The transcription factor p53 is under negative regulation by the ubiquitin ligase MDM2 and its close homologue MDM4. In the bound complex between MDM2 and p53, the transactivation domain of p53 adopts an amphipathic helical conformation which optimizes the spatial organization of three key hydrophobic residues (Phe19, Trp23, Leu26) for maximum interactions. The interaction with MDM2 is known to be abrogated by phosphorylation of Ser/Thr residues in the MDM2 N-terminal domain and in the p53 transactivation domain. In the latter, phosphorylation of Thr18 has been attributed to destabilize a key hbond between Thr18 and Asp21. This interaction has been thought to be critical for the formation of the helical conformation of the p53 transactivation domain. Molecular dynamics simulations of the p53 transactivation domain suggest that phosphorylation of either Thr18 or Ser20 does not disrupt its helical structure but does result in reduced affinities for MDM2. While interactions between the Thr18 and Asp21 are indeed broken due to charge-charge repulsions, the peptide has enough inherent flexibility to form alternate patterns of hbonds, resulting in the maintenance of helicity. Electrostatics of MDM2 reveal local anionic patches in the region where Thr18 docks. These suggest that repulsions will arise because the MDM2 surface will force the p53 to bind in a manner that will place the negatively charged phosphorylated Thr18 near this anionic region. A similar, albeit somewhat attenuated pattern of electrostatic modulations, is seen for a model of MDM4 that has been built. Mutants of MDM2 and MDM4 have been designed to attenuate this anionicity and have been computationally demonstrated to enhance the binding of the phosphorylated peptides.

p53 is a major tumor suppressor protein, that binds to, and is negatively regulated by MDM2. In tumors overexpressing MDM2, p53 function can be rescued through the disruption of the MDM2-p53 interactions by small molecules and peptides. It is known that MDM2 also binds p73 but not p63, the two homologues of p53. We dissect the structural and energetic reasons underlying this discrimination and have identified a peptide that is intrinsically less helical than p53 and yet has a higher affinity for MDM2. The increased disorder has been introduced by localizing a cationic residue in between two anionic residues, imparting a degree of frustration to the system. In addition, the introduction of a bulkier hydrophobic group towards the centre of the peptide enables the peptide to adapt a bound conformation that on the one hand is most strained, and yet enables the peptide to straddle the largest surface of MDM2, amongst all the peptides. Computations also reveal that this peptide is a dual inhibitor, binding also to MDMX. The computed affinity of the new peptide has been validated against MDM2 using fluorescence-based thermal shift assays.

ACKnowLeDGementSBII and IMCB are A-STAR institutes funded by BMRC. We thank Michael Schaefer for providing us with unpublished parameters for version 3 of the analytical continuum solvent method. AbStrACtCyclin dependent kinases (CDK) associate with cyclins to regulate cell cycle progression and gene transcription by phosphorylating key proteins. The different cyclin-CDK complexes display differences in substrate specificities with substrates binding across a shallow, hydrophobic and substrate-binding pocket known as the cyclin groove. However the mechanism underlying this differential substrate recognition remains largely unknown and cannot be explained merely on the basis of sequence variability. A subset of cyclins, cyclins A2, E1 and B1 despite being structurally and functionally similar, show marked differences in their interactions with recruitment peptides derived from their substrate or inhibitor proteins p27, p21, p57, E2F1, p53, pRb and p107. While these peptides (characterized by a cyclin binding motif of four residues ZRXL where Z and X are cationic residues) inhibit the activity of cyclins A2 and E1, no such inhibition is observed for cyclin B1.Electrostatic potentials of cyclins A2, E1 and B1 show that anionic regions of cyclins A2 and E1 enable them to bind peptides while cationic regions at homologous locations in cyclin B1 abrogate binding. These arise from charged residues that are conserved. Mutations that switch these characters are suggested. Computed energetics of binding confirms this. Deregulation of the enzymatic activity of this class of enzymes is a ubiquitous feature of human neoplasia, but attempts to exploit this therapeutically have been confounded by a lack of understanding of the precise specificity of the different cyclin complexes. Here we begin to clarify this issue by explaining the mechanism by which cyclin B1 escapes regulation by the p21 family of CDKIs.

In this paper, the performance of 6% and 18% attenuated phase-shifting masks (PSM) are investigated to assess their capabilities of printing O.12tm and O.lOjim polysilicon gates, using a 248nm scanner with a high NA of 0.68. The effect of off-axis illumination on process enhancement is also investigated. Simulations were done using PROLITHI3D Version 6.1.2. Experimentation was carried out using test masks with various line pitches. The effect of optical proximity correction (OPC) to enhance the overlapping process windows for 0. 12pm and O.1Otm was also studied.