First model of dimeric LRRK2: the challenge of unrevealing the structure of a multidomain Parkinson's-associated protein

2016 ◽  
Vol 44 (6) ◽  
pp. 1635-1641 ◽  
Author(s):  
Giambattista Guaitoli ◽  
Bernd K. Gilsbach ◽  
Francesco Raimondi ◽  
Christian Johannes Gloeckner
Keyword(s):  
Kinase Activity ◽  
Structural Model ◽  
Three Dimensional ◽  
Kinase Domain ◽  
Rational Drug Design ◽  
Dimensional Structure ◽  
Rational Drug ◽  
Its Gene ◽  
Lrrk2 Gene ◽  
Successful Approach

Mutations within the leucine-rich repeat kinase 2 (LRRK2) gene represent the most common cause of Mendelian forms of Parkinson's disease, among autosomal dominant cases. Its gene product, LRRK2, is a large multidomain protein that belongs to the Roco protein family exhibiting GTPase and kinase activity, with the latter activity increased by pathogenic mutations. To allow rational drug design against LRRK2 and to understand the cross-regulation of the G- and the kinase domain at a molecular level, it is key to solve the three-dimensional structure of the protein. We review here our recent successful approach to build the first structural model of dimeric LRRK2 by an integrative modeling approach.

scholarly journals Modelling the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase on adenylate kinase

1997 ◽  
Vol 321 (3) ◽  
pp. 615-621 ◽  
Author(s):  
Luc BERTRAND ◽  
Didier VERTOMMEN ◽  
Eric DEPIEREUX ◽  
Louis HUE ◽  
Mark H. RIDER ◽  
...  
Keyword(s):  
Adenylate Kinase ◽  
Structural Model ◽  
Three Dimensional ◽  
Kinase Domain ◽  
Multiple Alignment ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Conserved Residues ◽  
Nucleotide Binding Proteins ◽  
Sequence Similarities

Simultaneous multiple alignment of available sequences of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase revealed several segments of conserved residues in the 2-kinase domain. The sequence of the kinase domain was also compared with proteins of known three-dimensional structure. No similarity was found between the kinase domain of 6-phosphofructo-2-kinase and 6-phosphofructo-1-kinase. This questions the modelling of the 2-kinase domain on bacterial 6-phosphofructo-1-kinase that has previously been proposed [Bazan, Fletterick and Pilkis (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 9642Ő9646]. However, sequence similarities were found between the 2-kinase domain and several nucleotide-binding proteins, the most similar being adenylate kinase. A structural model of the 2-kinase domain based on adenylate kinase is proposed. It accommodates all the results of site-directed mutagenesis studies carried out to date on residues in the 2-kinase domain. It also allows residues potentially involved in catalysis and/or substrate binding to be predicted.

Characterization of an A-type cyclin-dependent kinase gene from Dendrobium candidum

Biologia ◽  
2012 ◽  
Vol 67 (2) ◽  
Author(s):  
Gang Zhang ◽  
Chao Song ◽  
Ming-Ming Zhao ◽  
Biao Li ◽  
Shun-Xing Guo
Keyword(s):  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Postembryonic Development ◽  
Kinase Domain ◽  
Dimensional Structure ◽  
Pcr Analysis ◽  
Kinase Gene ◽  
Multiple Sequence ◽  
Dendrobium Candidum ◽  
Rapid Amplification

AbstractCyclin-dependent kinases (CDKs) play an essential role in cell cycle regulation during the embryonic and postembryonic development of organisms. To better understand the molecular mechanisms of CDKs involved in embryogenesis regulation in the endangered medicinal plant Dendrobium candidum Wall. ex Lindl., a 1229-bp full-length cDNA of an A-type CDK gene, Denca;CDKA;1, was identified using 3′ rapid amplification of cDNA end (RACE) PCR. Denca;CDKA;1 was predicted to encode a 294 amino acid residue-long protein of 33.76 kDa with an isoelectric point of 7.72. The deduced Denca;CDKA;1 protein contained a conserved serine/threonine-protein kinase domain (S-TKc) and a canonical cyclinbinding “PSTAIRE” motif. Multiple sequence alignment indicated that members of CDKA family from various plants exhibited a high degree of sequence identity ranging from 82% to 93%. A neighbor-joining phylogenetic tree showed that Denca;CDKA;1 was clustered into the plant group and was distant from the animal and fungal groups. The modeled three-dimensional structure of Denca;CDKA;1 exhibited the similar functional structure of a fold consisting of β-sheets and α-helices joined by discontinuous random coils forming two relatively independent lobes. Quantitative real-time PCR analysis revealed that Denca;CDKA;1 transcripts were the most abundant in protocorm-like bodies with 4.76 fold, followed by that in roots (4.19 fold), seeds (2.57 fold), and stems (1.57 fold). This study characterized the novel Denca;CDKA;1 gene from D. candidum for the first time and the results will be useful for further functional determination of the gene.

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.

scholarly journals An Uncharacterized Member of the Ribokinase Family in Thermococcus kodakarensis Exhibits myo-Inositol Kinase Activity

2013 ◽  
Vol 288 (29) ◽  
pp. 20856-20867 ◽  
Author(s):  
Takaaki Sato ◽  
Masahiro Fujihashi ◽  
Yukika Miyamoto ◽  
Keiko Kuwata ◽  
Eriko Kusaka ◽  
...  
Keyword(s):  
Kinase Activity ◽  
Three Dimensional ◽  
Fold Increase ◽  
Adenosine Kinase ◽  
Dimensional Structure ◽  
Uncharacterized Protein ◽  
Thermococcus Kodakarensis ◽  
Sugar Phosphates ◽  
Biochemical Analyses ◽  
Physiological Substrates

Here we performed structural and biochemical analyses on the TK2285 gene product, an uncharacterized protein annotated as a member of the ribokinase family, from the hyperthermophilic archaeon Thermococcus kodakarensis. The three-dimensional structure of the TK2285 protein resembled those of previously characterized members of the ribokinase family including ribokinase, adenosine kinase, and phosphofructokinase. Conserved residues characteristic of this protein family were located in a cleft of the TK2285 protein as in other members whose structures have been determined. We thus examined the kinase activity of the TK2285 protein toward various sugars recognized by well characterized ribokinase family members. Although activity with sugar phosphates and nucleosides was not detected, kinase activity was observed toward d-allose, d-lyxose, d-tagatose, d-talose, d-xylose, and d-xylulose. Kinetic analyses with the six sugar substrates revealed high Km values, suggesting that they were not the true physiological substrates. By examining activity toward amino sugars, sugar alcohols, and disaccharides, we found that the TK2285 protein exhibited prominent kinase activity toward myo-inositol. Kinetic analyses with myo-inositol revealed a greater kcat and much lower Km value than those obtained with the monosaccharides, resulting in over a 2,000-fold increase in kcat/Km values. TK2285 homologs are distributed among members of Thermococcales, and in most species, the gene is positioned close to a myo-inositol monophosphate synthase gene. Our results suggest the presence of a novel subfamily of the ribokinase family whose members are present in Archaea and recognize myo-inositol as a substrate.

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.

scholarly journals Structural Model for 12-Helix Transporters Belonging to the Major Facilitator Superfamily

2003 ◽  
Vol 185 (5) ◽  
pp. 1712-1718 ◽  
Author(s):  
Teruhisa Hirai ◽  
Jürgen A. W. Heymann ◽  
Peter C. Maloney ◽  
Sriram Subramaniam
Keyword(s):  
Structural Model ◽  
Structural Information ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Bound State ◽  
Major Facilitator Superfamily ◽  
Dimensional Structure ◽  
Sequence Information ◽  
Major Facilitator ◽  
Related Proteins

ABSTRACT The major facilitator superfamily includes a large collection of evolutionarily related proteins that have been implicated in the transport of a variety of solutes and metabolites across the membranes of organisms ranging from bacteria to humans. We have recently reported the three-dimensional structure, at 6.5 Å resolution, of the oxalate transporter, OxlT, a representative member of this superfamily. In the oxalate-bound state, 12 helices surround a central cavity to form a remarkably symmetrical structure that displays a well-defined pseudo twofold axis perpendicular to the plane of the membrane as well as two less pronounced, mutually perpendicular pseudo twofold axes in the plane of the membrane. Here, we combined this structural information with sequence information from other members of this protein family to arrive at models for the arrangement of helices in this superfamily of transport proteins. Our analysis narrows down the number of helix arrangements from about a billion starting possibilities to a single probable model for the relative spatial arrangement for the 12 helices, consistent both with our structural findings and with the majority of previous biochemical studies on members of this superfamily.

scholarly journals O2- and NO-Sensing Mechanism through the DevSR Two-Component System in Mycobacterium smegmatis

2008 ◽  
Vol 190 (20) ◽  
pp. 6795-6804 ◽  
Author(s):  
Jin-Mok Lee ◽  
Ha Yeon Cho ◽  
Hyo Je Cho ◽  
In-Jeong Ko ◽  
Sae Woong Park ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
Kinase Activity ◽  
Binding Capacity ◽  
Three Dimensional ◽  
Heme Iron ◽  
Dimensional Structure ◽  
Comparison Analysis ◽  
Two Component System ◽  
Transport Chain ◽  
Autokinase Activity

ABSTRACT The DevS histidine kinase of Mycobacterium smegmatis contains tandem GAF domains (GAF-A and GAF-B) in its N-terminal sensory domain. The heme iron of DevS is in the ferrous state when purified and is resistant to autooxidation from a ferrous to a ferric state in the presence of O2. The redox property of the heme and the results of sequence comparison analysis indicate that DevS of M. smegmatis is more closely related to DosT of Mycobacterium tuberculosis than DevS of M. tuberculosis. The binding of O2 to the deoxyferrous heme led to a decrease in the autokinase activity of DevS, whereas NO binding did not. The regulation of DevS autokinase activity in response to O2 and NO was not observed in the DevS derivatives lacking its heme, indicating that the ligand-binding state of the heme plays an important role in the regulation of DevS kinase activity. The redox state of the quinone/quinol pool of the respiratory electron transport chain appears not to be implicated in the regulation of DevS activity. Neither cyclic GMP (cGMP) nor cAMP affected DevS autokinase activity, excluding the possibility that the cyclic nucleotides serve as the effector molecules to modulate DevS kinase activity. The three-dimensional structure of the putative GAF-B domain revealed that it has a GAF folding structure without cyclic nucleotide binding capacity.

Type I interferon structures: Possible scaffolds for the interferon-alpha receptor complex

2002 ◽  
Vol 80 (8) ◽  
pp. 1166-1173 ◽  
Author(s):  
Tattanahalli L Nagabhushan ◽  
Paul Reichert ◽  
Mark R Walter ◽  
Nicholas J Murgolo
Keyword(s):  
Structural Model ◽  
Structural Information ◽  
Three Dimensional ◽  
Cell Receptor ◽  
Type I Interferons ◽  
Dimensional Structure ◽  
Type I ◽  
Receptor Complex ◽  
X Ray Crystallography ◽  
Receptor Complexes

The structures of several type I interferons (IFNs) are known. We review the structural information known for IFN alphas and compare them to other interferons and cytokines. We also review the structural information known or proposed for IFN–cell receptor complexes. However, the structure of the IFN – cell receptor – IFN receptor2 (IFNAR2) and IFN receptor1 (IFNAR1) complex has not yet been determined. This paper describes a structural model of human IFN-IFNAR2/IFNAR1 complex using human IFN-α2b dimer as the ligand. Both the structures of recombinant human IFN-α2b and IFN-β were determined by X-ray crystallography as zinc-mediated dimers. Our proposed model was generated using human IFN-α2b dimer docked with IFNAR2/IFNAR1. We compare our model with the receptor complex models proposed for IFN-β and IFN-γ to contrast similarities and differences. The mutual binding sites of human IFN-α2b and IFNAR2/IFNAR1 complex are consistent with available mutagenesis studies.Key words: three dimensional structure, antiviral activity, receptor, interferon.

Rational Drug Design

2014 ◽  
Vol 4 (1) ◽  
pp. 59-85 ◽  
Author(s):  
Khaled H. Barakat ◽  
Michael Houghton ◽  
D. Lorne Tyrrel ◽  
Jack A. Tuszynski
Keyword(s):  
Drug Design ◽  
Rational Drug Design ◽  
Dimensional Structure ◽  
Computational Tools ◽  
Structure Based Drug Design ◽  
Practical Applications ◽  
3 Dimensional ◽  
Drug Candidates ◽  
The Past ◽  
Rational Drug

For the past three decades rationale drug design (RDD) has been developing as an innovative, rapid and successful way to discover new drug candidates. Many strategies have been followed and several targets with diverse structures and different biological roles have been investigated. Despite the variety of computational tools available, one can broadly divide them into two major classes that can be adopted either separately or in combination. The first class involves structure-based drug design, when the target's 3-dimensional structure is available or it can be computationally generated using homology modeling. On the other hand, when only a set of active molecules is available, and the structure of the target is unknown, ligand-based drug design tools are usually used. This review describes some recent advances in rational drug design, summarizes a number of their practical applications, and discusses both the advantages and shortcomings of the various techniques used.

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