High-Resolution Crystal Structures of Human Cyclin-Dependent Kinase 2 with and without ATP:  Bound Waters and Natural Ligand as Guides for Inhibitor Design

“…(19). The CDK2 portions, with the exception of the positioning of certain active-site residue side chains, in all the known complexes with ATP antagonists are practically identical to that found in the CDK2 apoenzyme [105], the ATP complex [105,106], and are very similar to that in the CDK2/cyclin A complex [107]. The inhibitor portions invariably bind into the deep ATP-binding cleft between the N-and C-terminal lobes of CDK2.…”

Section: Insights From Crystal Structures Between Cdk2 and Atp Antagomentioning

confidence: 70%

“…Another conserved Hbond in these complexes is that between the acidic C 8 position of the purine ring and the carbonyl The structures were generated by superimposition of the ATP-binding residues in CDK2 shown in (a). For ATP [106], staurosporin [43], and purvalanol B (only the main conformation shown) [32], the published crystal structure co-ordinates were used, flavonoid L868276 [109] and kenpaullone [110] were modelled. :b 10 20 30 40 50 60 CDK2 MENFQKVEKIGEGTYGVVYKARNKLTG-EVVALKKIR-LDTETEG---VPSTAIREISLLKELN---HPNIV CDK1 MEDYTKIEKIGEGTYGVVYKGRHKTTG-QVVAMKKIR-LESEEEG---VPSTAIREISLLKELR---HPNIV CDK4 MATSRYEPVAEIGVGAYGTVYKARDPHSG-HFVALKSVR-VPNGGGGGGGLPISTVREVALLRRLEAFEHPNVV CDK6 MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVR-VQTGEEG---MPLSTIREVAVLRHLETFEHPNVV CDK7 MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTN-QIVAIKKIK-LGHRSEAKDGINRTALREIKLLQELS---HPNII ERK2 MVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNK KLLDVIHT : 140 150 160 170 180 190 CDK2 GAIKLADFGLARAFGVPVR…”

Section: Purinesmentioning

confidence: 99%

“…ClustalW multiple sequence alignment was performed using the following sequences: CDK2, CDK2-human cell division protein kinase 2, sp|P24941|; CDK1, CC2-human cell division control protein 2 homolog, sp|P06493|; CDK4, CDK4-human cell division protein kinase 4 (EC 2.7.1.-) sp|P11802|; CDK6, CDK6-human cell division protein kinase, sp|Q00534|; CDK7, CDK7-human cell division protein kinase 7, sp|P50613|; ERK2, ERK2-human extracellular signal-regulated kinase 2, (mitogen-activated protein kinase 2), sp|P28482|; KPCa, KPCA-human protein kinase C, alpha type, sp|P17252|; KAPa, KAPA-human cAMP-dependent protein kinase, alphacatalytic subunit, sp|P17612|; KPBb, KGPB-human cGMP-dependent protein kinase, beta isozyme, sp|P14619|; EGFR, EGFR-human epidermal growth factor receptor precursor, sp|P00533|; SRC, SRC-human proto-oncogene tyrosine-protein kinase SRC (P60-SRC) (C-SRC), sp|P12931|. Sequence positions known to be involved in ATP interactions in the case of CDK2 are shaded [106]. The secondary structure designations refer to CDK2, as well.…”

Section: B8---: Al12:l12------------------------------:a4-------------mentioning

confidence: 99%

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Inhibitors of Cyclin-Dependent Kinases as Anti-Cancer Therapeutics

Fischer

Lane²

2000

CMC

141

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Initiation, progression, and completion of the cell cycle are regulated by various cyclin-dependent kinases (CDKs), which are thus critical for cell growth. Tumour development is closely associated with genetic alteration and deregulation of CDKs and their regulators, suggesting that inhibitors of CDKs may be useful anticancer therapeutics. Indeed, early results suggest that transformed and normal cells differ in their requirement for e.g. cyclin/CDK2 and that it may be possible to develop novel antineoplastic agents devoid of the general host toxicity observed with conventional cystostatic drugs. Numerous active-site inhibitors of CDKs have been studied; the main limitation with these ATP antagonists is kinase specificity for CDKs. However, screening of compound collections, as well as rational design based on enzyme-ligand complex crystal structures, are now yielding pre-clinical candidates, particularly certain purine and flavonoid analogues, with impressive potency and selectivity. Natural CDK inhibitors (CKIs), e.g. the tumour suppressor gene products p16 INK4 , p21 WAF1 , and p27 KIP1 , form the starting point for the design of mechanism-based CDK inhibitors. A number of these small proteins have been dissected and inhibitory lead peptides amenable to peptidomimetic development have been identified. Conversion of these peptides into pharmaceutically useful molecules is greatly aided by the recent elucidation of CKI/CDK crystal and solution structures. Additional interaction sites on CDKs being exploited for the purposes of inhibitor design include: phosphorylation/dephosphorylation sites, macromolecular substrate binding site, CKS regulatory subunit binding sites, cyclin-binding site, cellular localisation domain, and destruction box. Finally, progress has recently been made in the application of antisense technology in order to target CDK activity.

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“…the protein has a range of secondary structures and also it has a highly flexible fragment (37-48) based on its inactive free form of the X-ray crystallographic B-factor (PDB ID = 1HCL) (37). Functionally, this protein plays an important role in the regulation of many cellular events in eukaryotic (human in this context) cell cycle.…”

Section: Resultsmentioning

confidence: 99%

Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study

2016

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Protein flexibility probably is a phenomenon that can make the existence of the many protein conformations possible in contrast to a limited number. Many conformations in a protein are needed for doing many functions. For instance, based on searching IntAct PPI database with the UniprotKB accession number of hCDK2: P24941, hCDK2 has at least 200 different interactions with other proteins in addition to interactions by itself (1). As a structural characteristic, protein flexibility plays many functional roles with respect to different aspects of the proteins as well. Examples in this regard are enzyme catalysis and ligand-receptor interactions, substrate and ligand orientation, the turnover rate of the substrates, and reduction of the free energy barrier in the active sites (2).In structural bioinformatics tools, there are many instances regarding protein flexibility applications and usefulness; as an example, improvement of the small ligand-receptor docking (3,4 Background: Protein flexibility, which has been referred as a dynamic behavior has various roles in proteins' functions. Furthermore, for some developed tools in bioinformatics, such as protein-protein docking software, considering the protein flexibility, causes a higher degree of accuracy. Through undertaking the present work, we have accomplished the quantification plus analysis of the variations in the human Cyclin Dependent Kinase 2 (hCDK2) protein flexibility without affecting a significant change in its initial environment or the protein per se. Objectives:The main goal of the present research was to calculate variations in the flexibility for each residue of the hCDK2, analysis of their flexibility variations through clustering, and to investigate the functional aspects of the residues with high flexibility variations. Materials and Methods: Using Gromacs package (version 4.5.4), three independent molecular dynamics (MD) simulations of the hCDK2 protein (PDB ID: 1HCL) was accomplished with no significant changes in their initial environments, structures, or conformations, followed by Root Mean Square Fluctuations (RMSF) calculation of these MD trajectories. The amount of variations in these three curves of RMSF was calculated using two formulas.Results: More than 50% of the variation in the flexibility (the distance between the maximum and the minimum amount of the RMSF) was found at the region of Val-154. As well, there are other major flexibility fluctuations in other residues. These residues were mostly positioned in the vicinity of the functional residues. The subsequent works were done, as followed by clustering all hCDK2 residues into four groups considering the amount of their variability with respect to flexibility and their position in the RMSF curves. Conclusions:This work has introduced a new class of flexibility aspect of the proteins' residues. It could also help designing and engineering proteins, with introducing a new dynamic aspect of hCDK2, and accordingly, for the other similar globular proteins. In addition, it could provide a...

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High-Resolution Crystal Structures of Human Cyclin-Dependent Kinase 2 with and without ATP: Bound Waters and Natural Ligand as Guides for Inhibitor Design

Cited by 193 publications

References 33 publications

Structural Features of Proteins Responsible for Resistance of Tryptophan Residues to Nitrosylation

Structural Features of Proteins Responsible for Resistance of Tryptophan Residues to Nitrosylation

Inhibitors of Cyclin-Dependent Kinases as Anti-Cancer Therapeutics

Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study

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