Short runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4-6 adenine base pairs ('A-tracts') are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.

Optical Kerr effect spectroscopy has been employed to study the behavior of six symmetric-top liquids (acetonitrile, acetonitrile-d3, benzene, carbon disulfide, chloroform, and methyl iodide) over a broad range of temperatures. In all of the liquids, an exponential intermolecular response is observed on a time scale of a few hundreds of femtoseconds. Comparison of the temperature dependence of the time scale of this relaxation with the viscosity and single-molecule and collective orientational times in the liquids suggests that the exponential relaxation arises from motional narrowing.

The recently discovered scaling law for the relaxation times, ( ) ( )

Reactivation of the p53 cell apoptosis pathway through inhibition of the p53-hDM2 interaction is a viable approach to suppress tumor growth in many human cancers and stabilization of the helical structure of synthetic p53 analogs via a hydrocarbon cross-link (staple) has been found to lead to increased potency and inhibition of proteinprotein binding (J. Am. Chem. Soc. 129: 5298). However, details of the structure and dynamic stability of the stapled peptides are not well understood. Here, we use extensive all-atom molecular dynamics simulations to study a series of stapled a-helical peptides over a range of temperatures in solution. The peptides are found to exhibit substantial variations in predicted a-helical propensities that are in good agreement with the experimental observations. In addition, we find significant variation in local structural flexibility of the peptides with the position of the linker, which appears to be more closely related to the observed differences in activity than the absolute a-helical stability. These simulations provide new insights into the design of a-helical stapled peptides and the development of potent inhibitors of a-helical protein-protein interfaces.Key words: circular dichroism, drug design, hDM2, molecular dynamic simulations, p53, protein-protein interfaces, stapled peptide, a-helicity A renaissance of peptide drug discovery has emerged over the past several years. In particular, the identification of synthetically 'stapled' a-helical peptides having promising pharmacokinetic, metabolic stability, and cell-penetrating properties has sparked tremendous interest in their development for a plethora of therapeutic targets that have otherwise been deemed 'undruggable' by more conventional small-molecule strategies (1). To date, numerous examples of stapled peptides for varying therapeutic targets have been described, including p53 (2), BID BH3 (3,4), BAD BH3 (5), NOTCH (6), and HIV-1 capsid (7). Both single-turn (i + 4 fi i ) and double-turn (i + 7 fi i ) stapling chemistries are represented in these studies.Synthetic p53 peptides incorporating double-turn stapling chemistry have been previously described (2) and have provided insight to the evolution of a prototype series of cell-penetrating and in vitro biologically effective lead compounds. This series of peptides (Table 1) serves as the basis for the computational work presented here. These stapled p53 peptides have incorporated C a -methyl-amino acids having terminal olefin alkyl side chains of different lengths and chirality, such as (S)-CH 2 ) 3 -CH=CH 2 and (R)-CH 2 ) 6 -CH=CH 2 , which upon metathesis form an all-carbon macrocycle via an olefin linkage (see compound 8, Scheme 1). The structure-activity relationships of p53-stapled peptides 1-10 involve further amino acid modifications to decrease negative charge (i.e., Asp and Glu replacement by Asn and Gln, respectively) and facilitate cell penetration as well as point mutations to avoid nuclear export and ubiquitination (i.e., Lys replacement by Arg). In contrast,...

Experiments demonstrate that Mg2+ is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg2+ action on RNA is not well understood. We investigate the interplay between RNA and Mg2+ at atomic resolution through ten 2 microsecond explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including three stemloops, is very stable on this timescale. Simulations reveal that outer sphere coordinated Mg2+ ions fluctuate on the same time scale as the RNA, and that their dynamics couple. Locally, Mg2+ association affects RNA conformation through tertiary bridging interactions; globally, increasing Mg2+ concentration slows RNA fluctuations. Outer sphere Mg2+ ions responsible for these effects account for 80% of Mg2+ in our simulations. These ions are transiently bound to the RNA, maintaining interactions, but shuttled from site to site. Outer sphere Mg2+ are separated from the RNA by a single hydration shell, occupying a thin layer 3-5Å from the RNA. Distribution functions reveal outer sphere Mg2+ are positioned by electronegative atoms, hydration layers, and have a preference for the major groove. Diffusion analysis suggests transient outer sphere Mg2+ dynamics are glassy. Since outer sphere Mg2+ ions account for most of the Mg2+ in our simulations, these ions may change the paradigm of Mg2+-RNA interactions. Rather than a few inner sphere ions anchoring the RNA structure surrounded by a continuum of diffuse ions, we observe a layer of outer sphere coordinated Mg2+ that is transiently bound but strongly coupled to the RNA.