Effect of Mutation and Disulfide Bond Formation on the Catalytic Site of Monomeric Cytoglobin: A Molecular Level Insight

Razzokov, Jamoliddin; Fazliev, Sunnatullo; Yusupov, Maksudbek; Sharipov, Avez; Ruziev, Z. J.; Mamatkulov, Shavkat

doi:10.1615/plasmamed.2021041420

Cited by 4 publications

(6 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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.…”

Section: Non-reactive MD Simulations Of Proteinsmentioning

confidence: 99%

“…As mentioned in the previous section, CAP-generated RONS can penetrate cell membranes and increase intracellular levels of RONS, leading to nitro-oxidative damage to intracellular proteins. This section focuses on the modification of certain proteins that play key roles in diseases such as cancer [ 191 , 200 , 202 , 291 ], chronic wounds [ 200 , 202 ], and Alzheimer’s disease [ 195 ] by CAP-generated RONS, with the aim of treatment.…”

Section: Non-reactive MD Simulations Of Proteinsmentioning

confidence: 99%

“…These conformational changes in CYGB resulted in different interactions with ligands, such as suppressor drug-like molecules, which can affect intracellular oxidative stress [ 191 ]. Additionally, Razzokov et al demonstrated that the mutation of Lys 80 to Ala (L80A) also increased the accessibility of the CYGB binding pocket to the heme group, even in the absence of disulfide bond formation [ 200 ]. However, disulfide bond formation further enhanced the open accessibility of the binding pocket to the heme group.…”

Section: Non-reactive MD Simulations Of Proteinsmentioning

confidence: 99%

See 2 more Smart Citations

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

Ghasemitarei,

Ghorbi,

Yusupov

et al. 2023

Biomolecules

Self Cite

View full text Add to dashboard Cite

Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes.

show abstract

Section: Non-reactive MD Simulations Of Proteinsmentioning

confidence: 99%

Section: Non-reactive MD Simulations Of Proteinsmentioning

confidence: 99%

Section: Non-reactive MD Simulations Of Proteinsmentioning

confidence: 99%

See 1 more Smart Citation

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

Ghasemitarei,

Ghorbi,

Yusupov

et al. 2023

Biomolecules

Self Cite

View full text Add to dashboard Cite

show abstract

“…Studying interactions of ROS and RNS with biomolecules, cells and tissues is crucial to develop mechanistic insights which allow us to advance cancer treatment protocols. Moreover, a better understanding of redox balance in the cellular environment can point out to new therapeutic approaches [26]. Towards this end, de-coupling the biological effects of ROS and RNS is very important.…”

Section: Introductionmentioning

confidence: 99%

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

Razzokov

Fazliev

Erkinova

et al. 2022

J. Phys. D: Appl. Phys.

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…The interaction of CAP with water is a very complex physicochemical process resulting in UV radiation and numerous species with high chemical reactivity. Among the formed high-energy particles, reactive oxygen and nitrogen species (RONS) are particularly important, due to their wide variety of application areas, ranging from agriculture [ 5 , 6 , 7 , 8 , 9 , 10 ], to cancer [ 2 , 8 , 11 , 12 , 13 , 14 , 15 ], to the food industry [ 5 , 10 , 16 ]. Particularly in agriculture, it has been shown that PAW can be used to boost the stress tolerance [ 17 ], germination [ 18 , 19 ] and growth rate [ 20 ] of plants.…”

Section: Introductionmentioning

confidence: 99%

Mechanistic Insight into Permeation of Plasma-Generated Species from Vacuum into Water Bulk

Razzokov

Fazliev

Kodirov

et al. 2022

IJMS

Self Cite

View full text Add to dashboard Cite

Due to their potential benefits, cold atmospheric plasmas (CAPs), as biotechnological tools, have been used for various purposes, especially in medical and agricultural applications. The main effect of CAP is associated with reactive oxygen and nitrogen species (RONS). In order to deliver these RONS to the target, direct or indirect treatment approaches have been employed. The indirect method is put into practice via plasma-activated water (PAW). Despite many studies being available in the field, the permeation mechanisms of RONS into water at the molecular level still remain elusive. Here, we performed molecular dynamics simulations to study the permeation of RONS from vacuum into the water interface and bulk. The calculated free energy profiles unravel the most favourable accumulation positions of RONS. Our results, therefore, provide fundamental insights into PAW and RONS chemistry to increase the efficiency of PAW in biological applications.

show abstract

Effect of Mutation and Disulfide Bond Formation on the Catalytic Site of Monomeric Cytoglobin: A Molecular Level Insight

Cited by 4 publications

References 0 publications

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

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

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

Mechanistic Insight into Permeation of Plasma-Generated Species from Vacuum into Water Bulk

Contact Info

Product

Resources

About