Structural insights into how proteoglycans determine chemokine-CXCR1/CXCR2 interactions: progress and challenges

K Rajarathnam, UR Desai - Frontiers in immunology, 2020 - frontiersin.org
Proteoglycans (PGs), present in diverse environments, such as the cell membrane surface,
extracellular milieu, and intracellular granules, are fundamental to life. Sulfated …

pH-dependent random coil 1H, 13C, and 15N chemical shifts of the ionizable amino acids: a guide for protein pK a measurements

G Platzer, M Okon, LP McIntosh - Journal of biomolecular NMR, 2014 - Springer
The p K a values and charge states of ionizable residues in polypeptides and proteins are
frequently determined via NMR-monitored pH titrations. To aid the interpretation of the …

Physicochemical properties of ion pairs of biological macromolecules

J Iwahara, A Esadze, L Zandarashvili - Biomolecules, 2015 - mdpi.com
Ion pairs (also known as salt bridges) of electrostatically interacting cationic and anionic
moieties are important for proteins and nucleic acids to perform their function. Although …

A novel approach for nanobubble generation toward biomedical applications

L Ouyang, HHWB Hansen, H Cha, X Ji, J Zhang… - Colloids and Surfaces A …, 2024 - Elsevier
The stability of free-standing nanobubbles is a long-standing controversial problem due to
the Laplace pressure catastrophe at the nanoscale. In most industrial circumstances, a large …

Biophysical chemistry behind sickle cell anemia and the mechanism of voxelotor action

M Suhail - Scientific Reports, 2024 - nature.com
Sickle cell anemia disease has been a great challenge to the world in the present situation.
It occurs only due to the polymerization of sickle hemoglobin (HbS) having Pro–Val–Glu …

Dynamics and recognition within a protein–DNA complex: a molecular dynamics study of the SKN-1/DNA interaction

L Etheve, J Martin, R Lavery - Nucleic Acids Research, 2016 - academic.oup.com
Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1
bound to its cognate DNA site show that the protein–DNA interface undergoes significant …

Changes in conformational dynamics of basic side chains upon protein–DNA association

A Esadze, C Chen, L Zandarashvili, S Roy… - Nucleic acids …, 2016 - academic.oup.com
Basic side chains play major roles in recognition of nucleic acids by proteins. However,
dynamic properties of these positively charged side chains are not well understood. In this …

Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

L Etheve, J Martin, R Lavery - Nucleic acids research, 2016 - academic.oup.com
We have studied the dynamics of three transcription factor–DNA complexes using all-atom,
microsecond-scale MD simulations. In each case, the salt bridges and hydrogen bond …

New tools to probe the protein surface: ultrasmall gold nanoparticles carry amino acid binders

SB van der Meer, I Hadrovic, A Meiners… - The Journal of …, 2020 - ACS Publications
A strategy toward epitope-selective functionalized nanoparticles is introduced in the
following: ultrasmall gold nanoparticles (diameter of the metallic core about 2 nm) were …

Entropic enhancement of protein-DNA affinity by oxygen-to-sulfur substitution in DNA phosphate

L Zandarashvili, D Nguyen, KM Anderson, MA White… - Biophysical journal, 2015 - cell.com
Dithioation of DNA phosphate is known to enhance binding affinities, at least for some
proteins. We mechanistically characterized this phenomenon for the Antennapedia …