title: Ð¡ÑÐ¾Ñ Ð°ÑÑÐ¸ÑÐµÑÐºÐ¾Ðµ Ð¼Ð¾Ð´ÐµÐ»Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ðµ Ð¿Ð¾Ð¸ÑÐºÐ° ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÐ¼Ð¸ ÑÐ°ÐºÑÐ¾ÑÐ°Ð¼Ð¸ ÑÐ²Ð¾Ð¸Ñ ÑÐ°Ð¹ÑÐ¾Ð² ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ð½Ð° ÐÐÐ Ñ Ð¿Ð¾Ð¼Ð¾ÑÑÑ Ð¿Ð°ÐºÐµÑÐ° GRiP
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Stochastic modeling of the search by transcription factors for their target sites on DNA using the GRIP package.
Creators: name: ÐÑÐ½Ð³ÑÑÐ¾Ð², Ð¤ÑÐ´Ð¾Ñ
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2023
Subjects: ÑÑÐ¾Ñ Ð°ÑÑÐ¸ÑÐµÑÐºÐ¸Ðµ Ð¼Ð¾Ð´ÐµÐ»Ð¸
ÑÐºÑÐ¿ÑÐµÑÑÐ¸Ñ Ð³ÐµÐ½Ð¾Ð²
ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÐµ ÑÐ°ÐºÑÐ¾ÑÑ
ÑÐ°Ð¹ÑÑ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ
Ð°ÑÑÐ¸Ð½Ð¾ÑÑÑ
ÑÐ½ÐµÑÐ³Ð¸Ñ ÑÐ²ÑÐ·Ð¸
stochastic models
gene expression
transcription factors
target sites
affinity
binding energy

description: Ð¢ÐµÐ¼Ð° Ð²ÑÐ¿ÑÑÐºÐ½Ð¾Ð¹ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð¾Ð¹ ÑÐ°Ð±Ð¾ÑÑ: "Ð¡ÑÐ¾ÑÐ°ÑÑÐ¸ÑÐµÑÐºÐ¾Ðµ Ð¼Ð¾Ð´ÐµÐ»Ð¸ÑÐ¾Ð²Ð° Ð½Ð¸Ðµ Ð¿Ð¾Ð¸ÑÐºÐ° ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÐ¼Ð¸ ÑÐ°ÐºÑÐ¾ÑÐ°Ð¼Ð¸ ÑÐ²Ð¾Ð¸Ñ ÑÐ°Ð¹ÑÐ¾Ð² ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ð½Ð° ÐÐÐ Ñ Ð¿Ð¾Ð¼Ð¾ÑÑÑ Ð¿Ð°ÐºÐµÑ GRIP". Ð Ð°Ð±Ð¾ÑÐ° Ð¿Ð¾ÑÐ²ÑÑÐµÐ½Ð° Ð¼Ð¾Ð´ÐµÐ»Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ Ð¿ÑÐ¾ÑÐµÑÑÐ° Ð¿Ð¾Ð¸ÑÐºÐ° ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÐ¼Ð¸ ÑÐ°ÐºÑÐ¾ÑÐ°Ð¼Ð¸ ÑÐ²Ð¾Ð¸Ñ ÑÐµÐ»ÐµÐ²ÑÑ ÑÐ°Ð¹ÑÐ¾Ð², Ð° ÑÐ°ÐºÐ¶Ðµ Ð¼Ð¾Ð´Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¸ ÑÑÑÐµÑÑÐ²ÑÑÑÐµÐ¹ Ð¼Ð¾Ð´ÐµÐ»Ð¸ Ñ Ð´Ð°Ð»ÑÐ½ÐµÐ¹ÑÐ¸Ð¼ Ð°Ð½Ð°Ð»Ð¸Ð·Ð¾Ð¼ Ð¸Ð·Ð¼ÐµÐ½ÐµÐ½Ð¸Ð¹ Ð¸ Ð²ÑÑÐ²Ð»ÐµÐ½Ð¸ÐµÐ¼ Ð½Ð¾Ð²ÑÑ ÑÑÑÐµÐºÑÐ¾Ð². ÐÐ¾Ð´Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ñ ÑÐ¾ÑÑÐ¾ÑÐ»Ð° Ð² ÑÑÑÑÐµ Ð²ÑÐµÐ¼ÐµÐ½Ð¸ Ð¿ÐµÑÐµÑÐ¾Ð´Ð° Ð¼ÐµÐ¶Ð´Ñ ÑÐµÐ¶Ð¸Ð¼Ð°Ð¼Ð¸ Ð¿Ð¾Ð¸ÑÐºÐ° Ð¸ ÑÐ°ÑÐ¿Ð¾Ð·Ð½Ð°Ð²Ð°Ð½Ð¸Ñ Ð²Ð¾ Ð²ÑÐµÐ¼Ñ ÑÐ»ÑÑÐ°Ð¹Ð½ÑÑ Ð±Ð»ÑÐ¶Ð´Ð°Ð½Ð¸Ð¹ Ð¼Ð¾Ð»ÐµÐºÑÐ»Ñ ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½Ð¾Ð³Ð¾ ÑÐ°ÐºÑÐ¾ÑÐ° Ð¿Ð¾ ÐÐÐ. ÐÑÐµÐ´ Ð»Ð¾Ð¶ÐµÐ½Ð½Ð°Ñ Ð¼Ð¾Ð´Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ñ Ð±ÑÐ»Ð° ÑÐµÐ°Ð»Ð¸Ð·Ð¾Ð²Ð°Ð½Ð° Ñ Ð¿Ð¾Ð¼Ð¾ÑÑÑ Ð¼Ð¾Ð´Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¹ Ð¿Ð°ÐºÐµÑÐ° GRIP, Ð¾ÑÑÑÐµÑÑÐ²Ð»ÑÑÑÐµÐ³Ð¾ ÑÑÐ¾ÑÐ°ÑÑÐ¸ÑÐµÑÐºÑÑ ÑÐ¸Ð¼ÑÐ»ÑÑÐ¸Ñ ÑÐ°ÑÑÐ¼Ð°ÑÑÐ¸Ð²Ð°ÐµÐ¼Ð¾Ð³Ð¾ Ð¿ÑÐ¾ÑÐµÑÑÐ°. ÐÑÐ»Ð¸ Ð¿ÑÐ¾Ð²ÐµÐ´ÐµÐ½Ñ Ð²ÑÑÐ¸ÑÐ»Ð¸ÑÐµÐ»ÑÐ½ÑÐµ ÑÐºÑÐ¿ÐµÑÐ¸Ð¼ÐµÐ½ÑÑ Ð² ÑÐ°Ð¼ÐºÐ°Ñ Ð½Ð¾Ð²Ð¾Ð¹ Ð¼Ð¾Ð´ÐµÐ»Ð¸. ÐÐ½Ð°Ð»Ð¸Ð·Ð¸ÑÐ¾Ð²Ð° Ð»Ð¸ÑÑ Ð´Ð²Ðµ ÑÐ°ÑÐ°ÐºÑÐµÑÐ¸ÑÑÐ¸ÐºÐ¸ Ð¿ÑÐ¾ÑÐµÑÑÐ°: Ð²ÑÐµÐ¼Ñ Ð¿ÐµÑÐ²Ð¾Ð³Ð¾ Ð´Ð¾ÑÑÐ¸Ð¶ÐµÐ½Ð¸Ñ ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÐ¼ ÑÐ°ÐºÑÐ¾ÑÐ¾Ð¼ ÑÐ²Ð¾ÐµÐ³Ð¾ ÑÐ¿ÐµÑÐ¸ÑÐ¸ÑÐ½Ð¾Ð³Ð¾ ÑÐ°Ð¹ÑÐ° Ð¸ Ð²ÑÐµÐ¼Ñ Ð·Ð°Ð½ÑÑÐ¾ÑÑÐ¸ Ð²ÑÐµÑ ÑÐ°Ð¹ÑÐ¾Ð² ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ. Ð Ð½Ð¾Ð²Ð¾Ð¹ Ð¼Ð¾Ð´ÐµÐ»Ð¸ Ð¿Ð¾ÑÐ²Ð¸Ð»Ð¸ÑÑ Ð½ÐµÑÐ¿ÐµÑÐ¸ÑÐ¸ÑÐ½ÑÐµ ÑÐ°Ð¹ÑÑ Ñ ÑÐ²ÐµÐ»Ð¸ÑÐµÐ½Ð½ÑÐ¼ Ð²ÑÐµÐ¼ÐµÐ½ÐµÐ¼ Ð·Ð°Ð½ÑÑÐ¾ÑÑÐ¸. Ð­ÑÐ¾ Ð²ÑÐµÐ¼Ñ ÑÑÐ°Ð»Ð¾ ÑÐ¾Ð¿Ð¾ÑÑÐ°Ð²Ð¸Ð¼Ð¾ Ñ Ð²ÑÐµÐ¼ÐµÐ½ÐµÐ¼ Ð·Ð°Ð½ÑÑÐ¾ÑÑÐ¸ ÑÐ¿ÐµÑÐ¸ÑÐ¸ÑÐ½ÑÑ ÑÐ°Ð¹ÑÐ¾Ð². Ð¢Ð°ÐºÐ¾Ðµ Ð½Ð°Ð±Ð»ÑÐ´ÐµÐ½Ð¸Ðµ Ð¿Ð¾Ð·Ð²Ð¾Ð»ÑÐµÑ ÑÑÐ²ÐµÑÐ¶Ð´Ð°ÑÑ, ÑÑÐ¾ Ð¿Ð¾ÑÐ²Ð¸Ð»Ð¾ÑÑ Ð±Ð¾Ð»ÑÑÐµ ÑÑÑÐµÐº ÑÐ¸Ð²Ð½Ð¾-ÑÐ¿ÐµÑÐ¸ÑÐ¸ÑÐ½ÑÑ ÑÐ°Ð¹ÑÐ¾Ð², Ð½Ð° ÐºÐ¾ÑÐ¾ÑÑÑ Ð¼Ð¾Ð»ÐµÐºÑÐ»Ñ ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÑ ÑÐ°ÐºÑÐ¾ÑÐ¾Ð² ÑÐ¿Ð¾ÑÐ¾Ð±Ð½Ñ Ð²ÑÐ¿Ð¾Ð»Ð½ÑÑÑ ÑÐ²Ð¾Ð¸ Ð±Ð¸Ð¾Ð»Ð¾Ð³Ð¸ÑÐµÑÐºÐ¸Ðµ ÑÑÐ½ÐºÑÐ¸Ð¸. ÐÐ½Ð°Ð»Ð¸Ð· Ð¿Ð¾ÐºÐ°Ð·Ð°Ð», ÑÑÐ¾ ÑÑÐ°ÑÐ¸ ÑÑÐ¸ÑÐµÑÐºÐ¸ Ð·Ð½Ð°ÑÐ¸Ð¼Ð¾Ð³Ð¾ Ð¸Ð·Ð¼ÐµÐ½ÐµÐ½Ð¸Ñ Ð²ÑÐµÐ¼ÐµÐ½Ð¸ Ð¿ÐµÑÐ²Ð¾Ð³Ð¾ Ð´Ð¾ÑÑÐ¸Ð¶ÐµÐ½Ð¸Ñ Ð² Ð½Ð¾Ð²Ð¾Ð¹ Ð¼Ð¾Ð´ÐµÐ»Ð¸ Ð½Ðµ Ð¿ÑÐ¾Ð¸Ð·Ð¾ÑÐ»Ð¾. Ð¢Ð°ÐºÐ¸Ðµ ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÑ Ð¿Ð¾Ð·Ð²Ð¾Ð»ÑÑÑ ÑÑÐ²ÐµÑÐ¶Ð´Ð°ÑÑ, ÑÑÐ¾ Ð²ÑÐµÐ¼Ñ Ð¿ÐµÑÐµÑÐ¾Ð´Ð° Ð¼ÐµÐ¶Ð´Ñ ÑÐµÐ¶Ð¸Ð¼Ð°Ð¼Ð¸ Ð½Ðµ ÑÑÑÐµÑÑÐ²ÐµÐ½Ð½Ð¾ Ð²Ð»Ð¸ÑÐµÑ Ð½Ð° Ð²ÑÐµÐ¼Ñ Ð¿ÐµÑÐ²Ð¾Ð³Ð¾ Ð´Ð¾ÑÑÐ¸Ð¶ÐµÐ½Ð¸Ñ. ÐÐ¾Ð»ÑÑÐµÐ½Ð½ÑÐµ ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÑ Ð¼Ð¾Ð³ÑÑ Ð±ÑÑÑ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð½Ñ Ð´Ð»Ñ ÑÐ°Ð·ÑÐ°Ð±Ð¾ÑÐºÐ¸ Ð±Ð¾Ð»ÐµÐµ ÑÐ¾Ð²ÐµÑÑÐµÐ½Ð½ÑÑ Ð¼Ð¾Ð´ÐµÐ»ÐµÐ¹ ÑÐµÐ³ÑÐ»ÑÑÐ¸Ð¸ Ð³ÐµÐ½Ð¾Ð², ÑÑÐ¸ÑÑÐ²Ð°ÑÑÐ¸Ñ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÑ ÑÐ¾ÑÐ¼Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½ÑÑ ÐºÐ¾Ð¼Ð¿Ð»ÐµÐºÑÐ¾Ð² Ð¸Ð· ÑÑÐ°Ð½ÑÐºÑÐ¸Ð¿ÑÐ¸Ð¾Ð½Ð½ÑÑ ÑÐ°ÐºÑÐ¾ÑÐ¾Ð² Ð¸ ÑÐµÐ³ÑÐ»ÑÑÐ¾ÑÐ½Ð¾Ð¹ ÐÐÐ.
description: Theme of this work: "Stochastic modeling of the search by transcription factors for their target sites on DNA using the GRIP package".. The work is devoted to modeling the search process by transcription factors of their target sites, as well as modification of the existing model with further analysis of changes and identification of new effects. The modification consisted in taking into account the transition time between search and recognition modes during random walk of the transcription factor molecule along DNA. The proposed modification was implemented using modifications of the GRIP package, which performs stochastic modeling of the process under consideration. Computational experiments were carried out within the framework of the new model. Two characteristics of the process were analyzed: the time when the transcription factor first reached its specific site, and the time when all binding sites were occupied. In the new model, non-specific sites with increased occupancy time appeared. This time has become comparable to the time of specific sites. This observation suggests that there are more efficient specific sites where transcription factor molecules are able to perform their biological functions. The analysis showed that there were no statistically significant changes in the time of the first reach in the new model. Such results indicate that the transition time between conformations does not significantly affect the time of the first reach. The results obtained can be used to develop more advanced models of gene regulation that take into account the dynamics of the formation of molecular complexes from transcription factors and regulatory DNA.