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

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.

Download Full-text

Bach1, a heme-dependent transcription factor, reveals presence of multiple heme binding sites with distinct coordination structure

IUBMB Life ◽

10.1080/15216540701225941 ◽

2007 ◽

Vol 59 (8) ◽

pp. 542-551 ◽

Cited By ~ 62

Author(s):

Shusuke Hira ◽

Takeshi Tomita ◽

Toshitaka Matsui ◽

Kazuhiko Igarashi ◽

Masao Ikeda-Saito

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Heme Binding ◽

Coordination Structure

Download Full-text

Preferred heme binding sites of histidine-rich glycoprotein

Biochemistry ◽

10.1021/bi00342a034 ◽

1985 ◽

Vol 24 (21) ◽

pp. 5919-5924 ◽

Cited By ~ 16

Author(s):

Mary Kappel Burch ◽

William T. Morgan

Keyword(s):

Binding Sites ◽

Heme Binding

Download Full-text

Two Heme Binding Sites Are Involved in the Regulated Degradation of the Bacterial Iron Response Regulator (Irr) Protein

Journal of Biological Chemistry ◽

10.1074/jbc.m411664200 ◽

2004 ◽

Vol 280 (9) ◽

pp. 7671-7676 ◽

Cited By ~ 62

Author(s):

Jianhua Yang ◽

Koichiro Ishimori ◽

Mark R. O'Brian

Keyword(s):

Binding Sites ◽

Response Regulator ◽

Heme Binding ◽

Iron Response Regulator

Download Full-text

Spatial Relationship between L-Arginine and Heme Binding Sites of Endothelial Nitric-oxide Synthase

Journal of Biological Chemistry ◽

10.1074/jbc.271.52.33293 ◽

1996 ◽

Vol 271 (52) ◽

pp. 33293-33300 ◽

Cited By ~ 29

Author(s):

Vladimir Berka ◽

Pei-Feng Chen ◽

Ah-Lim Tsai

Keyword(s):

Nitric Oxide ◽

Nitric Oxide Synthase ◽

Binding Sites ◽

Endothelial Nitric Oxide Synthase ◽

Spatial Relationship ◽

Heme Binding ◽

Oxide Synthase ◽

Endothelial Nitric Oxide

Download Full-text

Structure-Function Analysis of the Bifunctional CcsBA Heme Exporter and CytochromecSynthetase

mBio ◽

10.1128/mbio.02134-18 ◽

2018 ◽

Vol 9 (6) ◽

Cited By ~ 3

Author(s):

Molly C. Sutherland ◽

Nathan L. Tran ◽

Dustin E. Tillman ◽

Joshua M. Jarodsky ◽

Jason Yuan ◽

...

Keyword(s):

Structure Function ◽

Binding Site ◽

Binding Sites ◽

Structural Model ◽

Function Analysis ◽

Integral Membrane Protein ◽

Covalent Attachment ◽

Heme Binding ◽

Heme Transport ◽

Heme Trafficking

ABSTRACTAlthough intracellular heme trafficking must occur for heme protein assembly, only a few heme transporters have been unequivocally discovered and nothing is known about their structure or mechanisms. Cytochromecbiogenesis in prokaryotes requires the transport of heme from inside to outside for stereospecific attachment to cytochromecvia two thioether bonds (at CXXCH). The CcsBA integral membrane protein was shown to transport and attach heme (and thus is a cytochromecsynthetase), but the structure and mechanisms underlying these two activities are poorly understood. We employed a new cysteine/heme crosslinking tool that traps endogenous heme in heme binding sites. We combined these data with a comprehensive imidazole correction approach (for heme ligand interrogation) to map heme binding sites. Results illuminate the process of heme transfer through the membrane to an external binding site (called the WWD domain). Using meta-genomic data (GREMLIN) and Rosetta modeling programs, a structural model of the transmembrane (TM) regions in CcsBA were determined. The heme mapping data were then incorporated to model the TM heme binding site (with TM-His1 and TM-His2 as ligands) and the external heme binding WWD domain (with P-His1 and P-His2 as ligands). Other periplasmic structure/function studies facilitated modeling of the full CcsBA protein as a framework for understanding the mechanisms. Mechanisms are proposed for heme transport from TM-His to WWD/P-His and subsequent stereospecific attachment of heme. A ligand exchange of the P-His1 for histidine of CXXCH at the synthetase active site is suggested.IMPORTANCEThe movement or trafficking of heme is critical for cellular functions (e.g., oxygen transport and energy production); however, intracellular heme is tightly regulated due to its inherent cytotoxicity. These factors, combined with the transient nature of transport, have resulted in a lack of direct knowledge on the mechanisms of heme binding and trafficking. Here, we used the cytochromecbiogenesis system II pathway as a model to study heme trafficking. System II is composed of two integral membrane proteins (CcsBA) which function to transport heme across the membrane and stereospecifically position it for covalent attachment to apocytochromec. We mapped two heme binding domains in CcsBA and suggest a path for heme trafficking. These data, in combination with metagenomic coevolution data, are used to determine a structural model of CcsBA, leading to increased understanding of the mechanisms for heme transport and the cytochromecsynthetase function of CcsBA.

Download Full-text

An extended-X-ray-absorption-fine-structure investigation of diferric transferrins and their iron-binding fragments

Biochemical Journal ◽

10.1042/bj2330479 ◽

1986 ◽

Vol 233 (2) ◽

pp. 479-484 ◽

Cited By ~ 21

Author(s):

R C Garratt ◽

R W Evans ◽

S S Hasnain ◽

P F Lindley

Keyword(s):

Aqueous Solution ◽

Fine Structure ◽

Binding Sites ◽

Rabbit Serum ◽

Iron Binding ◽

Structure Investigation ◽

X Ray ◽

Absorption Fine ◽

Spectral Profiles ◽

X Ray Absorption

Iron K-edge extended-X-ray-absorption-fine-structure (e.x.a.f.s.) spectra were recorded for diferric human and rabbit serum transferrins and for diferric chicken ovotransferrin in aqueous solution; for ovotransferrin e.x.a.f.s. spectra from the N-terminal and C-terminal domain fragments were also measured. The overall spectral profiles closely resemble one another, indicating similar iron-binding sites. The simulation of the diferric ovotransferrin spectrum suggests a first co-ordination shell consisting of six low-Z ligands (nitrogen/oxygen), two ligands at a distance of approx. 0.185 nm (1.85 A) and four ligands at approx. 0.204 nm (2.04 A). The two shorter distances may correspond to Fe-O (tyrosine), whereas the longer distance is consistent with Fe-N (histidine) and Fe-O (water). Detailed analysis of the spectra of the N-terminal and C-terminal fragments indicates a difference in the short ligand distance.

Download Full-text

THYROGLOBULIN IMMUNITY

Acta Endocrinologica ◽

10.1530/acta.0.0590159 ◽

1968 ◽

Vol 59 (1) ◽

pp. 159-171 ◽

Cited By ~ 3

Author(s):

A. K. Medda ◽

B. N. Premachandra

Keyword(s):

Immune Globulin ◽

Binding Sites ◽

Hind Limb ◽

Rana Catesbeiana ◽

Potent Inhibitor ◽

Protein Complexes ◽

Normal Serum ◽

Rabbit Serum ◽

Normal Rabbit Serum ◽

The Media

ABSTRACT Metamorphosis of Rana catesbeiana tadpoles immersed in a medium containing thyroxine (T4) occurred in 58 days, whereas 79 days were required for tadpoles treated with albumin + T4 complex in media, and at 121 days 50 % metamorphosis occurred in the group whose medium contained normal rabbit serum + T4. No metamorphosis occurred in tadpoles which had rabbit antiporcine thyroglobulin + T4 complex in media. Similarly the retardation of hind limb growth in comparison to the control at 58 days was most severe in animals treated with antithyroglobulin + T4 complex in media (74.3 % depression) followed by normal serum + T4 (60.1 % less) and bovine albumin + T4 complex (30 % inhibition) treated animals. In further investigations, in comparison to controls (only 125I-T4 in media), 62.4%, 77.0%, and 82.4% less 125I-T4 concentration was seen in viscera, tail, and carcass respectively of tadpoles treated with immune globulin + 125I-T4 in the media, whereas no change was seen in the group treated with normal gammaglobulin + 125I-T4 complex; similarly no changes in visceral 125I-T4 concentration were noted in groups whose media contained thyroglobulin in complex with 125I-T4. Present investigations therefore show that normal rabbit serum (apparently any good T4 binding protein) is a potent inhibitor of metamorphosis of tadpoles, the effectiveness mediated at least in part, on the inability of the larva to split thyroxine-protein complexes in their body. Antiporcine thyroglobulin rabbit serum was shown to be superior to normal rabbit serum in inhibiting tadpole metamorphosis, evidently due to additional T4 binding sites provided by the immune globulin. Available evidence indicates that antithyroglobulin binding of T4 is distinct and is evidently not due to thyroglobulin that may be in complex with the thyroid antibody.

Download Full-text

Effects of intrauterine instillation of antiserum to hCG during early pregnancy in mice

Acta Endocrinologica ◽

10.1530/acta.0.1070268 ◽

1984 ◽

Vol 107 (2) ◽

pp. 268-274 ◽

Cited By ~ 8

Author(s):

Narendra J. Joshi ◽

Tarala D. Nandedkar

Keyword(s):

Binding Sites ◽

Chorionic Gonadotrophin ◽

Human Chorionic Gonadotrophin ◽

Mouse Embryos ◽

Rabbit Serum ◽

Normal Rabbit Serum ◽

Cytotoxicity Test ◽

Implantation Sites ◽

Immunohistochemical Techniques

Abstract. Human chorionic gonadotrophin (hCG)-like activity has been reported in mouse and rabbit blastocysts. The presence of this hCG-like activity seems to be essential for nidation of the pre-implantation embryo. Binding sites for hCG were localised on day 4 mouse embryos by immunohistochemical techniques. Presence of hCG-like activity was confirmed by cytotoxicity test. The number of implantation sites was significantly reduced on day 8 of pregnancy. Prior treatment to day 4 mouse embryos with hCG antiserum, for 1 h in utero or in vitro and their subsequent transfer to uteri of synchronised pseudopregnant mice resulted in impaired implantation of embryos, compared to controls treated with normal rabbit serum (NRS). These results suggest that hCG-like activity present on the pre-implantation embryo may have a significant role in implantation of the embryo.

Download Full-text