scholarly journals Structural model of a putrescine-cadaverine permease from Trypanosoma cruzi predicts residues vital for transport and ligand binding

2013 ◽  
Vol 452 (3) ◽  
pp. 423-432 ◽  
Author(s):  
Radika Soysa ◽  
Hanka Venselaar ◽  
Jacqueline Poston ◽  
Buddy Ullman ◽  
Marie-Pierre Hasne
Keyword(s):  
Trypanosoma Cruzi ◽  
Structural Model ◽  
Three Dimensional ◽  
Salt Bridge ◽  
Homology Model ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Helical Structures ◽  
Structural Determinants ◽  
Key Residues

The TcPOT1.1 gene from Trypanosoma cruzi encodes a high affinity putrescine-cadaverine transporter belonging to the APC (amino acid/polyamine/organocation) transporter superfamily. No experimental three-dimensional structure exists for any eukaryotic member of the APC family, and thus the structural determinants critical for function of these permeases are unknown. To elucidate the key residues involved in putrescine translocation and recognition by this APC family member, a homology model of TcPOT1.1 was constructed on the basis of the atomic co-ordinates of the Escherichia coli AdiC arginine/agmatine antiporter crystal structure. The TcPOT1.1 homology model consisted of 12 transmembrane helices with the first ten helices organized in two V-shaped antiparallel domains with discontinuities in the helical structures of transmembrane spans 1 and 6. The model suggests that Trp241 and a Glu247–Arg403 salt bridge participate in a gating system and that Asn245, Tyr148 and Tyr400 contribute to the putrescine-binding pocket. To test the validity of the model, 26 site-directed mutants were created and tested for their ability to transport putrescine and to localize to the parasite cell surface. These results support the robustness of the TcPOT1.1 homology model and reveal the importance of specific aromatic residues in the TcPOT1.1 putrescine-binding pocket.

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 Discovery of Novel Inhibitors for Nek6 Protein through Homology Model Assisted Structure Based Virtual Screening and Molecular Docking Approaches

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
P. Srinivasan ◽  
P. Chella Perumal ◽  
A. Sudha
Keyword(s):  
Virtual Screening ◽  
Cell Cycle Progression ◽  
Three Dimensional ◽  
Homology Model ◽  
Mitotic Cell ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Amino Acid Residues ◽  
Relationship Of

Nek6 is a member of the NIMA (never in mitosis, gene A)-related serine/threonine kinase family that plays an important role in the initiation of mitotic cell cycle progression. This work is an attempt to emphasize the structural and functional relationship of Nek6 protein based on homology modeling and binding pocket analysis. The three-dimensional structure of Nek6 was constructed by molecular modeling studies and the best model was further assessed by PROCHECK, ProSA, and ERRAT plot in order to analyze the quality and consistency of generated model. The overall quality of computed model showed 87.4% amino acid residues under the favored region. A 3 ns molecular dynamics simulation confirmed that the structure was reliable and stable. Two lead compounds (Binding database ID: 15666, 18602) were retrieved through structure-based virtual screening and induced fit docking approaches as novel Nek6 inhibitors. Hence, we concluded that the potential compounds may act as new leads for Nek6 inhibitors designing.

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.

scholarly journals An Intramolecular Salt Bridge in Bacillus thuringiensis Cry4Ba Toxin Is Involved in the Stability of Helix α-3, Which Is Needed for Oligomerization and Insecticidal Activity

2017 ◽  
Vol 83 (20) ◽  
Author(s):  
Sabino Pacheco ◽  
Isabel Gómez ◽  
Jorge Sánchez ◽  
Blanca-Ines García-Gómez ◽  
Mario Soberón ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Double Point ◽  
Single Point ◽  
Three Dimensional ◽  
Point Mutations ◽  
Salt Bridge ◽  
Dimensional Structure ◽  
Cry Toxins ◽  
Content Type ◽  
Domain I

ABSTRACT Bacillus thuringiensis three-domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Here we identify an intramolecular salt bridge within helix α-3 of Cry4Ba (D111-K115) that is conserved in many members of the family of three-domain Cry toxins. Single point mutations such as D111K or K115D resulted in proteins severely affected in toxicity. These mutants were also altered in oligomerization, and the mutant K115D was more sensitive to protease digestion. The double point mutant with reversed charges, D111K-K115D, recovered both oligomerization and toxicity, suggesting that this salt bridge is highly important for conservation of the structure of helix α-3 and necessary to promote the correct oligomerization of the toxin. IMPORTANCE Domain I has been shown to be involved in oligomerization through helix α-3 in different Cry toxins, and mutations affecting oligomerization also elicit changes in toxicity. The three-dimensional structure of the Cry4Ba toxin reveals an intramolecular salt bridge in helix α-3 of domain I. Mutations that disrupt this salt bridge resulted in changes in Cry4Ba oligomerization and toxicity, while a double point reciprocal mutation that restored the salt bridge resulted in recovery of toxin oligomerization and toxicity. These data highlight the role of oligomer formation as a key step in Cry4Ba toxicity.

The Integrative Establishment of a Three-Dimensional Structure Model of Changling Gas Field in Changling Fault Depression

2014 ◽  
Vol 556-562 ◽  
pp. 3779-3782
Author(s):  
Xiao Yu Yu ◽  
Xue Li ◽  
Xiao Song Li ◽  
Guo Yi Zhang
Keyword(s):  
Structural Model ◽  
High Reliability ◽  
Three Dimensional ◽  
Physical Property ◽  
Modeling Technique ◽  
Dimensional Structure ◽  
Gas Field ◽  
3D Geological Modeling ◽  
Micro Features ◽  
Reservoir Description

The three-dimensional (3D) geological modeling technique which is considered as an important skill of fine reservoir description has been gaining more and more attention. On one hand, it can efficiently promote the transformation of reservoir description from two-dimensional (2D) to 3D, and from qualification to quantification as well. The 3D reservoir geological model can be used as basic geological knowledge in terms of adjusting well patterns and indicating remaining oil distribution, through reflecting the spatial distribution characteristics and the variation of the reservoir physical property. On the other hand, the 3D modeling technique specializes in the representation of local micro features in comparison of regular ways. This article aims at subtly describing the structural modeling of Changling gas field of Changling fault depression. The result of this case study shows that the establishment of structural model is consistent with the understanding of fault development which was proved during the process of producing gas, thus the structural model has high reliability. Therefore, the structural model is of great guiding significance for the design of new well and the well patter optimization.

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 Construction and validation of a homology model of the human voltage-gated proton channel hHV1

2013 ◽  
Vol 141 (4) ◽  
pp. 445-465 ◽  
Author(s):  
Kethika Kulleperuma ◽  
Susan M.E. Smith ◽  
Deri Morgan ◽  
Boris Musset ◽  
John Holyoake ◽  
...  
Keyword(s):  
Structural Model ◽  
Proton Translocation ◽  
External Solution ◽  
Homology Model ◽  
Structural Features ◽  
Proton Channel ◽  
Dimensional Structure ◽  
Internal Solution ◽  
Voltage Gated ◽  
Homology Models

The topological similarity of voltage-gated proton channels (HV1s) to the voltage-sensing domain (VSD) of other voltage-gated ion channels raises the central question of whether HV1s have a similar structure. We present the construction and validation of a homology model of the human HV1 (hHV1). Multiple structural alignment was used to construct structural models of the open (proton-conducting) state of hHV1 by exploiting the homology of hHV1 with VSDs of K+ and Na+ channels of known three-dimensional structure. The comparative assessment of structural stability of the homology models and their VSD templates was performed using massively repeated molecular dynamics simulations in which the proteins were allowed to relax from their initial conformation in an explicit membrane mimetic. The analysis of structural deviations from the initial conformation based on up to 125 repeats of 100-ns simulations for each system reveals structural features consistently retained in the homology models and leads to a consensus structural model for hHV1 in which well-defined external and internal salt-bridge networks stabilize the open state. The structural and electrostatic properties of this open-state model are compatible with proton translocation and offer an explanation for the reversal of charge selectivity in neutral mutants of Asp112. Furthermore, these structural properties are consistent with experimental accessibility data, providing a valuable basis for further structural and functional studies of hHV1. Each Arg residue in the S4 helix of hHV1 was replaced by His to test accessibility using Zn2+ as a probe. The two outermost Arg residues in S4 were accessible to external solution, whereas the innermost one was accessible only to the internal solution. Both modeling and experimental data indicate that in the open state, Arg211, the third Arg residue in the S4 helix in hHV1, remains accessible to the internal solution and is located near the charge transfer center, Phe150.

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.

Three-dimensional structure of β-momorcharin at 2.55 Å resolution

1999 ◽  
Vol 55 (6) ◽  
pp. 1144-1151 ◽  
Author(s):  
Yu-Ren Yuan ◽  
Yong-Ning He ◽  
Jian-Ping Xiong ◽  
Zong-Xiang Xia
Keyword(s):  
Active Site ◽  
Structural Model ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
Ribosome Inactivating Protein ◽  
Three Dimensional Structure ◽  
Replacement Method ◽  
Enzymatic Function ◽  
Molecular Replacement Method

β-Momorcharin (Mr ≃ 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of β-momorcharin has been determined using the molecular-replacement method and refined to 2.55 Å resolution. The final structural model gave an R factor of 17.2% and root-mean-square deviations of 0.016 Å and 1.76° from ideal bond lengths and bond angles, respectively. β-Momorcharin contains nine α-helices, two 310 helices and three β-sheets, and its overall structure is similar to those of other single-chained RIPs. Residues Tyr70, Tyr109, Glu158 and Arg161 are expected to define the active site of β-momorcharin as an rRNA N-glycosidase. The oligosaccharide is linked to the protein through an N-glycosidic bond, β-GlcNAc–(1-N)-Asn51, and stretches from the surface of the N-terminal domain far from the active site, which suggests that it should not play a role in enzymatic function. The oligosaccharide of each β-momorcharin molecule interacts with the protein through hydrogen bonds, although in the crystals most of these are intermolecular interactions with the protein atoms in an adjacent unit cell. This is the first example of an RIP structure which provides information about the three-dimensional structure and binding site of the oligosaccharide in the active chains of RIPs.

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