scholarly journals Dynamics and mechanism of dimer dissociation of photoreceptor UVR8

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Xiankun Li ◽  
Zheyun Liu ◽  
Haisheng Ren ◽  
Mainak Kundu ◽  
Frank W. Zhong ◽  
...  
Keyword(s):  
Charge Separation ◽  
Ultrafast Spectroscopy ◽  
Salt Bridge ◽  
Water Molecules ◽  
Interfacial Water ◽  
Biological Functions ◽  
Domino Effect ◽  
Light Sensing ◽  
Computational Calculations ◽  
Protective Processes

AbstractPhotoreceptors are a class of light-sensing proteins with critical biological functions. UVR8 is the only identified UV photoreceptor in plants and its dimer dissociation upon UV sensing activates UV-protective processes. However, the dissociation mechanism is still poorly understood. Here, by integrating extensive mutations, ultrafast spectroscopy, and computational calculations, we find that the funneled excitation energy in the interfacial tryptophan (Trp) pyramid center drives a directional Trp-Trp charge separation in 80 ps and produces a critical transient Trp anion, enabling its ultrafast charge neutralization with a nearby positive arginine residue in 17 ps to destroy a key salt bridge. A domino effect is then triggered to unzip the strong interfacial interactions, which is facilitated through flooding the interface by channel and interfacial water molecules. These detailed dynamics reveal a unique molecular mechanism of UV-induced dimer monomerization.

Interfacial water molecules in SH3 interactions: a revised paradigm for polyproline recognition

2012 ◽  
Vol 443 (1) ◽  
pp. 328-328
Author(s):  
J.M. Martin-Garcia ◽  
J. Ruiz-Sanz ◽  
I. Luque
Keyword(s):  
Water Molecules ◽  
Interfacial Water

scholarly journals Controlling charge separation in a novel donor–acceptor metal–organic framework via redox modulation

2014 ◽  
Vol 5 (12) ◽  
pp. 4724-4728 ◽  
Author(s):  
C. F. Leong ◽  
B. Chan ◽  
T. B. Faust ◽  
D. M. D'Alessandro
Keyword(s):  
Charge Transfer ◽  
Solid State ◽  
Charge Separation ◽  
Metal Organic Framework ◽  
Redox Modulation ◽  
Naphthalene Diimide ◽  
Computational Calculations ◽  
Donor Acceptor ◽  
Metal Organic ◽  
Organic Framework

Donor–acceptor charge transfer interactions in a tetrathiafulvalene–naphthalene diimide-based metal–organic framework (MOF) are interrogated using a complementary suite of solid state spectroscopic, electrochemical and spectroelectrochemical methods along with computational calculations.

scholarly journals Interfacial water molecules at biological membranes: Structural features and role for lateral proton diffusion

PLoS ONE ◽  
2018 ◽  
Vol 13 (2) ◽  
pp. e0193454 ◽  
Author(s):  
Trung Hai Nguyen ◽  
Chao Zhang ◽  
Ewald Weichselbaum ◽  
Denis G. Knyazev ◽  
Peter Pohl ◽  
...  
Keyword(s):  
Biological Membranes ◽  
Structural Features ◽  
Water Molecules ◽  
Interfacial Water ◽  
Proton Diffusion

Spontaneous protein desorption from self-assembled monolayer (SAM)-coated gold nanoparticles

2018 ◽  
Vol 20 (1) ◽  
pp. 68-74 ◽  
Author(s):  
Ranran Tian ◽  
Mengbo Luo ◽  
Jingyuan Li
Keyword(s):  
Gold Nanoparticles ◽  
Lateral Diffusion ◽  
Water Molecules ◽  
Interfacial Water ◽  
Self Assembled Monolayer ◽  
Adsorption Affinity ◽  
Self Assembled

Interfacial water molecules and lateral diffusion of protein reduce the adsorption affinity of protein and promote protein desorption.

scholarly journals Applications of vibrational spectroscopy in the study of flavin-based photoactive proteins

2011 ◽  
Vol 25 (6) ◽  
pp. 261-269 ◽  
Author(s):  
Jiang Li ◽  
Teizo Kitagawa
Keyword(s):  
Signal Transduction ◽  
Raman Spectroscopy ◽  
Blue Light ◽  
Reaction Mechanisms ◽  
Flavin Adenine Dinucleotide ◽  
Spectroscopic Studies ◽  
Biological Functions ◽  
Light Sensing ◽  
Infrared And Raman Spectroscopy ◽  
Sensitive Tool

Flavin cofactor is known to perform diverse biological functions. Recently, its role as a photoreceptor has been identified. So far, three classes of photoactive flavoproteins have been recognized: phototropin with LOV (Light, Oxygen and Voltage) domain, blue light sensory protein with BLUF (Blue Light sensing Using Flavin adenine dinucleotide) domain and photolyase/cryptochrome protein with PHR (Photolyase Homology Region) domain. Photochemistry of flavin is the key to unravel the reaction mechanisms of photoactive flavoproteins in their biological functions such as DNA repair or signal transduction. Vibrational (Infrared and Raman) spectroscopy is a useful and sensitive tool to investigate the photochemistry of flavin in protein environments and has significantly contributed to elucidate the reaction mechanisms of these photoactive proteins. This study will survey recent advances in vibrational spectroscopic studies on this topic and remaining questions to be answered.

scholarly journals Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools

Glycobiology ◽  
2020 ◽  
Vol 30 (8) ◽  
pp. 516-527
Author(s):  
Balaji Nagarajan ◽  
Nehru Viji Sankaranarayanan ◽  
Umesh R Desai
Keyword(s):  
Force Fields ◽  
Protein Recognition ◽  
Water Molecules ◽  
Biological Functions ◽  
Computational Simulations ◽  
Rigorous Analysis ◽  
Protein Targets ◽  
End Distance ◽  
Heparan Sulfates ◽  
The Comparative Study

Abstract Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.

Water Structure on Mica Surfaces: Investigating the Effect of Cations

2019 ◽  
Author(s):  
Jiarun Zhou ◽  
Nurun Nahar Lata ◽  
Sapna Sarupria ◽  
will cantrell
Keyword(s):  
Divalent Cations ◽  
Water Structure ◽  
Ice Nucleation ◽  
Water Molecules ◽  
Interfacial Water ◽  
Ice Nucleation Protein ◽  
Naturally Occurring ◽  
Air Interface ◽  
Bulk Structure ◽  
Dynamics Simulations

We studied thin films of water at the mica-air interface using infrared spectroscopy and molecular dynamics simulations. We investigate the influence of ions on interfacial water by exchanging the naturally occurring K<sup>+</sup> ion with H<sup>+</sup>/Na<sup>+</sup>, Ca<sup>2+</sup>, and Mg<sup>2+</sup>. The experiments do not show a difference in the bulk structure (<i>i. e.</i> in the infrared spectra), but indicate that water is more strongly attracted to the Mg<sup>2+</sup> mica. The simulations reveal that the cation-water interactions significantly influence the microscopic arrangement of water on mica. Our results indicate that the divalent cations result in strong water-mica interactions, which leads to longer hydrogen bond lifetimes and larger hydrogen bonded clusters of interfacial water molecules. These results have implications for surface-mediated processes such as heterogeneous ice nucleation, protein assembly and catalysis.

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