The presence of native contacts in the denatured state of many proteins suggests that elements of the biologically active structure of these molecules are formed during the initial stage of the folding process. The rapidity with which these events take place makes it difficult to study them in vitro, but, by the same token, suitable for studies in silico. With the help of all-atom, explicit solvent, molecular dynamics simulations we have followed in time, starting from elongated structureless conformations, the early events in the folding of src-SH3 domain and of proteins G, L, and CI2. It is observed that within the first 50 ns two important events take place, essentially independent of each other: hydrophobic collapse and formation of a few selected native contacts. The same contacts are also found in simulations carried out in the presence of guanidinium chloride in order to reproduce the conditions used to characterize experimentally the denatured state and testify to the fact that these contacts are to be considered a resilient characterizing property of the denaturated state.

Early events in protein folding : is there something more than hydrophobic burst? / C. Camilloni, L. Sutto, D. Provasi, G. Tiana, R.A. Broglia. - In: PROTEIN SCIENCE. - ISSN 0961-8368. - 17:8(2008 Aug), pp. 1424-1433. [10.1110/ps.035105.108]

Early events in protein folding : is there something more than hydrophobic burst?

C. Camilloni;L. Sutto;D. Provasi;G. Tiana;R.A. Broglia
2008-08

Abstract

The presence of native contacts in the denatured state of many proteins suggests that elements of the biologically active structure of these molecules are formed during the initial stage of the folding process. The rapidity with which these events take place makes it difficult to study them in vitro, but, by the same token, suitable for studies in silico. With the help of all-atom, explicit solvent, molecular dynamics simulations we have followed in time, starting from elongated structureless conformations, the early events in the folding of src-SH3 domain and of proteins G, L, and CI2. It is observed that within the first 50 ns two important events take place, essentially independent of each other: hydrophobic collapse and formation of a few selected native contacts. The same contacts are also found in simulations carried out in the presence of guanidinium chloride in order to reproduce the conditions used to characterize experimentally the denatured state and testify to the fact that these contacts are to be considered a resilient characterizing property of the denaturated state.
Molecular mechanics/dynamics; Protein structure/folding
Settore FIS/03 - Fisica della Materia
Settore FIS/04 - Fisica Nucleare e Subnucleare
Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin)
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/43359
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