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THE ARABIDOPSIS THALIANA POLY(ADP-RIBOSE) POLYMERASES 1 AND 2 MODIFY DNA BY ADP-RIBOSYLATING TERMINAL PHOSPHATE RESIDUES

Taipakova, Sabira; Kuanbay, Aigerim; Saint-Pierre, Christine; Gasparutto, Didier; Baiken, Yeldar; Groisman, Regina; Ishchenko, Alexander A.; Saparbaev, Murat; Bissenbaev, Amangeldy K. (Frontiers Media, 2020-11-26)

Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyze the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor ...
DNA-HISTONE CROSS-LINKS: FORMATION AND REPAIR

Pachva, Manideep C.; Kisselev, Alexei F.; Matkarimov, Bakhyt T.; Saparbaev, Murat; Groisman, Regina (Frontiers Media, 2020-12-21)

The nucleosome is a stretch of DNA wrapped around a histone octamer. Electrostatic interactions and hydrogen bonds between histones and DNA are vital for the stable organization of nucleosome core particles, and for the ...
The Human DNA glycosylases NEIL1 and NEIL3 Excise Psoralen-Induced DNA-DNA Cross-Links in a Four-Stranded DNA Structure

Martin, Peter R.; Couvé, Sophie; Zutterling, Caroline; Albelazi, Mustafa S.; Groisman, Regina; Matkarimov, Bakhyt T.; Parsons, Jason L.; Elder, Rhoderick H.; Saparbaev, Murat K. (Nature Research, 2017)

Interstrand cross-links (ICLs) are highly cytotoxic DNA lesions that block DNA replication and transcription by preventing strand separation. Previously, we demonstrated that the bacterial and human DNA glycosylases Nei ...
Insight into DNA substrate specificity of PARP1-catalysed DNA poly(ADP-ribosyl)ation

Matkarimov, Bakhyt T.; Matta, Elie; Kiribayeva, Assel; Khassenov, Bekbolat; Ishchenko, Alexander A. (Springer Nature, 2020-02-28)

DNA-dependent poly(ADP-ribose) polymerases (PARPs) PARP1, PARP2 and PARP3 act as DNA break sensors signalling DNA damage. Upon detecting DNA damage, these PARPs use nicotine adenine dinucleotide as a substrate to synthesise ...
Characterization of DNA ADP-ribosyltransferase activities of PARP2 and PARP3: new insights into DNA ADP-ribosylation

Zarkovic, Gabriella; Belousova, Ekaterina; Talhaoui, Ibtissam; Saint-Pierre, Christine; Kutuzov, Mikhail M.; Matkarimov, Bakhyt; Biard, Denis; Gasparutto, Didier; Lavrik, Olga I.; Ishchenko, Alexander A. (Oxford University Press, 2018-01)

Poly(ADP-ribose) polymerases (PARPs) act as DNA break sensors and catalyze the synthesis of polymers of ADP-ribose (PAR) covalently attached to acceptor proteins at DNA damage sites. It has been demonstrated that both ...
Determining the optimal number of independent components for reproducible transcriptomic data analysis

Kairov, Ulykbek; Cantini, Laura; Greco, Alessandro; Molkenov, Askhat; Czerwinska, Urszula; Barillot, Emmanuel; Zinovyev, Andrei (BioMed Central, 2017)

Background: Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the ...
Aberrant DNA glycosylase-initiated repair pathway of free radicals induced DNA damage: implications for age-related diseases and natural aging

Matkarimov, B.; Saparbaev, M. (Biopolymers and Cell. doi: http://dx.doi.org/10.7124/bc.000943, 2017)

Aerobic cellular respiration generates reactive oxygen species (ROS), which can damage macro-molecules including lipids, proteins and DNA. It was proposed that aging is a consequence of accumulation of naturally occurring ...
Самоорганизация дипептидного производного в гидрогели и криогели для биомедицинских целей

Берилло, Дмитрий (RAM Trade company, 2016)

Способность биомолекул к молекулярному узнаванию в природных системах выработана в процессе эволюции. Недавние исследования выявили библиотеки пептидов с селективным сродством к самоструктурированию (самоорганизацией ...
Включение важнейших многочастичных взаимодействий в силовое поле AMBER и оптимизация энергетических параметров обновленного поля

Гарбузинский (Garbuzinskiy), С.А. ( S.A.); Маткаримов (Matkarimov), Б.Т. (B.Т.); Финкельштейн ( Finkelstein), А.В. (A.V.) (Математическая биология и биоинформатика, 2015)

Разработана новая функциональная форма для силового поля невалентных взаимодействий, учитывающая, наряду с традиционными членами, как наведенную парциальными зарядами поляризацию всех атомов, так и трехчастичные дисперсионные ...
Включение важнейших многочастичных взаимодействий в силовое поле АМБЕР и применение обновленного поля к молекулярно-динамическим расчетам

Маткаримов (Matkarimov), Б.Т. (Bakhyt); Балабаев (Balabaev), Н.К.(N.K.); Гарбузинский (Garbuzinskiy), С.А. ( S.A.); Галзитская (Galzitskaya), О.В. (O.V.); Глякина (Glyakina), А.В. (A.V.); Финкельштейн ( Finkelstein), А.В. (A.V.); Маткаримов (Matkarimov), Б.Т. (B.Т.) (Математическая биология и биоинформатика, 2015)

Выведены формулы для расчета потенциалов и сил в новом силовом поле невалентных взаимодействий, включающем, наряду с традиционными членами, наведенную парциальными зарядами поляризацию всех атомов и трехчастичные ...
Aberrant repair initiated by mismatch-specific thymine-DNA glycosylases provides a mechanism for the mutational bias observed in CpG islands

Talhaoui, Ibtissam; Couve, Sophie; Gros, Laurent; Ishchenko, Alexander A.; Matkarimov, Bakhyt; Saparbaev, Murat K. (Nucleic Acids Research, 2014-04-01)

The human thymine-DNA glycosylase (TDG) initiates the base excision repair (BER) pathway to remove spontaneous and induced DNA base damage. It was first biochemically characterized for its ability to remove T mispaired ...
Oxidatively Generated Guanine(C8)-Thymine(N3) Intrastrand Cross-links in Double-stranded DNA Are Repaired by Base Excision Repair Pathways*

Talhaoui, Ibtissam; Shafirovich, Vladimir; Liu, Zhi; Saint-Pierre, Christine; Akishev, Zhiger; Matkarimov, Bakhyt T.; Gasparutto, Didier; Geacintov, Nicholas E.; Saparbaev, Murat (The Journal of Biological Chemistry, 2015-04-15)

Oxidatively generated guanine radical cations in DNA can undergo various nucleophilic reactions including the formation of C8-guanine cross-links with adjacent or nearby N3-thymines in DNA in the presence of O2. The ...
Role of viruses in the development of breast cancer

Alibek, Kenneth; Kakpenova, Ainur; Mussabekova, Assel; Sypabekova, Marzhan; Karatayeva, Nargis (Infectious Agents and Cancer, 2013-09-02)

The most common cancer worldwide among women is breast cancer. The initiation, promotion, and progression of this cancer result from both internal and external factors. The International Agency for Research on Cancer stated ...
The role of infectious agents in urogenital cancers

Alibek, Kenneth; Karatayeva, Nargis; Bekniyazov, Ildar (BioMed Central, 2012-12-03)

Since the late 1990s, infectious agents have been thought to play a role in the pathogenesis of approximately 15% of cancers. It is now widely accepted that infection of stomach tissue with the bacteria Helicobacter pylori ...
Синтез, строение и свойства гидразидов β-аминопропановой кислоты и их производных

Berillo (Берилло), Dmitriy (Дмитрий) (КазНУ им. аль-Фараби, 2010)

Настоящая работа посвящена комплексному исследованию в области синтеза потенциально биологически активных веществ на основе гидразидов и нитрилов α-( и β-)-аминопропановых кислот, установлению закономерностей их гетероциклизации ...
Synthesis of trans-porphyrin dimers for nonlinear optics

Baptayev, Bakhytzhan; Tauanov, Zhandos; Bissengaliyeva, Moldir; Zhakiyeva, Zhanar; Berillo, Dmitriy; Adilov, Salimgerey (“NURIS”, Nazarbayev University, Astana, Kazakhstan, 2014)

Following the development of the idea of octupolar molecules as nonlinear optical materials a variety of compounds have been reported. Trans-porphyrins have a great potential to self-order into octupolar symmetry. Nonlinear ...