Cyclin-dependent kinase 2 (CDK2) is the most thoroughly studied of the cyclin-dependent kinases that regulate essential cellular processes, including the cell cycle, and it has become a model for studies of regulatory mechanisms at the molecular level. This contribution identifies flexible and rigid regions of CDK2 based on temperature B-factors acquired from both X-ray data and molecular dynamics simulations. In addition, the biological relevance of the identified flexible regions and their motions is explored using information from the essential dynamics analysis related to conformational changes of CDK2 and knowledge of its biological function(s). The conserved regions of CMGC protein kinases' primary sequences are located in the most rigid regions identified in our analyses, with the sole exception of the absolutely conserved G13 in the tip of the glycine-rich loop. The conserved rigid regions are important for nucleotide binding, catalysis, and substrate recognition. In contrast, the most flexible regions correlate with those where large conformational changes occur during CDK2 regulation processes. The rigid regions flank and form a rigid skeleton for the flexible regions, which appear to provide the plasticity required for CDK2 regulation. Unlike the rigid regions (which as mentioned are highly conserved) no evidence of evolutionary conservation was found for the flexible regions.

• MeSH
• adenosintrifosfát chemie   metabolismus   MeSH
• cyklin-dependentní kinasa 2 genetika   chemie   metabolismus   MeSH
• financování organizované MeSH
• kinetika MeSH
• konformace proteinů MeSH
• konzervovaná sekvence MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• molekulární evoluce MeSH
• molekulární modely MeSH
• sekvence aminokyselin MeSH
• termodynamika MeSH
• Check Tag
• lidé MeSH

The structures of fully active cyclin-dependent kinase-2 (CDK2) complexed with ATP and peptide substrate, CDK2 after the catalytic reaction, and CDK2 inhibited by phosphorylation at Thr14/Tyr15 were studied using molecular dynamics (MD) simulations. The structural details of the CDK2 catalytic site and CDK2 substrate binding box were described. Comparison of MD simulations of inhibited complexes of CDK2 was used to help understand the role of inhibitory phosphorylation at Thr14/Tyr15. Phosphorylation at Thr14/Tyr15 causes ATP misalignment for the phosphate-group transfer, changes in the Mg(2+) coordination sphere, and changes in the H-bond network formed by CDK2 catalytic residues (Asp127, Lys129, Asn132). The inhibitory phosphorylation causes the G-loop to shift from the ATP binding site, which leads to opening of the CDK2 substrate binding box, thus probably weakening substrate binding. All these effects explain the decrease in kinase activity observed after inhibitory phosphorylation at Thr14/Tyr15 in the G-loop. Interaction of the peptide substrate, and the phosphorylated peptide product, with CDK2 was also studied and compared. These results broaden hypotheses drawn from our previous MD studies as to why a basic residue (Arg/Lys) is preferred at the P(+2) substrate position.

• MeSH
• cyklin-dependentní kinasa 2 antagonisté a inhibitory   chemie   metabolismus   MeSH
• financování organizované MeSH
• fosforylace MeSH
• katalytická doména MeSH
• lidé MeSH
• sekundární struktura proteinů MeSH
• threonin chemie   metabolismus   MeSH
• tyrosin chemie   metabolismus   MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH

A detailed analysis is presented of the dynamics of human CDK5 in complexes with the protein activator p25 and the purine-like inhibitor roscovitine. These and other findings related to the activation of CDK5 are critically reviewed from a molecular perspective. In addition, the results obtained on the behavior of CDK5 are compared with data on CDK2 to assess the differences and similarities between the two kinases in terms of (i) roscovitine binding, (ii) regulatory subunit association, (iii) conformational changes in the T-loop following CDK/regulatory subunit complex formation, and (iv) specificity in CDK/regulatory subunit recognition. An energy decomposition analysis, used for these purposes, revealed why the binding of p25 alone is sufficient to stabilize the extended active T-loop conformation of CDK5, whereas the equivalent conformational change in CDK2 requires both the binding of cyclin A and phosphorylation of the Thr(160) residue. The interaction energy of the CDK5 T-loop with p25 is about 26 kcal.mol(-1) greater than that of the CDK2 T-loop with cyclin A. The binding pattern between CDK5 and p25 was compared with that of CDK2/cyclin A to find specific regions involved in CDK/regulatory subunit recognition. The analyses performed revealed that the alphaNT-helix of cyclin A interacts with the alpha6-alpha7 loop and the alpha7 helix of CDK2, but these regions do not interact in the CDK5/p25 complex. Further differences between the CDK5/p25 and CDK2/cyclin A systems studied are discussed with respect to their specific functionality.

• MeSH
• chemické modely MeSH
• cyklin A chemie   metabolismus   MeSH
• cyklin-dependentní kinasa 2 metabolismus   MeSH
• cyklin-dependentní kinasa 5 metabolismus   MeSH
• financování organizované MeSH
• fosforylace MeSH
• fylogeneze MeSH
• inhibitory proteinkinas farmakologie   chemie   MeSH
• konformace proteinů MeSH
• lidé MeSH
• molekulární konformace MeSH
• molekulární modely MeSH
• proteiny buněčného cyklu chemie   MeSH
• proteiny nervové tkáně metabolismus   MeSH
• puriny farmakologie   chemie   MeSH
• sekundární struktura proteinů MeSH
• stereoizomerie MeSH
• substrátová specifita MeSH
• terciární struktura proteinů MeSH
• threonin chemie   MeSH
• tyrosin chemie   MeSH
• vodíková vazba MeSH
• Check Tag
• lidé MeSH

Vysokoškolská učebnice, která se zaměřuje na anorganickou chemii. Obsahuje praktické laboratorní úkoly.; Předložená publikace má za cíl pomocí praktických úloh demonstrovat vlastnosti prvků periodického systému a jejich využití při syntéze anorganických a koordinačních sloučenin. Studenti si tak mohou rozšířit praktické dovednosti získané v průběhu předmětu Laboratorní technika a využít teoretické poznatky získané v rámci předmětu Anorganická chemie. Preparativní úkoly jsou rozděleny do jedenácti kapitol, které obsahují stručný teoretický úvpd a sadu praktických úkolů věnovaných dané skupině prvků. Každý úkol obsahuje kromě postupu i stručný teoretický úvod a popis použitých chemických sloučenin z hlediska jejich vlastností, praktického využití a možných bezpečnostních rizik při práci s nimi.

• MeSH
• anorganická chemie MeSH
• chemické techniky analytické MeSH

• Konspekt
• Chemie. Mineralogické vědy
• Učební osnovy. Vyučovací předměty. Učebnice
• NLK Obory
• chemie, klinická chemie
• NLK Publikační typ
• učebnice vysokých škol
• laboratorní cvičení