Frustration in Biomolecules

Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with a finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of "frustration" in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and how structure connects to function. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding, how a large part of the biological functions of proteins are related to subtle local frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. We hope to illustrate how Frustration is a fundamental concept in relating function to structural biology.Comment: 97 pages, 30 figure

Structural motifs of biomolecules

Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularityfree self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules.Comment: 13 pages, 5 figure

Electron collisions with biomolecules

We report on results of recent studies of collisions of low-energy electrons with nucleobases and other DNA constituents. A particular focus of these studies has been the identification and characterization of resonances that play a role in electron attachment leading to strand breaks in DNA. Comparison of the calculated resonance positions with results of electron transmission measurements is quite encouraging. However, the higher-lying π* resonances of the nucleobases appear to be of mixed elastic and core-excited character. Such resonant channel coupling raises the interesting possibility that the higher π*resonances in the nucleobases may promote dissociation of DNA by providing doorway states to triplet excited states

Spin-boson models for quantum decoherence of electronic excitations of biomolecules and quantum dots in a solvent

We give a theoretical treatment of the interaction of electronic excitations (excitons) in biomolecules and quantum dots with the surrounding polar solvent. Significant quantum decoherence occurs due to the interaction of the electric dipole moment of the solute with the fluctuating electric dipole moments of the individual molecules in the solvent. We introduce spin boson models which could be used to describe the effects of decoherence on the quantum dynamics of biomolecules which undergo light-induced conformational change and on biomolecules or quantum dots which are coupled by Forster resonant energy transfer.Comment: More extended version, to appear in Journal of Physics: Condensed Matter. 13 pages, 3 figure

Multi-wavelength fluorescence sensing with integrated waveguides in an optofluidic chip

Femtosecond-laser-written integrated waveguides enable multi-wavelength fluorescence sensing of flowing biomolecules in an optofluidic chip. Fluorescence from differently labeled biomolecules with distinct absorption wavelengths, encoded by uniquely modulating each excitation beam, is detected by a color-blind photodetector, and the origin of each signal is unraveled by Fourier analysis

Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems

Biomolecules carry out very specialized tasks inside the cell where energies involved are few tens of k_BT, small enough for thermal fluctuations to be relevant in many biomolecular processes. In this paper I discuss a few concepts and present some experimental results that show how the study of fluctuation theorems applied to biomolecules contributes to our understanding of the nonequilibrium thermal behavior of small systems.Comment: Proceedings of the 22nd Statphys Conference 2004 (Bangalore,India). Invited contributio

Interactions of slow electrons with biomolecules

We report on results of computational studies of the interaction of slow electrons with the purine and pyrimidine bases of DNA, as well as with their associated nucleosides and nucleotides. The calculations focus on characterisation of the π* resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. High-level studies of the π* resonances in pyrazine, a close analogue of the pyrimidine bases, indicate that the higher-energy π* resonances in these bases may in fact contain large admixtures of core-excited character built on low-lying triplet states. Decay into such triplet states may provide a mechanism for damage to DNA