生物大分子
Specific binding of proteins to DNA is one of the most common ways in which gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a…
We analyzed folding routes predicted by a variational model in terms of a generalized formalism of the capillarity scaling theory for 28 two-state proteins. The scaling exponent ranged from 0.2 to 0.45 with an average of 0.33. This average…
Natively unstructured proteins defy the classical "one sequence-one structure" paradigm of protein science. Monomers of these proteins in pathological conditions can aggregate in the cell, a process that underlies socially relevant…
While designing oligonucleotide-based microarrays, cross-hybridization between surface-bound oligos and non-intended labeled targets is probably the most difficult parameter to predict. Although literature describes rules-of-thumb…
In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum arc- and stack-length. That is, we study the numbers of RNA pseudoknot structures with arc-length $\ge 3$, stack-length $\ge \sigma$ and in which there…
In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum stack-length. We show that the numbers of $k$-noncrossing structures without isolated base pairs are significantly smaller than the number of all…
Miniaturization is a hallmark of modern technologies. Notably, this feature has not spared molecular biology and its potential applications. Towards developing more effective therapeutics against cancer, studies began to explore more than a…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6),…
We present the results of our numerical analysis of a "composite" model of DNA which generalizes a well-known elementary torsional model of Yakushevich by allowing bases to move independently from the backbone. The model shares with the…
What are proteins made from, as the working parts of the living cells protein machines? To answer this question, we need a technology to disassemble proteins onto elementary func-tional details and to prepare lumped description of such…
Time has come for a survey of our knowledge on the physical interaction between the growth-promoting insulin molecule and retinoblastoma tumor suppressor protein (RB). Theoretical and experimental observations over the past 15 years…
A recently proposed model of non-autocatalytic reactions in dipeptide reactions leading to spontaneous symmetry breaking and homochirality is examined. The model is governed by activation, polymerization, epimerization and depolymerization…
Although conservation of thermodynamics is much less studied than of sequences and structures, thermodynamic details are biophysical features different from but as important as structural features. As a succession of previous research which…
Background. Dramatic increases in RNA structural data have made it possible to recognize its conformational preferences much better than a decade ago. This has created an opportunity to use discrete restraint-based conformational sampling…
Background. All-atom crystallographic refinement of proteins is a laborious manually driven procedure, as a result of which, alternative and multiconformer interpretations are not routinely investigated. Results. We describe efficient loop…
We demonstrate that a common-line method can assemble a 3D oversampled diffracted intensity distribution suitable for high-resolution structure solution from a set of measured 2D diffraction patterns, as proposed in experiments with an…
The isotopic composition, for example, 14C/12C, 13C/12C, 2H/1H, 15N/14N and 18O/16O, of the elements of matter is heterogeneous. It is ruled by physical, chemical and biological mechanisms. Isotopes can be employed to follow the fate of…
Simple theoretical concepts and models have been helpful to understand the folding rates and routes of single-domain proteins. As reviewed in this article, a physical principle that appears to underly these models is loop closure.
The authors address the problem of downhill protein folding in the framework of a simple statistical mechanical model, which allows an exact solution for the equilibrium and a semianalytical treatment of the kinetics. Focusing on protein…