Frustration in biomolecules
Biomolecules are the prime information processing elements of living matter. Most of these
inanimate systems are polymers that compute their own structures and dynamics using as …
inanimate systems are polymers that compute their own structures and dynamics using as …
Modeling structural dynamics of biomolecular complexes by coarse-grained molecular simulations
Conspectus Due to hierarchic nature of biomolecular systems, their computational modeling
calls for multiscale approaches, in which coarse-grained (CG) simulations are used to …
calls for multiscale approaches, in which coarse-grained (CG) simulations are used to …
An engineered hypercompact CRISPR-Cas12f system with boosted gene-editing activity
Compact CRISPR-Cas systems offer versatile treatment options for genetic disorders, but
their application is often limited by modest gene-editing activity. Here we present …
their application is often limited by modest gene-editing activity. Here we present …
Building transcription factor binding site models to understand gene regulation in plants
Transcription factors (TFs) are key cellular components that control gene expression. They
recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to …
recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to …
Protein diffusion along Protein and DNA lattices: role of electrostatics and disordered regions
Diffusion is a pervasive process present in a broad spectrum of cellular reactions. Its
mathematical description has existed for nearly two centuries and permits the construction of …
mathematical description has existed for nearly two centuries and permits the construction of …
Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble
L Zandarashvili, A Esadze, D Vuzman… - Proceedings of the …, 2015 - National Acad Sciences
Although engineering of transcription factors and DNA-modifying enzymes has drawn
substantial attention for artificial gene regulation and genome editing, most efforts focus on …
substantial attention for artificial gene regulation and genome editing, most efforts focus on …
Electrostatics, structure prediction, and the energy landscapes for protein folding and binding
While being long in range and therefore weakly specific, electrostatic interactions are able to
modulate the stability and folding landscapes of some proteins. The relevance of …
modulate the stability and folding landscapes of some proteins. The relevance of …
Charge engineering improves the performance of bst DNA polymerase fusions
The charge states of proteins can greatly influence their stabilities and interactions with
substrates, and the addition of multiple charges (supercharging) has been shown to be a …
substrates, and the addition of multiple charges (supercharging) has been shown to be a …
Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1
L Zandarashvili, D Vuzman, A Esadze… - Proceedings of the …, 2012 - National Acad Sciences
Egr-1 is an inducible transcription factor that recognizes 9-bp target DNA sites via three zinc
finger domains and activates genes in response to cellular stimuli such as synaptic signals …
finger domains and activates genes in response to cellular stimuli such as synaptic signals …
Ion counting demonstrates a high electrostatic field generated by the nucleosome
In eukaryotes, a first step towards the nuclear DNA compaction process is the formation of a
nucleosome, which is comprised of negatively charged DNA wrapped around a positively …
nucleosome, which is comprised of negatively charged DNA wrapped around a positively …