pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4, PLoS Comput. Biol, vol.8, p.1002761, 2012. ,
Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites, IUBMB Life, vol.53, pp.85-98, 2002. ,
On the solubility of proteins as a function of pH: Mathematical development and application. Fluid Phase Equilibr, vol.306, pp.242-250, 2011. ,
A universal trend of amino acid gain and loss in protein evolution, Nature, vol.433, pp.633-638, 2005. ,
, Protein Modelling
pH-dependent properties of SOD studied through mutants on Lys-136, Inorg. Chem, vol.32, pp.1403-1406, 1993. ,
pH-dependent insertion of proteins into membranes: B-chain mutation of diphtheria toxin that inhibits membrane translocation, Glu-349--Lys, Proc. Natl. Acad. Sci, vol.89, pp.6202-6206, 1992. ,
A novel mechanism of tumorigenesis involving pHdependent destabilization of a mutant p53 tetramer, Nat. Struct. Biol, vol.9, pp.12-16, 2001. ,
Analysis of the pH-dependent Folding and Stability of Histidine Point Mutants Allows Characterization of the Denatured State and Transition State for Protein Folding, J. Mol. Biol, vol.345, pp.163-173, 2005. ,
Histidine Residues in the Na+-coupled Ascorbic Acid Transporter-2 (SVCT2) Are Central Regulators of SVCT2 Function, Modulating pH Sensitivity, Transporter Kinetics, Na+ Cooperativity, Conformational Stability, and Subcellular Localization, J. Biol. Chem, vol.285, pp.36471-36485, 2010. ,
Fluorescence Enhancement of a Microbial Rhodopsin via Electronic Reprogramming, J. Am. Chem. Soc, vol.141, pp.262-271, 2018. ,
Photochromicity of Anabaena Sensory Rhodopsin, an Atypical Microbial Receptor with a cis-Retinal Lightadapted Form, J. Biol. Chem, vol.280, pp.14663-14668, 2005. ,
PH-Dependent Photoreaction Pathway of the All-Trans Form of Anabaena Sensory Rhodopsin, J. Phys. Chem. B, vol.117, pp.2053-2060, 2013. ,
pH Dependence of Anabaena Sensory Rhodopsin: Retinal Isomer Composition, Rate of Dark Adaptation, and Photochemistry, J. Phys. Chem. B, vol.118, pp.8995-9006, 2014. ,
Cytoplasmic Shuttling of Protons in Anabaena Sensory Rhodopsin: Implications for Signaling Mechanism, J. Mol. Biol, vol.358, pp.686-700, 2006. ,
Structural Determinants of Spectral Tuning in Retinal ProteinsBacteriorhodopsin vs Sensory Rhodopsin II, J. Phys. Chem. B, vol.105, pp.10124-10131, 2001. ,
The Protonation State of the Glu-71/Asp-80 Residues in the KcsA Potassium Channel: A First-Principles QM/MM Molecular Dynamics Study, Biophys. J, vol.93, pp.2315-2324, 2007. ,
Mechanism of Spectral Tuning in Green-Absorbing Proteorhodopsin, Biochemistry, vol.46, pp.12679-12686, 2007. ,
The Protonation State of Glu181 in Rhodopsin Revisited: Interpretation of Experimental Data on the Basis of QM/MM Calculations, J. Phys. Chem. B, vol.114, pp.11338-11352, 2010. ,
A Conserved Protonation-Induced Switch can Trigger Ionic-Lock Formation in Adrenergic Receptors, J. Mol. Biol, vol.397, pp.1339-1349, 2010. ,
Protonation effects on the UV/Vis absorption spectra of imatinib: A theoretical and experimental study, Spectrochim. Acta A, vol.129, pp.326-332, 2014. ,
On the Influence of the Protonation States of Active Site Residues on AChE Reactivation: A QM/MM Approach, vol.18, pp.666-675, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01644385
QM/MM simulations provide insight into the mechanism of bioluminescence triggering in ctenophore photoproteins, PLOS ONE, vol.12, pp.1-19, 2017. ,
Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores, Chem. Rev, vol.117, pp.13502-13565, 2017. ,
QM/MM Investigation for Protonation States in a Bilin Reductase PcyA-Biliverdin IX? Complex, ChemPhysChem, vol.19, pp.1809-1813, 2018. ,
Protonation state and fine structure of the active site determine the reactivity of dehydratase: hydration and isomerization of ?-myrcene catalyzed by linalool dehydratase/isomerase from Castellaniella defragrans, Phys. Chem. Chem. Phys, vol.20, pp.17342-17352, 2018. ,
Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics, J. Chem. Theory Comput, vol.8, pp.4393-4404, 2012. ,
All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water, J. Chem. Theory Comput, vol.12, pp.5411-5421, 2016. ,
Calculating Absorption Shifts for Retinal Proteins: Computational Challenges, J. Phys. Chem. B, vol.109, pp.3606-3615, 2005. ,
Mechanism of color tuning in retinal protein: SAC-CI and QM/MM study, Chem. Phys. Lett, vol.414, pp.239-242, 2005. ,
Spectral Tuning in Visual Pigments: An ONIOM(QM:MM) Study on Bovine Rhodopsin and its Mutants, J. Phys. Chem. B, vol.112, p.18473437, 2008. ,
Electrostatic Control of the Photoisomerization Efficiency and Optical Properties in Visual Pigments: On the Role of Counterion Quenching, J. Am. Chem. Soc, vol.131, pp.5172-5186, 2009. ,
The opsin shift and mechanism of spectral tuning in rhodopsin, J. Comput. Chem, vol.32, pp.854-865, 2011. ,
A Configuration Interaction Picture for a Molecular Environment Using Localized Molecular Orbitals: The Excited States of Retinal Proteins, J. Chem. Theory Comput, vol.8, pp.4452-4461, 2012. ,
Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle, J. Am. Chem. Soc, vol.136, pp.3842-3851, 2014. ,
Electrostatic versus Resonance Interactions in Photoreceptor Proteins: The Case of Rhodopsin, J. Phys. Chem. Lett, vol.7, pp.4547-4553, 2016. ,
First-Order Interacting Space Approach to Excited-State Molecular Interaction: Solvatochromic Shift of p-Coumaric Acid and Retinal Schiff Base, J. Chem. Theory Comput, vol.14, pp.3643-3655, 2018. ,
Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement, J. Chem. Theory Comput, vol.15, pp.3134-3152, 2019. ,
Role of the Molecular Environment in Flavoprotein Color and Redox Tuning: QM Cluster versus QM/MM Modeling, J. Chem. Theory Comput, vol.11, pp.3878-3894, 2015. ,
pH-Dependent pKa Values in Proteins -A Theoretical Analysis of Protonation Energies with Practical Consequences for Enzymatic Reactions ,
, J. Phys. Chem. B, vol.114, 1994.
pKa values and redox potentials of proteins. What do they mean?, Biol. Chem, p.394, 2013. ,
Sampling the protonation states: the pH-dependent UV absorption spectrum of a polypeptide dyad, Phys. Chem. Chem. Phys, vol.20, pp.23252-23261, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02091888
Anabaena Sensory Rhodopsin: A Photochromic Color Sensor at 2.0 . Science, vol.306, pp.1390-1393, 2004. ,
, , 2016.
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation, J. Chem. Theory Comput, vol.10, pp.1341-1352, 2014. ,
Simmerling, C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB, J. Chem. Theory Comput, vol.11, pp.3696-3713, 2015. ,
Structural Changes during the Formation of Early Intermediates in the Bacteriorhodopsin Photocycle, Biophys. J, vol.83, pp.1281-1297, 2002. ,
Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters, J. Mol. Mod, vol.19, pp.1-32, 2013. ,
Molecular orbital theory for the excited states of transition metal complexes, J. Chem. Soc., Farad. Trans, vol.2, p.1839, 1972. ,
Stewart Computational Chemistry ,
a surface-hopping program for nonadiabatic molecular dynamics, WIRES Computat. Mol. Sci, vol.4, pp.26-33, 2014. ,
NEWTON-X: a package for Newtonian dynamics close to the crossing seam, 2015. ,
Automatic Rhodopsin Modeling as a Tool for HighThroughput Computational Photobiology, J. Chem. Theory Comput, vol.12, pp.6020-6034, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01409070
The multi-state CASPT2 method, Chem. Phys. Lett, vol.288, pp.299-306, 1998. ,
pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin, Phys. Chem. Chem. Phys, vol.19, pp.14073-14084, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01774207
, , 2017.
The Hill equation revisited: uses and misuses, The FASEB Journal, vol.11, pp.835-841, 1997. ,
Intramolecular photo-induced charge transfer in visual retinal chromophore mimics: electron density-based indices at the TD-DFT and post-HF levels, Theor. Chem. Acc, p.96, 2016. ,
The UV-visible action-absorption spectrum of all-trans and 11-cis protonated Schiff base retinal in the gas Phase, Phys. Chem. Chem. Phys, vol.20, pp.7190-7194, 2018. ,
Solid-state NMR spectroscopy structure determination of a lipid-embedded heptahelical membrane protein, Nat. Methods, vol.10, p.10071012, 2013. ,