Folding of proteins in Go models with angular interactions

Cieplak, Marek; Hoang, Trinh Xuan

doi:10.1016/j.physa.2003.08.034

Cited by 9 publications

(14 citation statements)

References 27 publications

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“…The specificity corrections could be implemented if known reliably. Replacing the Lennard-Jones potential in the contacts by a 10-12 interaction yields equivalent results both in folding 44 and in stretching. 29 An improved simulation might involve enhancing the strength of contacts that correspond to a disulfide bridge that is present in the I1 domain.…”

Section: Model and Methodsmentioning

confidence: 97%

Mechanical properties of the domains of titin in a Go-like model

Cieplak

Pastore²,

Hoang

2005

The Journal of Chemical Physics

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Comparison of properties of three domains of titin, I1, I27, and I28, in a simple geometry-based model shows that despite a high structural homology between their native states different domains show similar but distinguishable mechanical properties. Folding properties of the separate domains are predicted to be diversified which reflects sensitivity of the kinetics to the details of native structures. The Go-like model corresponding to the experimentally resolved native structure of the I1 domain is found to provide the biggest thermodynamic and mechanical stability compared to the other domains studied here. We analyze elastic, thermodynamic, and kinetic properties of several structures corresponding to the I28 domain as obtained through homology-based modeling. We discuss the ability of the models of the I28 domain to reproduce experimental results qualitatively. A strengthening of contacts that involve hydrophobic amino acids does not affect theoretical comparisons of the domains. Tandem linkages of up to five identical or different domains unravel in a serial fashion at low temperatures. We study the nature of the intermediate state that arises in the early stages of the serial unraveling and find it to qualitatively agree with the results of Marszalek et al.

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Section: Model and Methodsmentioning

confidence: 97%

Mechanical properties of the domains of titin in a Go-like model

Cieplak

Pastore²,

Hoang

2005

The Journal of Chemical Physics

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“…V CHIR favors native values of the dihedral angles ( 11 ). The model considered here has similar properties ( 18 ) to the model with the 10–12 contact potentials of Clementi et al ( 19 ).…”

Section: Methodsmentioning

confidence: 78%

BSDB: the biomolecule stretching database

Sikora

Sułkowska

Witkowski

et al. 2010

Nucleic Acids Research

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We describe the Biomolecule Stretching Data Base that has been recently set up at http://www.ifpan.edu.pl/BSDB/. It provides information about mechanostability of proteins. Its core is based on simulations of stretching of 17 134 proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force–displacement patterns, and the sequencing of the contact-rupturing events. We also summarize the possible types of the mechanical clamps, i.e. the motifs which are responsible for a protein's resistance to stretching.

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“…The native contacts are identified as in Ref. 13,14,42 , i.e., by using an overlap criterion 43 applied to the coordinates of all heavy atoms in the native structure. The heavy atoms are assigned enlarged van der Waals spheres and if there is a pair of atoms for which one finds spheres that overlap in the native state then the corresponding pair of amino acids is considered as forming a native contact.…”

Section: Methodsmentioning

confidence: 99%

“…To study thermodynamic properties of the CS dimers, we performed overdamped Langevin dynamics simulations using in-house software 15,42 . The simulations were carried out at 31 different temperatures T distributed uniformly in the interval from 0.1 ǫ/k B to 0.7 ǫ/k B .…”

Section: Methodsmentioning

confidence: 99%

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Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

Różycki

Cieplak

2014

The Journal of Chemical Physics

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We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.

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Folding of proteins in Go models with angular interactions

Cited by 9 publications

References 27 publications

Mechanical properties of the domains of titin in a Go-like model

Mechanical properties of the domains of titin in a Go-like model

BSDB: the biomolecule stretching database

Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

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