Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins

Protein Science : a Publication of the Protein Society
V Z SpassovA D Karshikoff

Abstract

The three-dimensional optimization of the electrostatic interactions between the charged amino acid residues and the peptide partial charges was studied by Monte-Carlo simulations on a set of 127 nonhomologous protein structures with known atomic coordinates. It was shown that this type of interaction is very well optimized for all proteins in the data set, which suggests that they are a valuable driving force, at least for the native side-chain conformations. Similar to the optimization of the charge-charge interactions (Spassov VZ, Karshikoff AD, Ladenstein R, 1995, Protein Sci 4:1516-1527), the optimization effect was found more pronounced for enzymes than for proteins without enzymatic function. The asymmetry in the interactions of acidic and basic groups with the peptide dipoles was analyzed and a hypothesis was proposed that the properties of peptide dipoles are a factor contributing to the natural selection of the basic amino acids in the chemical composition of proteins.

References

Jun 8, 1978·Nature·W G HolH J Berendsen
May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Mar 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·J AqvistA Warshel
Mar 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·M K Gilson, B Honig
Aug 5, 1987·Journal of Molecular Biology·S MillerC Chothia
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
Sep 1, 1994·Protein Science : a Publication of the Protein Society·V Z SpassovR Ladenstein
Aug 1, 1995·Protein Science : a Publication of the Protein Society·V Z SpassovR Ladenstein
May 1, 1995·Protein Engineering·J BobergM Vihinen
Nov 1, 1996·Protein Science : a Publication of the Protein Society·L A PlesniakL P McIntosh

❮ Previous
Next ❯

Citations

Mar 23, 2002·Protein Science : a Publication of the Protein Society·Yury N Vorobjev, Jan Hermans
Sep 12, 2001·Trends in Biochemical Sciences·A Karshikoff, R Ladenstein
Sep 10, 2005·Nature Biotechnology·Philipp Holliger, Peter J Hudson
Jul 3, 2007·Nature Biotechnology·Jeffrey C MillerEdward J Rebar
Apr 19, 2005·Nature Structural & Molecular Biology·Jirí LísalRoman Tuma
Jun 19, 2002·Protein Science : a Publication of the Protein Society·Petras J Kundrotas, Andrey Karshikoff
May 22, 2002·Protein Science : a Publication of the Protein Society·Ulrich ZachariaeAndrey Karshikoff
Jan 11, 2001·Protein Science : a Publication of the Protein Society·D Petrey, B Honig
Jan 22, 2005·Acta Pharmacologica Sinica·Roland E Kontermann
May 27, 2005·Acta Pharmacologica Sinica·Jonathan S Marvin, Zhenping Zhu
Jul 21, 2007·Journal of Biomedicine & Biotechnology·Jing ZhaoRong-Qiao He
May 17, 2005·Proceedings of the National Academy of Sciences of the United States of America·Daniel R RipollHarold A Scheraga
May 27, 2011·Cellular and Molecular Life Sciences : CMLS·Anirban Banerji, Indira Ghosh
Mar 9, 2005·Biochimica Et Biophysica Acta·A ShoshevaE Alexov
Apr 28, 2005·Journal of Molecular Biology·Jinrang KimM R Gunner
Aug 19, 2007·Biophysical Journal·Kelly BrockEmil Alexov
Sep 27, 2002·Biophysical Journal·Roxana E GeorgescuMarilyn R Gunner
May 9, 2003·Protein Engineering·Angel Mozo-VillaríasEnrique Querol
May 5, 2011·Chemistry : a European Journal·Xinying JiaGottfried Otting

❮ 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.