生物大分子
Zinc is found saturated in the deposited Amyloid-beta (AB) peptide plaques in brains of patients subjected to Alzheimer disease (AD). Zinc binding to AB promotes aggregations, including the toxic soluble AB species. Up to now, only the…
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…
"Pull moves" is a popular move set for lattice polymer model simulations. We show that the proof given for its reversibility earlier is flawed, and some moves are irreversible, which leads to biases in the parameters estimated from the…
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental…
Upon studying the B-Factors of all the atoms of all non-redundant proteins belonging to 76 most commonly found structural domains of all four major structural classes, it was found that the residue mobility has decreased during the course…
Motivation: Protein surface roughness is fractal in nature. Mass, hydrophobicity, polarizability distributions of protein interior are fractal too, as are the distributions of dipole moments, aromatic residues, and many other structural…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
A relationship between the preexponent of the rate constant and the distribution over activation barrier energies for enzymatic/protein reactions is revealed. We consider an enzyme solution as an ensemble of individual molecules with…
In this article it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free…
We introduce Modulated Orientation Sensitive Terahertz Spectroscopy (MOSTS) that can both increase contrast between adjacent modes and remove the broad band librational background to allow mode identification for large macro molecules such…
A method is presented for measuring anisotropic THz response for small crystals, Crystal Anisotropy Terahertz Microscopy (CATM). Sucrose CATM measurements find the expected anisotropic phonon resonances. CATM measurements of protein…
The evidence that Flowering Locus T (FT) protein and its paralog Twin Sister of FT, act as the long distance floral stimulus, or at least that they are part of it in diverse plant species, has attracted much attention in recent years.…
Fifteen years ago Monique Tirion showed that the low-frequency normal modes of a protein are not significantly altered when non-bonded interactions are replaced by Hookean springs, for all atom pairs whose distance is smaller than a given…
Sensory rhodopsin II (SRII) is a seven helix protein that belongs to the rhodopsin protein family. Light induced conformational changes govern SRII's function. These changes are related to the photo cycle of the protein that is comprised of…
During this era of new drug designing, medicinal plants had become a very interesting object of further research. Pharmacology screening of active compound of medicinal plants would be time consuming and costly. Molecular docking is one of…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…