PMID: 22587122May 17, 2012Paper

Soliton concepts and protein structure

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Andrei KrokhotinXubiao Peng

Abstract

Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion from a relatively small number of components. Here we propose that the modular building blocks are made of the dark soliton solution of a generalized discrete nonlinear Schrödinger equation. We find that practically all protein loops can be obtained simply by scaling the size and by joining together a number of copies of the soliton, one after another. The soliton has only two loop-specific parameters, and we compute their statistical distribution in the Protein Data Bank (PDB). We explicitly construct a collection of 200 sets of parameters, each determining a soliton profile that describes a different short loop. The ensuing profiles cover practically all those proteins in PDB that have a resolution which is better than 2.0 Å, with a precision such that the average root-mean-square distance between the loop and its soliton is less than the experimental B-factor fluctuation distance. We also present two examples that describe how the loop library can be employed both to model and to analyze folded proteins.

References

May 21, 1977·Journal of Theoretical Biology·A S Davydov
Dec 1, 1992·Protein Science : a Publication of the Protein Society·L HolmG Vriend
Jan 1, 1984·Annual Review of Biophysics and Bioengineering·G A Petsko, D Ringe
Dec 5, 2006·Nucleic Acids Research·Helen BermanJohn L Markley
Sep 29, 2009·Nucleic Acids Research·Sven Griep, Uwe Hobohm
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Maxim ChernodubAntti J Niemi
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ulf H DanielssonAntti J Niemi
May 24, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Shuangwei HuXubiao Peng
Jul 30, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Shuangwei HuAntti J Niemi

❮ Previous
Next ❯

Citations

Mar 13, 2014·The Journal of Chemical Physics·Andrey KrokhotinAntti J Niemi
Oct 5, 2013·The Journal of Chemical Physics·Konrad HinsenAntti J Niemi
May 10, 2013·The Journal of Chemical Physics·Andrey KrokhotinXubiao Peng
Jul 27, 2012·The Journal of Chemical Physics·Andrey KrokhotinHarold A Scheraga
Jan 21, 2014·The Journal of Chemical Physics·Andrey KrokhotinHarold A Scheraga
Feb 2, 2015·The Journal of Chemical Physics·Jianfeng HeAntti J Niemi
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Martin LundgrenFan Sha
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Andrey KrokhotinAntti J Niemi
Jul 11, 2013·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Andrey KrokhotinXubiao Peng
Nov 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M LundgrenAntti J Niemi
Oct 30, 2015·BMC Structural Biology·Xubiao PengAntti J Niemi
Jan 14, 2017·Physical Review. E·Xubiao PengAntti J Niemi
Oct 12, 2019·Scientific Reports·Dmitry MelnikovAra Sedrakyan
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Martin Lundgren, Antti J Niemi
Apr 29, 2021·Journal of Chemical Theory and Computation·Adam K SieradzanGia G Maisuradze
Jun 12, 2021·Biophysical Chemistry·Yanchun Li, Xubiao Peng
Apr 10, 2020·The Journal of Physical Chemistry. B·Khatuna KachlishviliGia G Maisuradze

❮ 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.

© 2021 Meta ULC. All rights reserved