scholarly journals Molecular Modeling of Chemosensory Protein 3 from Spodoptera litura and Its Binding Property with Plant Defensive Metabolites

2020 ◽  
Vol 21 (11) ◽  
pp. 4073
Author(s):  
Sujata Singh ◽  
Chetna Tyagi ◽  
Irfan A. Rather ◽  
Jamal S.M. Sabir ◽  
Md. Imtaiyaz Hassan ◽  
...  
Keyword(s):  
Host Plant ◽  
Spodoptera Litura ◽  
Management Strategies ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Chemical Signals ◽  
Dimensional Structure ◽  
Binding Property ◽  
Plant Metabolites ◽  
Modeled Structure

Chemosensory perception in insects involves a broad set of chemosensory proteins (CSPs) that identify the bouquet of chemical compounds present in the external environment and regulate specific behaviors. The current study is focused on the Spodoptera litura (Fabricius) chemosensory-related protein, SlitCSP3, a midgut-expressed CSP, which demonstrates differential gene expression upon different diet intake. There is an intriguing possibility that SlitCSP3 can perceive food-derived chemical signals and modulate insect feeding behavior. We predicted the three-dimensional structure of SlitCSP3 and subsequently performed an accelerated molecular dynamics (aMD) simulation of the best-modeled structure. SlitCSP3 structure has six α-helices arranged as a prism and a hydrophobic binding pocket predominated by leucine and isoleucine. We analyzed the interaction of selected host plant metabolites with the modeled structure of SlitCSP3. Out of two predicted binding pockets in SlitCSP3, the plant-derived defensive metabolites 2-b-D-glucopyranosyloxy-4-hydroxy-7-methoxy-1, 4-benzoxazin-3-one (DIMBOA), 6-Methoxy-2–benzoxazolinone (MBOA), and nicotine were found to interact preferably to the hydrophobic site 1, compared to site 2. The current study provides the potential role of CSPs in recognizing food-derived chemical signals, host-plant specialization, and adaptation to the varied ecosystem. Our work opens new perspectives in designing novel pest-management strategies. It can be further used in the development of CSP-based advanced biosensors.

scholarly journals Structure of the Lectin Mannose 6-Phosphate Receptor Homology (MRH) Domain of Glucosidase II, an Enzyme That Regulates Glycoprotein Folding Quality Control in the Endoplasmic Reticulum

2013 ◽  
Vol 288 (23) ◽  
pp. 16460-16475 ◽  
Author(s):  
Linda J. Olson ◽  
Ramiro Orsi ◽  
Solana G. Alculumbre ◽  
Francis C. Peterson ◽  
Ivan D. Stigliano ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Mannose Residue ◽  
Glucosidase Ii ◽  
Mannose 6 Phosphate ◽  
First Time ◽  
Conserved Residue

Here we report for the first time the three-dimensional structure of a mannose 6-phosphate receptor homology (MRH) domain present in a protein with enzymatic activity, glucosidase II (GII). GII is involved in glycoprotein folding in the endoplasmic reticulum. GII removes the two innermost glucose residues from the Glc3Man9GlcNAc2 transferred to nascent proteins and the glucose added by UDP-Glc:glycoprotein glucosyltransferase. GII is composed of a catalytic GIIα subunit and a regulatory GIIβ subunit. GIIβ participates in the endoplasmic reticulum localization of GIIα and mediates in vivo enhancement of N-glycan trimming by GII through its C-terminal MRH domain. We determined the structure of a functional GIIβ MRH domain by NMR spectroscopy. It adopts a β-barrel fold similar to that of other MRH domains, but its binding pocket is the most shallow known to date as it accommodates a single mannose residue. In addition, we identified a conserved residue outside the binding pocket (Trp-409) present in GIIβ but not in other MRHs that influences GII glucose trimming activity.

Hemoglobin Biosynthesis in Vitreoscilla stercoraria DW: Cloning, Expression, and Characterization of a New Homolog of a Bacterial Globin Gene

1998 ◽  
Vol 64 (6) ◽  
pp. 2220-2228 ◽  
Author(s):  
Meenal Joshi ◽  
Shekhar Mande ◽  
Kanak L. Dikshit
Keyword(s):  
Globin Gene ◽  
Three Dimensional ◽  
Fold Increase ◽  
Binding Pocket ◽  
Growth Conditions ◽  
Dimensional Structure ◽  
Strictly Aerobic ◽  
Coding Region ◽  
Oxygen Control ◽  
Constitutive Production

ABSTRACT In the strictly aerobic, gram-negative bacteriumVitreoscilla strain C1, oxygen-limited growth conditions create a more than 50-fold increase in the expression of a homodimeric heme protein which was recognized as the first bacterial hemoglobin (Hb). The recently determined crystal structure ofVitreoscilla Hb has indicated that the heme pocket of microbial globins differs from that of eukaryotic Hbs. In an attempt to understand the diverse functions of Hb-like proteins in prokaryotes, we have cloned and characterized the gene (vgb) encoding an Hb-like protein from another strain of Vitreoscilla,V. stercoraria DW. Several silent changes were observed within the coding region of the V. stercoraria vgb gene. Apart from that, V. stercoraria Hb exhibited interesting differences between the A and E helices. Compared to its Hb counterpart from Vitreoscilla strain C1, the purified preparation ofV. stercoraria Hb displays a slower autooxidation rate. The differences between Vitreoscilla Hb and V. stercoraria Hb were mapped onto the three-dimensional structure of Vitreoscilla Hb, which indicated that the four changes, namely, Ile7Val, Ile9Thr, Ile10Ser, and Leu62Val, present within theV. stercoraria Hb fall in the region where the A and E helices contact each other. Therefore, alteration in the relative orientation of the A and E helices and the corresponding conformational change in the heme binding pocket of V. stercoraria Hb can be correlated to its slower autooxidation rate. In sharp contrast to the oxygen-regulated biosynthesis of Hb in Vitreoscillastrain C1, production of Hb in V. stercoraria has been found to be low and independent of oxygen control, which is supported by the absence of a fumarate and nitrate reductase regulator box within the V. stercoraria vgb promoter region. Thus, the regulation mechanisms of the Hb-encoding gene appear to be quite different in the two closely related species ofVitreoscilla. The relatively slower autooxidation rate ofV. stercoraria Hb, lack of oxygen sensitivity, and constitutive production of Hb suggest that it may have some other function(s) in the cellular physiology of V. stercorariaDW, together with facilitated oxygen transport, predicted for earlier reported Vitreoscilla Hb.

scholarly journals KNApSAcK-3D: A Three-Dimensional Structure Database of Plant Metabolites

2013 ◽  
Vol 54 (2) ◽  
pp. e4-e4 ◽  
Author(s):  
Kensuke Nakamura ◽  
Naoki Shimura ◽  
Yuuki Otabe ◽  
Aki Hirai-Morita ◽  
Yukiko Nakamura ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Plant Metabolites ◽  
Three Dimensional Structure ◽  
Structure Database

Unliganded GroEL at 2.8 Å: structure and functional implications

1995 ◽  
Vol 348 (1323) ◽  
pp. 113-119 ◽  
Keyword(s):  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Outer Diameter ◽  
Central Channel ◽  
Crystal Forms ◽  
Monoclinic Form ◽  
C Terminus ◽  
Ligand Free ◽  
Dyad Symmetry

The three-dimensional structure of the E. coli chaperonin, GroEL, has been determined crystallo-graphically and refined to 2.7 Å in two crystal forms: an orthorhombic form from high salt and a monoclinic form from polyethylene glycol. The former is ligand free, the latter is both liganded with ATP analogues and ligand free. These structures provide a structural scaffold upon which to interpret extensive mutagenesis and biochemical studies. GroEL contains two sevenfold rotationally symmetric rings of identical 547-amino acid subunits. The rings are arranged ‘back-to-back’ with exact dyad symmetry to form a stubby cylinder that is 146 Å high with an outer diameter of about 143 Å. The cylinder has a substantial central channel that is unobstructed for the entire length of the cylinder and has a diameter of about 45 Å except for large bulges that lead into a sevenfold symmetric array of elliptical side windows in each ring. Each subunit is composed of three distinct domains: (i) an ‘equatorial’ domain that contains the N- and C-terminus and the ATP-binding pocket, .(ii) an ‘apical domain’ that forms the opening of the central channel and contains poorly ordered segments that mutational studies implicate in binding unfolded polypeptides and GroES, and (iii) an intermediate domain tht connects the other two domains and may serve to transmit allosteric adjustments.

Molecular and cellular biology of thyrotropin-releasing hormone receptors

1996 ◽  
Vol 76 (1) ◽  
pp. 175-191 ◽  
Author(s):  
M. C. Gershengorn ◽  
R. Osman
Keyword(s):  
Hormone Receptors ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Amino Acid Sequences ◽  
Thyrotropin Releasing Hormone ◽  
Cellular Biology ◽  
Dimensional Structure ◽  
Releasing Hormone ◽  
G Protein Coupled ◽  
Trh Receptor

Thyrotropin-releasing hormone (TRH) receptor (TRH-R) complementary DNAs have been cloned from several species. The deduced amino acid sequences are compatible with TRH-R being a seven-transmembrane-spanning G protein-coupled receptor. These complementary DNAs and reagents derived from them have permitted detailed study of TRH-R biology at the molecular and cellular levels. Studies that have been performed since 1990 are reviewed in this article under the following headings: TRH-R gene, tissue distribution of TRH-R, primary structure of TRH-Rs, three-dimensional structure of the TRH-R binding pocket, TRH-R and G proteins, TRH-R activation, TRH desensitization, TRH-R endocytosis, and regulation of TRH-R number. It is evident that many new insights into the structure, function, and regulation of TRH-Rs have been gained in the last several years but that our understanding of these processes is incomplete. We look forward to even greater progress in the future.

scholarly journals FpvA-Mediated Ferric Pyoverdine Uptake in Pseudomonas aeruginosa: Identification of Aromatic Residues in FpvA Implicated in Ferric Pyoverdine Binding and Transport

2005 ◽  
Vol 187 (24) ◽  
pp. 8511-8515 ◽  
Author(s):  
Jiang-Sheng Shen ◽  
Valérie Geoffroy ◽  
Shadi Neshat ◽  
Zongchao Jia ◽  
Allison Meldrum ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Aromatic Residues ◽  
Three Dimensional Structure

ABSTRACT A number of aromatic residues were seen to cluster in the upper portion of the three-dimensional structure of the FpvA ferric pyoverdine receptor of Pseudomonas aeruginosa, reminiscent of the aromatic binding pocket for ferrichrome in the FhuA receptor of Escherichia coli. Alanine substitutions in three of these, W362, W391, and F795, markedly compromised ferric pyoverdine binding and transport, consistent with a role of FpvA in ferric pyoverdine recognition.

Molecular cloning, sequence characteristics, and tissue expression analysis of glucagon receptor gene in Bama minipig

2020 ◽  
Vol 100 (3) ◽  
pp. 536-546
Author(s):  
Cuiping An ◽  
Kaiyi Zhang ◽  
Wenjuan Zhu ◽  
Yanzhen Bi ◽  
Tianwen Wu ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Receptor Gene ◽  
Three Dimensional ◽  
Salt Bridge ◽  
Binding Pocket ◽  
Tissue Expression ◽  
Dimensional Structure ◽  
Glucagon Receptor ◽  
Tissue Expression Analysis ◽  
Glucose And Lipid Metabolism

Recent studies have shown that the glucagon receptor (GCGR) plays an important role in the development of type 2 diabetes mellitus. Both pigs and humans exhibit significantly similar behaviors in their glucose and lipid metabolism. In this study, the obtained Bama minipig GCGR coding sequence was 1437 bp encoding 479 amino acids (AA), which demonstrated higher sequence homology with humans than other species. It showed the highest expression profile in the liver, followed by the lung and kidney. In addition, the three-dimensional structure analysis showed that the porcine GCGR protein also had a classic sevenfold transmembrane region and a stalk region at the N-terminus for ligand binding. The stalk region of GCGR possessed five AA variations. The ligand binding pocket of GCGR has one AA variation in the key region, none of which affected the glucagon binding verified by the crystal structure mutagenesis in humans. There was no variation found in the region of membrane anchoring, hydrophobic bond, salt bridge, and hydrogen bond. However, the Gly40Ser mutation in mice resulted in major diseases, meaning that pigs are more suitable for the evaluation of GCGR-related drugs than mice.

scholarly journals The future: genetics advances in MEN1 therapeutic approaches and management strategies

2017 ◽  
Vol 24 (10) ◽  
pp. T119-T134 ◽  
Author(s):  
Sunita K Agarwal
Keyword(s):  
Genetic Testing ◽  
Tumor Suppressor ◽  
Mouse Models ◽  
Target Genes ◽  
Molecular Genetic ◽  
Management Strategies ◽  
Tumor Development ◽  
Three Dimensional ◽  
Suppressor Gene ◽  
Dimensional Structure

The identification of the multiple endocrine neoplasia type 1 (MEN1) gene in 1997 has shown that germline heterozygous mutations in theMEN1gene located on chromosome 11q13 predisposes to the development of tumors in the MEN1 syndrome. Tumor development occurs upon loss of the remaining normal copy of theMEN1gene in MEN1-target tissues. Therefore,MEN1is a classic tumor suppressor gene in the context of MEN1. This tumor suppressor role of the protein encoded by theMEN1gene, menin, holds true in mouse models with germline heterozygousMen1loss, wherein MEN1-associated tumors develop in adult mice after spontaneous loss of the remaining non-targeted copy of theMen1gene. The availability of genetic testing for mutations in theMEN1gene has become an essential part of the diagnosis and management of MEN1. Genetic testing is also helping to exclude mutation-negative cases in MEN1 families from the burden of lifelong clinical screening. In the past 20 years, efforts of various groups world-wide have been directed at mutation analysis, molecular genetic studies, mouse models, gene expression studies, epigenetic regulation analysis, biochemical studies and anti-tumor effects of candidate therapies in mouse models. This review will focus on the findings and advances from these studies to identifyMEN1germline and somatic mutations, the genetics of MEN1-related states, several protein partners of menin, the three-dimensional structure of menin and menin-dependent target genes. The ongoing impact of all these studies on disease prediction, management and outcomes will continue in the years to come.

scholarly journals Structural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase

2016 ◽  
Vol 198 (10) ◽  
pp. 1499-1512 ◽  
Author(s):  
Sonali Dhindwal ◽  
Leticia Gomez-Gil ◽  
David B. Neau ◽  
Thi Thanh My Pham ◽  
Michel Sylvestre ◽  
...  
Keyword(s):  
Polychlorinated Biphenyl ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Degradation Pathway ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Biphenyl Dioxygenase ◽  
Pcb Congeners ◽  
Biphenyl Degradation ◽  
Insight Into

ABSTRACTBiphenyl dioxygenase, the first enzyme of the biphenyl catabolic pathway, is a major determinant of which polychlorinated biphenyl (PCB) congeners are metabolized by a given bacterial strain. Ongoing efforts aim to engineer BphAE, the oxygenase component of the enzyme, to efficiently transform a wider range of congeners. BphAEII9, a variant of BphAELB400in which a seven-residue segment,335TFNNIRI341, has been replaced by the corresponding segment of BphAEB356,333GINTIRT339, transforms a broader range of PCB congeners than does either BphAELB400or BphAEB356, including 2,6-dichlorobiphenyl, 3,3′-dichlorobiphenyl, 4,4′-dichlorobiphenyl, and 2,3,4′-trichlorobiphenyl. To understand the structural basis of the enhanced activity of BphAEII9, we have determined the three-dimensional structure of this variant in substrate-free and biphenyl-bound forms. Structural comparison with BphAELB400reveals a flexible active-site mouth and a relaxed substrate binding pocket in BphAEII9that allow it to bind different congeners and which could be responsible for the enzyme's altered specificity. Biochemical experiments revealed that BphAEII9transformed 2,3,4′-trichlorobiphenyl and 2,2′,5,5′-tetrachlorobiphenyl more efficiently than did BphAELB400and BphAEB356. BphAEII9also transformed the insecticide dichlorodiphenyltrichloroethane (DDT) more efficiently than did either parental enzyme (apparentkcat/Kmof 2.2 ± 0.5 mM−1s−1, versus 0.9 ± 0.5 mM−1s−1for BphAEB356). Studies of docking of the enzymes with these three substrates provide insight into the structural basis of the different substrate selectivities and regiospecificities of the enzymes.IMPORTANCEBiphenyl dioxygenase is the first enzyme of the biphenyl degradation pathway that is involved in the degradation of polychlorinated biphenyls. Attempts have been made to identify the residues that influence the enzyme activity for the range of substrates among various species. In this study, we have done a structural study of one variant of this enzyme that was produced by family shuffling of genes from two different species. Comparison of the structure of this variant with those of the parent enzymes provided an important insight into the molecular basis for the broader substrate preference of this enzyme. The structural and functional details gained in this study can be utilized to further engineer desired enzymatic activity, producing more potent enzymes.

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