338 results match your criteria Journal of Structural and Functional Genomics [Journal]


Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

J Struct Funct Genomics 2016 Dec 12;17(4):147-154. Epub 2017 Jan 12.

Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.

Protein database search for public databases is a fundamental step in the target selection of proteins in structural and functional genomics and also for inferring protein structure, function, and evolution. Most database search methods employ amino acid substitution matrices to score amino acid pairs. The choice of substitution matrix strongly affects homology detection performance. Read More

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http://link.springer.com/10.1007/s10969-016-9210-4
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http://dx.doi.org/10.1007/s10969-016-9210-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5274646PMC
December 2016
9 Reads

Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery.

J Struct Funct Genomics 2016 Dec 6;17(4):111-133. Epub 2017 Jan 6.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

More than 800 G protein-coupled receptor (GPCR) genes have been discovered in the human genome. Towards the next step in GPCR research, we performed a knowledge-driven analysis of orphan class-A GPCRs that may serve as novel targets in drug discovery. We examined the relationship between 61 orphan class-A GPCR genes and diseases using the Online Mendelian Inheritance in Man (OMIM) database and the DDSS tool. Read More

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http://dx.doi.org/10.1007/s10969-016-9212-2DOI Listing
December 2016
8 Reads

Special issue: big data analyses in structural and functional genomics.

J Struct Funct Genomics 2016 12;17(4):67

Graduate School of Humanities and Sciences, Ochanomizu University, Otsuka, Bunkyo, Tokyo, 112-8610, Japan.

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http://dx.doi.org/10.1007/s10969-016-9213-1DOI Listing
December 2016
8 Reads

Classification of ligand molecules in PDB with graph match-based structural superposition.

J Struct Funct Genomics 2016 Dec 23;17(4):135-146. Epub 2016 Dec 23.

Department of Bioscience, Nagahama Institute of Bio-science and Technology, 1266 Tamura, Nagahama, 526-0829, Japan.

The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom-atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set. Read More

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http://dx.doi.org/10.1007/s10969-016-9209-xDOI Listing
December 2016
4 Reads

VaProS: a database-integration approach for protein/genome information retrieval.

J Struct Funct Genomics 2016 Dec 23;17(4):69-81. Epub 2016 Dec 23.

National Institute of Genetics, Shizuoka, 411-8540, Mishima, Japan.

Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein-protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. Read More

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http://dx.doi.org/10.1007/s10969-016-9211-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5274651PMC
December 2016
13 Reads

NLDB: a database for 3D protein-ligand interactions in enzymatic reactions.

J Struct Funct Genomics 2016 Dec 16;17(4):101-110. Epub 2016 Aug 16.

Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan.

NLDB (Natural Ligand DataBase; URL: http://nldb.hgc.jp ) is a database of automatically collected and predicted 3D protein-ligand interactions for the enzymatic reactions of metabolic pathways registered in KEGG. Read More

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http://dx.doi.org/10.1007/s10969-016-9206-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5274645PMC
December 2016
7 Reads

HOMCOS: an updated server to search and model complex 3D structures.

Authors:
Takeshi Kawabata

J Struct Funct Genomics 2016 Dec 13;17(4):83-99. Epub 2016 Aug 13.

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

The HOMCOS server ( http://homcos.pdbj.org ) was updated for both searching and modeling the 3D complexes for all molecules in the PDB. Read More

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http://dx.doi.org/10.1007/s10969-016-9208-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5274653PMC
December 2016
6 Reads

Successful completion of a semi-automated enzyme-free cloning method.

J Struct Funct Genomics 2016 Sep 9;17(2-3):57-66. Epub 2016 Aug 9.

GSK Vaccines, Siena, 53100, Italy.

Nowadays, in scientific fields such as Structural Biology or Vaccinology, there is an increasing need of fast, effective and reproducible gene cloning and expression processes. Consequently, the implementation of robotic platforms enabling the automation of protocols is becoming a pressing demand. The main goal of our study was to set up a robotic platform devoted to the high-throughput automation of the polymerase incomplete primer extension cloning method, and to evaluate its efficiency compared to that achieved manually, by selecting a set of bacterial genes that were processed either in the automated platform (330) or manually (94). Read More

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http://dx.doi.org/10.1007/s10969-016-9207-zDOI Listing
September 2016
7 Reads

Structural mapping of Kelch13 mutations associated with artemisinin resistance in malaria.

J Struct Funct Genomics 2016 Sep 11;17(2-3):51-6. Epub 2016 Jul 11.

Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi, 110067, India.

Mutations in Plasmodium falciparum gene kelch13 (pfkelch13) are strongly and causally associated with resistance to anti-malarial drug artemisinin, but their effects on PfKelch13 structure and function remain unclear. Utilizing the publicly available three-dimensional structure of PfKech13 (PDB ID: 4yy8), we find that most of the mutations in its propeller domain occur in two spatial clusters. Of these, one cluster is enriched in surface exposed residues which may drive PfKelch13-centered protein interactions, and the second cluster mostly contains residues which are buried and whose mutations may destabilize PfKelch13 structure. Read More

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http://dx.doi.org/10.1007/s10969-016-9205-1DOI Listing
September 2016
9 Reads

Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation.

J Struct Funct Genomics 2016 Sep 11;17(2-3):39-49. Epub 2016 Jul 11.

Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.

We present a new method for predicting protein-ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Read More

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http://dx.doi.org/10.1007/s10969-016-9204-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5002282PMC
September 2016
23 Reads

Expression, purification, and crystallization of Schizosaccharomyces pombe eIF2B.

J Struct Funct Genomics 2016 Mar 29;17(1):33-8. Epub 2016 Mar 29.

Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Tight control of protein synthesis is necessary for cells to respond and adapt to environmental changes rapidly. Eukaryotic translation initiation factor (eIF) 2B, the guanine nucleotide exchange factor for eIF2, is a key target of translation control at the initiation step. The nucleotide exchange activity of eIF2B is inhibited by the stress-induced phosphorylation of eIF2. Read More

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http://dx.doi.org/10.1007/s10969-016-9203-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833825PMC
March 2016
7 Reads

Premeltons in DNA.

Authors:
Henry M Sobell

J Struct Funct Genomics 2016 Mar 16;17(1):17-31. Epub 2016 Mar 16.

Departments of Chemistry and Molecular Biophysics, University of Rochester, Rochester, NY, 14642, USA.

Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. Read More

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http://dx.doi.org/10.1007/s10969-016-9202-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833827PMC
March 2016
12 Reads

The impact of structural genomics: the first quindecennial.

J Struct Funct Genomics 2016 Mar 2;17(1):1-16. Epub 2016 Mar 2.

Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA, 22908, USA.

The period 2000-2015 brought the advent of high-throughput approaches to protein structure determination. With the overall funding on the order of $2 billion (in 2010 dollars), the structural genomics (SG) consortia established worldwide have developed pipelines for target selection, protein production, sample preparation, crystallization, and structure determination by X-ray crystallography and NMR. These efforts resulted in the determination of over 13,500 protein structures, mostly from unique protein families, and increased the structural coverage of the expanding protein universe. Read More

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http://dx.doi.org/10.1007/s10969-016-9201-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834271PMC
March 2016
12 Reads

Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes.

J Struct Funct Genomics 2015 Dec 15;16(3-4):113-28. Epub 2015 Dec 15.

Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, 9700 S Cass Ave., Argonne, IL, 60439, USA.

Multiprotein complexes play essential roles in all cells and X-ray crystallography can provide unparalleled insight into their structure and function. Many of these complexes are believed to be sufficiently stable for structural biology studies, but the production of protein-protein complexes using recombinant technologies is still labor-intensive. We have explored several strategies for the identification and cloning of heterodimers and heterotrimers that are compatible with the high-throughput (HTP) structural biology pipeline developed for single proteins. Read More

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http://dx.doi.org/10.1007/s10969-015-9200-yDOI Listing
December 2015
8 Reads

Automated protein motif generation in the structure-based protein function prediction tool ProMOL.

J Struct Funct Genomics 2015 Dec 16;16(3-4):101-11. Epub 2015 Nov 16.

School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY, USA.

ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. Read More

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http://dx.doi.org/10.1007/s10969-015-9199-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684744PMC
December 2015
37 Reads
1 Citation

Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies.

J Struct Funct Genomics 2015 Jun 9;16(2):67-80. Epub 2015 Apr 9.

The Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin at Madison, 433 Babcock Dr., Madison, WI, 53706, USA.

Vectors designed for protein production in Escherichia coli and by wheat germ cell-free translation were tested using 21 well-characterized eukaryotic proteins chosen to serve as controls within the context of a structural genomics pipeline. The controls were carried through cloning, small-scale expression trials, large-scale growth or synthesis, and purification. Successfully purified proteins were also subjected to either crystallization trials or (1)H-(15)N HSQC NMR analyses. Read More

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http://dx.doi.org/10.1007/s10969-015-9198-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430420PMC
June 2015
19 Reads

Crystal structures of Mycobacterial MeaB and MMAA-like GTPases.

J Struct Funct Genomics 2015 Jun 2;16(2):91-9. Epub 2015 Apr 2.

Beryllium, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bainbridge Island, WA, 98110, USA,

The methylmalonyl Co-A mutase-associated GTPase MeaB from Methylobacterium extorquens is involved in glyoxylate regulation and required for growth. In humans, mutations in the homolog methylmalonic aciduria associated protein (MMAA) cause methylmalonic aciduria, which is often fatal. The central role of MeaB from bacteria to humans suggests that MeaB is also important in other, pathogenic bacteria such as Mycobacterium tuberculosis. Read More

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http://dx.doi.org/10.1007/s10969-015-9197-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631608PMC
June 2015
14 Reads

Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT.

J Struct Funct Genomics 2015 Jun 24;16(2):55-65. Epub 2015 Mar 24.

RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.

ZFAT is a transcriptional regulator, containing eighteen C2H2-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structures of the thirteen individual ZFAT zinc-fingers (ZF) and the tandemly arrayed zinc-fingers in the regions from ZF2 to ZF5, by NMR spectroscopy. ZFAT has eight uncommon bulged-out helix-containing zinc-fingers, and six of their structures (ZF4, ZF5, ZF6, ZF10, ZF11, and ZF13) were determined. Read More

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http://link.springer.com/content/pdf/10.1007%2Fs10969-015-91
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http://link.springer.com/10.1007/s10969-015-9196-3
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http://dx.doi.org/10.1007/s10969-015-9196-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427657PMC
June 2015
7 Reads

Crystal structure of the MazG-related nucleoside triphosphate pyrophosphohydrolase from Thermotoga maritima MSB8.

J Struct Funct Genomics 2015 Jun 11;16(2):81-9. Epub 2015 Mar 11.

Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, 560 029, India,

The MazG family proteins, which are highly conserved in bacteria, are nucleoside triphosphate pyrophosphohydrolases that hydrolyze all canonical nucleoside triphosphates, and are also involved in removing noncanonical nucleoside triphosphates to prevent their incorporation into DNA or RNA. The primary structure of TM0360 from Thermotoga maritima MSB8 suggested that TM0360 is a MazG-related nucleoside triphosphate pyrophosphohydrolase. The crystal structure of the TM0360 protein was determined by the MAD technique at 2. Read More

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http://link.springer.com/10.1007/s10969-015-9195-4
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http://dx.doi.org/10.1007/s10969-015-9195-4DOI Listing
June 2015
12 Reads

Annotation of proteins of unknown function: initial enzyme results.

J Struct Funct Genomics 2015 Mar 29;16(1):43-54. Epub 2015 Jan 29.

College of Science, RIT, Rochester, NY, USA.

Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having "unknown function". Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed. Read More

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http://dx.doi.org/10.1007/s10969-015-9194-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332402PMC
March 2015
12 Reads
4 Citations

A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.).

J Struct Funct Genomics 2015 Mar 25;16(1):25-41. Epub 2015 Jan 25.

RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.

The putative translation elongation factor Mbar_A0971 from the methanogenic archaeon Methanosarcina barkeri was proposed to be the pyrrolysine-specific paralogue of EF-Tu ("EF-Pyl"). In the present study, the crystal structures of its homologue from Methanosarcina mazei (MM1309) were determined in the GMPPNP-bound, GDP-bound, and apo forms, by the single-wavelength anomalous dispersion phasing method. The three MM1309 structures are quite similar (r. Read More

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http://dx.doi.org/10.1007/s10969-015-9193-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329189PMC
March 2015
7 Reads

Expression, purification, crystallization, and preliminary X-ray crystallographic studies of the human adiponectin receptors, AdipoR1 and AdipoR2.

J Struct Funct Genomics 2015 Mar 10;16(1):11-23. Epub 2015 Jan 10.

RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.

The adiponectin receptors (AdipoR1 and AdipoR2) are membrane proteins with seven transmembrane helices. These receptors regulate glucose and fatty acid metabolism, thereby ameliorating type 2 diabetes. The full-length human AdipoR1 and a series of N-terminally truncated mutants of human AdipoR1 and AdipoR2 were expressed in insect cells. Read More

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http://dx.doi.org/10.1007/s10969-014-9192-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329188PMC
March 2015
29 Reads

X-ray structure of the mature ectodomain of phogrin.

J Struct Funct Genomics 2015 Mar 26;16(1):1-9. Epub 2014 Nov 26.

Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina.

Phogrin/IA-2β and ICA512/IA-2 are two paralogs receptor-type protein-tyrosine phosphatases (RPTP) that localize in secretory granules of various neuroendocrine cells. In pancreatic islet β-cells, they participate in the regulation of insulin secretion, ensuring proper granulogenesis, and β-cell proliferation. The role of their cytoplasmic tail has been partially unveiled, while that of their luminal region remains unclear. Read More

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http://dx.doi.org/10.1007/s10969-014-9191-0DOI Listing
March 2015
11 Reads

Development of a hexahistidine-3× FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris.

J Struct Funct Genomics 2014 Dec 15;15(4):191-9. Epub 2014 Nov 15.

Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.

We developed a method for efficient chromosome tagging in Pichia pastoris, using a useful tandem affinity purification (TAP) tag. The TAP tag, designated and used here as the THF tag, contains a thrombin protease cleavage site for removal of the TAP tag and a hexahistidine sequence (6× His) followed by three copies of the FLAG sequence (3× FLAG) for affinity purification. Using this method, THF-tagged RNA polymerases I, II, and III were successfully purified from P. Read More

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http://dx.doi.org/10.1007/s10969-014-9190-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237914PMC
December 2014
24 Reads

Structural characterization of the putative ABC-type 2 transporter from Thermotoga maritima MSB8.

J Struct Funct Genomics 2014 Dec 12;15(4):215-22. Epub 2014 Oct 12.

Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.

This study describes the structure of the putative ABC-type 2 transporter TM0543 from Thermotoga maritima MSB8 determined at a resolution of 2.3 Å. In comparative sequence-clustering analysis, TM0543 displays similarity to NatAB-like proteins, which are components of the ABC-type Na(+) efflux pump permease. Read More

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http://link.springer.com/10.1007/s10969-014-9189-7
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http://dx.doi.org/10.1007/s10969-014-9189-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239177PMC
December 2014
11 Reads

Crystal structures of the S6K1 kinase domain in complexes with inhibitors.

J Struct Funct Genomics 2014 Sep 31;15(3):153-64. Epub 2014 Jul 31.

RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.

Ribosomal protein S6 kinase 1 (S6K1) is a serine/threonine protein kinase that plays an important role in the PIK3/mTOR signaling pathway, and is implicated in diseases including diabetes, obesity, and cancer. The crystal structures of the S6K1 kinase domain in complexes with staurosporine and the S6K1-specific inhibitor PF-4708671 have been reported. In the present study, five compounds (F108, F109, F176, F177, and F179) were newly identified by in silico screening of a chemical library and kinase assay. Read More

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http://dx.doi.org/10.1007/s10969-014-9188-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125821PMC
September 2014
30 Reads

A new manual dispensing system for in meso membrane protein crystallization with using a stepping motor-based dispenser.

J Struct Funct Genomics 2014 Sep 24;15(3):165-71. Epub 2014 Jul 24.

RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan,

A reliable and easy to use manual dispensing system has been developed for the in meso membrane protein crystallization method. The system consists of a stepping motor-based dispenser with a new microsyringe system for dispensing, which allows us to deliver any desired volume of highly viscous lipidic mesophase in the range from ~50 to at least ~200 nl. The average, standard deviation, and coefficient of variation of 20 repeated deliveries of 50 nl cubic phase were comparable to those of a current robotic dispensing. Read More

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http://dx.doi.org/10.1007/s10969-014-9187-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125823PMC
September 2014
5 Reads

Structural and functional analysis of the anti-malarial drug target prolyl-tRNA synthetase.

J Struct Funct Genomics 2014 Dec 22;15(4):181-90. Epub 2014 Jul 22.

Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India.

Aminoacyl-tRNA synthetases (aaRSs) drive protein translation in cells and hence these are essential enzymes across life. Inhibition of these enzymes can halt growth of an organism by stalling protein translation. Therefore, small molecule targeting of aaRS active sites is an attractive avenue from the perspective of developing anti-infectives. Read More

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http://dx.doi.org/10.1007/s10969-014-9186-xDOI Listing
December 2014
5 Reads

Solution NMR structures of immunoglobulin-like domains 7 and 12 from obscurin-like protein 1 contribute to the structural coverage of the Human Cancer Protein Interaction Network.

J Struct Funct Genomics 2014 Dec 3;15(4):209-14. Epub 2014 Jul 3.

Department of Chemistry, The State University of New York at Buffalo and Northeast Structural Genomics Consortium, Buffalo, NY, 14260, USA.

High-quality solution NMR structures of immunoglobulin-like domains 7 and 12 from human obscurin-like protein 1 were solved. The two domains share 30% sequence identity and their structures are, as expected, rather similar. The new structures contribute to structural coverage of human cancer associated proteins. Read More

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http://link.springer.com/10.1007/s10969-014-9185-y
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http://dx.doi.org/10.1007/s10969-014-9185-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945113PMC
December 2014
9 Reads

Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network.

J Struct Funct Genomics 2014 Dec 19;15(4):201-7. Epub 2014 Jun 19.

Department of Chemistry, The State University of New York at Buffalo and Northeast Structural Genomics Consortium, Buffalo, NY, 14260, USA.

High-quality solution NMR structures of three homeodomains from human proteins ALX4, ZHX1 and CASP8AP2 were solved. These domains were chosen as targets of a biomedical theme project pursued by the Northeast Structural Genomics Consortium. This project focuses on increasing the structural coverage of human proteins associated with cancer. Read More

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http://link.springer.com/content/pdf/10.1007/s10969-014-9184
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http://link.springer.com/10.1007/s10969-014-9184-z
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http://dx.doi.org/10.1007/s10969-014-9184-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239167PMC
December 2014
8 Reads

Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin.

J Struct Funct Genomics 2014 Jun 17;15(2):63-71. Epub 2014 Jun 17.

Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India.

Malaria parasites inevitably develop drug resistance to anti-malarials over time. Hence the immediacy for discovering new chemical scaffolds to include in combination malaria drug therapy. The desirable attributes of new chemotherapeutic agents currently include activity against both liver and blood stage malaria parasites. Read More

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http://dx.doi.org/10.1007/s10969-014-9182-1DOI Listing
June 2014
2 Reads

The crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein CAE31940 from proteobacterium Bordetella bronchiseptica RB50, and evolutionary insight into the NMT1/THI5 family.

J Struct Funct Genomics 2014 Jun 8;15(2):73-81. Epub 2014 Jun 8.

Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.

We report a 2.0 Å structure of the CAE31940 protein, a proteobacterial NMT1/THI5-like domain-containing protein. We also discuss the primary and tertiary structure similarity with its homologs. Read More

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http://dx.doi.org/10.1007/s10969-014-9180-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115252PMC
June 2014
8 Reads

Crystal structure of tRNA m(1)A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine.

J Struct Funct Genomics 2014 Sep 4;15(3):173-80. Epub 2014 Jun 4.

RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.

The N (1)-methyladenosine residue at position 58 of tRNA is found in the three domains of life, and contributes to the stability of the three-dimensional L-shaped tRNA structure. In thermophilic bacteria, this modification is important for thermal adaptation, and is catalyzed by the tRNA m(1)A58 methyltransferase TrmI, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. We present the 2. Read More

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http://dx.doi.org/10.1007/s10969-014-9183-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125815PMC
September 2014
13 Reads

Substrate selectivity of bacterial monoacylglycerol lipase based on crystal structure.

J Struct Funct Genomics 2014 Sep 4;15(3):83-9. Epub 2014 Jun 4.

Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan,

Lipases, which are conserved from bacteria to mammals, catalyze the hydrolysis of acylglycerol to free fatty acids and glycerol. Monoacylglycerol lipase (MGL) specifically catalyzes the hydrolysis of monoacylglycerol. Although there have been numerous studies of the structure of lipases, there have been few studies of MGL. Read More

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http://dx.doi.org/10.1007/s10969-014-9181-2DOI Listing
September 2014
7 Reads

Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR.

J Struct Funct Genomics 2014 Sep 20;15(3):117-24. Epub 2014 Apr 20.

FEI Company, 5350 N.E. Dawson Creek Drive, Hillsboro, OR, 97124, USA,

Cryo-transmission electron microscopy (Cryo-TEM) and particularly single particle analysis is rapidly becoming the premier method for determining the three-dimensional structure of protein complexes, and viruses. In the last several years there have been dramatic technological improvements in Cryo-TEM, such as advancements in automation and use of improved detectors, as well as improved image processing techniques. While Cryo-TEM was once thought of as a low resolution structural technique, the method is currently capable of generating nearly atomic resolution structures on a routine basis. Read More

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http://dx.doi.org/10.1007/s10969-014-9179-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125826PMC
September 2014
5 Reads

Conformational landscapes for KMSKS loop in tyrosyl-tRNA synthetases.

J Struct Funct Genomics 2014 Jun 11;15(2):45-61. Epub 2014 Apr 11.

Structural and Computational Biology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India.

Protein synthesis requires accurate charging of tRNA with cognate amino acid as catalyzed by aminoacyl-tRNA synthetases. Crystal structures of tyrosyl-tRNA synthetase (YRSs) show remarkably diverse conformations for the KMSKS loop, hitherto classified as "open" and "closed". This traditional classification implied that the KMSKS loop adopts different conformations depending on occupancy of active site pocket. Read More

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http://dx.doi.org/10.1007/s10969-014-9178-xDOI Listing
June 2014
3 Reads

Crystal structure of the eukaryotic translation initiation factor 2A from Schizosaccharomyces pombe.

J Struct Funct Genomics 2014 Sep 26;15(3):125-30. Epub 2014 Feb 26.

Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

The eukaryotic translation initiation factor 2A (eIF2A) was identified as a factor that stimulates the binding of methionylated initiator tRNA (Met-tRNA i (Met) ) to the 40S ribosomal subunit, but its physiological role remains poorly defined. Recently, eIF2A was shown to be involved in unconventional translation initiation from CUG codons and in viral protein synthesis under stress conditions where eIF2 is inactivated. We determined the crystal structure of the WD-repeat domain of Schizosaccharomyces pombe eIF2A at 2. Read More

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http://dx.doi.org/10.1007/s10969-014-9177-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125824PMC
September 2014
31 Reads

Structural characterization of a hypothetical protein: a potential agent involved in trimethylamine metabolism in Catenulispora acidiphila.

J Struct Funct Genomics 2014 Mar 22;15(1):33-40. Epub 2014 Feb 22.

Department of Molecular Pharmacology and Biological Chemistry, Northwestern Feinberg School of Medicine, Chicago, IL, 60611, USA.

Catenulispora acidiphila is a newly identified lineage of actinomycetes that produces antimicrobial activities and represents a promising source of novel antibiotics and secondary metabolites. Among the discovered protein coding genes, 68 % were assigned a putative function, while the remaining 32 % are genes encoding "hypothetical" proteins. Caci_0382 is one of the "hypothetical" proteins that has very few homologs. Read More

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http://dx.doi.org/10.1007/s10969-014-9176-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3955178PMC
March 2014
9 Reads
2 Citations

Complete backbone and DENQ side chain NMR assignments in proteins from a single experiment: implications to structure-function studies.

J Struct Funct Genomics 2014 Mar 18;15(1):25-32. Epub 2014 Feb 18.

Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India.

Resonance assignment is the first and the most crucial step in all nuclear magnetic resonance (NMR) investigations on structure-function relationships in biological macromolecules. Often, the assignment exercise has to be repeated several times when specific interactions with ligands, substrates etc., have to be elucidated for understanding the functional mechanisms. Read More

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http://dx.doi.org/10.1007/s10969-014-9175-0DOI Listing
March 2014
8 Reads

Arabinose 5-phosphate covalently inhibits transaldolase.

J Struct Funct Genomics 2014 Mar 9;15(1):41-4. Epub 2014 Feb 9.

Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.

Arabinose 5-phosphate (A5P) is the aldopentose version of the ketohexose fructose 6-phosphate (F6P), having identical stereochemistry but lacking atoms corresponding to the 1-carbon and 1-hydroxyl. Despite structural similarity and conservation of the reactive portion of F6P, F6P acts as a substrate whereas A5P is reported to be an inhibitor of transaldolase. To address the lack of A5P reactivity we determined a crystal structure of the Francisella tularensis transaldolase in complex with A5P. Read More

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http://dx.doi.org/10.1007/s10969-014-9174-1DOI Listing
March 2014
3 Reads

Principal components analysis of protein sequence clusters.

J Struct Funct Genomics 2014 Mar 5;15(1):1-11. Epub 2014 Feb 5.

Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.

Sequence analysis of large protein families can produce sub-clusters even within the same family. In some cases, it is of interest to know precisely which amino acid position variations are most responsible for driving separation into sub-clusters. In large protein families composed of large proteins, it can be quite challenging to assign the relative importance to specific amino acid positions. Read More

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http://dx.doi.org/10.1007/s10969-014-9173-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982804PMC
March 2014
3 Reads

Structural genomics studies of human caries pathogen Streptococcus mutans.

J Struct Funct Genomics 2014 Sep 29;15(3):91-9. Epub 2014 Jan 29.

State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China,

Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. Read More

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http://dx.doi.org/10.1007/s10969-014-9172-3DOI Listing
September 2014
30 Reads

Carboxylic acids in crystallization of macromolecules: learning from successful crystallization experiments.

J Struct Funct Genomics 2014 Mar 23;15(1):13-24. Epub 2014 Jan 23.

Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA.

The production of macromolecular crystals suitable for structural analysis is one of the most important and limiting steps in the structure determination process. Often, preliminary crystallization trials are performed using hundreds of empirically selected conditions. Carboxylic acids and/or their salts are one of the most popular components of these empirically derived crystallization conditions. Read More

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http://dx.doi.org/10.1007/s10969-014-9171-4DOI Listing
March 2014
4 Reads

Evaluation of intensity and pulse width of different moderators for designing a new diffractometer for protein crystals with large unit cells in J-PARC/MLF.

J Struct Funct Genomics 2014 Sep 18;15(3):131-5. Epub 2014 Jan 18.

Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki, 319-1195, Japan,

We plan to design a high-resolution biomacromolecule neutron time-of-flight diffractometer, which allows us to collect data from crystals with unit cells above 250 Å, in the materials and life science experimental facility at the Japan Proton Accelerator Research Complex. This new diffractometer can be used for a detailed analysis of large proteins such as membrane proteins and supermolecular complex. A quantitative comparison of the intensity and pulse width of a decoupled moderator (DM) against a coupled moderator (CM) considering the pulse width time resolution indicated that the DM satisfies the criteria for our diffractometer rather than the CM. Read More

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http://link.springer.com/10.1007/s10969-014-9170-5
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http://dx.doi.org/10.1007/s10969-014-9170-5DOI Listing
September 2014
6 Reads

Structural insights of post-translational modification sites in the proteome of Thermus thermophilus.

J Struct Funct Genomics 2014 Sep 10;15(3):137-51. Epub 2014 Jan 10.

Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan,

Phosphorylation and acetylation are the most prevalent post-translational modifications (PTMs) detected in not only eukaryotes but also bacteria. We performed phosphoproteome and acetylome analyses of proteins from an extremely thermophilic eubacterium Thermus thermophilus HB8, and identified numerous phosphorylation and acetylation sites. To facilitate the elucidation of the structural aspects of these PTM events, we mapped the PTM sites on the known tertiary structures for the respective proteins and their homologs. Read More

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http://dx.doi.org/10.1007/s10969-013-9169-3DOI Listing
September 2014
13 Reads

Conformational variation of the translocon enhancing chaperone SecDF.

J Struct Funct Genomics 2014 Sep 25;15(3):107-15. Epub 2013 Dec 25.

BRI and ITRI, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8568, Japan,

The Sec translocon facilitates transportation of newly synthesized polypeptides from the cytoplasm to the lumen/periplasm across the phospholipid membrane. Although the polypeptide-conducting machinery is formed by the SecYEG-SecA complex in bacteria, its transportation efficiency is markedly enhanced by SecDF. A previous study suggested that SecDF assumes at least two conformations differing by a 120° rotation in the spatial orientation of the P1 head subdomain to the rigid base, and that the conformational dynamics plays a critical role in polypeptide translocation. Read More

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http://dx.doi.org/10.1007/s10969-013-9168-4DOI Listing
September 2014
9 Reads

Carbohydrate recognition by rotaviruses.

J Struct Funct Genomics 2014 Sep 19;15(3):101-6. Epub 2013 Nov 19.

Institute for Glycomics, Griffith University, Gold Coast campus, QLD, 4222, Australia,

Rotaviruses are a global health concern causing severe childhood diarrhea. Though the mechanisms mediating rotavirus cell entry require further characterisation, it is acknowledged that an essential and critical step in rotavirus infection is the virus cell attachment via initial recognition of cell surface carbohydrate-containing receptors. This review summarises the current knowledge about recognition of glycan receptors by rotaviruses. Read More

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http://dx.doi.org/10.1007/s10969-013-9167-5DOI Listing
September 2014
3 Reads

The crystal structure of sterol carrier protein 2 from Yarrowia lipolytica and the evolutionary conservation of a large, non-specific lipid-binding cavity.

J Struct Funct Genomics 2013 Dec 17;14(4):145-53. Epub 2013 Nov 17.

Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina.

Sterol carrier protein 2 (SCP2), a small intracellular domain present in all forms of life, binds with high affinity a broad spectrum of lipids. Due to its involvement in the metabolism of long-chain fatty acids and cholesterol uptake, it has been the focus of intense research in mammals and insects; much less characterized are SCP2 from other eukaryotic cells and microorganisms. We report here the X-ray structure of Yarrowia lipolytica SCP2 (YLSCP2) at 2. Read More

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http://dx.doi.org/10.1007/s10969-013-9166-6DOI Listing
December 2013
7 Reads

New LIC vectors for production of proteins from genes containing rare codons.

J Struct Funct Genomics 2013 Dec 22;14(4):135-44. Epub 2013 Sep 22.

Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL, 60439, USA.

In the effort to produce proteins coded by diverse genomes, structural genomics projects often must express genes containing codons that are rare in the production strain. To address this problem, genes expressing tRNAs corresponding to those codons are typically coexpressed from a second plasmid in the host strain, or from genes incorporated into production plasmids. Here we describe the modification of a series of LIC pMCSG vectors currently used in the high-throughput (HTP) production of proteins to include crucial tRNA genes covering rare codons for Arg (AGG/AGA) and Ile (AUA). Read More

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http://dx.doi.org/10.1007/s10969-013-9163-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933008PMC
December 2013
10 Reads

Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct α-helical architecture and provides first structural representative of protein domain family PF14203.

J Struct Funct Genomics 2013 Dec 19;14(4):155-60. Epub 2013 Sep 19.

Department of Chemistry, The State University of New York at Buffalo and Northeast Structural Genomics Consortium, Buffalo, NY, 14260, USA.

A high-quality structure of the 68-residue protein CD1104B from Clostridium difficile strain 630 exhibits a distinct all α-helical fold. The structure presented here is the first representative of bacterial protein domain family PF14203 (currently 180 members) of unknown function (DUF4319) and reveals that the side-chains of the only two strictly conserved residues (Glu 8 and Lys 48) form a salt bridge. Moreover, these two residues are located in the vicinity of the largest surface cleft which is predicted to contribute to a surface area involved in protein-protein interactions. Read More

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http://dx.doi.org/10.1007/s10969-013-9164-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844015PMC
December 2013
10 Reads