scholarly journals How water-mediated hydrogen bonds affect chlorophyll a/b selectivity in Water-Soluble Chlorophyll Protein

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Alessandro Agostini ◽  
Elena Meneghin ◽  
Lucas Gewehr ◽  
Danilo Pedron ◽  
Daniel M. Palm ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Binding Sites ◽  
Photophysical Properties ◽  
Water Soluble ◽  
Variable Degree ◽  
Formyl Group ◽  
Hydrogen Bond Networks ◽  
Conformational Freedom ◽  
Chlorophyll Protein ◽  
Hydrogen Bonded

AbstractThe Water-Soluble Chlorophyll Protein (WSCP) of Brassicaceae is a remarkably stable tetrapyrrole-binding protein that, by virtue of its simple design, is an exceptional model to investigate the interactions taking place between pigments and their protein scaffold and how they affect the photophysical properties and the functionality of the complexes. We investigated variants of WSCP from Lepidium virginicum (Lv) and Brassica oleracea (Bo), reconstituted with Chlorophyll (Chl) b, to determine the mechanisms by which the different Chl binding sites control their Chl a/b specificities. A combined Raman and crystallographic investigation has been employed, aimed to characterize in detail the hydrogen-bond network involving the formyl group of Chl b. The study revealed a variable degree of conformational freedom of the hydrogen bond networks among the WSCP variants, and an unexpected mixed presence of hydrogen-bonded and not hydrogen-bonded Chls b in the case of the L91P mutant of Lv WSCP. These findings helped to refine the description of the mechanisms underlying the different Chl a/b specificities of WSCP versions, highlighting the importance of the structural rigidity of the Chl binding site in the vicinity of the Chl b formyl group in granting a strong selectivity to binding sites.

Hydrogen bond effect on the photophysical properties of 2-ureido-4[1H]-pyrimidinone quadruple hydrogen bonded systems

RSC Advances ◽  
2015 ◽  
Vol 5 (46) ◽  
pp. 36279-36287 ◽  
Author(s):  
Jun-Sheng Chen ◽  
Feng-Jiao Zhao ◽  
Yang Yang ◽  
Tian-Shu Chu
Keyword(s):  
Hydrogen Bond ◽  
Photophysical Properties ◽  
Hydrogen Bonded Systems ◽  
Bond Effect ◽  
Hydrogen Bonded

Two different hydrogen bond effects on the photophysical properties of UPy systems in different solutions have been studied.

Structures of yeast peroxisomal Δ3,Δ2-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole

2015 ◽  
Vol 71 (11) ◽  
pp. 2178-2191 ◽  
Author(s):  
Goodluck U. Onwukwe ◽  
M. Kristian Koski ◽  
Petri Pihko ◽  
Werner Schmitz ◽  
Rik K. Wierenga
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Hydrogen Bond ◽  
Side Chain ◽  
Oxyanion Hole ◽  
Substrate Analogues ◽  
Hydrogen Bond Networks ◽  
Wide Range ◽  
Coa Thioesters ◽  
Loop 2 ◽  
Hydrogen Bonded

Δ3,Δ2-Enoyl-CoA isomerases (ECIs) catalyze the shift of a double bond from 3Z- or 3E-enoyl-CoA to 2E-enoyl-CoA. ECIs are members of the crotonase superfamily. The crotonase framework is used by many enzymes to catalyze a wide range of reactions on acyl-CoA thioesters. The thioester O atom is bound in a conserved oxyanion hole. Here, the mode of binding of acyl-CoA substrate analogues to peroxisomal Saccharomyces cerevisiae ECI (ScECI2) is described. The best defined part of the bound acyl-CoA molecules is the 3′,5′-diphosphate-adenosine moiety, which interacts with residues of loop 1 and loop 2, whereas the pantetheine part is the least well defined. The catalytic base, Glu158, is hydrogen-bonded to the Asn101 side chain and is further hydrogen-bonded to the side chain of Arg100 in the apo structure. Arg100 is completely buried in the apo structure and a conformational change of the Arg100 side chain appears to be important for substrate binding and catalysis. The oxyanion hole is formed by the NH groups of Ala70 (loop 2) and Leu126 (helix 3). The O atoms of the corresponding peptide units, Gly69 O and Gly125 O, are both part of extensive hydrogen-bond networks. These hydrogen-bond networks are a conserved feature of the crotonase oxyanion hole and their importance for catalysis is discussed.

scholarly journals Proton-Binding Motifs of Membrane-Bound Proteins: From Bacteriorhodopsin to Spike Protein S

2021 ◽  
Vol 9 ◽  
Author(s):  
Ana-Nicoleta Bondar
Keyword(s):  
Hydrogen Bond ◽  
Binding Sites ◽  
Coupled Model ◽  
Protein S ◽  
Specific Protein ◽  
Spike Protein ◽  
Sequence Motifs ◽  
Proton Binding ◽  
Hydrogen Bond Networks ◽  
Membrane Bound

Membrane-bound proteins that change protonation during function use specific protein groups to bind and transfer protons. Knowledge of the identity of the proton-binding groups is of paramount importance to decipher the reaction mechanism of the protein, and protonation states of prominent are studied extensively using experimental and computational approaches. Analyses of model transporters and receptors from different organisms, and with widely different biological functions, indicate common structure-sequence motifs at internal proton-binding sites. Proton-binding dynamic hydrogen-bond networks that are exposed to the bulk might provide alternative proton-binding sites and proton-binding pathways. In this perspective article I discuss protonation coupling and proton binding at internal and external carboxylate sites of proteins that use proton transfer for function. An inter-helical carboxylate-hydroxyl hydrogen-bond motif is present at functionally important sites of membrane proteins from archaea to the brain. External carboxylate-containing H-bond clusters are observed at putative proton-binding sites of protonation-coupled model proteins, raising the question of similar functionality in spike protein S.

scholarly journals Neutron crystal structure of human FPPS complexed with risedronate

2014 ◽  
Vol 70 (a1) ◽  
pp. C1220-C1220
Author(s):  
Takeshi Yokoyama ◽  
Andreas Ostermann ◽  
Mineyuki Mizuguchi ◽  
Nobuo Niimura ◽  
Tobias Schrader ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Neutron Diffraction ◽  
Antitumor Agents ◽  
Structural Characteristics ◽  
Water Soluble ◽  
Water Molecules ◽  
Protonation State ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Hydrogen Bond Networks

Nitrogen-containing bisphosphonates (N-BPs), such as risedronate and zoledronate, are currently used as clinical drug for bone-resorption diseases and are potent inhibitor of farnesyl pyrophosphate synthase (FPPS). The potential of N-BPs as antitumor agents has also been suggested by the several in vitro and in vivo preclinical studies. However, BP drugs limit their therapeutic use to bone-related diseases, because BPs are highly charged and water soluble molecules. X-ray crystallographic analyses of FPPS with N-BPs have revealed that N-BPs bind to FPPS with three magnesium ions and several water molecules. In order to develop a novel FPPS inhibitor, the hydrogen-bond networks formed by FPPS, BPs and water molecules are necessary to be elucidated. To understand the structural characteristics of N-BPs bound to FPPS, including hydrogen atoms and hydration by water, neutron diffraction studies were initiated using BIODIFF at the Heinz Maier-Leibnitz Zentrum (MLZ). FPPS-risedronate complex crystals of approximate dimensions 2.8 × 2.5 × 1.5 mm (~ 3.5 mm3) were obtained by repeated macro-seeding. Monochromatic neutron diffraction data were collected to 2.4 Å resolution with 98.4% overall completeness and 10.7% Rmerge. As a result of X-ray/neutron joint refinment, R and Rfree values for the neutron data were 19.6 and 23.3%, respectively. This neutron structure clearly reveals the protonation state of risedronate, hydration in the inhibitor-binding region. Furthermore, the amide H/D exchange analysis showed that there is a highly rigid region which regulate the structural change upon the binding of the ligands. Here we will discuss the detailed hydrogen-bond network and the protonation state of FPPS and risedronate.

Probing the Structural Features and the Micro-heterogeneity of Various Deep Eutectic Solvents and their Water Dilutions by the Photophysical Behaviour of Two Fluorophores

2020 ◽  
Author(s):  
Matteo Tiecco ◽  
Irene Di Guida ◽  
Pier Luigi Gentili ◽  
Raimondo Germani ◽  
Carmela Bonaccorso ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Transient Absorption ◽  
Photophysical Properties ◽  
Deep Eutectic Solvents ◽  
Structural Features ◽  
Solvation Dynamics ◽  
Structured Systems ◽  
Reduced Viscosity ◽  
Bond Network ◽  
Fluorescent Molecules

<div><div><div><p>The structural features of a series of diverse Deep Eutectic Solvents (DESs) have been investigated and characterized by means of two fluorescent probes. The spectral and photophysical properties of the latter are strictly dependent on the experienced environment, so that they can provide insights into the polarity, viscosity, hydrogen-bond network, and micro-heterogeneity of the various DESs.</p><p>In fact, the investigated DESs exhibit a variety of properties with regards to their hydrophilicity, acidity, and hydrogen-bond ability, and these details were deeply probed by the two fluorescent molecules. The effect of the addition of water, which is a key strategy for tuning the properties of these structured systems, was also tested. In particular, the excited state dynamics of the probes, measured by femtosecond-resolved transient absorption, proved instrumental in understanding the changes in the structural properties of the DESs, namely reduced viscosity and enhanced heterogeneity, as the water percentage increases. Differences between the various DESs in terms of both local microheterogeneity and bulk viscosity also emerged from the peculiar multi-exponential solvation dynamics undergone by the excited states of the probes.</p></div></div></div>

Probing the Structural Features and the Micro-heterogeneity of Various Deep Eutectic Solvents and their Water Dilutions by the Photophysical Behaviour of Two Fluorophores

2020 ◽  
Author(s):  
Matteo Tiecco ◽  
Irene Di Guida ◽  
Pier Luigi Gentili ◽  
Raimondo Germani ◽  
Carmela Bonaccorso ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Transient Absorption ◽  
Photophysical Properties ◽  
Deep Eutectic Solvents ◽  
Structural Features ◽  
Solvation Dynamics ◽  
Structured Systems ◽  
Reduced Viscosity ◽  
Bond Network ◽  
Fluorescent Molecules

<div><div><div><p>The structural features of a series of diverse Deep Eutectic Solvents (DESs) have been investigated and characterized by means of two fluorescent probes. The spectral and photophysical properties of the latter are strictly dependent on the experienced environment, so that they can provide insights into the polarity, viscosity, hydrogen-bond network, and micro-heterogeneity of the various DESs.</p><p>In fact, the investigated DESs exhibit a variety of properties with regards to their hydrophilicity, acidity, and hydrogen-bond ability, and these details were deeply probed by the two fluorescent molecules. The effect of the addition of water, which is a key strategy for tuning the properties of these structured systems, was also tested. In particular, the excited state dynamics of the probes, measured by femtosecond-resolved transient absorption, proved instrumental in understanding the changes in the structural properties of the DESs, namely reduced viscosity and enhanced heterogeneity, as the water percentage increases. Differences between the various DESs in terms of both local microheterogeneity and bulk viscosity also emerged from the peculiar multi-exponential solvation dynamics undergone by the excited states of the probes.</p></div></div></div>

High proton conductivity in a nickel(ii) complex and its hybrid membrane

2019 ◽  
Vol 48 (6) ◽  
pp. 2190-2196 ◽  
Author(s):  
Shuai-Liang Yang ◽  
Yue-Ying Yuan ◽  
Fei Ren ◽  
Chen-Xi Zhang ◽  
Qing-Lun Wang
Keyword(s):  
Hydrogen Bond ◽  
Proton Conductivity ◽  
Hybrid Membrane ◽  
Water Molecules ◽  
Hybrid Membranes ◽  
High Proton Conductivity ◽  
High Proton ◽  
Hydrogen Bond Networks

A novel 2D nickel(ii) complex (1) has been successfully synthesized using a 2,2′-bipyridyl, polycarboxylsulfonate ligand H4SBTC and Ni2+ ions. Owing to the presence of abundant water molecules, hydrogen bond networks and other protons, 1 and its hybrid membranes demonstrate high proton conductivity.

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