Pathfinder: protein folding pathway prediction based on conformational sampling

Z Huang, X Cui, Y Xia, K Zhao… - PLoS Computational …, 2023 - journals.plos.org
The study of protein folding mechanism is a challenge in molecular biology, which is of great
significance for revealing the movement rules of biological macromolecules, understanding …

Protein–peptide binding energetics under crowded conditions

SS Stadmiller, JS Aguilar, S Parnham… - The Journal of Physical …, 2020 - ACS Publications
Nearly all biological processes, including strictly regulated protein–protein interactions
fundamental in cell signaling, occur inside living cells where the concentration of …

Amyloid properties of the mouse egg zona pellucida

N Egge, A Muthusubramanian, GA Cornwall - PLoS One, 2015 - journals.plos.org
The zona pellucida (ZP) surrounding the oocyte is an extracellular fibrillar matrix that plays
critical roles during fertilization including species-specific gamete recognition and protection …

Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain

A Cámara-Artigas - Archives of Biochemistry and Biophysics, 2016 - Elsevier
Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold
and function. In the early 1960s this phenomenon was postulated for the oligomers of …

Inhibition of c-Src/p38 MAPK pathway ameliorates renal tubular epithelial cells apoptosis in db/db mice

H Wu, Y Shi, X Deng, Y Su, C Du, J Wei, Y Ren… - Molecular and cellular …, 2015 - Elsevier
Renal tubular epithelial cells (RTEC) apoptosis, which plays a key role in the pathogenesis
and progression of diabetic nephropathy (DN), is believed to be contributive to the …

Nickel Ligation of the N-Terminal Amine of HypA Is Required for Urease Maturation in Helicobacter pylori

HQ Hu, RC Johnson, DS Merrell, MJ Maroney - Biochemistry, 2017 - ACS Publications
The human pathogen Helicobacter pylori requires nickel for colonization of the acidic
environment of the stomach. HypA, a Ni metallochaperone that is typically associated with …

Small molecule AX-024 reduces T cell proliferation independently of CD3ϵ/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3. 1 domain

K Richter, AC Rufer, M Muller, D Burger… - Journal of Biological …, 2020 - ASBMB
Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck
(noncatalytic region of tyrosine kinase) to the CD3ϵ subunit of the TCR. The interaction was …

First 3-D structural evidence of a native-like intertwined dimer in the acylphosphatase family

S Martínez-Rodríguez, A Cámara-Artigas… - Biochemical and …, 2023 - Elsevier
Abstract Acylphosphatase (AcP, EC 3.6. 1.7) is a small model protein conformed by a
ferredoxin-like fold, profoundly studied to get insights into protein folding and aggregation …

A database overview of metal‐coordination distances in metalloproteins

M Bazayeva, C Andreini, A Rosato - … Crystallographica Section D …, 2024 - journals.iucr.org
Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of
biological processes. For this reason, their experimental characterization is crucial to obtain …

Osmolyte effects on the growth of amyloid fibrils

AN Muttathukattil, G Reddy - The Journal of Physical Chemistry B, 2016 - ACS Publications
Understanding the role of naturally occurring protective osmolytes, such as trimethylamine N-
oxide (TMAO), in the growth of amyloid fibrils implicated in neurodegenerative diseases is …