dorsal/arxiv
View SchemaChirality and Protein Folding
| Authors | Joanna I. Kwiecinska, Marek Cieplak |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0412001 |
| URL | https://arxiv.org/abs/q-bio/0412001 |
| DOI | 10.1088/0953-8984/17/18/013 |
Abstract
There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are established, i.e. whether the interacting amino acids come closer than some characteristic distance. We use Go-like models of proteins and show that such simple criteria may prompt one to declare folding even though fragments of the resulting conformations have a wrong sense of chirality. We propose that a better condition of folding should augment the simple criteria with the requirement that most of the local values of the chirality should be nearly native. The kinetic discrepancy between the simple and compound criteria can be substantially reduced in the Go-like models by providing the Hamiltonian with a term which favors native values of the local chirality. We study the effects of this term as a function of its amplitude and compare it to other models such as with the side groups and with the angle-dependent potentials.
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"abstract": "There are several simple criteria of folding to a native state in model\nproteins. One of them involves crossing of a threshold value of the RMSD\ndistance away from the native state. Another checks whether all native contacts\nare established, i.e. whether the interacting amino acids come closer than some\ncharacteristic distance. We use Go-like models of proteins and show that such\nsimple criteria may prompt one to declare folding even though fragments of the\nresulting conformations have a wrong sense of chirality. We propose that a\nbetter condition of folding should augment the simple criteria with the\nrequirement that most of the local values of the chirality should be nearly\nnative. The kinetic discrepancy between the simple and compound criteria can be\nsubstantially reduced in the Go-like models by providing the Hamiltonian with a\nterm which favors native values of the local chirality. We study the effects of\nthis term as a function of its amplitude and compare it to other models such as\nwith the side groups and with the angle-dependent potentials.",
"arxiv_id": "q-bio/0412001",
"authors": [
"Joanna I. Kwiecinska",
"Marek Cieplak"
],
"categories": [
"q-bio.BM",
"cond-mat.stat-mech"
],
"doi": "10.1088/0953-8984/17/18/013",
"title": "Chirality and Protein Folding",
"url": "https://arxiv.org/abs/q-bio/0412001"
},
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