Helical Contributions Mediate Light-Activated Conformational Change in the LOV2 Domain of <i>Avena sativa</i> Phototropin 1

Algae, plants, bacteria, and fungi contain flavin-binding light-oxygen-voltage (LOV) domains that function as blue light sensors to control cellular responses to light. In the second LOV domain of phototropins, called LOV2 domains, blue light illumination leads to covalent bond formation between protein and flavin that induces the dissociation and unfolding of a C-terminally attached α helix (Jα) and the N-terminal helix (A′α). To date, the majority of studies on these domains have focused on versions that contain truncations in the termini, which creates difficulties when extrapolating to the much larger proteins that contain these domains. Here, we study the influence of deletions and extensions of the A′α helix of the LOV2 domain of Avena sativa phototropin 1 (AsLOV2) on the light-triggered structural response of the protein by Fourier-transform infrared difference spectroscopy. Deletion of the A′α helix abolishes the light-induced unfolding of Jα, whereas extensions of the A′α helix lead to an attenuated structural change of Jα. These results are different from shorter constructs, indicating that the conformational changes in full-length phototropin LOV domains might not be as large as previously assumed, and that the well-characterized full unfolding of the Jα helix in AsLOV2 with short A′α helices may be considered a truncation artifact. It also suggests that the N- and C-terminal helices of phot-LOV2 domains are necessary for allosteric regulation of the phototropin kinase domain and may provide a basis for signal integration of LOV1 and LOV2 domains in phototropins

Scaling in many-body systems and proton structure function

The observation of scaling in processes in which a weakly interacting probe delivers large momentum ${\bf q}$ to a many-body system simply reflects the dominance of incoherent scattering off target constituents. While a suitably defined scaling function may provide rich information on the internal dynamics of the target, in general its extraction from the measured cross section requires careful consideration of the nature of the interaction driving the scattering process. The analysis of deep inelastic electron-proton scattering in the target rest frame within standard many-body theory naturally leads to the emergence of a scaling function that, unlike the commonly used structure functions $F_1$ and $F_2$, can be directly identified with the intrinsic proton response.Comment: 11 pages, 4 figures. Proceedings of the 11th Conference on Recent Progress in Many-Body Theories, Manchester, UK, July 9-13 200

Momentum distributions in liquid helium

The appearance of the superfluid phase, with its unique macroscopic properties, and the success of the 'two-fluid' model in describing the transport properties are intimately linked to the Bose statistics obeyed by /sup 4/He atoms. The most direct signature of the Bose condensate is in the single particle momentum distribution n(p). In the normal liquid the momentum distribution has a broad Gaussian shape, as predicted for classical systems, with a width determined by the quantum zero point motion. In the superfluid phase a new feature appears, the Bose condensate. The condensate appears as a delta-function singularity in n(p) with an intensity proportional to n/sub 0/, the condensate fraction. There has been extensive experimental work attempting to verify the existence of the condensate. Hohenberg and Platzman originally suggested that inelastic neutron scattering at high momentum transfer Q, where the Impulse Approximation IA can be used to directly relate the observed scattering to n(p), could provide a means of directly observing the condensate. In this review we will concentrate on recent experimental studies that utilize the large flux of high energy neutrons available at spallation neutron sources. These sources, which have become available only recently, have made it possible to make detailed measurements at large enough momentum transfers that the conditions for the Impulse Approximation are approximately satisfied. While deviations from the IA are still present at these higher Q's, they are more amenable to theoretical treatment and detailed predictions are available. Thus, even though no distinct condensate peak is observed, for the first time excellent agreement with the theoretical predictions for n(p) can be obtained. 50 refs., 12 figs

Momentum distributions in ^3He-^4He liquid mixtures

We present variational calculations of the one-body density matrices and momentum distributions for ^3He-^4He mixtures in the zero temperature limit, in the framework of the correlated basis functions theory. The ground-state wave function contains two- and three-body correlations and the matrix elements are computed by (Fermi)Hypernetted Chain techniques. The dependence on the ^3He concentration (x_3) of the ^4He condensate fraction $(n_0^{(4)})$ and of the ^3He pole strength (Z_F) is studied along the P=0 isobar. At low ^3He concentration, the computed ^4He condensate fraction is not significantly affected by the ^3He statistics. Despite of the low x_3 values, Z_F is found to be quite smaller than that of the corresponding pure ^3He because of the strong ^3He-^4He correlations and of the overall, large total density \rho. A small increase of $n_0^{(4)}$ along x_3 is found, which is mainly due to the decrease of \rho respect to the pure ^4He phase.Comment: 23 pages, 7 postscript figures, Revte

Description of recent large-qq neutron inclusive scattering data from liquid 4^4He

We report dynamical calculations for large-$q$ structure functions of liquid $^4$He at $T$=1.6 and 2.3 K and compare those with recent MARI data. We extend those calculations far beyond the experimental range q\le 29\Ain in order to study the approach of the response to its asymptotic limit for a system with interactions having a strong short-range repulsion. We find only small deviations from theoretical $1/q$ behavior, valid for smooth $V$. We repeat an extraction by Glyde et al of cumulant coefficients from data. We argue that fits determine the single atom momentum distribution, but express doubt as to the extraction of meaningful Final State Interaction parameters.Comment: 37 pages, 13 postscript fig

Momentum distribution of liquid helium

We have obtained the one--body density matrix and the momentum distribution $n(p)$ of liquid $^4$He at $T=3D0^o$K from Diffusion Monte Carlo (DMC) simulations, using trial functions optimized via the Euler Monte Carlo (EMC) method. We find a condensate fraction smaller than in previous calculations. Though we do not explicitly include long--range correlations in our calculations, we get a momentum distribution at long wavelength which is compatible with the presence of long--range correlations in the exact wave function. We have also studied $^3$He, using fixed--node DMC, with nodes and trial functions provided by the EMC. In particular, we analyze the momentum distribution $n(p)$ with respect to the discontinuity $Z$ as well as the singular behavior, at the Fermi surface. We also show that an approximate factorization of the one-body density matrix $\rho(r)\simeq \rho_0(r)\rho_B(r)$ holds, with $\rho_0(r)$ and $\rho_B(r)$ respectively the density matrix of the ideal Fermi gas and the density matrix of a Bose $^3$He.Comment: 10 pages, REVTeX, 12 figure

Energetic Components of Cooperative Protein Folding

A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative helical formation and contact energies based on a 5-letter alphabet are found to be insufficient to satisfy calorimetric and other experimental criteria for two-state folding. Such proteinlike behaviors are predicted, however, by models with polypeptide-like local conformational restrictions and environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

An Estimate of the Numbers and Density of Low-Energy Structures (or Decoys) in the Conformational Landscape of Proteins

The conformational energy landscape of a protein, as calculated by known potential energy functions, has several minima, and one of these corresponds to its native structure. It is however difficult to comprehensively estimate the actual numbers of low energy structures (or decoys), the relationships between them, and how the numbers scale with the size of the protein.We have developed an algorithm to rapidly and efficiently identify the low energy conformers of oligo peptides by using mutually orthogonal Latin squares to sample the potential energy hyper surface. Using this algorithm, and the ECEPP/3 potential function, we have made an exhaustive enumeration of the low-energy structures of peptides of different lengths, and have extrapolated these results to larger polypeptides.We show that the number of native-like structures for a polypeptide is, in general, an exponential function of its sequence length. The density of these structures in conformational space remains more or less constant and all the increase appears to come from an expansion in the volume of the space. These results are consistent with earlier reports that were based on other models and techniques