Anomalous orientation-dependent effective pair interaction among histidine and other amino acid residues in metalloproteins: breakdown of the hydropathy scale index

Biochemistry
Arnab Mukherjee, Biman Bagchi

Abstract

Hydropathy scale is widely used to obtain a measure of the effective interaction between any two amino acid residues in proteins and is based on the assumption that attraction between two hydrophobic groups and repulsion between hydrophilic groups (in water) can be translated straightforwardly to protein environment. Here we employ a recently developed statistical mechanical approach combined with the Protein Data Bank to obtain both distance- and orientation-dependent potential of mean force (ODPMF). This allowed us to explore effective pair potential among many amino acid residues and to examine the validity of the hydropathy scale in modeling the interaction among amino acid residues. We find that in some cases, like Phe-Phe and Lys-Lys, the hydropathy scale approach is largely obeyed. However, we also observe many unexpected pair interactions which defy the trend given by published hydropathy scales. An example of the former is the arginine-arginine (Arg-Arg) pair interaction which is found to be strongly and surprisingly attractive at short separation, even though it is the most hydrophilic residue. Here the head-to-head (see text) interaction is also stabilized. Tryptophan residues also exhibit strong attractive interacti...Continue Reading

References

May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Mar 21, 1997·Journal of Molecular Biology·F Melo, E Feytmans
May 22, 1998·Journal of Molecular Biology·F Melo, E Feytmans
Jun 28, 2002·Journal of Chemical Information and Computer Sciences·Davor JuretićDamir Zucić
Oct 31, 2002·Journal of the American Chemical Society·Steve ScheinerJayasree Pattanayak
Feb 13, 2003·Journal of the American Chemical Society·Artëm Masunov, Themis Lazaridis
Apr 2, 2003·Biophysical Journal·Alessandro PintarSándor Pongor
Jul 23, 2005·The Journal of Chemical Physics·Arnab MukherjeeBiman Bagchi

❮ Previous
Next ❯

Citations

Feb 15, 2008·The Journal of Physical Chemistry. B·Sten O Nilsson LillGrover L Waldrop
Oct 12, 2011·The Journal of Physical Chemistry. B·Olga Yuzlenko, Themis Lazaridis
Oct 10, 2014·The Journal of Chemical Physics·Rikhia GhoshBiman Bagchi
Aug 30, 2008·Protein Science : a Publication of the Protein Society·Igor MochalkinGrover L Waldrop
Apr 6, 2018·Physical Chemistry Chemical Physics : PCCP·Rudra N SamajdarAninda J Bhattacharyya
Sep 18, 2010·The Journal of Physical Chemistry. B·Saikat BanerjeeBiman Bagchi

❮ 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.