Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2

2020 ◽  
Author(s):  
Suliman Adam ◽  
Christian Wiebeler ◽  
Igor Schapiro
Keyword(s):  
Hydrogen Bonding ◽  
Absorption Spectrum ◽  
Schiff Base ◽  
Absorption Maximum ◽  
Rational Design ◽  
Blue Shift ◽  
Spectral Shift ◽  
Structural Basis ◽  
Neural Cells ◽  
Structural Factors

Channelrhodopsins are photosensitive proteins that trigger flagella motion in single cell algae and have been successfully utilized in optogenetic applications. In optogenetics light is used to activate neural cells in living organisms, which can be achieved by exploiting the ion channel signaling of channelrhodopsins. Tailoring channelrhodopsins for such applications includes the tuning of the absorption maximum. In order to establish rational design and to obtain a desired spectral shift, a basic understanding of the absorption spectrum is required. We have studied the chimera C1C2 as a representative of this protein family and the first member with an available crystal structure. For this purpose, we sampled the conformations of C1C2 using QM/MM molecular dynamics, and subjected the resulting snapshots of the trajectory to excitation energy calculations using ADC(2) and simplified TD-DFT. In contrast to previous reports, we found that different hydrogen-bonding networks—involving the retinal protonated Schiff base, the putative counterions E162 and D292 as well as water molecules—had only a small impact on the absorption spectrum. However, in case of deprotonated E162 increasing the distance to the Schiff base hydrogen-bonding partner led to a systematic blue shift. The β-ionone ring rotation was identified as another important contributor. Yet the most important factor was found to be the bond length alternation and bond order alternation that were linearly correlated to the absorption maximum by up to 62 % and 82 %, respectively. We ascribe this novel insight into the structural basis of the absorption spectrum to our enhanced protein setup that includes membrane embedding as well as long and extensive sampling.

scholarly journals Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2

2020 ◽  
Author(s):  
Suliman Adam ◽  
Christian Wiebeler ◽  
Igor Schapiro
Keyword(s):  
Hydrogen Bonding ◽  
Absorption Spectrum ◽  
Schiff Base ◽  
Absorption Maximum ◽  
Rational Design ◽  
Blue Shift ◽  
Spectral Shift ◽  
Structural Basis ◽  
Neural Cells ◽  
Structural Factors

Channelrhodopsins are photosensitive proteins that trigger flagella motion in single cell algae and have been successfully utilized in optogenetic applications. In optogenetics light is used to activate neural cells in living organisms, which can be achieved by exploiting the ion channel signaling of channelrhodopsins. Tailoring channelrhodopsins for such applications includes the tuning of the absorption maximum. In order to establish rational design and to obtain a desired spectral shift, a basic understanding of the absorption spectrum is required. We have studied the chimera C1C2 as a representative of this protein family and the first member with an available crystal structure. For this purpose, we sampled the conformations of C1C2 using QM/MM molecular dynamics, and subjected the resulting snapshots of the trajectory to excitation energy calculations using ADC(2) and simplified TD-DFT. In contrast to previous reports, we found that different hydrogen-bonding networks—involving the retinal protonated Schiff base, the putative counterions E162 and D292 as well as water molecules—had only a small impact on the absorption spectrum. However, in case of deprotonated E162 increasing the distance to the Schiff base hydrogen-bonding partner led to a systematic blue shift. The β-ionone ring rotation was identified as another important contributor. Yet the most important factor was found to be the bond length alternation and bond order alternation that were linearly correlated to the absorption maximum by up to 62 % and 82 %, respectively. We ascribe this novel insight into the structural basis of the absorption spectrum to our enhanced protein setup that includes membrane embedding as well as long and extensive sampling.

Analysis of the Visual Spectrum of Methyl Orange in Solvents and in Hydrophobic Binding Sites

1973 ◽  
Vol 51 (4) ◽  
pp. 628-635 ◽  
Author(s):  
Richard L. Reeves ◽  
Robert S. Kaiser ◽  
Mary S. Maggio ◽  
Edward A. Sylvestre ◽  
William H. Lawton
Keyword(s):  
Hydrogen Bonding ◽  
Methyl Orange ◽  
Organic Solvents ◽  
Absorption Maximum ◽  
Low Frequency ◽  
Blue Shift ◽  
Frequency Component ◽  
High Frequency Component ◽  
Surfactant Micelle ◽  
Aqueous Solvent

The absorption curves of methyl orange (MO) and analogous p-aminophenylazobenzenes in organic and aqueous organic solvents are shown to consist of two severely overlapping bands. The curves have been resolved into two skewed component bands using a regression method. The blue shift of the absorption maximum obtained when organic solvents are added to aqueous solutions of MO, or when MO is bound to bovine serum albumin or a surfactant micelle, is the result of a change in relative intensities of the component bands. The low-frequency component is assigned to a π1 → π1* transition of a solvate in which there is specific hydrogen-bonding interaction between solvent and the azo nitrogens, and the high-frequency component to a π1 → π1* transition of a solvate in which the interaction is absent. The low-frequency component is favored by aqueous solvent compositions and by low temperatures. The free energies of interconversion of the species in various hydrogen-bonding solvents are correlated by the solvent surface tension but not by the dielectric constant. The results show that the shift in absorption maximum accompanying binding to a protein or micelle should be interpreted as a shift in an equilibrium rather than as a shift in transition energy.

scholarly journals Lokiarchaeota archaeon schizorhodopsin-2 (LaSzR2) is an inward proton pump displaying a characteristic feature of acid-induced spectral blue-shift

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Keiichi Kojima ◽  
Susumu Yoshizawa ◽  
Masumi Hasegawa ◽  
Masaki Nakama ◽  
Marie Kurihara ◽  
...  
Keyword(s):  
Schiff Base ◽  
Proton Pump ◽  
Flash Photolysis ◽  
Blue Shift ◽  
Spectroscopic Studies ◽  
Spectral Shift ◽  
Bulk Solution ◽  
Proton Pumps ◽  
Ph Titration ◽  
Retinal Chromophore

AbstractThe photoreactive protein rhodopsin is widespread in microorganisms and has a variety of photobiological functions. Recently, a novel phylogenetically distinctive group named ‘schizorhodopsin (SzR)’ has been identified as an inward proton pump. We performed functional and spectroscopic studies on an uncharacterised schizorhodopsin from the phylum Lokiarchaeota archaeon. The protein, LaSzR2, having an all-trans-retinal chromophore, showed inward proton pump activity with an absorption maximum at 549 nm. The pH titration experiments revealed that the protonated Schiff base of the retinal chromophore (Lys188, pKa = 12.3) is stabilised by the deprotonated counterion (presumably Asp184, pKa = 3.7). The flash-photolysis experiments revealed the presence of two photointermediates, K and M. A proton was released and uptaken from bulk solution upon the formation and decay of the M intermediate. During the M-decay, the Schiff base was reprotonated by the proton from a proton donating residue (presumably Asp172). These properties were compared with other inward (SzRs and xenorhodopsins, XeRs) and outward proton pumps. Notably, LaSzR2 showed acid-induced spectral ‘blue-shift’ due to the protonation of the counterion, whereas outward proton pumps showed opposite shifts (red-shifts). Thus, we can distinguish between inward and outward proton pumps by the direction of the acid-induced spectral shift.

scholarly journals Ligand-induced activation of human TRPM2 requires the terminal ribose of ADPR and involves Arg1433 and Tyr1349

2017 ◽  
Vol 474 (13) ◽  
pp. 2159-2175 ◽  
Author(s):  
Ralf Fliegert ◽  
Joanna M. Watt ◽  
Anja Schöbel ◽  
Monika D. Rozewitz ◽  
Christelle Moreau ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Transient Receptor Potential ◽  
Therapeutic Potential ◽  
Receptor Potential ◽  
Transient Receptor Potential Channel ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Pharmacological Intervention ◽  
Hydroxyl Groups

TRPM2 (transient receptor potential channel, subfamily melastatin, member 2) is a Ca2+-permeable non-selective cation channel activated by the binding of adenosine 5′-diphosphoribose (ADPR) to its cytoplasmic NUDT9H domain (NUDT9 homology domain). Activation of TRPM2 by ADPR downstream of oxidative stress has been implicated in the pathogenesis of many human diseases, rendering TRPM2 an attractive novel target for pharmacological intervention. However, the structural basis underlying this activation is largely unknown. Since ADP (adenosine 5′-diphosphate) alone did not activate or antagonize the channel, we used a chemical biology approach employing synthetic analogues to focus on the role of the ADPR terminal ribose. All novel ADPR derivatives modified in the terminal ribose, including that with the seemingly minor change of methylating the anomeric-OH, abolished agonist activity at TRPM2. Antagonist activity improved as the terminal substituent increasingly resembled the natural ribose, indicating that gating by ADPR might require specific interactions between hydroxyl groups of the terminal ribose and the NUDT9H domain. By mutating amino acid residues of the NUDT9H domain, predicted by modelling and docking to interact with the terminal ribose, we demonstrate that abrogating hydrogen bonding of the amino acids Arg1433 and Tyr1349 interferes with activation of the channel by ADPR. Taken together, using the complementary experimental approaches of chemical modification of the ligand and site-directed mutagenesis of TRPM2, we demonstrate that channel activation critically depends on hydrogen bonding of Arg1433 and Tyr1349 with the terminal ribose. Our findings allow for a more rational design of novel TRPM2 antagonists that may ultimately lead to compounds of therapeutic potential.

scholarly journals Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kazutoshi Tani ◽  
Ryo Kanno ◽  
Yuki Makino ◽  
Malgorzata Hall ◽  
Mizuki Takenouchi ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Reaction Center ◽  
Absorption Maximum ◽  
Light Harvesting ◽  
Ring Structure ◽  
Structural Basis ◽  
Multiple Forms ◽  
Closed Ring ◽  
Reaction Center Complex ◽  
Ca Ions

Abstract The light-harvesting-reaction center complex (LH1-RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970 exhibits an LH1 absorption maximum at 960 nm, the most red-shifted absorption for any bacteriochlorophyll (BChl) a-containing species. Here we present a cryo-EM structure of the strain 970 LH1-RC complex at 2.82 Å resolution. The LH1 forms a closed ring structure composed of sixteen pairs of the αβ-polypeptides. Sixteen Ca ions are present in the LH1 C-terminal domain and are coordinated by residues from the αβ-polypeptides that are hydrogen-bonded to BChl a. The Ca2+-facilitated hydrogen-bonding network forms the structural basis of the unusual LH1 redshift. The structure also revealed the arrangement of multiple forms of α- and β-polypeptides in an individual LH1 ring. Such organization indicates a mechanism of interplay between the expression and assembly of the LH1 complex that is regulated through interactions with the RC subunits inside.

Mode of Binding of Pyridoxal Phosphate to 5-Aminolevulinate Synthase

1978 ◽  
Vol 33 (11-12) ◽  
pp. 1003-1005
Author(s):  
Dhirendra L. Nandi
Keyword(s):  
Schiff Base ◽  
Absorption Maximum ◽  
Pyridoxal Phosphate ◽  
Spectral Shift ◽  
Sulfhydryl Reagents ◽  
Absorption Bands ◽  
Aminolevulinate Synthase ◽  
Predominant Species ◽  
Sh Group ◽  
Combined Data

5-Aminolevulinate synthase of Khodopseudomonas spheroides interacts with its cofactor, pyridoxal phosphate, and shows an absorption maximum at 430 nm with a probable shoulder at 320 -330 nm. The enzyme-PLP complex absorb­ing at 430 nm is the predominant species at pH 7.2 and can be reduced by NaBH4 at neutral pH with a spectral shift of the absorption maximum to 325 nm. These data suggests the formation of a Schiff base rather than a substituted aldimine between the enzyme and pyridoxal phosphate. The decrease in absorption at 430 nm and increase in absorption at 325 nm by the addition of 2-mercaptoethanol seem to sup­port Schiff base structures for the absorption bands at 430 nm and 320 -330 nm. Both pyridoxal phosphate and glycine can equally protect the enzyme from inactivation by sulfhydryl reagents. The inhibition by p-chloromercuribenzo- ate versus PLP and glycine is noncompetitive and that by N-ethylmaleimide is noncompetitive with glycine and compet­itive with PLP. These results suggest either a conformational change in the presence of substrates or loss of affinity by the enzyme for PLP, rather than an interaction of PLP with a -SH group of the enzyme. The combined data seems to eliminate the possibility of the formation of a thiohemiacetal or a substituted aldimine and support rather strongly the formation of a Schiff base between the enzyme and pyridoxal phosphate.

scholarly journals Structural basis for no spectral shift of heliorhodopsin by counterion mutation

2020 ◽  
Author(s):  
Tatsuki Tanaka ◽  
Manish Singh ◽  
Wataru Shihoya ◽  
Keitaro Yamashita ◽  
Hideki Kandori ◽  
...  
Keyword(s):  
Absorption Spectrum ◽  
Absorption Spectra ◽  
Interaction Network ◽  
Spectral Shift ◽  
Structural Basis ◽  
Spectral Studies ◽  
Transmembrane Helices ◽  
Wild Type ◽  
Covalently Bonded ◽  
Light Energy Absorption

AbstractMicrobial rhodopsins comprise an opsin protein with seven transmembrane helices and a retinal as the chromophore. An all-trans retinal is covalently-bonded to a lysine residue through the retinal Schiff base (RSB) and stabilized by a negatively-charged counterion. The distance between the RSB and counterion is closely related to the light energy absorption. However, in heliorhodopsin-48C12 (HeR-48C12), while Glu107 acts as the counterion, E107D mutation exhibits an identical absorption spectrum to the wild-type, suggesting that the distance does not affect its absorption spectra. Here we present the 2.6 Å resolution crystal structure of the Thermoplasmatales archaeon HeR E108D mutant, which also has an identical absorption spectrum to the wild-type. The structure revealed that D108 does not form a hydrogen bond with the RSB, and its counterion interaction becomes weaker. Alternatively, serine cluster, S78, S112, and S238 form a distinct interaction network around the RSB. The absorption spectra of the E to D and S to A double mutants suggested that S112 influences the spectral shift by compensating for the weaker counterion interaction. Our structural and spectral studies have revealed the unique spectral shift mechanism of HeR and clarified the physicochemical properties of HeRs.

Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Biological Molecules ◽  
Conformational Space ◽  
X Ray Crystallography ◽  
Simple Strategy ◽  
Induced Folding ◽  
Π Stacking ◽  
Varying Length ◽  
Dynamics Simulations

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.

Hierarchy of π-Stacking Determines the Conformational Preference of Bis-Squaraines

2020 ◽  
Author(s):  
Abhishek Singh ◽  
Reman K. Singh ◽  
G Naresh Patwari
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Biological Molecules ◽  
Conformational Space ◽  
X Ray Crystallography ◽  
Simple Strategy ◽  
Induced Folding ◽  
Π Stacking ◽  
Varying Length ◽  
Dynamics Simulations

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are ideal molecules for designing foldable modules that can mimic the secondary structures of bio-molecules. The π-stacking induced folding of bis-squaraines tethered using aliphatic primary and secondary-diamine linkers of varying length is explored with a simple strategy of invoking small perturbations involving the length linkers and degree of substitution. Solution phase NMR investigations in combination with molecular dynamics simulations suggest that bis-squaraines predominantly exist as extended conformations. Structures elucidated by X-ray crystallography confirmed a variety of folded and extended secondary conformations including hairpin turns and 𝛽-sheets which are determined by the hierarchy of π-stacking relative to N–H···O hydrogen bonds.

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