Understanding the effect of nitrosylation on dynamics of human epidermal growth factor: a µs simulation study

Abstract

Advancements of plasma science, such as the development of cold atmospheric plasmas made it possible to easily generate reactive oxygen and nitrogen species (RONS) and apply them to biological media under ambient conditions. Studying the interactions of RONS with biomolecules is a central topic of plasma medicine. One of the main targets of plasma medicine is to take control over signaling proteins such as human epidermal growth factor (hEGF) which is an important protein in cancer treatment and wound healing. The oxidative damage of RONS on various proteins, including hEGF, was investigated using molecular dynamics (MD) simulations. However, another effect of RONS – nitrosative damage – is left unexplored. Plasma treatment can induce substantial damage via nitrosylation by reactive nitrogen species. Thus, elucidating the effects of nitrosylation on protein structures is crucial, especially in plasma medicine. Here, we perform MD simulations to explore the effect of nitrosylation on the conformation of hEGF. We carried out MD simulations with different degrees of modifications of hEGF structures to mimic short and long plasma exposure times. Our results show that nitrosylation induces conformational changes in hEGF and the breakage of disulfide bonds which might modulate the binding of hEGF with its receptor. But the structural stability of hEGF remains almost unchallenged to the nitrosative damage, even to the disruption of disulfide bonds. The results assist plasma medicine applications in cancer treatment and wound healing by modulating plasma treatment time and chemical compositions of plasma-generated RONS to mediate effective oxidation of the biological environment and develop optimal treatment protocols.

Effects of Nitro-Oxidative Stress on Biomolecules: Part 1—Non-Reactive Molecular Dynamics Simulations

“…Depending on their specific functions, proteins possess an active site domain that contains specific amino acid residues crucial for their activities [ 187 ]. Modifications in protein structures, such as amino acid mutations [ 188 , 189 ] or oxidation and nitration induced by RONS interactions [ 36 , 80 , 190 , 191 , 192 , 193 , 194 , 195 , 196 ], can directly or indirectly affect the active sites and, subsequently, the protein functions [ 197 ]. Understanding the impact of such modifications on protein structure and function at the atomic scale is challenging to investigate experimentally.…”

“…This review focuses on papers that have employed MD simulations to investigate the effects of oxidation and nitration of amino acid residues in proteins due to interactions with CAP on their functions. Many of these proteins are significant in cancer therapy, as CAP can selectively kill certain types of cancer cells while causing less damage to normal cells, which makes this method appropriate for cancer therapy [ 36 , 80 , 190 , 191 , 192 , 194 , 198 , 199 , 200 , 201 , 202 ]. This selectivity may be attributed to specific proteins and phospholipids (mentioned earlier) found in cancer cells, which are adapted to the high metabolic activity of these cells.…”

“…In many cases, the presence of mutated, overexpressed, or underexpressed proteins compared to their normal counterparts plays a key role in the selectivity of CAP treatment. Additionally, some of these proteins, along with others relevant to Alzheimer’s disease [ 195 ], wound healing [ 36 , 194 ], and viral and bacterial infections [ 203 , 204 , 205 ], are discussed here. The consistency between MD simulations and experimental results in most studies demonstrates that MD simulations are a reliable and cost-effective method for investigating and predicting the effects of CAP on protein structures, and subsequently on cells and tissues.…”

“…Since these proteins are located on the cell membrane, they are among the first to be affected by CAP. In this section, we will review the nitro-oxidation of five transmembrane proteins—AQP1 [ 80 ], xC − antiporter [ 189 , 190 ], CD44 [ 199 ], CD47 [ 192 ], and EGFR [ 36 , 194 ]—that have undergone structural changes or experienced alterations in their related ligands due to RONS generated by CAP. These proteins play a significant role in CAP treatment and have been investigated using MD simulations.…”

“…This protein plays a crucial role in cell proliferation, survival, and differentiation, which is useful for wound healing and is part of the healing process. However, in cancer cells, this mechanism acts against the treatment and allows the cancer cells to progress in the body [ 36 , 194 , 244 , 245 , 246 ]. Overexpression of EGFR has been observed in many cancer types, which affects the cell cycle by inducing these mechanisms [ 244 , 247 ].…”