scholarly journals Spectral Tuning of Chlorophylls in Proteins – Electrostatics vs. Ring Deformation

2020 ◽  
Author(s):  
Yigal Lahav ◽  
Dror Noy ◽  
Igor Schapiro
Keyword(s):  
Absorption Spectra ◽  
Conformational Dynamics ◽  
Spectral Shift ◽  
Water Soluble ◽  
Conformational Sampling ◽  
Protein Electrostatics ◽  
Spectral Tuning ◽  
Photosynthetic Complexes ◽  
Artificial Protein ◽  
Ring Deformation

In photosynthetic complexes, tuning of chlorophyll light-absorption spectra by the protein environment is crucial to their efficiency and robustness. Water Soluble Chlorophyll-binding Proteins from <i>Brassicaceae</i> (WSCPs) are useful for studying spectral tuning mechanisms due to their symmetric homotetramer structure, the ability to rigorously modify the chlorophyll’s protein surroundings, and the availability of crystal structures. Here, we present a rigorous analysis based on hybrid Quantum Mechanics and Molecular Mechanics simulations with conformational sampling to quantify the relative contributions of steric and electrostatic factors to the absorption spectra of WSCP-chlorophyll complexes. We show that when considering conformational dynamics, chlorophyll ring deformation accounts for about one-third of the spectral shift, whereas protein electrostatics accounts for the remaining two-thirds. From a practical perspective, protein electrostatics is easier to manipulate than chlorophyll conformations, thus, it may be more readily implemented in designing artificial protein-chlorophyll complexes with desired spectral shift.

scholarly journals Spectral Tuning of Chlorophylls in Proteins – Electrostatics vs. Ring Deformation

2020 ◽  
Author(s):  
Yigal Lahav ◽  
Dror Noy ◽  
Igor Schapiro
Keyword(s):  
Absorption Spectra ◽  
Conformational Dynamics ◽  
Spectral Shift ◽  
Water Soluble ◽  
Conformational Sampling ◽  
Protein Electrostatics ◽  
Spectral Tuning ◽  
Photosynthetic Complexes ◽  
Artificial Protein ◽  
Ring Deformation

In photosynthetic complexes, tuning of chlorophyll light-absorption spectra by the protein environment is crucial to their efficiency and robustness. Water Soluble Chlorophyll-binding Proteins from <i>Brassicaceae</i> (WSCPs) are useful for studying spectral tuning mechanisms due to their symmetric homotetramer structure, the ability to rigorously modify the chlorophyll’s protein surroundings, and the availability of crystal structures. Here, we present a rigorous analysis based on hybrid Quantum Mechanics and Molecular Mechanics simulations with conformational sampling to quantify the relative contributions of steric and electrostatic factors to the absorption spectra of WSCP-chlorophyll complexes. We show that when considering conformational dynamics, chlorophyll ring deformation accounts for about one-third of the spectral shift, whereas protein electrostatics accounts for the remaining two-thirds. From a practical perspective, protein electrostatics is easier to manipulate than chlorophyll conformations, thus, it may be more readily implemented in designing artificial protein-chlorophyll complexes with desired spectral shift.

scholarly journals Spectral Tuning of Chlorophylls in Proteins – Electrostatics vs. Ring Deformation

2021 ◽  
Author(s):  
Yigal Lahav ◽  
Dror Noy ◽  
Igor Schapiro
Keyword(s):  
Absorption Spectra ◽  
Light Absorption ◽  
Binding Proteins ◽  
Water Soluble ◽  
Spectral Tuning ◽  
Photosynthetic Complexes ◽  
Protein Environment ◽  
Ring Deformation

: In photosynthetic complexes, tuning of chlorophyll light-absorption spectra by the protein environment is crucial to their efficiency and robustness. Water Soluble Chlorophyll-binding Proteins from Brassicaceae (WSCPs) are useful for...

scholarly journals Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis

2018 ◽  
Vol 115 (45) ◽  
pp. 11525-11530 ◽  
Author(s):  
Marcelo E. Guerin ◽  
Guillaume Stirnemann ◽  
David Giganti
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Conformational Sampling ◽  
Enzymatic Reactions ◽  
Sequence Specificity ◽  
Proteomics Data ◽  
Conformational Entropy ◽  
Substrate Peptide ◽  
The Impact

An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino acid sequence specificity of these enzymatic reactions in vivo, because the target peptide must be disordered to accommodate the specific enzyme-binding site. Here, we were able to control the conformation of a single-molecule peptide chain by applying mechanical force to activate and monitor its specific cleavage by a model protease. We found that the conformational entropy impacts the reaction in two distinct ways. First, the flexibility and accessibility of the substrate peptide greatly increase upon mechanical unfolding. Second, the conformational sampling of the disordered peptide drives the specific recognition, revealing force-dependent reaction kinetics. These results support a mechanism of peptide recognition based on conformational selection from an ensemble that we were able to quantify with a torsional free-energy model. Our approach can be used to predict how entropy affects site-specific modifications of proteins and prompts conformational and mechanical selectivity.

Catalytic Oxidation of 2-Mercaptoethanol by Cationic Water-soluble Phthalocyaninatocobalt(II) Complexes

1997 ◽  
Vol 01 (04) ◽  
pp. 309-313 ◽  
Author(s):  
MUTSUMI KIMURA ◽  
YUJI YAMAGUCHI ◽  
TOSHIKI KOYAMA ◽  
KENJI HANABUSA ◽  
HIROFUSA SHIRAI
Keyword(s):  
Catalytic Activity ◽  
Catalytic Oxidation ◽  
Absorption Spectra ◽  
Positive Charge ◽  
Alkyl Chain ◽  
Solvent Polarity ◽  
Water Soluble ◽  
Uv Absorption Spectra ◽  
Alkyl Chains ◽  
The Stability

The cationic amphiphilic cobalt(II) phthalocyanines have been prepared, and are characterized by UV-absorption spectra in water and organic solvents and in their mixtures. The monomer–dimer transformation equilibrium was affected by solvent polarity and the length of the alkyl chains in the amphiphilic parts. All complexes are efficient catalysts for the oxidation of 2-mercaptoethanol in the presence of dioxygen. The positive charge around the complex increases the acceleration of the dissociation of 2-mercaptoethanol under neutral pH. The catalytic activity is affected by the length of the alkyl chain; consequently the stability of aggregation between cobalt(II) phthalocyanines, as catalysts for the oxidation of 2-mercaptoethanol, can be changed.

scholarly journals Effect of Some Substituents Increasing the Solubility of Zn(II) and Al(III) Phthalocyanines on Their Photophysical Properties

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
A. A. Chernonosov ◽  
E. A. Ermilov ◽  
B. Röder ◽  
L. I. Solovyova ◽  
O. S. Fedorova
Keyword(s):  
Absorption Spectra ◽  
Structural Changes ◽  
Water Solubility ◽  
Transient Absorption ◽  
Photophysical Properties ◽  
Water Soluble ◽  
Quantum Yields ◽  
Carboxyl Groups ◽  
Transient Absorption Spectra ◽  
Photochemical Properties

Water solubility of phthalocyanines (Pcs) usually increases by the introduction of charged or carboxy substituents in the peripheral positions of the macrocycle. As a result, such structural changes influence their photophysical and photochemical properties as photosensitizers. Phthalocyanines substituted with four or eight terminal carboxyl groups and having in some cases additional eight positive charges (water soluble phthalocyanines) were studied in order to evaluate the spectroscopic and photophysical effects of these side residues on the chromophore properties. The quantum yield of singlet oxygen (O12) generation, the triplet-triplet absorption, and the transient absorption spectra were measured and linked to the structure of the substituents. It was shown that charged substituents did not change the quantum yields ofO12generation but decrease its lifetimes. The introduction of the charged substituents not only increases the water solubility but also significantly changes absorption, fluorescence, and transient absorption spectra of water soluble Pcs.

scholarly journals Inter-domain dynamics and fibrinolytic activity of matrix metalloprotease-1

2019 ◽  
Author(s):  
Lokender Kumar ◽  
Joan Planas-Iglesias ◽  
Chase Harms ◽  
Sumaer Kamboj ◽  
Derek Wright ◽  
...  
Keyword(s):  
Single Molecule ◽  
Blood Clot ◽  
Conformational Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Primary Component ◽  
Water Soluble ◽  
Matrix Metalloprotease ◽  
Allosteric Control ◽  
Domain Dynamics

AbstractThe roles of protein conformational dynamics and allostery in function are well-known. However, the roles that inter-domain dynamics have in function are not entirely understood. We used matrix metalloprotease-1 (MMP1) as a model system to study the relationship between inter-domain dynamics and activity because MMP1 has diverse substrates. Here we focus on fibrin, the primary component of a blood clot. Water-soluble fibrinogen, following cleavage by thrombin, self-polymerize to form water-insoluble fibrin. We studied the inter-domain dynamics of MMP1 on fibrin without crosslinks using single-molecule Forster Resonance Energy Transfer (smFRET). We observed that the distance between the catalytic and hemopexin domains of MMP1 increases or decreases as the MMP1 activity increases or decreases, respectively. We modulated the activity using 1) an active site mutant (E219Q) of MMP1, 2) MMP9, another member of the MMP family that increases the activity of MMP1, and 3) tetracycline, an inhibitor of MMP1. We fitted the histograms of smFRET values to a sum of two Gaussians and the autocorrelations to an exponential and power law. We modeled the dynamics as a two-state Poisson process and calculated the kinetic rates from the histograms and autocorrelations. Activity-dependent inter-domain dynamics may enable allosteric control of the MMP1 function.

scholarly journals New homologues of Brassicaceae water‐soluble chlorophyll proteins shed light on chlorophyll binding, spectral tuning, and molecular evolution

FEBS Journal ◽  
2019 ◽  
Vol 287 (5) ◽  
pp. 991-1004 ◽  
Author(s):  
Vadivel Prabahar ◽  
Livnat Afriat‐Jurnou ◽  
Irina Paluy ◽  
Yoav Peleg ◽  
Dror Noy
Keyword(s):  
Molecular Evolution ◽  
Water Soluble ◽  
Spectral Tuning ◽  
Shed Light

scholarly journals PHOTOSYNTHETIC ACTION SPECTRA OF MARINE ALGAE

1950 ◽  
Vol 33 (4) ◽  
pp. 389-422 ◽  
Author(s):  
F. T. Haxo ◽  
L. R. Blinks
Keyword(s):  
Absorption Spectra ◽  
Green Algae ◽  
Red Algae ◽  
Marine Algae ◽  
Monochromatic Light ◽  
Action Spectrum ◽  
Water Soluble ◽  
Good Correspondence ◽  
Oxygen Determination ◽  
Action Spectra

A polarographic oxygen determination, with tissue in direct contact with a stationary platinum electrode, has been used to measure the photosynthetic response of marine algae. These were exposed to monochromatic light, of equal energy, at some 35 points through the visible spectrum (derived from a monochromator). Ulva and Monostroma (green algae) show action spectra which correspond very closely to their absorption spectra. Coilodesme (a brown alga) shows almost as good correspondence, including the spectral region absorbed by the carotenoid, fucoxanthin. In green and brown algae, light absorbed by both chlorophyll and carotenoids seems photosynthetically effective, although some inactive absorption by carotenoids is indicated. Action spectra for a wide variety of red algae, however, show marked deviations from their corresponding absorption spectra. The photosynthetic rates are high in the spectral regions absorbed by the water-soluble "phycobilin" pigments (phycoerythrin and phycocyanin), while the light absorbed by chlorophyll and carotenoids is poorly utilized for oxygen production. In red algae containing chiefly phycoerythrin, the action spectrum closely resembles that of the water-extracted pigment, with peaks corresponding to its absorption maxima (495, 540, and 565 mµ). Such algae include Delesseria, Schizymenia, and Porphyrella. In the genus Porphyra, there is a series P. nereocystis, P. naiadum, and P. perforata, with increasingly more phycocyanin and less phycoerythrin: the action spectra reflect this, with increasing activity in the orange-red region (600 to 640 mµ) where phycocyanin absorbs. In all these red algae, photosynthesis is almost minimal at 435 mµ and 675 mµ, where chlorophyll shows maximum absorption. Although the chlorophylls (and carotenoids) are present in quantities comparable to the green algae, their function is apparently not that of a primary light absorber; this role is taken over by the phycobilins. In this respect the red algae (Rhodophyta) appear unique among photosynthetic plants.

Histochemistry and UV-microspectrometry of cell walls of untreated and ammonia-treated barley straw

1998 ◽  
Vol 78 (3) ◽  
pp. 437-443 ◽  
Author(s):  
Masakazu Goto ◽  
Keiji Takabe ◽  
Isao Abe
Keyword(s):  
Absorption Spectra ◽  
Cell Walls ◽  
Spring Barley ◽  
Parenchyma Cell ◽  
Water Soluble ◽  
Barley Straw ◽  
Ir Absorption ◽  
Ammonia Treatment ◽  
Vessel Walls ◽  
Lignin Structure

Histochemical staining reactions with acid phloroglucinol and ultraviolet (UV) absorption spectra of the individual cell walls in spring barley straw (Hordeum vulgare L.) were investigated in combination with spectrometric measurements of the dioxane-water soluble lignin. Changes in lignin structure of barley straw with ammonia treatment were also investigated. Parenchyma and metaxylem vessel walls in untreated straw stained red with acid phloroglucinol and had higher absorbances around 550 nm than did epidermis and sclerenchyma cell walls, being consistent with the λmax of coniferylaldehyde. Following a reductive treatment, the lignins isolated from untreated barley straw showed an increase in UV absorbance at 280 nm and a decrease in that around 320 nm. These regions in UV and IR absorption spectra are assigned to conjugated carbonyl groups as shown by the narrowing of the IR absorption band at 1660 cm−1, and this was consistent with the staining observation of the specific tissue walls. UV microspectrometry indicated that parenchyma cell walls were much less lignified tissues than metaxylem and protoxylem vessel walls and probably epidermal cell walls. The lignins isolated from untreated and ammonia-treated straw had similar values for empirical formulae of the C9 units, phenolic hydroxyl and methoxyl group contents, and molecular weight, although the lignin of ammonia-treated straw had a slightly higher contents of nitrogen and hydrogen. The IR bands of 1730–1680 cm−1 in ammonia-treated straw lignin also disappeared. Therefore, ammonia appeared to react with the carbon atoms of the propane side-chain. Key words: Ammonia treatment, barley straw, lignin distribution, lignin structure, staining with acid phloroglucinol, ultraviolet microspectrometry

Novel porphyrin-labelled poly(N-isopropylacrylamides): syntheses from bromoalkyl-containing prepolymers and physicochemical properties

2000 ◽  
Vol 04 (06) ◽  
pp. 579-587 ◽  
Author(s):  
YURI S. AVLASEVICH ◽  
TIMOUR A. CHEVTCHOUK ◽  
VALERY N. KNYUKSHTO ◽  
OLEG G. KULINKOVICH ◽  
KONSTANTIN N. SOLOVYOV
Keyword(s):  
Phase Transition ◽  
Phase Separation ◽  
Physicochemical Properties ◽  
Absorption Spectra ◽  
Polymer Solutions ◽  
Soret Band ◽  
Water Soluble ◽  
Absorption Bands ◽  
Aqueous Polymer ◽  
Peak Intensity

Novel water-soluble tetraarylporphyrin-labelled polymers have been synthesized by the reaction of bromoalkyl-containing poly(N-isopropylacrylamides) with 5-(4-pyridyl)-10,15,20-tri(4-methoxyphenyl) porphyrin. Corresponding Zn -porphyrin-containing polymers have also been prepared. Phase transition diagrams show that aqueous polymer solutions exhibit phase separation upon heating. Absorption spectra of the porphyrin-labelled polymers have been recorded in water and organic solvents. It is found that the absorption bands in aqueous polymer solutions are broadened and shifted bathochromically, the peak intensity of the Soret band in the polymer spectra being strongly lowered in water. Fluorescence properties of the polymers are briefly reported.

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