pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

NV Di Russo, DA Estrin, MA Martí… - PLoS computational …, 2012 - journals.plos.org
The acid-base behavior of amino acids is an important subject of study due to their
prominent role in enzyme catalysis, substrate binding and protein structure. Due to …

Short-Range π–π Stacking Assembly on P25 TiO2 Nanoparticles for Enhanced Visible-Light Photocatalysis

W Wei, D Liu, Z Wei, Y Zhu - ACS Catalysis, 2017 - ACS Publications
Utilization of the renewable solar fuel based on a perylenetetracarboxylic acid diimide
(PTCDI)–semiconductor composite represents an effective method to solve the energy crisis; …

THz absorption spectroscopy of solvated β-lactoglobulin

H Vondracek, J Dielmann-Gessner, W Lubitz… - The Journal of …, 2014 - pubs.aip.org
The influence of β-lactoglobulin (βLG) on the fast sub-picosecond collective hydration
dynamics in the solvent was investigated by THz absorption spectroscopy as a function of …

Mycobacterial and human ferrous nitrobindins: Spectroscopic and reactivity properties

G De Simone, A di Masi, A Pesce, M Bolognesi… - International Journal of …, 2021 - mdpi.com
Structural and functional properties of ferrous Mycobacterium tuberculosis (Mt-Nb) and
human (Hs-Nb) nitrobindins (Nbs) were investigated. At pH 7.0 and 25.0° C, the unliganded …

Underlying thermodynamics of pH-dependent allostery

NV Di Russo, MA Martí, AE Roitberg - The Journal of Physical …, 2014 - ACS Publications
Understanding the effects of coupling protein protonation and conformational states is
critical to the development of drugs targeting pH sensors and to the rational engineering of …

Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125

DJA de Armiño, S Di Lella, D Montepietra… - Protein …, 2024 - Wiley Online Library
Due to the low temperature, the Antarctic marine environment is challenging for protein
functioning. Cold‐adapted organisms have evolved proteins endowed with higher flexibility …

Nitrite dismutase reaction mechanism: Kinetic and spectroscopic investigation of the interaction between nitrophorin and nitrite

C He, BD Howes, G Smulevich, S Rumpel… - Journal of the …, 2015 - ACS Publications
Nitrite is an important metabolite in the physiological pathways of NO and other nitrogen
oxides in both enzymatic and nonenzymatic reactions. The ferric heme b protein nitrophorin …

[HTML][HTML] Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7

M Knipp, H Ogata, G Soavi, G Cerullo, A Allegri… - …, 2015 - ncbi.nlm.nih.gov
Nitrophorins represent a unique class of heme proteins that are able to perform the delicate
transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH …

pH-dependent picosecond structural dynamics in the distal pocket of nitrophorin 4 investigated by 2D IR spectroscopy

M Cheng, JF Brookes, WR Montfort… - The Journal of Physical …, 2013 - ACS Publications
Nitrophorin 4 (NP4) belongs to a family of pH-sensitive, nitric oxide (NO) transporter proteins
that undergo a large structural change from a closed to an open conformation at high pH to …

Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations

S Abbruzzetti, F Spyrakis, A Bidon-Chanal… - Physical Chemistry …, 2013 - pubs.rsc.org
The presence of cavities and tunnels in the interior of proteins, in conjunction with the
structural plasticity arising from the coupling to the thermal fluctuations of the protein …