Revisiting the interaction of heme with hemopexin

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Milena Sophie Detzel ◽  
Benjamin Franz Schmalohr ◽  
Francèl Steinbock ◽  
Marie-Thérèse Hopp ◽  
Anuradha Ramoji ◽  
...  
Keyword(s):  
Binding Sites ◽  
Protective Factor ◽  
Homology Model ◽  
Binding Pocket ◽  
Heme Binding ◽  
Vis Spectroscopy ◽  
Erythrocyte Lysis ◽  
Peptide Models ◽  
High Concentrations ◽  
Displacement Assays

Abstract In hemolytic disorders, erythrocyte lysis results in massive release of hemoglobin and, subsequently, toxic heme. Hemopexin is the major protective factor against heme toxicity in human blood and currently considered for therapeutic use. It has been widely accepted that hemopexin binds heme with extraordinarily high affinity of <1 pM in a 1:1 ratio. However, several lines of evidence point to a higher stoichiometry and lower affinity than determined 50 years ago. Here, we re-analyzed these data. SPR and UV/Vis spectroscopy were used to monitor the interaction of heme with the human protein. The heme-binding sites of hemopexin were characterized using hemopexin-derived peptide models and competitive displacement assays. We obtained a K D value of 0.32 ± 0.04 nM and the ratio for the interaction was determined to be 1:1 at low heme concentrations and at least 2:1 (heme:hemopexin) at high concentrations. We were able to identify two yet unknown potential heme-binding sites on hemopexin. Furthermore, molecular modelling with a newly created homology model of human hemopexin suggested a possible recruiting mechanism by which heme could consecutively bind several histidine residues on its way into the binding pocket. Our findings have direct implications for the potential administration of hemopexin in hemolytic disorders.

scholarly journals Revisiting the interaction of heme with hemopexin: Recommendations for the responsible use of an emerging drug

2020 ◽  
Author(s):  
Milena S. Detzel ◽  
Benjamin F. Syllwasschy ◽  
Francèl Steinbock ◽  
Anuradha Ramoji ◽  
Marie-Thérèse Hopp ◽  
...  
Keyword(s):  
Binding Sites ◽  
Protective Factor ◽  
Biomedical Application ◽  
Homology Model ◽  
Binding Pocket ◽  
Heme Binding ◽  
High Affinity ◽  
Erythrocyte Lysis ◽  
Peptide Models ◽  
Displacement Assays

AbstractIn hemolytic disorders, erythrocyte lysis results in massive release of hemoglobin and, subsequently, toxic heme. Hemopexin is the major protective factor against heme toxicity in human blood and currently considered for therapeutic use. It has been widely accepted that hemopexin binds heme with extraordinarily high affinity in a 1:1 ratio. Here we show that hemopexin binds heme with lower affinity than previously assumed and that the interaction ratio tends to 2:1 (heme:hemopexin) or above. The heme-binding sites of hemopexin were characterized using hemopexin-derived peptide models and competitive displacement assays. In addition, in silico molecular modelling with a newly created homology model of human hemopexin allowed us to propose a recruiting mechanism by which heme consecutively binds to several histidine residues and is finally funnelled into the high-affinity binding pocket. Our findings have direct implications for the biomedical application of hemopexin and its potential administration in hemolytic disorders.

Spectroscopic characterization of the heme binding (GAF) domain of two sensor kinases from Methanosarcina acetivorans

2019 ◽  
Vol 23 (07n08) ◽  
pp. 930-942
Author(s):  
Kerstin Fiege ◽  
Christian Twittenhoff ◽  
Kathrin Kwiatkowski ◽  
Nicole Frankenberg-Dinkel
Keyword(s):  
Spectroscopic Characterization ◽  
Binding Pocket ◽  
Cysteine Residue ◽  
Site Directed Mutagenesis ◽  
Heme Binding ◽  
Methanosarcina Acetivorans ◽  
Vis Spectroscopy ◽  
Sensor Kinases ◽  
Covalently Linked ◽  
Heme Cofactor

The sensor kinases MsmS and RdmS from the methanogenic archaeon Methanosarcina acetivorans are multidomain proteins containing a covalently linked heme cofactor. This cofactor is connected via a single cysteine residue in a GAF domain. Although both proteins were shown to display a redox-dependent control of the downstream kinase module, this property appears to be independent of the heme cofactor. We therefore envision an additional sensor role for the heme cofactor. In order to learn more about the heme binding pocket and its constitution, UV-vis spectroscopy in combination with site-directed mutagenesis was performed on the isolated heme-binding sGAF2 domain and the full-length protein. The data indicate a 6-coordinated heme with a proximal histidine ligand and a smaller ligand, likely a water molecule on the distal site. The latter is also thought to be the sensory site and is shown to easily undergo ligand exchange.

scholarly journals In Silico Identification of Cholesterol Binding Motifs in the Chemokine Receptor CCR3

Membranes ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 570
Author(s):  
Evan van van Aalst ◽  
Jotham Koneri ◽  
Benjamin J. Wylie
Keyword(s):  
Chemokine Receptor ◽  
Binding Sites ◽  
In Silico ◽  
Chemokine Receptors ◽  
Homology Model ◽  
Binding Pocket ◽  
Coarse Grained ◽  
Class A ◽  
Inflammatory Conditions ◽  
Cholesterol Binding

CC motif chemokine receptor 3 (CCR3) is a Class A G protein-coupled receptor (GPCR) mainly responsible for the cellular trafficking of eosinophils. As such, it plays key roles in inflammatory conditions, such as asthma and arthritis, and the metastasis of many deadly forms of cancer. However, little is known about how CCR3 functionally interacts with its bilayer environment. Here, we investigate cholesterol binding sites in silico through Coarse-Grained Molecular Dynamics (MD) and Pylipid analysis using an extensively validated homology model based on the crystal structure of CCR5. These simulations identified several cholesterol binding sites containing Cholesterol Recognition/Interaction Amino Acid Consensus motif (CRAC) and its inversion CARC motifs in CCR3. One such site, a CARC site in TM1, in conjunction with aliphatic residues in TM7, emerged as a candidate for future investigation based on the cholesterol residency time within the binding pocket. This site forms the core of a cholesterol binding site previously observed in computational studies of CCR2 and CCR5. Most importantly, these cholesterol binding sites are conserved in other chemokine receptors and may provide clues to cholesterol regulation mechanisms in this subfamily of Class A GPCRs.

Functional Involvement of Thrombospondin in Platelet Aggregation Induced by Low Versus High Concentrations of Thrombin

1986 ◽  
Vol 55 (01) ◽  
pp. 136-142 ◽  
Author(s):  
K J Kao ◽  
David M Shaut ◽  
Paul A Klein
Keyword(s):  
Platelet Aggregation ◽  
Binding Sites ◽  
Inhibitory Effect ◽  
Activated Platelets ◽  
Low Concentrations ◽  
Platelet Binding ◽  
Functional Involvement ◽  
Thrombin Activation ◽  
Platelet Aggregates ◽  
High Concentrations

SummaryThrombospondin (TSP) is a major platelet secretory glycoprotein. Earlier studies of various investigators demonstrated that TSP is the endogenous platelet lectin and is responsible for the hemagglutinating activity expressed on formaldehyde-fixed thrombin-treated platelets. The direct effect of highly purified TSP on thrombin-induced platelet aggregation was studied. It was observed that aggregation of gel-filtered platelets induced by low concentrations of thrombin (≤0.05 U/ml) was progressively inhibited by increasing concentrations of exogenous TSP (≥60 μg/ml). However, inhibition of platelet aggregation by TSP was not observed when higher than 0.1 U/ml thrombin was used to activate platelets. To exclude the possibility that TSP inhibits platelet aggregation by affecting thrombin activation of platelets, three different approaches were utilized. First, by using a chromogenic substrate assay it was shown that TSP does not inhibit the proteolytic activity of thrombin. Second, thromboxane B2 synthesis by thrombin-stimulated platelets was not affected by exogenous TSP. Finally, electron microscopy of thrombin-induced platelet aggregates showed that platelets were activated by thrombin regardless of the presence or absence of exogenous TSP. The results indicate that high concentrations of exogenous TSP (≥60 μg/ml) directly interfere with interplatelet recognition among thrombin-activated platelets. This inhibitory effect of TSP can be neutralized by anti-TSP Fab. In addition, anti-TSP Fab directly inhibits platelet aggregation induced by a low (0.02 U/ml) but not by a high (0.1 U/ml) concentration of thrombin. In conclusion, our findings demonstrate that TSP is functionally important for platelet aggregation induced by low (≤0.05 U/ml) but not high (≥0.1 U/ml) concentrations of thrombin. High concentrations of exogenous TSP may univalently saturate all its platelet binding sites consequently interfering with TSP-crosslinking of thrombin-activated platelets.

scholarly journals A protein with multiple heme-binding sites from rabbit serum.

1982 ◽  
Vol 257 (7) ◽  
pp. 3925-3931 ◽  
Author(s):  
K Tsutsui ◽  
G C Mueller
Keyword(s):  
Binding Sites ◽  
Rabbit Serum ◽  
Heme Binding

Furosemide-sensitive thallium fluxes in smooth muscle of rabbit uterus

1983 ◽  
Vol 245 (6) ◽  
pp. F778-F783
Author(s):  
A. Johns ◽  
S. V. Cutshaw
Keyword(s):  
Smooth Muscle ◽  
Binding Sites ◽  
Rank Order ◽  
Chloride Concentration ◽  
Cation Binding ◽  
Exchange System ◽  
Total Uptake ◽  
Low Concentrations ◽  
Chloride Pump ◽  
High Concentrations

The furosemide-sensitive uptake of thallium represents approximately equal to 50% of the total uptake of thallium by rabbit uterus and requires Cl- and Na+. The furosemide-sensitive uptake of thallium is stimulated by other ions at low concentrations with the rank order Li+ greater than Tl+ greater than K+ = Rb+ greater than Cs+ and is inhibited by these ions at high concentrations with the rank order Tl+ greater than K+ = Rb+ greater than Cs+ greater than Li+, suggesting multiple cation binding sites on the carrier. Uptake of 36Cl- is inhibited by furosemide in the presence of ouabain. Thallium efflux and 36Cl efflux in the presence of ouabain is inhibited by furosemide. The chloride concentration regulates the proportion of thallium uptake that is ouabain sensitive and furosemide sensitive without altering the total uptake. It is suggested that the furosemide-sensitive uptake of thallium reflects a Na+-Cl- -K+ exchange system that could be classified as a cotransport or countertransport of any two of these ions and also could be the smooth muscle chloride pump.

scholarly journals Etomidate and Etomidate Analog Binding and Positive Modulation of γ-Aminobutyric Acid Type A Receptors

2018 ◽  
Vol 129 (5) ◽  
pp. 959-969 ◽  
Author(s):  
Megan McGrath ◽  
Zhiyi Yu ◽  
Selwyn S. Jayakar ◽  
Celena Ma ◽  
Mansi Tolia ◽  
...  
Keyword(s):  
Steric Hindrance ◽  
Gabaa Receptors ◽  
Binding Sites ◽  
Phenyl Ring ◽  
Type A ◽  
Binding Pocket ◽  
Aminobutyric Acid ◽  
Substituent Group ◽  
Acid Type ◽  
Site Selective

Abstract Editor’s Perspective What We Already Know about This Topic What This Article Tells Us That Is New Background Naphthalene-etomidate, an etomidate analog containing a bulky phenyl ring substituent group, possesses very low γ-aminobutyric acid type A (GABAA) receptor efficacy and acts as an anesthetic-selective competitive antagonist. Using etomidate analogs containing phenyl ring substituents groups that range in volume, we tested the hypothesis that this unusual pharmacology is caused by steric hindrance that reduces binding to the receptor’s open state. Methods The positive modulatory potencies and efficacies of etomidate and phenyl ring–substituted etomidate analogs were electrophysiology defined in oocyte-expressed α1β3γ2L GABAA receptors. Their binding affinities to the GABAA receptor’s two classes of transmembrane anesthetic binding sites were assessed from their abilities to inhibit receptor labeling by the site-selective photolabels 3[H]azi-etomidate and tritiated R-5-allyl-1-methyl-5-(m-trifluoromethyl-diazirynylphenyl) barbituric acid. Results The positive modulatory activities of etomidate and phenyl ring–substituted etomidate analogs progressively decreased with substituent group volume, reflecting significant decreases in both potency (P = 0.005) and efficacy (P &lt; 0.0001). Affinity for the GABAA receptor’s two β+ − α– anesthetic binding sites similarly decreased with substituent group volume (P = 0.003), whereas affinity for the receptor’s α+ – β–/γ+ – β– sites did not (P = 0.804). Introduction of the N265M mutation, which is located at the β+ − α– binding sites and renders GABAA receptors etomidate-insensitive, completely abolished positive modulation by naphthalene-etomidate. Conclusions Steric hindrance selectively reduces phenyl ring–substituted etomidate analog binding affinity to the two β+ − α– anesthetic binding sites on the GABAA receptor’s open state, suggesting that the binding pocket where etomidate’s phenyl ring lies becomes smaller as the receptor isomerizes from closed to open.

Refinement of a Homology Model of the μ-Opioid Receptor Using Distance Constraints from Intrinsic and Engineered Zinc-Binding Sites†

Biochemistry ◽  
2004 ◽  
Vol 43 (27) ◽  
pp. 8700-8710 ◽  
Author(s):  
Carol B. Fowler ◽  
Irina D. Pogozheva ◽  
Harry LeVine ◽  
Henry I. Mosberg
Keyword(s):  
Opioid Receptor ◽  
Binding Sites ◽  
Homology Model ◽  
Zinc Binding ◽  
Distance Constraints ◽  
Μ Opioid Receptor

scholarly journals Off-pathway 3D-structure provides protection against spontaneous Asn/Asp isomerization: shielding proteins Achilles heel

2020 ◽  
Vol 53 ◽  
Author(s):  
András Láng ◽  
Imre Jákli ◽  
Kata Nóra Enyedi ◽  
Gábor Mező ◽  
Dóra K. Menyhárd ◽  
...  
Keyword(s):  
Protective Factor ◽  
Structural Integrity ◽  
3D Structure ◽  
Nucleophilic Attack ◽  
Structural Element ◽  
Backbone Conformation ◽  
Peptide Models ◽  
Geometric Descriptors ◽  
Restricted Mobility ◽  
Methylene Group

Abstract Spontaneous deamidation prompted backbone isomerization of Asn/Asp residues resulting in – most cases – the insertion of an extra methylene group into the backbone poses a threat to the structural integrity of proteins. Here we present a systematical analysis of how temperature, pH, presence of charged residues, but most importantly backbone conformation and dynamics affect isomerization rates as determined by nuclear magnetic resonance in the case of designed peptide-models. We demonstrate that restricted mobility (such as being part of a secondary structural element) may safeguard against isomerization, but this protective factor is most effective in the case of off-pathway folds which can slow the reaction by several magnitudes compared to their on-pathway counterparts. We show that the geometric descriptors of the initial nucleophilic attack of the isomerization can be used to classify local conformation and contribute to the design of stable protein drugs, antibodies or the assessment of the severity of mutations.

scholarly journals BionoiNet: ligand-binding site classification with off-the-shelf deep neural network

2020 ◽  
Vol 36 (10) ◽  
pp. 3077-3083
Author(s):  
Wentao Shi ◽  
Jeffrey M Lemoine ◽  
Abd-El-Monsif A Shawky ◽  
Manali Singha ◽  
Limeng Pu ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Ligand Binding ◽  
Binding Sites ◽  
Protein Structures ◽  
Supplementary Information ◽  
Heme Binding ◽  
Unseen Data ◽  
Ligand Binding Sites ◽  
Binding Pockets

Abstract Motivation Fast and accurate classification of ligand-binding sites in proteins with respect to the class of binding molecules is invaluable not only to the automatic functional annotation of large datasets of protein structures but also to projects in protein evolution, protein engineering and drug development. Deep learning techniques, which have already been successfully applied to address challenging problems across various fields, are inherently suitable to classify ligand-binding pockets. Our goal is to demonstrate that off-the-shelf deep learning models can be employed with minimum development effort to recognize nucleotide- and heme-binding sites with a comparable accuracy to highly specialized, voxel-based methods. Results We developed BionoiNet, a new deep learning-based framework implementing a popular ResNet model for image classification. BionoiNet first transforms the molecular structures of ligand-binding sites to 2D Voronoi diagrams, which are then used as the input to a pretrained convolutional neural network classifier. The ResNet model generalizes well to unseen data achieving the accuracy of 85.6% for nucleotide- and 91.3% for heme-binding pockets. BionoiNet also computes significance scores of pocket atoms, called BionoiScores, to provide meaningful insights into their interactions with ligand molecules. BionoiNet is a lightweight alternative to computationally expensive 3D architectures. Availability and implementation BionoiNet is implemented in Python with the source code freely available at: https://github.com/CSBG-LSU/BionoiNet. Supplementary information Supplementary data are available at Bioinformatics online.

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