Miroslav Pinak

Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site.

Clustered DNA damage sites induced by ionizing radiation have been suggested to have serious consequences to organisms, such as cancer, due to their reduced probability to be repaired by the enzymatic repair machinery of the cell. Although experimental results have revealed that clustered DNA damage sites effectively retard the efficient function of repair enzymes, it remains unclear as to what particular factors influence this retardation. In this study, approaches based on molecular dynamics (MD) simulation have been applied to examine conformational changes and energetic properties of DNA molecules containing clustered damage sites consisting of two lesioned sites, namely 7,8‐dihydro‐8‐oxoguanine (8‐oxoG) and apurinic/apyrimidinic (AP) site, located within a few base pairs of each other. After 1 ns of MD simulation, one of the six DNA molecules containing a clustered damage site develops specific characteristic features: sharp bending at the lesioned site and weakening or complete loss of electrostatic interaction energy between 8‐oxoG and bases located on the complementary strand. From these results it is suggested that these changes would make it difficult for the repair enzyme to bind to the lesions within the clustered damage site and thereby result in a reduction of its repair capacity.

Electrostatic energy analysis of 8-oxoguanine DNA lesion-molecular dynamics study

One nanosecond molecular dynamics (MD) simulation was performed for two DNA segments each composed of 30 base pairs. In one DNA segment the native guanines at nucleotides positions 17 and 19 were replaced with two 8-oxoguanines (8-oxoG) (8-oxoG is mutagenic DNA oxo-lesion). The analysis of results was focused on the electrostatic energy that is supposed to be significant factor causing the disruption of DNA base stacking in DNA duplex and may also serve as a signal toward the repair enzyme informing the presence of the lesion. The repulsive interaction between 8-oxoG and the entire DNA molecule was observed, which caused the extrahelical position of 8-oxoG (position 19). The repulsive electrostatic interaction between both 8-oxoG lesions contributed to the flipping out of one 8-oxoG and to the local instability of the lesioned DNA region. The electrostatic potential at the surface of DNA close to the lesions has more negative value than the same region on the native DNA. This electrostatic potential may signal presence of the lesion to the repair enzyme. In the simulation of native DNA segment, no significant structural changes were observed and B-DNA structure was well preserved throughout the MD simulation.

8-oxoguanine lesioned B-DNA molecule complexed with repair enzyme hOGG1: A molecular dynamics study

The molecular dynamics (MD) simulation of DNA mutagenic oxidative lesion, 7,8‐dihydro‐8‐oxoguanine (8‐oxoG), complexed with the repair enzyme, human oxoguanine glycosylase 1 (hOGG1), was performed for 1 nanosecond (ns) in order to describe the dynamical process of DNA‐enzyme complex formation. After 900 picoseconds of MD the lesioned DNA and enzyme formed a complex that lasted until the end of the simulation at 1 ns. The complex was mainly represented by the overlapping van der Waals surfaces of DNA and enzyme molecules. The amino group of arginine 324 was located close to the phosphodiester bond of the nucleotide with 8‐oxoG enabling chemical reactions between amino acid and lesion. The broken hydrogen bonds resulting in locally collapsed B‐DNA structure were observed at the lesion site. The phosphodiester bond at C5′ of 8‐oxoG was displaced to the position close to the amino group of arginine 324. The water‐mediated hydrogen bond network was formed in each contact area between DNA and enzyme, further enhancing the stability of the complex. In the background simulation of the identical molecular system with the native DNA, neither the complex nor the water‐ mediated hydrogen bond network was observed.

Molecular dynamics simulation of thymine glycol-lesioned DNA reveals specific hydration at the lesion

One nanosecond molecular dynamics (MD) simulation of a thymine glycol (TG)‐lesioned part of human lymphoblast AG9387 was performed to determine structural changes in DNA molecule caused by the presence of a lesion. These changes can be significant for proper recognition of lesions by a repair enzyme. Thymine glycol is the DNA oxidative lesion formed by addition of OH radicals to C5 and C6 atoms of the thymine base. This lesion is known as causing Cockayne Syndrome—inherited genetic disorder. Distribution of water molecules in a hydration shell around the DNA molecule was analyzed for its contribution to the recognition of the TG lesion by the repair enzyme. The results of MD simulation show there is a specific DNA structural configuration formed at the lesion. After 500 ps the DNA is bent in a kink at the TG site. This change dislocates the glycosyl bond at C5′ to a position closer to the DNA surface, and thus its atoms are more exposed to the surrounding water shell. The increased number of water molecules that are close to the TG site indicates that the glycosyl bond may be easily contacted by the repair enzyme. In addition, the higher number of water molecules at the TG site substantiates the importance of water‐mediated hydrogen bonds created between the repair enzyme and the DNA upon formation of the complex.

Hydration at the TD Damaged Site of DNA and its Role in the Formation of Complex with T4 Endonuclease V

Abstract An analysis of the distribution of water around DNA surface focusing on the role of the distribution of water molecules in the proper recognition of damaged site by repair enzyme T4 Endonuclease V was performed. The native DNA dodecamer, dodecamer with the thymine dimer (TD) and complex of DNA and part of repair enzyme T4 Endonuclease V were examined throughout the 500 ps of molecular dynamics simulation. During simulation the number of water molecules close to the DNA atoms and the residence time were calculated. There is an increase in number of water molecules lying in the close vicinity to TD if compared with those lying close to two native thymines (TT). Densely populated area with water molecules around TD is one of the factors detected by enzyme during scanning process. The residence time was found higher for molecule of the complex and the six water molecules were found occupying the stabile positions between the TD and catalytic center close to atoms P, C3′ and N3. These molecules originate water mediated hydrogen bond network that contribute to the stability of complex required for the onset of repair process.

Computational determination of radiation damage effects on DNA structure

Molecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.

Molecular Dynamics of 8‐oxoguanine Lesioned B‐DNA Molecule — Structure and Energy Analysis

The molecular dynamics (MD) simulation of DNA mutagenic oxidative lesion — 7,8‐dihydro‐8‐oxoguanine (8‐oxoG), complexed with the repair enzyme — human oxoguanine glycosylase 1 (hOGG1) was performed for 1 nanosecond (ns) in order to describe the dynamical process of DNA‐enzyme complex formation. After 900 picoseconds of MD the lesioned DNA and enzyme formed a complex that lasted until the end of the simulation at 1 ns. The amino group of arginine 324 was located close to the phosphodiester bond of nucleotide with 8‐oxoG enabling chemical reactions between amino acid and lesion. Phosphodiester bond at C5′ of 8‐oxoG was displaced to the position close to the amino group of arginine 324. In the background simulation of the identical molecular system with the native DNA, neither the complex nor the water mediated hydrogen bond network were observed. The electrostatic energy is supposed to be significant factor causing the disruption of DNA base stacking in DNA duplex and may also to serve as a signal toward th...