Correlating topology and thermodynamics to predict protein structure sensitivity to point mutations

• Autorzy: Rodriguez P. M. , Stratmann D. , Duprat E. , Papandreou N. , Acuna R. , Lacroix Z. , Chomilier J.

Identyfikatory

DOI

10.1515/bams-2018-0026

• Języki publikacji: EN

Abstrakty

EN

The relation between distribution of hydrophobic amino acids along with protein chains and their structure is far from being completely understood. No reliable method allows ab initio prediction of the folded structure from this distribution of physicochemical properties, even when they are highly degenerated by considering only two classes: hydrophobic and polar. Establishment of long-range hydrophobic three dimension (3D) contacts is essential for the formation of the nucleus, a key process in the early steps of protein folding. Thus, a large number of 3D simulation studies were developed to challenge this issue. They are nowadays evaluated in a specific chapter of the molecular modeling competition, Critical Assessment of Protein Structure Prediction. We present here a simulation of the early steps of the folding process for 850 proteins, performed in a discrete 3D space, which results in peaks in the predicted distribution of intra-chain noncovalent contacts. The residues located at these peak positions tend to be buried in the core of the protein and are expected to correspond to critical positions in the sequence, important both for folding and structural (or similarly, energetic in the thermodynamic hypothesis) stability. The degree of stabilization or destabilization due to a point mutation at the critical positions involved in numerous contacts is estimated from the calculated folding free energy difference between mutated and native structures. The results show that these critical positions are not tolerant towards mutation. This simulation of the noncovalent contacts only needs a sequence as input, and this paper proposes a validation of the method by comparison with the prediction of stability by well-established programs.

Słowa kluczowe

EN

folding nucleus; free energy; protein mutation; stability

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2018
• Tom: Vol. 14, no. 3
• Strony: art. no. 20180026
• Opis fizyczny: Bibliogr. 66 poz., rys., tab.

Twórcy

autor

Rodriguez P. M.

• IMPMC, UPMC, CNRS, MNHN, Paris, France

autor

Stratmann D.

• IMPMC, UPMC, CNRS, MNHN, Paris, France

autor

Duprat E.

• IMPMC, UPMC, CNRS, MNHN, Paris, France

autor

Papandreou N.

• Physics Department, AUA, Athens, Greece

autor

Acuna R.

• Scientific Data Management, ASU, Tempe, AZ, USA

autor

Lacroix Z.

• Scientific Data Management, ASU, Tempe, AZ, USA

autor

Chomilier J.

• IMPMC, UPMC, CNRS, MNHN, Paris, France

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Uwagi

EN

Supplementary Material: The online version of this article offers supplementary material (DOI: https://doi.org/10.1515/bams-2018-0026).

PL

Opracowanie rekordu w ramach umowy 509/P-DUN/2018 ze środków MNiSW przeznaczonych na działalność upowszechniającą naukę (2019).