The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins

Biophysical Journal
Y Y ShamA Warshel

Abstract

The effect of the reorganization of the protein polar groups on charge-charge interaction and the corresponding effective dielectric constant (epsilon(eff)) is examined by the semimicroscopic version of the Protein Dipole Langevin Dipoles (PDLD/S) method within the framework of the Linear Response Approximation (LRA). This is done by evaluating the interactions between ionized residues in the reaction center of Rhodobacter sphaeroides, while taking into account the protein reorganization energy. It is found that an explicit consideration of the protein relaxation leads to a significant increase in epsilon(eff) and that semimicroscopic models that do not take this relaxation into account force one to use a large value for the so-called "protein dielectric constant," epsilon(p), of the Poisson-Boltzmann model or for the corresponding epsilon(in) in the PDLD/S model. An additional increase in epsilon(eff) is expected from the reorganization of ionized residues and from changes in the degree of water penetration. This finding provides further support for the idea that epsilon(in) (or epsilon(p)) represents contributions that are not considered explicitly. The present study also provides a systematic illustration of the nature of ep...Continue Reading

References

Nov 1, 1978·Proceedings of the National Academy of Sciences of the United States of America·A Warshel
Sep 29, 1978·Science·M F Perutz
Jan 1, 1990·Annual Review of Biophysics and Biophysical Chemistry·K A Sharp, B Honig
Jan 1, 1985·Annual Review of Biophysics and Biophysical Chemistry·J B Matthew
Aug 1, 1984·Quarterly Reviews of Biophysics·A Warshel, S T Russell
Aug 15, 1980·Journal of Molecular Biology·D C Rees
Jun 5, 1982·Journal of Molecular Biology·J Warwicker, H C Watson
Aug 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·A WarshelA K Churg
Apr 1, 1995·Current Opinion in Structural Biology·M K Gilson
Mar 1, 1993·Proteins·A S YangB Honig
Feb 1, 1996·Quarterly Reviews of Biophysics·H Nakamura

❮ Previous
Next ❯

Citations

Feb 1, 2011·Journal of Mathematical Biology·Zhan ChenG W Wei
Jul 29, 2005·Photosynthesis Research·Anna DillerJörg Matysik
May 23, 2002·Biophysical Journal·Carolyn A FitchBertrand García-Moreno E
Oct 13, 2006·Biophysical Chemistry·B Roux, T Simonson
Oct 13, 2006·Biophysical Chemistry·S BoreschO Steinhauser
Jun 19, 1998·Current Opinion in Structural Biology·A Warshel, A Papazyan
Sep 16, 2000·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·M MitevaB Atanasov
Dec 12, 2012·Quarterly Reviews of Biophysics·Pengyu RenNathan A Baker
Sep 9, 2010·Journal of the American Chemical Society·Maybelle K GoJohn P Richard
Dec 1, 2011·The Journal of Physical Chemistry. B·Hanzhong Liu, Shuanghong Huo
Aug 9, 2008·Physical Chemistry Chemical Physics : PCCP·Feng DongNathan A Baker
Mar 5, 2009·The Journal of Chemical Physics·I V Leontyev, A A Stuchebrukhov
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·J J Havranek, P B Harbury
Jun 23, 2001·Protein Science : a Publication of the Protein Society·F L Da SilvaR Penfold
Apr 23, 2002·Protein Science : a Publication of the Protein Society·Kelly K LeeBertrand García-Moreno E
Apr 22, 2003·Annual Review of Biochemistry·Daniel A KrautDaniel Herschlag
Dec 23, 2009·The Journal of Chemical Physics·A Mandal, K L C Hunt
Jun 25, 2010·The Journal of Chemical Physics·Georgios N PatargiasJohn H Harding
Aug 15, 2015·Molecular Based Mathematical Biology·Jaydeep P BardhanPeter Brune
Oct 13, 2010·Journal of Computational Physics·Zhan ChenG W Wei
Sep 2, 2004·Protein Science : a Publication of the Protein Society·Andrei L LomizeH I Mosberg
Nov 11, 2011·Proteins·Vernon Couch, Alexei Stuchebrukhov
Aug 31, 2002·Biophysical Journal·Sandeep Kumar, Ruth Nussinov
Jul 17, 2003·Proteins·Anton BurykinArieh Warshel
Mar 29, 2008·Protein Science : a Publication of the Protein Society·Michael J HarmsBertrand García-Moreno
Dec 3, 2014·Journal of Photochemistry and Photobiology. B, Biology·Jun TamogamiNaoki Kamo

❮ 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.