Electrostatic interactions in protein structure, folding, binding, and condensation

HX Zhou, X Pang - Chemical reviews, 2018 - ACS Publications
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …

Eukaryotic transcription factors: paradigms of protein intrinsic disorder

L Staby, C O'Shea, M Willemoës, F Theisen… - Biochemical …, 2017 - portlandpress.com
Gene-specific transcription factors (TFs) are key regulatory components of signaling
pathways, controlling, for example, cell growth, development, and stress responses. Their …

Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins

X Wang, LS Bigman, HM Greenblatt, B Yu… - Nucleic acids …, 2023 - academic.oup.com
In eukaryotes, many DNA/RNA-binding proteins possess intrinsically disordered regions
(IDRs) with large negative charge, some of which involve a consecutive sequence of …

Simple methods and rational design for enhancing aptamer sensitivity and specificity

P Kalra, A Dhiman, WC Cho, JG Bruno… - Frontiers in molecular …, 2018 - frontiersin.org
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity
and specificity. However, conventional SELEX (Systematic Evolution of Ligands by …

Structure and RNA-binding of the helically extended Roquin CCCH-type zinc finger

JN Tants, L Oberstrass, JE Weigand… - Nucleic Acids …, 2024 - academic.oup.com
Zinc finger (ZnF) domains appear in a pool of structural contexts and despite their small size
achieve varying target specificities, covering single-stranded and double-stranded DNA and …

Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

M Stracy, J Schweizer, DJ Sherratt, AN Kapanidis… - Molecular cell, 2021 - cell.com
Despite their diverse biochemical characteristics and functions, all DNA-binding proteins
share the ability to accurately locate their target sites among the vast excess of non-target …

Protein diffusion along Protein and DNA lattices: role of electrostatics and disordered regions

LS Bigman, Y Levy - Annual review of biophysics, 2023 - annualreviews.org
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 …

[HTML][HTML] Dynamics in Cre-loxP site-specific recombination

MP Foster, MJ Benedek, TD Billings… - Current opinion in …, 2024 - Elsevier
Cre recombinase is a phage-derived enzyme that has found utility for precise manipulation
of DNA sequences. Cre recognizes and recombines pairs of loxP sequences characterized …

Poly (ADP-ribose) polymerase 1 searches DNA via a 'monkey bar'mechanism

J Rudolph, J Mahadevan, P Dyer, K Luger - Elife, 2018 - elifesciences.org
Poly (ADP-ribose) polymerase 1 (PARP1) is both a first responder to DNA damage and a
chromatin architectural protein. How PARP1 rapidly finds DNA damage sites in the context …

Foldamer tertiary structure through sequence-guided protein backbone alteration

KL George, WS Horne - Accounts of chemical research, 2018 - ACS Publications
Conspectus The prospect of recreating the complex structural hierarchy of protein folding in
synthetic oligomers with backbones that are artificial in covalent structure (“foldamers”) has …