Polymer collapse, protein folding, and the percolation threshold

Journal of Computational Chemistry
Hagai Meirovitch

Abstract

We study the transition of polymers in the dilute regime from a swollen shape at high temperatures to their low-temperature structures. The polymers are modeled by a single self-avoiding walk (SAW) on a lattice for which l of the monomers (the H monomers) are self-attracting, i.e., if two nonbonded H monomers become nearest neighbors on the lattice they gain energy of interaction (epsilon = -/epsilon/); the second type of monomers, denoted P, are neutral. This HP model was suggested by Lau and Dill (Macromolecules 1989, 22, 3986-3997) to study protein folding, where H and P are the hydrophobic and polar amino acid residues, respectively. The model is simulated on the square and simple cubic (SC) lattices using the scanning method. We show that the ground state and the sharpness of the transition depend on the lattice, the fraction g of the H monomers, as well as on their arrangement along the chain. In particular, if the H monomers are distributed at random and g is larger than the site percolation threshold of the lattice, a collapsed transition is very likely to occur. This conclusion, drawn for the lattice models, is also applicable to proteins where an effective lattice with coordination number between that of the SC lattic...Continue Reading

References

Apr 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·D A Hinds, M Levitt
Apr 3, 1990·Biochemistry·D G Covell, R L Jernigan
Oct 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·A KolinskiR Yaris
Jun 1, 1997·Protein Science : a Publication of the Protein Society·C Tanford
Oct 23, 1997·Protein Science : a Publication of the Protein Society·G Raghunathan, R L Jernigan
Jun 18, 1998·Folding & Design·E I Shakhnovich
Nov 1, 1993·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·I Chang, H Meirovitch
Aug 3, 1987·Physical Review Letters·B Duplantier, H Saleur
Jul 1, 1999·Protein Science : a Publication of the Protein Society·K A Dill

❮ Previous
Next ❯

Citations

Apr 26, 2011·Journal of Theoretical Biology·Li Tai Fang
Dec 28, 2010·Ultramicroscopy·Hossein Nejat Pishkenari, Ali Meghdari
Nov 10, 2004·Journal of Molecular Biology·Jiangbo MiaoHagai Meirovitch
Nov 9, 2004·Biomacromolecules·Yves Termonia

❮ 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.