+ 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

Simulating energy flow in biomolecules: application to tuna cytochrome c

, : Simulating energy flow in biomolecules: application to tuna cytochrome c. Biophysical Journal 75(1): 60-69

By constructing a continuity equation of energy flow, one can utilize results from a molecular dynamics simulation to calculate the energy flux or flow in different parts of a biomolecule. Such calculations can yield useful insights into the pathways of energy flow in biomolecules. The method was first tested on a small system of a cluster of 13 argon atoms and then applied to the study of the pathways of energy flow after a tuna ferrocytochrome c molecule was oxidized. Initially, energy propagated faster along the direction perpendicular to the heme plane. This was due to an efficient through-bond mechanism, because the heme iron in cytochrome c was covalently bonded to a cysteine and a histidine. For the oxidation of cytochrome c, electrostatic interactions also facilitated a long-range through-space mechanism of energy flow. As a result, polar or charged groups that were further away from the oxidation site could receive energy earlier than nonpolar groups closer to the site. Another bridging mechanism facilitating efficient long-range responses to cytochrome c oxidation involved the coupling of far-off atoms with atoms that were nearer to, and interacted directly with, the oxidation site. The different characteristics of these energy transfer mechanisms defied a simple correlation between the time that the excess energy of the oxidation site first dissipated to an atom and the distance of the atom from the oxidation site. For tuna cytochrome c, all of the atoms of the protein had sensed the effects of the oxidation within approximately 40 fs. For the length scale of energy transfer considered in this study, the speed of the energy propagation in the protein was on the order of 10(5) m/s.


PMID: 9649368

DOI: 10.1016/S0006-3495(98)77495-8

Other references

Czaplicki, S.; Stanowski, E.; Szepietowski, J., 1964: Blood groups in cholelithiasis, gastric cancer and ulcer. The report deals with studies on the relation between the ABO blood groups and the occurrence of cholelithiasis (621 cases) gastric cancer (83 cases) and gastric and duodenal ulcer (276 cases). Clinical diagnosis was confirmed in all the cases by...

Chernenko, L.; Gilinskaia, E.; Putilova, I.; Gorin, L., 1975: Investigation of polydispersion of agar and agaroid by the method of molecular-weight distribution. Izvestiia vysshikh uchebnykh zavedenii Pishchevaia tekhnologiia: 26-28

Wang,; Ge, S., 1998: A karyotype study on five species of Adenophora. In this paper, chromosome numbers and karyotypes of five species of Adenophora are reported for the first time. The species under study are native to China. The results are as follows: 2n = 34 = 28m+4sm(2sat)+2st(2sat) for A. borealis; 2n = 34 = 2...

Li, L.; Abou-Hamad, E.; Anjum, D.H.; Zhou, L.; Laveille, P.V.; Emsley, L.; Basset, J-Marie., 2015: Well-defined mono(η(3)-allyl)nickel complex ≡MONi(η(3)-C3H5) (M = Si or Al) grafted onto silica or alumina: a molecularly dispersed nickel precursor for syntheses of supported small size nickel nanoparticles. Preparing evenly-dispersed small size nickel nanoparticles over inert oxides remains a challenge today. In this context, a versatile method to prepare supported small size nickel nanoparticles (ca. 1-3 nm) with narrow size distribution via a surfa...

Fichte, Be, 1970: The new land. Spring 25 (2) 46-47

Storozhuk P.G., 1970: The small intestine section in dogs under the action of protein rich food stimulants. Voprosy Pitaniya 29(6): 39-43

Anderson, S., 1970: Taxonomic status of the woodrat, Neotoma albigula, in southern Chihuahua, Mexico. Misc. Publs Mus. nat. Hist. Univ. Kans, 51,1969: 25-50

Sun, B.; Fan, N.; Nie, S.; Zhang, M.; Huang, X.; He, H.; Rosenheck, R.A., 2014: Attitudes towards people with mental illness among psychiatrists, psychiatric nurses, involved family members and the general population in a large city in Guangzhou, China. Stigma towards people with mental illness is believed to be widespread in low and middle income countries. This study assessed the attitudes towards people with mental illness among psychiatrists, psychiatric nurses, involved family members of pat...

Anahosur, K.H.; Naik, S.T.; Nadaf, S.K., 1987: Correlation and path coefficient analyses of loss in seed weight due to charcoal rot in sorghum. Among 5 parameters considered to assess the resistant nature of a genotype to Macrophomina phaseolina, correlation and path coefficient analyses revealed that percentage lodging had a strong and positive association with loss in seed wt. It is con...

Mckillop, W.B.; Harrison, A.D., 1980: Hydrobiological studies of eastern lesser antillean islands 5. st lucia fresh water habitats water chemistry and distribution of fresh water mollusks. The field biology of the freshwater mollusks of St. Lucia is discussed. Monthly population densities over 2 yr are given for Biomphalaria glabrata, Pyrgophorus parvulus and Pisidium punctiferum. Marsh populations of B. glabrata are stable and acti...