Cytochrome c aggregation: A dataset at and far from the isoelectric point

Marilena Carbone; Alessandro Nucara; Marina Carbonaro

doi:10.1016/j.dib.2019.104842

Cytochrome c aggregation: A dataset at and far from the isoelectric point

Data Brief. 2019 Nov 18:28:104842. doi: 10.1016/j.dib.2019.104842. eCollection 2020 Feb.

Authors

Marilena Carbone¹, Alessandro Nucara², Marina Carbonaro³

Affiliations

¹ Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy.
² Department of Physics, Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.
³ Council for Agricultural Research and Economics (CREA), Research Centre for Food and Nutrition, Via Ardeatina 546, 00178, Rome, Italy.

Abstract

We present SEM, ThT fluorescence and circular dichroism (CD) data of amyloidogenic aggregates of cytochrome c (cyt c).This protein is of outmost relevance in many biochemical processes, such as respiratory chain in mitochondria and cells apoptosis. The present data focus on polymorphism of the protein aggregates obtained at the isoelectric point (IP) and by changing the environmental pH above and below the IP, the protein concentration and the base. The SEM images provide evidence for a large variety of structures, depending on the pH and on protein concentration: mature amyloid fibrils and overstructured platelets are distinguishable in the aggregates below IP, and relatively high cyt c concentration, whereas inhomogeneous amyloid formations are observed above it. At pH 10, i.e. close to IP, only characteristic protein particulates at the micrometric scale are observed. SEM and Fluorescence data have been acquired in dried drops of protein solution, prepared in different bases: TRIS-HCl, at the different pH values, or NaOH (pH 13). Along with this, at relatively low cyt c concentration compact layered structures are visible below the IP, though still made of a thin fibrils reticulate, whereas above the IP, also at low cyt c concentration, granulates structures are present, merging into compact layer, alongside with platelets and mature fibers. These areas are characterized by diffuse ThT-fluorescence and typical fibrils. The loss of the predominant alpha helix secondary structure was verified by CD spectra. Besides the intrinsic scientific relevance, this data collection provides a set of images useful for spectroscopists to discriminate among different morphologic protein formations and suggests pathways for the achievement of different kinds of cytochrome c aggregates. These data are add-ons of the paper published in the International Journal of Biomacromolecules, 138 (2019) 106-115, https://doi.org/10.1016/j.ijbiomac.2019.07.060.

Keywords: Aggregates; Cytochrome c; Particulates; Protein fibrils; SEM images; ThT fluorescence.