Walczak, Jan M Antosiewicz
Mar 5, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Maciej DługoszAndrew D Robertson
Oct 14, 2004·Journal of Computational Chemistry·John MonganJ Andrew McCammon
Apr 20, 2005·Current Opinion in Structural Biology·John Mongan, David A Case
Aug 5, 2005·Proteins·Jorge A VilaHarold A Scheraga

❮ Previous
Next ❯

Citations

Apr 27, 2010·The European Physical Journal. E, Soft Matter·M Aguilella-Arzo, V M Aguilella
Oct 13, 2006·Annual Review of Physical Chemistry·Harold A ScheragaAdam Liwo
Mar 26, 2013·Biophysical Chemistry·Andreja Mirtič, Jože Grdadolnik
Feb 6, 2007·Biophysical Journal·Joanna MakowskaHarold A Scheraga
Nov 18, 2015·Journal of Chemical Theory and Computation·Tim Meyer, Ernst-Walter Knapp
Dec 2, 2011·The Journal of Physical Chemistry. B·Joanna MakowskaLech Chmurzyński

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.