A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII

Author(s)

Hassan, Ayaz ^[1] ; Macedo, Lucyano J. A. ^[1] ; de Souza, Joao C. P. ^[2] ; Lima, Filipe C. D. A. ^[3] ; Crespilho, Frank N. ^[1]

Affiliation

^[1] Univ Sao Paulo, Sao Carlos Inst Chem, BR-13560970 Sao Paulo - Brazil

^[2] Goiano Fed Inst Educ Sci & Technol, Campus Rio Verde, BR-75901970 Goias - Brazil

^[3] Fed Inst Educ Sci & Technol Sao Paulo, Campus Matao, BR-15991502 Sao Paulo - Brazil

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 10, n. 1 FEB 6 2020.
• Web of Science Citations: 0

Abstract

Endonuclease III (EndoIII) is a DNA glycosylase that contains the {[}4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe-S bonds of the {[}4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300cm(-1)) were used independently to study the structural changes in EndoIII and the behavior of the {[}4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe-S (sulfide) and Fe-S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe-S bond lengths upon DNA binding, both of the Fe-S (sulfide) and Fe-S (thiolate) bonds in the {[}4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix. (AU)

• FAPESP's process: 17/20493-2 - Study of metalloenzymes through electrochemistry coupled to vibrational spectroscopy
• Grantee: Lucyano Jefferson Alves de Macêdo
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 13/14262-7 - Nanostructured films from biologically-relevant materials
• Grantee: Osvaldo Novais de Oliveira Junior
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 15/16672-3 - Development of High Performance Bioelectrodes for Application in Miniaturized Biofuel Cell
• Grantee: Frank Nelson Crespilho
• Support Opportunities: Regular Research Grants
• FAPESP's process: 16/25806-6 - Interaction between biomolecules and nanostructures: electrochemistry, interfaces and surfaces
• Grantee: Ayaz Hassan
• Support Opportunities: Scholarships in Brazil - Post-Doctoral