生物大分子
An intense controversy has surrounded the mechanism of voltage-gating in ion channels. We interpreted the two leading models of voltage-gating with respect to the thermodynamic energetics of membrane insertion of the voltage-sensing…
Polymers can be modeled as open polygonal paths and their closure generates knots. Knotted proteins detection is currently achieved via high-throughput methods based on a common framework insensitive to the handedness of knots. Here we…
We inspect the geometry of proteins by identifying their backbones as framed polygons. We find that the left-handed helix region of the Ramachandran map for non-glycyl residues corresponds to an isolated and highly localized sector in the…
The lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding CI and CRO proteins. Here we address the Physics of this transition in terms of an energy function that…
We present a rigidity analysis on a large number of X-ray crystal structures of the enzyme HIV-1 protease using the 'pebble game' algorithm of the software FIRST. We find that although the rigidity profile remains similar across a…
The problem of DNA-DNA interaction mediated by divalent counterions is studied using computer simulation. Although divalent counterions cannot condense free DNA molecules in solution, we show that if DNA configurational entropy is…
Nanospray and collisionally-induced dissociation are used to evaluate the presence and absence of interstrand co-chelation of zinc ions in dimers of metallothionein. As was reported in a previous publication from this laboratory,…
Lasso peptides constitute a class of bioactive peptides sharing a knotted structure where the C-terminal tail of the peptide is threaded through and trapped within an N-terminalmacrolactamring. The structural characterization of lasso…
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction…
While slowly turning the ends of a single molecule of DNA at constant applied force, a discontinuity was recently observed at the supercoiling transition, when a small plectoneme is suddenly formed. This can be understood as an abrupt…
It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.). These properties are…
We apply the Wako-Saito-Munoz-Eaton model to the study of Myotrophin, a small ankyrin repeat protein, whose folding equilibrium and kinetics have been recently characterized experimentally. The model, which is a native-centric with binary…
A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…
We present a theoretical investigation on possible selection of olfactory receptors (ORs) as sensing components of nanobiosensors. Accordingly, we generate the impedance spectra of the rat OR I7 in the native and activated state and analyze…
We propose a mechanism that explains in a simple and natural form the l-homochiralization of prebiotic aminoacids in a volume of water where a geothermal gradient exists.
We perform a quantum mechanical study of the peptides that are part of the LH2 complex from Rhodopseudomonas acidophila, a non-sulfur purple bacteria that has the ability of producing chemical energy from photosynthesis. The electronic…
Many physical and chemical processes, such as folding of biopolymers, are best described as dynamics on large combinatorial energy landscapes. A concise approximate description of dynamics is obtained by partitioning the micro-states of the…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
The performance of single folding predictors and combination scores is critically evaluated. We test mean packing, mean pairwise energy and the new index gVSL2 on a dataset of 743 folded proteins and 81 natively unfolded proteins. These…
Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg/ml. This high density requires substantial compression of the normal B form…