Biophysical Reviews and Letters

We have studied the collective dynamics of leucine-rich repeat (LRR) proteins using an elastic network approximation. The slowest mode of the porcine ribonuclease inhibitor (pRI) protein could be visualized as bending fluctuations of a curved elastic strip leading to a planar opening–closing motion of the horseshoe which largely corresponded to the deformation of the protein on ligand binding. The second slowest mode however exhibited a significant out of plane splaying. The distribution of the lowest eigenvalues of different LRR proteins as a function of their repeat number was found to be close to the dispersion curve obtained from pRI whereas that of the leucine-rich variant (LRV) protein showed considerable deviation. The differing mechanical properties of these structurally similar solenoid proteins may have relevance to their function.

In spite of the numerous experimental and theoretical studies on green fluorescent protein and its modifications, there is still no definitive answer to the central question: why such systems exhibit enhanced fluorescence. Based upon detailed quantum-chemical estimations, we advocate the following hypothesis. In the green fluorescent protein ground electronic state, the protein surrounding strains the chromophore with respect to its native intramolecular conformational preference in vacuo or in solution. Absorbing a photon of the proper wavelength not only causes a joint proton–electron transfer in and around the chromophore, but also increases the intrinsic strain of the latter. Since conformational relaxation of such a structure will not require any additional energy input, the energy gained by the chromophore cannot be dissipated into the chromophore's internal non-radiative degrees of freedom, and thus it returns as a fluorescence emission.

The ten years since the first publication of the structure from bovine heart mitochondria in 1997 have significantly broadened our structural knowledge of cytochrome bc₁ and b₆f complexes from various organisms under a variety of conditions providing unprecedented mechanistic insights into the function of these essential enzymes. Still many questions remain. The bifurcated electron transfer at the quinol oxidation (Q_P) site is one of the most difficult and unresolved problems. Intertwined with it, the proton translocation pathway and the quinol oxidation chemistry have remained focuses of intense research. Structural studies of mitochondrial bc₁ complexes have not only provided an atomic view of the bc₁ complex, defining many critical, functionally important features such as the locations of the Q_P and Q_N sites, but have also offered a number of important clues to mechanistic issues leading to the formulation of the "conformational switch of ISP" hypothesis. Intensive biochemical, genetic, and biophysical studies coupled with structural investigations have provided strong support for this hypothesis. The recent structure determination of the bc₁ from the photosynthetic bacterium R. sphaeroides promises further insight.

Many prokaryotic nucleoid proteins bend DNA and form extended helical protein-DNA fibers rather than condensed structures. On the other hand, it is known that such proteins (such as bacterial HU) strongly promote DNA condensation by macromolecular crowding. Using theoretical arguments, we show that this synergy is a simple consequence of the larger diameter and lower net charge density of the protein-DNA filaments as compared to naked DNA, and hence, should be quite general. To illustrate this generality, we use light-scattering to show that the 7kDa basic archaeal nucleoid protein Sso7d from Sulfolobus solfataricus (known to sharply bend DNA) likewise does not significantly condense DNA by itself. However, the resulting protein-DNA fibers are again highly susceptible to crowding-induced condensation. Clearly, if DNA-bending nucleoid proteins fail to condense DNA in dilute solution, this does not mean that they do not contribute to DNA condensation in the context of the crowded living cell.

The Protein Data Bank (PDB) is the most important depository of protein structural information, containing more than 45,000 deposited entries today. Because of its inhomogeneous structure, its fully automated processing is almost impossible. In a previous work, we cleaned and re-structured the entries in the Protein Data Bank, and from the result we have built the RS-PDB database. Using the RS-PDB database, we draw a Ramachandran-plot from 6,593 "perfect" polypeptide chains found in the PDB, containing 1,192,689 residues. This is a more than tenfold increase in the size of data analyzed before this work. The density of the data points makes it possible to draw a logarithmic heat map enhanced Ramachandran map, showing the fine inner structure of the right-handed α-helix region.

Mapping entry and exit pathways of gases in proteins is now carried out using a combination of crystallographic, spectroscopic and computational techniques. Recent technological advances have brought about a broad range of software packages that can map diffusion pathways in several different classes of proteins, the results of which can be verified experimentally. We review some of the software packages used to study diffusion pathways in different proteins and discuss some common applications. It is anticipated that this review will serve as a useful resource in choosing the software package best suited to one's need to study a problem on diffusion pathways for diatomic molecules while providing the necessary background for this purpose.

Both microscopic and macroscopic worlds are plentiful in knotted and linked structures. But even at the mesoscopic level, works in molecular topology have shown that Nature builds DNA molecules, which form actual knots and links between themselves. Qualitative similarities may be observed between forms of the microscopic world, as well as between those of the macroscopic world; and by extracting the structures, it is possible to study their dynamics thanks to topological methods and techniques. The aim of this paper is to show that knots and links are ubiquitous scale-independent objects carrying a tremendous amount of precious information on the emergence of new forms and structures especially in living matter. In fact, knotting and unknotting are "universal" principles underlying these forms and structures. This study is focused on showing that differential geometry and topological knot's theory can be used, notably (a) to describe three-dimensional structures of DNA and protein-DNA complexes, and (b) to explain how geometrical supercoiling occur in the most fundamental supra-molecular structures and why it is essential for their biological activity.