Biomolecules
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a…
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both…
Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that…
Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as…
Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in…
Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk of preterm labour, and its associated malodour impacts the quality of life for many women. Clinical diagnosis primarily relies on microscopy to presumptively detect a…
We discuss the gauge field theory approach to protein structure study, which allows a natural way to introduce collective degrees of freedom and nonlinear topological structures. Local symmetry of proteins and its breaking in the medium is…
Considerable mechanistic insight has been gained into amyloid aggregation; however, a large class of non-amyloid protein aggregates are considered 'amorphous,' and in most cases little is known about their mechanisms. Amorphous aggregation…
A free energy landscape estimation-method based on Bayesian inference is presented and used for comparing the efficiency of thermally enhanced sampling methods with respect to regular molecular dynamics, where the simulations are carried…
Artificial neural networks (ANNs) have gained a well-deserved popularity among machine learning tools upon their recent successful applications in image- and sound processing and classification problems. ANNs have also been applied for…
Because of the limitations of classical silicon based computational technology, several alternatives to traditional method in form of unconventional computing have been proposed. In this paper we will focus on DNA computing which is showing…
Collapsin response mediator protein CRMP2 (gene: DPYSL2) is crucial for neuronal development. The homotetrameric CRMP2 complex is regulated via two mechanisms, first by phosphorylation at, and second by reduction and oxidation of the Cys504…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
We propose to combine a mean field approach with all atom molecular dynamics into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic level precision. As an example we investigate…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
Many of the most important processes in cells take place on and across membranes. With the rise of an impressive array of powerful quantitative methods for characterizing these membranes, it is an opportune time to reflect on the structure…
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins.…
Protein allostery requires dynamical structural correlations. Physical origin of which, however, remain elusive despite intensive studies during last two decades. Based on analysis of molecular dynamics (MD) simulation trajectories for ten…
Summary: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make modeling simpler, but largely exclude users from the process. We present an…
We study the conformational freedom of a protein made by two rigid domains connected by a flexible linker. The conformational freedom is represented as an unknown probability distribution on the space of allowed states. A new algorithm for…