As a protein originally found in plant pathogenic bacteria, transcription activator-like effectors (TALEs) can be fused with the cleaving domain of restriction endonuclease (For example Fok I) to form artificial nucleases named TALENs. These proteins are dependent on variable numbers of tandem Repeats of TALEs to recognize and bind DNA sequences. Each of these repeats consists of a set of approximately 34 amino acids, composed of about 32 conserved amino acids and 2 highly variable amino acids called repeat variant di-residues (RVDs). RVDs distinguish one TALE from another and can make TALEs have a simple cipher for the one-to-one recognition for proteins and DNA bases. Based on this, in theory, artificially constructed TALENs could recognize and break DNA sites specifically and arbitrarily to perform gene knockout, insertion or modification. We reviewed the development of this technology in multi-level and multi species, and its advantages and disadvantages compared with ZFNs and CRISPR/Cas technology. We also address its special advantages in industrial microbe breeding, vector construction, targeting precision, high efficiency of editing and biological safety.
Amino Acid Motifs ; Biotechnology ; DNA ; chemistry ; Endonucleases ; chemistry ; Tandem Repeat Sequences ; Trans-Activators ; chemistry

OBJECTIVETo evaluate the impact of surface modification on the DNA-binding ability of nano-hydroxyapatite (nHA).

METHODSChemical co-precipitation-hydrothermal synthesis was utilized to prepare the nHA particles, and polyethylenimine (PEI) was used for surface modification of the nHA. Transmission electron microscopic (TEM) observation and zeta potential detection of the nHA were carried out before and after surface modification. The abilities of the nanoparticles, at different pH values and different concentrations, for DNA-binding and DNA protection against nuclease digestion were assessed before and after surface modification by electrophoresis.

RESULTSTEM observation showed a short rod-like morphology of PEI-modified nHA with uniform particle size and good dispersion; the nHA without the modification tended to aggregate with poor dispersion. With a positive zeta potential, the PEI-modified nHA showed an obviously enhanced ability of DNA binding at different pH values and concentrations, with strong capacity to protect the DNA against Dnase I digestion. At the concentration of 250 µg/ml and a pH value of 7.0, the nHA-PEI showed an optimal efficiency of DNA-binding and DNA protection.

CONCLUSIONnHA with surface modification by PEI can serve as an effective vector for DNA binding and transfer.

Amino Acid Motifs ; DNA ; chemistry ; Durapatite ; chemistry ; Gene Transfer Techniques ; Genetic Vectors ; Nanoparticles ; chemistry ; Polyethyleneimine ; chemistry

Amino Acid Motifs ; DEAD-box RNA Helicases ; chemistry ; Humans ; Protein Domains ; Structure-Activity Relationship

The WD40 domain exhibits a β-propeller architecture, often comprising seven blades. The WD40 domain is one of the most abundant domains and also among the top interacting domains in eukaryotic genomes. In this review, we will discuss the identification, definition and architecture of the WD40 domains. WD40 domain proteins are involved in a large variety of cellular processes, in which WD40 domains function as a protein-protein or protein-DNA interaction platform. WD40 domain mediates molecular recognition events mainly through the smaller top surface, but also through the bottom surface and sides. So far, no WD40 domain has been found to display enzymatic activity. We will also discuss the different binding modes exhibited by the large versatile family of WD40 domain proteins. In the last part of this review, we will discuss how post-translational modifications are recognized by WD40 domain proteins.
Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Humans ; Molecular Sequence Data ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Proteins ; chemistry ; metabolism ; Repetitive Sequences, Amino Acid

Types of cofactor independency for newly found oxidoreductases sequences are usually determined by experimental analysis. These experimental methods are both time-consuming and costly. With the explosion of oxidoreductases sequences entering into the databanks, it is highly desirable to explore the feasibility of selectively classifying newly found oxidoreductases into their respective cofactor independency classes by means of an automated method. In this study, we proposed a modified Chou's pseudo-amino acid composition method to extract features from sequences and the k-nearest neighbor was used as the classifier, and the results were very encouraging. When lambda = 48, w = 0.1, the areas under the ROC curve of k-nearest neighbor in 10-fold cross-validation was 0.9536; and the success rate was 92.0%, which was 3.5% higher than that of pseudo-amino acid composition. It was also better than all the other 7 feature extraction methods. Our results showed that predicting the cofactors of oxidoreductases was feasible and the modified pseudo-amino acid composition method may be a useful method for extracting features from protein sequences.
Amino Acid Motifs ; Amino Acids ; analysis ; Coenzymes ; chemistry ; Computational Biology ; Models, Chemical ; Oxidoreductases ; chemistry ; Predictive Value of Tests

Phospholipase D (PLD) catalyzes the hydrolysis of phosphatidylcholine to generate the lipid second messenger, phosphatidic acid. PLD is localized in most cellular organelles, where it is likely to play different roles in signal transduction. PLD1 is primarily localized in vesicular structures such as endosomes, lysosomes and autophagosomes. However, the factors defining its localization are less clear. In this study, we found that four hydrophobic residues present in the N-terminal HKD catalytic motif of PLD1, which is involved in intramolecular association, are responsible for vesicular localization. Site-directed mutagenesis of the residues dramatically disrupted vesicular localization of PLD1. Interestingly, the hydrophobic residues of PLD1 are also involved in the interruption of its nuclear localization. Mutation of the residues increased the association of PLD1 with importin-beta, which is known to mediate nuclear importation, and induced the localization of PLD1 from vesicles into the nucleus. Taken together, these data suggest that the hydrophobic amino acids involved in the interdomain association of PLD1 are required for vesicular localization and disturbance of its nuclear localization.
Amino Acid Motifs ; Amino Acid Sequence ; Amino Acids/chemistry ; Cell Nucleus/*enzymology ; Endosomes/enzymology ; HEK293 Cells ; Humans ; Hydrophobic and Hydrophilic Interactions ; Lysosomes/enzymology ; Phagosomes/enzymology ; Phospholipase D/chemistry/*metabolism ; Protein Interaction Domains and Motifs ; Protein Transport ; Transport Vesicles/*enzymology

Sequence comparison of the RNA-dependent RNA polymerase of human caliciviruses (HuCVs) from Korean children with gastroenteritis revealed significant genetic variation among them. cDNA clones were produced from the HuCVs collected from pediatric population during a period of 1987-1994. The application of reverse transcription-polymerase chain reaction (RT-PCR) using primers directed to the RNA-dependent RNA polymerase region within ORF1 of Norwalk virus (NV) showed that 13.7% of HuCVs yielded PCR products of similar size to the NV prototype, NV8Flla/68/US, with exceptions of HuCV185/87/Korea and HuCV1115/90/Korea. Computer analyses showed that the PCR products had a continuous protein encoding frame on the positive strand, and contained GLPSG and YGDD amino acid motifs at the predicted distance from primers. Alignment of the amino acid sequences of HuCVs with previously published sequences for Snow Mountain agent (SMA), NV, and Sapporo/82/Japan indicated that these strains can be divided into four major genogroups. There were 10 (45%) SMA-like CVs, one (4.5%) NV-like HuCVs, two (9%) Sapporo-like HuCVs, and nine (41%) unidentified HuCVs. This fourth genogroup should be investigated further. HuCV185/87/Korea and HuCV1115/90/Korea, Sapporo-like CVs, were genetically distinct from previously characterized HuCVs and more closely related to known animal CVs. One of the animal CV-like strain, HuCV185/87/Korea, showed nucleotide and amino acid homology of only 67% and 73% with the prototype Sapporo/82/Japan. Further characterization of animal and human CV genomes and studies of possible cross-transmission of CVs from animals to humans are likely to be beneficial in understanding the epidemiology of HuCVs.
Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Child ; Clone Cells ; DNA, Complementary ; Epidemiology ; Gastroenteritis ; Genetic Variation ; Genome ; Genotype ; Humans* ; Korea* ; Norwalk virus ; Polymerase Chain Reaction ; RNA Replicase ; Snow

Knowledge of the evolution of pathogens is of great medical and biological significance to the prevention, diagnosis, and therapy of infectious diseases. In order to understand the origin and evolution of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus), we collected complete genome sequences of all viruses available in GenBank, and made comparative analyses with the SARS-CoV. Genomic signature analysis demonstrates that the coronaviruses all take the TGTT as their richest tetranucleotide except the SARS-CoV. A detailed analysis of the forty-two complete SARS-CoV genome sequences revealed the existence of two distinct genotypes, and showed that these isolates could be classified into four groups. Our manual analysis of the BLASTN results demonstrates that the HE (hemagglutinin-esterase) gene exists in the SARS-CoV, and many mutations made it unfamiliar to us.
Amino Acid Motifs ; Amino Acid Substitution ; Base Composition ; Codon ; genetics ; Computational Biology ; DNA Mutational Analysis ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome, Viral ; Phylogeny ; SARS Virus ; genetics

Scansite is a short linear motif-based scanning approach established in the latest two years. It's accessible over the World Wide Web and can be used to identify sequence motifs likely to be phosphorylated by specific protein kinases or likely to bind to specific protein domains such as 14-3-3, SH2 and SH3 domains. The usage and function of the potent approach were reviewed and compared with previously established tools for phosphorylation prediction. The facing problems and application outlook of Scansite in prediction of cell signaling networks within proteomes were also presented.
Amino Acid Motifs ; Amino Acid Sequence ; Databases, Factual ; Internet ; Molecular Sequence Data ; Phosphorylation ; Protein Structure, Tertiary ; Proteins ; chemistry ; metabolism ; Signal Transduction

Integrins are allosteric cell adhesion receptors that cycle from a low to a high affinity ligand binding state, a complex process of receptor activation that is of particular importance in blood cells such as platelets or leukocytes. Here we highlight recent progress in the understanding of the molecular pathways that regulate integrin activation in platelets and leukocytes, with a special focus on the structural changes in platelet integrin αIIbβ3 brought about by key intracellular proteins, namely talin and kindlins, that are of crucial importance in the regulation of integrin function. Evidence that the small GTPase Rap1 and its guanine exchange factor CalDAG-GEF1, together with RIAM, a Rap1GTP adaptor protein, promote the interaction of talin with the integrin β subunit, has greatly contributed to fill the gap in our understanding of the signaling pathway from G-coupled agonist receptors and their phospholipase C-dependant second messengers, to integrin activation. Studies of patients with the rare blood cell disorder LAD-III have contributed to the identification of kindlins as new co-regulators of the talin-dependent integrin activation process in platelets and leukocytes, underlining the relevance for the in-depth investigation of patients with rare genetic blood cell disorders.
Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Adhesion ; Cytoskeleton ; metabolism ; Humans ; Intracellular Signaling Peptides and Proteins ; metabolism ; Models, Molecular ; Molecular Sequence Data ; Platelet Glycoprotein GPIIb-IIIa Complex ; metabolism ; Protein Interaction Domains and Motifs ; Recombinant Proteins ; metabolism ; Sequence Alignment ; Talin ; metabolism