Dataset Information

In silico Evaluation of Crosslinking Effects on Denaturant m(eq) values and ?Cp upon Protein Unfolding.

ABSTRACT: Important thermodynamic parameters including denaturant equilibrium m values (m(eq)) and heat capacity changes (?Cp) can be predicted based on changes in Solvent Accessible Surface Area (SASA) upon unfolding. Crosslinks such as disulfide bonds influence the stability of the proteins by decreasing the entropy gain as well as reduction of SASA of unfolded state. The aim of the study was to develop mathematical models to predict the effect of crosslinks on ?SASA and ultimately on m(eq) and ?Cp based on in silico methods. Changes of SASA upon computationally simulated unfolding were calculated for a set of 45 proteins with known m(eq) and ?Cp values and the effect of crosslinks on ?SASA of unfolding was investigated. The results were used to predict the m(eq) of denaturation for guanidine hydrochloride and urea, as well as ?Cp for the studied proteins with overall error of 20%, 31% and 17%, respectively. The results of the current study were in close agreement with those obtained from the previous studies.

SUBMITTER: Hamzeh-Mivehroud M

PROVIDER: S-EPMC3558204 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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In silico Evaluation of Crosslinking Effects on Denaturant m(eq) values and ΔCp upon Protein Unfolding.

Hamzeh-Mivehroud Maryam M Alizade Ali Akbar AA Ahmadifar Monire M Dastmalchi Siavoush S

Avicenna journal of medical biotechnology 20120101 1

Important thermodynamic parameters including denaturant equilibrium m values (m(eq)) and heat capacity changes (ΔCp) can be predicted based on changes in Solvent Accessible Surface Area (SASA) upon unfolding. Crosslinks such as disulfide bonds influence the stability of the proteins by decreasing the entropy gain as well as reduction of SASA of unfolded state. The aim of the study was to develop mathematical models to predict the effect of crosslinks on ΔSASA and ultimately on m(eq) and ΔCp base ...[more]

PMID: 23408172

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Project description:Human phenylalanine hydroxylase (PAH) is a metabolic enzyme involved in the catabolism of L-Phe in liver. Loss of conformational stability and decreased enzymatic activity in PAH variants result in the autosomal recessive disorder phenylketonuria (PKU), characterized by developmental and psychological problems if not treated early. One current therapeutic approach to treat PKU is based on pharmacological chaperones (PCs), small molecules that can displace the folding equilibrium of unstable PAH variants toward the native state, thereby rescuing the physiological function of the enzyme. Understanding the PAH folding equilibrium is essential to develop new PCs for different forms of the disease. We investigate here the urea and the thermal-induced denaturation of full-length PAH and of a truncated form lacking the regulatory and the tetramerization domains. For either protein construction, two distinct transitions are seen in chemical denaturation followed by fluorescence emission, indicating the accumulation of equilibrium unfolding intermediates where the catalytic domains are partly unfolded and dissociated from each other. According to analytical centrifugation, the chemical denaturation intermediates of either construction are not well-defined species but highly polydisperse ensembles of protein aggregates. On the other hand, each protein construction similarly shows two transitions in thermal denaturation measured by fluorescence or differential scanning calorimetry, also indicating the accumulation of equilibrium unfolding intermediates. The similar temperatures of mid denaturation of the two constructions, together with their apparent lack of response to protein concentration, indicate the catalytic domains are unfolded in the full-length PAH thermal intermediate, where they remain associated. That the catalytic domain unfolds in the first thermal transition is relevant for the choice of PCs identified in high throughput screening of chemical libraries using differential scanning fluorimetry.

Dataset Information

In silico Evaluation of Crosslinking Effects on Denaturant m(eq) values and ?Cp upon Protein Unfolding.

Publications

In silico Evaluation of Crosslinking Effects on Denaturant m(eq) values and ΔCp upon Protein Unfolding.

Similar Datasets

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