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Dynamics of Biomolecules: Combining Neutron, MD-Simulations and Dielectrics Spectroscopy Studies

A. P. Sokolov

Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA and
Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA


We present an attempt to classify different dynamic processes in biological macromolecules on the ns-ps time scale. It is based on analysis of quasileastic neutron scattering (QENS) data, dielectric relaxation spectroscopy and MD-simulations studies of dynamics of proteins, RNA and DNA. We identify four relaxation processes in dynamics of biomolecules on the picoseconds-nanosecond time scale: (i) fast picosecond relaxation that is strongly coupled to the solvent dynamics and is traditionally ascribed to a caged motion of residues; (ii) methyl groups dynamics that seems to play an important role in proteins; (iii) “localized diffusion” that seems to be strongly coupled to dynamics of hydration water; (iv) larger scale relaxation process in the ns-time scale that we ascribed to motions of domains or secondary structures. The microscopic nature of these processes and their dependence on hydration water are discussed. We propose a general picture of biomolecular dynamics on the ps-ns time scale. At the end we emphasize the difference in dynamics between proteins and nucleic acids and address the question of their evolutionary evolvements.

Affymetrix Human Transcriptome Array 2.0, New Transcriptome Analysis Software (TAC) and Comparisons to RNA-Seq!
Research has shown that the tens of thousands of human genes contain hundreds of thousands of exons, which produce hundreds of thousands of different transcript isoforms. Until now, measuring and analyzing these transcript isoforms has been nearly impossible due to technology limitations, sample input requirements, and lack of analysis capabilities/tools.
Designed to empower next-generation expression profiling studies, GeneChip Human Transcriptome Array 2.0 (HTA 2.0) provides the ability to go beyond gene-level expression profiling by providing the coverage and accuracy required to accurately detect all known transcript isoforms produced by a gene.
This high-resolution array design contains >6.0 million probes covering coding transcripts and non-coding transcripts. 70% of the probes on this array cover exons for coding transcripts, and the remaining 30% of probes on the array cover exon-exon splice junctions and non-coding transcripts.
The free TAC software is designed and intended for investigators allowing quick and easy visualization and detection of the transcriptome.
In this talk I will try to illustrate how most researchers who run RNA-Seq do not sequence deep enough and are missing important changes which are easily accessible on microarrays.

Amos Grundwag
Manager, Genomics and BioInformatics.
Biotechnology Department.
Eisenberg Bros. Ltd.
Tel: +972 (0)3 9777037
Mobile: +972 (0)528 910960

What is an optimal particle shape for scattering, e.g., shape causing minimal extinction among those of equal volume and randomly oriented? Guided by the isoperimetric property of a sphere, relevant in the geometrical optics limit of scattering by large particles, we examine an analogous question in the low frequency (induced dipole moment) approximation, seeking to disentangle electric and geometric contributions. To that end, a simple proof is supplied of spherical optimality for a coated ellipsoidal particle and a monotonic increase with asphericity is shown in the low frequency regime for orientation-averaged induced dipole moments and scattering cross-sections. Physical insight is obtained from the Rayleigh-Gans (transparent) limit and eccentricity expansions. We propose linking low and high frequency regime in a single sweeping minimum principle valid for all size parameters, provided that reasonable size distributions wash out the Mie resonances. This proposal is further supported by the sum rule for integrated extinction. Implications for environmental remote sensing are discussed throughout the talk.