Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same way so that the folding features of a protein are determined only by the geometry of its native conformation. We present an extended version of a C{alpha}-based Go model where different residues interact with different energies. The model is used to calculate the thermodynamics of three small proteins (Protein G, Src-SH3, and CI2) and the effect of mutations ({Delta}{Delta}GU-N, {Delta}{Delta}G{ddagger}-N, {Delta}{Delta}G{ddagger}-U, and {varphi}-values) on the wild-type sequence. The model allows us to investigate some of the most controversial areas in protein folding, such as its earliest stages and the nature of the unfolded state, subjects that have lately received particular attention.

Sequence of events in folding mechanism: Beyond the Go model / L. Sutto, G. Tiana, R. A. Broglia. - In: PROTEIN SCIENCE. - ISSN 0961-8368. - 15:7(2006), pp. 1638-1652. [10.1110/ps.052056006]

Sequence of events in folding mechanism: Beyond the Go model

L. Sutto
Primo
;
G. Tiana
Secondo
;
R.A. Broglia
Ultimo
2006

Abstract

Simplified Go models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same way so that the folding features of a protein are determined only by the geometry of its native conformation. We present an extended version of a C{alpha}-based Go model where different residues interact with different energies. The model is used to calculate the thermodynamics of three small proteins (Protein G, Src-SH3, and CI2) and the effect of mutations ({Delta}{Delta}GU-N, {Delta}{Delta}G{ddagger}-N, {Delta}{Delta}G{ddagger}-U, and {varphi}-values) on the wild-type sequence. The model allows us to investigate some of the most controversial areas in protein folding, such as its earliest stages and the nature of the unfolded state, subjects that have lately received particular attention.
Mutation free energy; Protein folding; Simplified model
Settore FIS/04 - Fisica Nucleare e Subnucleare
Settore FIS/03 - Fisica della Materia
2006
http://www.proteinscience.org/cgi/reprint/15/7/1638
Article (author)
File in questo prodotto:
Non ci sono file associati a questo prodotto.
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/23714
Citazioni
  • ???jsp.display-item.citation.pmc??? 7
  • Scopus 34
  • ???jsp.display-item.citation.isi??? 31
social impact