geoscience.net logo
+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

Proteins fold by subdiffusion of the order parameter


, : Proteins fold by subdiffusion of the order parameter. Journal of Physical Chemistry. B 113(48): 15886-15894

It is shown that the folding of a C(alpha) model of chymotyprsin inhibitor (CI2) protein cannot be described by either diffusion (Smoluchowski equation, SE) or a normal-diffusion continuous time random walk of a single order parameter under the influence of the thermodynamic force. The reason for these failures is that the order parameter follows subdiffusion. A theory is proposed based on the idea that an ordinary SE holds along a contour representative of the folding pathways, and that displacements along the contour obey a fractal relationship to, and are longer than, those along the reaction coordinate defined by the order parameter. With a new, constraint-free method to determine the order-parameter-dependent diffusion constant, and statistical temperature molecular dynamics (STMD) enhanced sampling of the free energy, the fractal SE theory is completely characterized by short-time simulations, and its predictions are in quantitative agreement with simulated long-time folding dynamics. Thus, the fractal SE may serve as an accelerated algorithm to study the folding of proteins too slow to be simulated directly.

US$19.90

PMID: 19902909

DOI: 10.1021/jp907009r


Other references

Dinis da Gama, A., 2007: The decline of surgery in the new millenium. Revista Portuguesa de Cirurgia Cardio-Toracica E Vascular 13(4): 195-195

Goncalves, M.; Schapher, M.; Iro, H.; Wuest, W.; Mantsopoulos, K.; Koch, M., 2017: Value of Sonography in the Diagnosis of Sialolithiasis: Comparison With the Reference Standard of Direct Stone Identification. The aim of this study was to assess the effectiveness of sonography for diagnosing sialolithiasis in comparison with the existing reference standard of direct identification of a stone. A total of 659 glands with signs of obstructive sialadenopath...

Engler, M., 1955: Mephenesin (tolserol) and mephenesin carbamate in spastic conditions. Journal of Mental Science 101(423): 391-398

Frider, B.; Silva, M.; Viola, L., 2011: Renal failure, hemodialysis and renal transplant. Acta Gastroenterologica Latinoamericana 35 Suppl 1: S13-S14

Palatinus, L., 1983: The spread of rusts (P. graminis, P. recondita and P. striiformis) on winter wheat in irrigated fields. The stand was irrigated by spraying from mid-May to mid-June. During the 3-yr period of investigation, irrigation increased infection by Puccinia graminis on variety Yubileinaya by an av. of 2.4% and on Sava by 1.52%. Infection by P. recondita inc...

Breyer H G.; Faensen M.; Rahmanzadeh R., 1985: Do posttraumatic coxarthroses following femoral head and acetabulum fractures depend on the time of operation. Zeitschrift fuer Orthopaedie und ihre Grenzgebiete 123(4): 705

Leck, Charles, Reviewer, 1991: New Jersey at the crossroads of migration (book review). The Auk 108: 5-6

Kubo, M.; Imai, A.; Nishiyama, T.; Ishikawa, M.; Sato, Y.; Kurata, T.; Hiwatashi, Y.; Reski, R.; Hasebe, M., 2014: System for stable β-estradiol-inducible gene expression in the moss Physcomitrella patens. Inducible transgene expression provides a useful tool to analyze gene function. The moss Physcomitrellapatens is a model basal land plant with well-developed research tools, including a high efficiency of gene targeting and substantial genomics re...

Brodo, I., M.; Lewis, C.; Craig, B., 2007: Xanthoria parietina, a coastal lichen, rediscovered in Ontario. Xanthoria parietina, a conspicuous orange foliose lichen, has been doubtfully recorded as part of the Ontario lichen flora because the previous documented reports were very old (1868 and 1917) and it had never been reported since. Here, we docume...

Laine, J.; Minkkinen, K.; Trettin, C., 2009: Direct human impacts on the peatland carbon sink. Northern peatlands occupy over 3 million km2 globally and contain the largest carbon (C) pool (typically >100 kg C m(-2) ) among terrestrial ecosystems. Agriculture, forestry, and peat harvesting are the principal human-induced activities that...