Constrained versus unconstrained folding free-energy landscapes

Coluzza, Ivan

doi:10.1080/00268976.2015.1043031

Cited by 6 publications

(9 citation statements)

References 49 publications

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“…The role of non-native interactions in protein folding has been explored by several authors, with many studies agreeing on a functional role played by these interactions [75–80] , while others concluding they play essentially no active part [81] . A recent contribution by Best and co-workers, which analyzed a set of classical MD trajectories of nine proteins obtained by the Shaw group, concluded that non-native interactions are irrelevant to the mechanism of folding in most cases [82] .…”

Section: Introductionmentioning

confidence: 99%

Knotted proteins: A tangled tale of Structural Biology

Faísca

2015

Computational and Structural Biotechnology Journal

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Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research.

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Section: Introductionmentioning

confidence: 99%

Knotted proteins: A tangled tale of Structural Biology

Faísca

2015

Computational and Structural Biotechnology Journal

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“…If the size of the alphabet is reduced, the construction of folding proteins requires an optimization step of amino acid sequence along the chain [62,82,83]; for this reason these methods are often referred as "protein design". Comparing designed proteins with Go-proteins, Coluzza recently shown that, close to the folded state, Go and designed proteins behaves in a very similar manner [84]. Since we are interested in measuring the stability regions defined by the environmental condition at which the trial protein is at least 90% folded, Go-models are an appropriate protein representation, and, at this stage, we do not require to perform the laborious work of protein design to obtain general results.…”

Section: Models and Methodsmentioning

confidence: 99%

How the stability of a folded protein depends on interfacial water properties and residue-residue interactions

Bianco

Pagès-Gelabert

Coluzza

et al. 2017

Journal of Molecular Liquids

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Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T -P thermodynamic plane outside which the biomolecule is denaturated. It is known that the extension and shape of the SR depend on i) the specific protein residue-residue interactions in the native state of the amino acids sequence and ii) the water properties at the hydration interface. Here we analyze by Monte Carlo simulations of different coarse-grained protein models in explicit water how changes in i) and ii) affect the SR. We show that the solvent properties ii) are essential to rationalize the SR shape at low T and high P and that our finding are robust with respect to parameter changes and with respect to different protein models. These results can help in developing new strategies for the design of novel synthetic biopolymers.

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“…39 Hence, the configurational space close to the native state is modelled accurately. 40 All attractive interactions (residueresidue and opposite charged residue-NP) are represented with a sigmoidal-type potential U ATT used in coarse-grained protein models to represent residue-residue interactions. 40 U ATT ¼ 1 1:0 þ e À2:5 rcÀr…”

Section: Simulationsmentioning

confidence: 99%