Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Direct evidence of acid-driven protein desolvation.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 123, Issue 10, Page e2525949123, Year 2026
Publish date	Mar 10, 2026
Authors	Farzad Hamdi / Ioannis Skalidis / Inken Kaja Schwerin / Jaydeep Belapure / Dmitry A Semchonok / Fotis L Kyrilis / Christian Tüting / Johannes Müller / Georg Künze / Panagiotis L Kastritis /
PubMed Abstract	Water and its ability to modulate the protonation states of biomolecules govern the physical chemistry of life, dictating their metabolic functions. However, how amino acid protonation alters protein ...Water and its ability to modulate the protonation states of biomolecules govern the physical chemistry of life, dictating their metabolic functions. However, how amino acid protonation alters protein hydration and solubility is an open question since Kuntz and Kauzmann proposed p-driven protein desolvation in 1974. Here, in a series of high-resolution cryoelectron microscopy structures of a protein complex at different p values (from p 9.0 to 3.5), we examined thousands of observable hydration sites. Cryoelectron microscopy data, in agreement with constant-p molecular dynamics simulations, show that nearly half of protein-bound waters exchanged with the bulk solvent upon acidification, with ~100 waters lost per p unit per molecule. The loss of waters was most significant around the side chains of glutamate and aspartate residues while specific polar residues, mostly asparagine, anchored persistent waters. A positionally conserved hydration layer was observed across all p conditions, accounting for 40% of resolved waters. Those waters displayed denser packing than less persistent waters, forming a p-independent solvation shell. Acid-induced water exchange also displaced bound iron, providing a mechanistic link between solvation and metal release. Our findings demonstrate the core principles of acid-driven protein desolvation, resolving a 50-y-old biochemical hypothesis.
External links	Proc Natl Acad Sci U S A / PubMed:41785322 / PubMed Central
Methods	EM (single particle)
Resolution	1.89 - 2.08 Å
Structure data	54951 9sjr EMDB-54951, PDB-9sjr: Cryo-EM structure of Human Apoferritin at pH 3.5 Method: EM (single particle) / Resolution: 1.99 Å 54952 9sjs EMDB-54952, PDB-9sjs: Cryo-EM structure of Human Apoferritin at pH 4 Method: EM (single particle) / Resolution: 2.06 Å 54953 9sjt EMDB-54953, PDB-9sjt: Cryo-EM structure of Human Apoferritin at pH 5 Method: EM (single particle) / Resolution: 1.96 Å 54954 9sju EMDB-54954, PDB-9sju: Cryo-EM structure of Human Apoferritin at pH 7 Method: EM (single particle) / Resolution: 2.08 Å 54955 9sjv EMDB-54955, PDB-9sjv: Cryo-EM structure of Human Apoferritin at pH 9 Method: EM (single particle) / Resolution: 1.89 Å
Chemicals	ChemComp-FE: Unknown entry ChemComp-MG: Unknown entry ChemComp-HOH: WATER
Source	homo sapiens (human)
Keywords	METAL BINDING PROTEIN / Apoferritin / Ferritin / Metal storage / Low pH