• Humans
• Gene Transfer Techniques
• Genetic Therapy
• Nucleic Acids/genetics
• Pandemics
• Animals
• Mammals

• Endoribonuclease
• RNA digestion.
• RNase
• hTRIR
• methylated RNA
• ribonuclease

• Humans
• Methylation
• Ribonucleases/metabolism
• Ribonucleases/genetics
• RNA/metabolism
• RNA/genetics

• 2022BCE054 Department of Science and Technology, Hubei Provincial People's Government

• RNA integrity
• mRNA
• polysome profiling
• ribosome
• translation

• A29252 Cancer Research UK
• A25233 Cancer Research UK
• A27603 Cancer Research UK
• A29996 Cancer Research UK
• C48702 Cancer Research UK
• 30062 Cancer Research UK
• 29252 Cancer Research UK
• 24388 Cancer Research UK

• Blood coagulation
• endoribonuclease
• extracellular RNA
• inflammation
• pancreatic-type ribonuclease
• stress

• Bone marrow failures
• Cancer
• Deadenylase
• PARN
• Ribonuclease
• Telomere dysfunction
• mRNA degradation pathways

In this review, we summarise the evidence for a role of the ribonuclease angiogenin in the pathophysiology of neurodegenerative disorders, with a specific focus on Parkinson’s disease (PD). Angiogenin is a stress-induced, secreted ribonuclease with both nuclear and cytosolic activities. Loss-of-function mutations in the angiogenin gene (ANG) have been initially discovered in familial cases of amyotrophic lateral sclerosis (ALS), however, variants in ANG have subsequently been identified in PD and Alzheimer’s disease. Delivery of angiogenin protein reduces neurodegeneration and delays disease progression in in vitro and in vivo models of ALS and in vitro models of PD. In the nucleus, angiogenin promotes ribosomal RNA transcription. Under stress conditions, angiogenin also translocates to the cytosol where it cleaves non-coding RNA into RNA fragments, in particular transfer RNAs (tRNAs). Stress-induced tRNA fragments have been proposed to have multiple cellular functions, including inhibition of ribosome biogenesis, inhibition of protein translation and inhibition of apoptosis. We will discuss recent evidence of tRNA fragment accumulation in PD, as well as their potential neuroprotective activities.

• angiogenin
• neuroprotection
• ribonuclease
• ribosomal RNA (rRNA)
• tRNA-derived fragments (tRFs)
• transfer RNA (tRNA)

• RNase oligomers
• antitumor activity
• cytotoxicity
• domain swapping
• ribonucleases

• Antineoplastic Agents/pharmacology
• Drug Design
• Endocytosis
• Protein Domains
• Protein Multimerization
• RNA/metabolism
• Ribonucleases/antagonists & inhibitors
• Ribonucleases/chemistry
• Ribonucleases/metabolism

• Angiogenin
• Extracellular RNA
• Receptor tyrosine kinase
• Ribonuclease
• Ribosomal RNA
• Transfer RNA

• CD30
• ImmunoRNase
• RNases 1 to 8
• antibody-based therapy
• human RNase A superfamily
• human antibody
• lymphoma

The Ribonuclease A Superfamily is composed of cationic peptides that are secreted by immune cells and epithelial tissues. Although their physiological roles are unclear, several members of the vertebrate Ribonuclease A Superfamily demonstrate antimicrobial and immune modulation activities. The objective of this review is to provide an overview of the published literature on the Ribonuclease A Superfamily with an emphasis on each peptide’s regulation, antimicrobial properties, and immunomodulatory functions. As additional insights emerge regarding the mechanisms in which these ribonucleases eradicate invading pathogens and modulate immune function, these ribonucleases may have the potential to be developed as a novel class of therapeutics for some human diseases.

• infection
• inflammation
• innate immunity
• ribonuclease A superfamily
• ribonucleases

• Angiogenin
• Cancer
• Epidermal growth factor receptor
• Ligand
• Receptor tyrosine kinase
• Ribonuclease
• Serum biomarker
• Targeted therapy
• Tyrosine kinase inhibitor

• Humans
• Ligands
• Multigene Family/genetics
• Multigene Family/physiology
• Protein Binding
• Receptor Protein-Tyrosine Kinases/genetics
• Receptor Protein-Tyrosine Kinases/metabolism
• Ribonucleases/genetics
• Ribonucleases/metabolism

• CA211615 NIH HHS
• P30 CA016672 NCI NIH HHS
• CA201777 NIH HHS
• CA016672 NIH HHS
• U01 CA201777 NCI NIH HHS
• CA186892 NIH HHS
• R01 CA211615 NCI NIH HHS
• T32 CA186892 NCI NIH HHS
• National Institutes of Health
• Breast Cancer Research Foundation
• Ministry of Health and Welfare

The ribonuclease A superfamily is a vertebrate-specific family of proteins that encompasses eight functional members in humans. The proteins are secreted by diverse innate immune cells, from blood cells to epithelial cells and their levels in our body fluids correlate with infection and inflammation processes. Recent studies ascribe a prominent role to secretory RNases in the extracellular space. Extracellular RNases endowed with immuno-modulatory and antimicrobial properties can participate in a wide variety of host defense tasks, from performing cellular housekeeping to maintaining body fluid sterility. Their expression and secretion are induced in response to a variety of injury stimuli. The secreted proteins can target damaged cells and facilitate their removal from the focus of infection or inflammation. Following tissue damage, RNases can participate in clearing RNA from cellular debris or work as signaling molecules to regulate the host response and contribute to tissue remodeling and repair. We provide here an overall perspective on the current knowledge of human RNases’ biological properties and their role in health and disease. The review also includes a brief description of other vertebrate family members and unrelated extracellular RNases that share common mechanisms of action. A better knowledge of RNase mechanism of actions and an understanding of their physiological roles should facilitate the development of novel therapeutics.

• RNA
• extracellular
• infection
• inflammation
• innate immunity
• ribonucleases

Angiogenin (ANG), a member of the RNase superfamily (also known as RNase 5) has neurotrophic, neuroprotective and angiogenic activities. Recently it has also been shown to be important in stem cell homeostasis. Mutations in ANG are associated with neurodegenerative diseases such as Amyotrophic Lateral Sclerosis (ALS) and Fronto-temporal dementia (FTD). ANG is a secreted protein which is taken up by cells and translocated to the nucleus. However, the import pathway/s through which ANG is taken up is/are still largely unclear. We have characterised the uptake of ANG in neuronal, astrocytic and microglial cell lines as well as primary neurons and astrocytes using pharmacological agents as well as dominant negative dynamin and Rab5 to perturb uptake and intracellular trafficking. We find that uptake of ANG is largely clathrin/dynamin independent and microtubule depolymerisation has a marginal effect. Perturbation of membrane ruffling and macropinocytosis significantly inhibited ANG uptake suggesting an uptake mechanism similar to RNase A. Our findings shed light on why mutations which do not overtly affect RNase activity but cause impaired localization are associated with neurodegenerative disease.

• Amyotrophic Lateral Sclerosis/metabolism
• Animals
• Astrocytes/drug effects
• Astrocytes/metabolism
• Cell Line
• Clathrin/metabolism
• Dynamins/metabolism
• Humans
• Membrane Microdomains/drug effects
• Membrane Microdomains/metabolism
• Mice
• Microglia/drug effects
• Microglia/metabolism
• Neurons/drug effects
• Neurons/metabolism
• Ribonuclease, Pancreatic/pharmacokinetics

We describe the first human RNase 6 crystal structure in complex with sulfate anions. Kinetic analysis, site-directed mutagenesis and molecular dynamics simulations identified novel substrate recognition and cleavage sites.

Human RNase 6 is a cationic secreted protein that belongs to the RNase A superfamily. Its expression is induced in neutrophils and monocytes upon bacterial infection, suggesting a role in host defence. We present here the crystal structure of RNase 6 obtained at 1.72 Å (1 Å=0.1 nm) resolution, which is the first report for the protein 3D structure and thereby setting the basis for functional studies. The structure shows an overall kidney-shaped globular fold shared with the other known family members. Three sulfate anions bound to RNase 6 were found, interacting with residues at the main active site (His¹⁵, His¹²² and Gln¹⁴) and cationic surface-exposed residues (His³⁶, His³⁹, Arg⁶⁶ and His⁶⁷). Kinetic characterization, together with prediction of protein–nucleotide complexes by molecular dynamics, was applied to analyse the RNase 6 substrate nitrogenous base and phosphate selectivity. Our results reveal that, although RNase 6 is a moderate catalyst in comparison with the pancreatic RNase type, its structure includes lineage-specific features that facilitate its activity towards polymeric nucleotide substrates. In particular, enzyme interactions at the substrate 5′ end can provide an endonuclease-type cleavage pattern. Interestingly, the RNase 6 crystal structure revealed a novel secondary active site conformed by the His³⁶–His³⁹ dyad that facilitates the polynucleotide substrate catalysis.

• RNase A superfamily
• RNase k6
• kinetic characterization
• molecular dynamics
• protein crystallography
• sulfate anion

• Eosinophil
• Evolution
• Macrophage
• Ribonuclease
• Toll-like receptor (TLR)

• Amino Acid Sequence
• Animals
• Base Sequence
• DNA Primers
• Eosinophil Cationic Protein/chemistry
• Eosinophil Cationic Protein/genetics
• Eosinophil Cationic Protein/metabolism
• Immunity, Innate
• Macrophages/immunology
• Macrophages/metabolism
• Mice
• Mice, Inbred BALB C
• Mice, Inbred C57BL
• Molecular Sequence Data
• Phylogeny
• Sequence Homology, Amino Acid
• Spleen/cytology

• Z01 AI000746 Intramural NIH HHS
• Z01 AI000942 Intramural NIH HHS

• orthologues
• ribonucleases
• rnase a
• evolutionary conservation
• rna

• Amino Acid Sequence
• Animals
• Catalytic Domain
• Evolution, Molecular
• Humans
• Models, Molecular
• Molecular Sequence Data
• Nuclear Magnetic Resonance, Biomolecular
• Ribonucleases/chemistry
• Ribonucleases/metabolism

• R01 GM105978 NIGMS NIH HHS

The ribonuclease (RNase) A superfamily is a vertebrate-specific gene family. Because of a massive expansion that occurred during the early mammalian evolution, extant mammals in general have much more RNase genes than nonmammalian vertebrates. Mammalian RNases have been associated with diverse physiological functions including digestion, cytotoxicity, angiogenesis, male reproduction, and host defense. However, it is still uncertain when their expansion occurred and how a wide array of functions arose during their evolution. To answer these questions, we generate a compendium of all RNase genes identified in 20 complete mammalian genomes including the platypus, Ornithorhynchus anatinus. Using this, we delineate 13 ancient RNase gene lineages that arose before the divergence between the monotreme and the other mammals (∼220 Ma). These 13 ancient gene lineages are differentially retained in the 20 mammals, and the rate of protein sequence evolution is highly variable among them, which suggest that they have undergone extensive functional diversification. In addition, we identify 22 episodes of recent expansion of RNase genes, many of which have signatures of adaptive functional differentiation. Exemplifying this, bursts of gene duplication occurred for the RNase1, RNase4, and RNase5 genes of the little brown bat (Myotis lucifugus), which might have contributed to the species’ effective defense against heavier pathogen loads caused by its communal roosting behavior. Our study illustrates how host-defense systems can generate new functions efficiently by employing a multigene family, which is crucial for a host organism to adapt to its ever-changing pathogen environment.

• adaptive evolution
• angiogenin
• gene duplication
• gene sorting
• host defense
• positive selection

Human ribonucleases A (hRNaseA) superfamily consists of thirteen members with high-structure similarities but exhibits divergent physiological functions other than RNase activity. Evolution of hRNaseA superfamily has gained novel functions which may be preserved in a unique region or domain to account for additional molecular interactions. hRNase3 has multiple functions including ribonucleolytic, heparan sulfate (HS) binding, cellular binding, endocytic, lipid destabilization, cytotoxic, and antimicrobial activities. In this study, three putative multifunctional regions, ³⁴RWRCK³⁸ (HBR1), ⁷⁵RSRFR⁷⁹ (HBR2), and ¹⁰¹RPGRR¹⁰⁵ (HBR3), of hRNase3 have been identified employing in silico sequence analysis and validated employing in vitro activity assays. A heparin binding peptide containing HBR1 is characterized to act as a key element associated with HS binding, cellular binding, and lipid binding activities. In this study, we provide novel insights to identify functional regions of hRNase3 that may have implications for all hRNaseA superfamily members.

• Amino Acids/genetics
• Binding Sites
• Evolution, Molecular
• Fungal Proteins/genetics
• Gene Dosage/drug effects
• Gene Duplication/drug effects
• Genes, Duplicate/genetics
• Glucosides/pharmacology
• Hydrolysis/drug effects
• Maltose/metabolism
• Models, Molecular
• Multigene Family/genetics
• Saccharomyces cerevisiae/drug effects
• Saccharomyces cerevisiae/enzymology
• Saccharomyces cerevisiae/genetics
• Saccharomyces cerevisiae/growth & development
• Selection, Genetic
• Substrate Specificity/drug effects
• alpha-Glucosidases/genetics

AIM: To study the association between inflammatory bowel disease (IBD) and genetic variations in eosinophil protein X (EPX) and eosinophil cationic protein (ECP).

METHODS: DNA was extracted from ethylene diamine tetraacetic acid blood of 587 patients with Crohn’s disease (CD), 592 with ulcerative colitis (UC) and 300 healthy subjects. The EPX405 (G > C, rs2013109), ECP434 (G > C, rs2073342) and ECP562 (G > C, rs2233860) gene polymorphisms were analysed, by the 5’-nuclease allelic discrimination assay. For determination of intracellular content of EPX and ECP in granulocytes, 39 blood samples was collected and extracted with a buffer containing cetyltrimethylammonium bromide. The intracellular content of EPX was analysed using an enzyme-linked immunosorbent assay. The intracellular content of ECP was analysed with the UniCAP^® system as described by the manufacturer. Statistical tests for calculations of results were χ² test, Fisher’s exact test, ANOVA, Student-Newman-Keuls test, and Kaplan-Meier survival curve with Log-rank test for trend, the probability values of P < 0.05 were considered statistically significant.

RESULTS: The genotype frequency for males with UC and with an age of disease onset of ≥ 45 years (n = 57) was for ECP434 and ECP562, GG = 37%, GC = 60%, CC = 4% and GG = 51%, GC = 49%, CC = 0% respectively. This was significantly different from the healthy subject’s genotype frequencies of ECP434 (GG = 57%, GC = 38%, CC = 5%; P = 0.010) and ECP562 (GG = 68%, GC = 29%,CC = 3%; P = 0.009). The genotype frequencies for females, with an age of disease onset of ≥ 45 years with CD (n = 62), was for the ECP434 and ECP562 genotypes GG = 37%, GC = 52%, CC = 11% and GG = 48%, GC = 47% and CC = 5% respectively. This was also statistically different from healthy controls for both ECP434 (P = 0.010) and ECP562 (P = 0.013). The intracellular protein concentration of EPX and ECP was calculated in μg/10⁶ eosinophils and then correlated to the EPX 405 genotypes. The protein content of EPX was highest in the patients with the CC genotype of EPX405 (GG = 4.65, GC = 5.93, and CC = 6.57) and for ECP in the patients with the GG genotype of EPX405 (GG = 2.70, GC = 2.47 and CC = 1.90). ANOVA test demonstrated a difference in intracellular protein content for EPX (P = 0.009) and ECP (P = 0.022). The age of disease onset was linked to haplotypes of the EPX405, ECP434 and ECP562 genotypes. Kaplan Maier curve showed a difference between haplotype distributions for the females with CD (P = 0.003). The highest age of disease onset was seen in females with the EPX405CC, ECP434GC, ECP562CC haplotype (34 years) and the lowest in females with the EPX405GC, ECP434GC, ECP562GG haplotype (21 years). For males with UC there was also a difference between the highest and lowest age of the disease onset (EPX405CC, ECP434CC, ECP562CC, mean 24 years vs EPX405GC, ECP434GC, ECP562GG, mean 34 years, P = 0.0009). The relative risk for UC patients with ECP434 or ECP562-GC/CC genotypes to develop dysplasia/cancer was 2.5 (95%CI: 1.2-5.4, P = 0.01) and 2.5 (95%CI: 1.1-5.4, P = 0.02) respectively, compared to patients carrying the GG-genotypes.

CONCLUSION: Polymorphisms of EPX and ECP are associated to IBD in an age and gender dependent manner, suggesting an essential role of eosinophils in the pathophysiology of IBD.

• Eosinophil derived neurotoxin
• RNase 2
• RNase 3
• Single nucleotide polymorphism
• Inflammation bowel disease
• Crohn’s disease
• Ulcerative colitis

• ribonuclease
• polymorphism

• Alleles
• Amino Acid Sequence
• Animals
• COS Cells
• Chlorocebus aethiops
• Genetic Variation
• Humans
• Molecular Sequence Data
• Polymorphism, Single Nucleotide
• Ribonucleases/genetics
• Sequence Analysis, DNA
• Transcription Initiation Site
• Transfection

• Z01-AI00942 NIAID NIH HHS

• Algorithms
• Amino Acid Motifs
• Amino Acid Sequence
• Animals
• Antibodies, Monoclonal
• Antibody Specificity
• Cattle
• Computational Biology
• Epitope Mapping/statistics & numerical data
• Humans
• Mice
• Models, Molecular
• Molecular Sequence Data
• Peptides/chemistry
• Peptides/genetics
• Peptides/immunology
• Ribonuclease, Pancreatic/chemistry
• Ribonuclease, Pancreatic/genetics
• Ribonuclease, Pancreatic/immunology
• Sequence Analysis, Protein/statistics & numerical data

Mammalian spermatozoa become fully motile and fertile during transit through the luminal fluid of the epididymis. At least 200 proteins are present in the epididymal lumen, but the potential roles of these luminal proteins in male fertility are unknown. Investigation of the function of these proteins will elucidate the mechanism of sperm maturation, and also provide new drug targets for male contraception. We cloned RNase9 from a human epididymis cDNA library for characterization and analysis of its functions.

It was predicted that human RNase9 gene was located on chromosome 14q11.2 and encoded a 205 amino acids protein with a signal peptide of 26 amino acids at the N-terminus. The protein had eight conserved cysteine residues characteristic of the RNase A family members and several potential post-translational modification sites.

At the transcriptional level, RNase9 was expressed in a wide variety of tissues, and the expression was higher in men than in boys. RNase9 was localized to the post-equatorial region of the sperms' head. Immunofluorescence staining showed that RNase9 protein was present mostly in the epithelium of the epididymal tubule. Recombinant RNase9 had no ribonuclease activity. In addition, RNase9 had no detectable effect on sperm motility and fertilization as demonstrated by blocking spermatozoa with anti-RNase9 polyclonal serum.

RNase9 is expressed in a wide variety of tissues. It is located on the post-equatorial region of the sperm head and the epithelium of epididymal tubule. Although RNase9 belongs to the RNase A family, it has no ribonuclease activity.

Human eosinophil-derived neurotoxin (edn) and eosinophil cationic protein (ecp) are members of a subfamily of primate ribonuclease (rnase) genes. Although they are generated by gene duplication event, distinct edn and ecp expression profile in various tissues have been reported.

In this study, we obtained the upstream promoter sequences of several representative primate eosinophil rnases. Bioinformatic analysis revealed the presence of a shared 34-nucleotide (nt) sequence stretch located at -81 to -48 in all edn promoters and macaque ecp promoter. Such a unique sequence motif constituted a region essential for transactivation of human edn in hepatocellular carcinoma cells. Gel electrophoretic mobility shift assay, transient transfection and scanning mutagenesis experiments allowed us to identify binding sites for two transcription factors, Myc-associated zinc finger protein (MAZ) and SV-40 protein-1 (Sp1), within the 34-nt segment. Subsequent in vitro and in vivo binding assays demonstrated a direct molecular interaction between this 34-nt region and MAZ and Sp1. Interestingly, overexpression of MAZ and Sp1 respectively repressed and enhanced edn promoter activity. The regulatory transactivation motif was mapped to the evolutionarily conserved -74/-65 region of the edn promoter, which was guanidine-rich and critical for recognition by both transcription factors.

Our results provide the first direct evidence that MAZ and Sp1 play important roles on the transcriptional activation of the human edn promoter through specific binding to a 34-nt segment present in representative primate eosinophil rnase promoters.

A novel protein family, designated hereafter as RNase κ (kappa) family, has been recently introduced with the characterization of the specific Cc RNase, isolated from the insect Ceratitis capitata. The human ortholog of this family consists of 98 amino acids and shares > 98% identity with its mammalian counterparts. This RNase is encoded by a single-copy gene found to be expressed in a wide spectrum of normal and cancer tissues. The cDNA of the human ribonuclease has been isolated and subcloned into a variety of prokaryotic expression vectors, but most efforts to express it caused a severe toxic effect. On the other hand, the expression of the human RNase by the use of the methylotrophic yeast Pichia pastoris system resulted in the production of a highly active recombinant enzyme. Using a 30-mer 5′-end-labeled RNA probe as substrate, the purified enzyme seems to preferentially cleave ApU and ApG phosphodiester bonds, while it hydrolyzes UpU bonds at a lower rate. Based on amino acid sequence alignment and substrate specificity data, as well as the complete resistance of the recombinant protein to the placental ribonuclease inhibitor, we concluded that the human RNase κ is a novel endoribonuclease distinct from other known ribonucleases.

• Animals
• Base Sequence
• Cloning, Molecular
• Conserved Sequence
• DNA, Complementary/isolation & purification
• Endoribonucleases/chemistry
• Endoribonucleases/genetics
• Endoribonucleases/metabolism
• Escherichia coli/genetics
• Humans
• Molecular Sequence Data
• Pichia/genetics
• RNA, Messenger/metabolism
• Ribonucleases/chemistry
• Ribonucleases/genetics
• Ribonucleases/metabolism
• Sequence Alignment
• Substrate Specificity

• Animals
• Biological Evolution
• History, 20th Century
• History, 21st Century
• Humans
• Molecular Biology/history
• Molecular Biology/methods
• Paleontology/methods
• Systems Biology/history

• Animals
• Anti-Infective Agents/chemistry
• Anti-Infective Agents/pharmacology
• Bacteria/drug effects
• Bacteria/growth & development
• Bacteria/metabolism
• Humans
• Immunity, Innate/drug effects
• Immunity, Innate/immunology
• Models, Biological
• Molecular Structure
• Peptides/chemistry
• Peptides/pharmacology
• Proteins/chemistry
• Proteins/pharmacology
• Ribonuclease, Pancreatic/chemistry
• Ribonuclease, Pancreatic/pharmacology

• Amino Acid Sequence
• Animals
• Anti-Bacterial Agents/metabolism
• Cloning, Molecular
• Evolution, Molecular
• Fishes/genetics
• Fishes/metabolism
• Gene Expression
• Genome
• Humans
• Liver/enzymology
• Microbial Sensitivity Tests
• Molecular Sequence Data
• RNA, Transfer/metabolism
• Ribonuclease, Pancreatic/genetics
• Ribonucleases/classification
• Ribonucleases/genetics
• Ribonucleases/physiology
• Tissue Distribution
• Vertebrates
• Zebrafish/genetics
• Zebrafish/metabolism
• Zebrafish/microbiology

• GM67030 NIGMS NIH HHS

• Amino Acid Sequence
• Androgens/metabolism
• Androgens/pharmacology
• Animals
• Base Sequence
• Cloning, Molecular
• DNA, Complementary/genetics
• Epididymis/cytology
• Epididymis/drug effects
• Epididymis/enzymology
• Gene Expression Regulation, Enzymologic/drug effects
• Inflammation/enzymology
• Male
• Molecular Sequence Data
• RNA, Messenger/analysis
• RNA, Messenger/metabolism
• Rats
• Ribonuclease, Pancreatic/analysis
• Ribonuclease, Pancreatic/chemistry
• Ribonuclease, Pancreatic/metabolism
• Ribonucleases
• Sequence Homology, Amino Acid
• Spermatozoa/enzymology
• Testosterone Propionate/pharmacology
• Vas Deferens/enzymology
• Vas Deferens/surgery
• Vasectomy

• 1R03TW01490 FIC NIH HHS

• Amino Acid Sequence
• Gram-Negative Bacteria/drug effects
• Gram-Positive Bacteria/drug effects
• Humans
• Microbial Sensitivity Tests
• Molecular Sequence Data
• Recombinant Proteins/genetics
• Recombinant Proteins/metabolism
• Recombinant Proteins/pharmacology
• Ribonuclease, Pancreatic/genetics
• Ribonuclease, Pancreatic/metabolism
• Ribonuclease, Pancreatic/pharmacology

• Amino Acid Sequence
• Animals
• Cysteine/genetics
• Disulfides/chemistry
• Evolution, Molecular
• Hominidae
• Humans
• Molecular Sequence Data
• Placenta/enzymology
• Pregnancy Proteins/chemistry
• Pregnancy Proteins/genetics
• Pregnancy Proteins/metabolism
• Recombinant Proteins/genetics
• Ribonucleases/chemistry
• Ribonucleases/genetics
• Ribonucleases/metabolism
• Sequence Alignment

• Animals
• Cattle
• Endoribonucleases/immunology
• Evolution, Molecular
• Humans
• Immunity, Innate/genetics
• Multigene Family
• Phylogeny
• Ribonuclease, Pancreatic/immunology
• Ribonucleases/genetics
• Ribonucleases/immunology
• Skin/immunology

• Intramural NIH HHS

• Analysis of Variance
• Anti-HIV Agents/pharmacology
• Cell Culture Techniques/methods
• Eosinophil-Derived Neurotoxin/pharmacology
• Gene Expression/drug effects
• HIV Infections/metabolism
• HIV-1/drug effects
• HIV-1/physiology
• Humans
• Immunologic Factors/pharmacology
• Macrophages/metabolism
• Macrophages/virology
• Microscopy, Confocal
• Recombinant Proteins/pharmacology
• Ribonuclease, Pancreatic/pharmacology
• Ribonucleases/pharmacology
• Statistics, Nonparametric
• T-Lymphocytes/metabolism
• T-Lymphocytes/virology
• Virus Replication/drug effects

• Intramural NIH HHS

We provide a ‘R_EMUS’ (reinforced merging techniques for unique peptide segments) web server for identification of the locations and compositions of unique peptide segments from a set of protein family sequences. Different levels of uniqueness are determined according to substitutional relationship in the amino acids, frequency of appearance and biological properties such as priority for serving as candidates for epitopes where antibodies recognize. R_EMUS also provides interactive visualization of 3D structures for allocation and comparison of the identified unique peptide segments. Accuracy of the algorithm was found to be 70% in terms of mapping a unique peptide segment as an epitope. The R_EMUS web server is available at and the PC version software can be freely downloaded either at or . User guide and working examples for PC version are available at , and details of the proposed algorithm can be referred to the documents as described previously [H. T. Chang, T. W. Pai, T. C. Fan, B. H. Su, P. C. Wu, C. Y. Tang, C. T. Chang, S. H. Liu and M. D. T. Chang (2006) BMC Bioinformatics, 7, 38 and T. W. Pai, B. H. Su, P. C. Wu, M. D. T. Chang, H. T. Chang, T. C. Fan and S. H. Liu (2006) J. Bioinform. Comput. Biol., 4, 75–92].

• Algorithms
• Epitopes/chemistry
• Humans
• Internet
• Peptides/chemistry
• Peptides/immunology
• Sequence Analysis, Protein/methods
• Software

• Biopsy, Needle
• Cell Cycle Proteins
• Female
• Gene Expression
• Humans
• Intracellular Signaling Peptides and Proteins
• Placenta/chemistry
• Placental Lactogen/genetics
• Polymerase Chain Reaction
• Proteins/genetics
• RNA/analysis
• RNA/isolation & purification

• ES-11597 NIEHS NIH HHS
• HD-45675 NICHD NIH HHS

• Amino Acid Sequence
• Animals
• Cattle
• Dogs
• Evolution, Molecular
• Gene Duplication
• Marsupialia/genetics
• Opossums
• Phylogeny
• Ribonuclease, Pancreatic/genetics
• Sequence Alignment
• Sequence Analysis, DNA

• GM67030 NIGMS NIH HHS

Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with high sequence identity may acquire differential functions other than the common catalytic ability. It is probable that each of their variable regions consists of a unique peptide motif (UPM), which selectively interacts with other cellular proteins, rendering additional biological activities. The ability to identify and localize such UPMs is paramount in recognizing the characteristic role of each member of a protein family.

We have developed a reinforced merging algorithm (RMA) with which non-gapped UPMs were identified in a variety of query protein sequences including members of human ribonuclease A (RNaseA), epidermal growth factor receptor (EGFR), matrix metalloproteinase (MMP), and Sma-and-Mad related protein families (Smad). The UPMs generally occupy specific positions in the resolved 3-D structures, especially the loop regions on the structural surfaces. These motifs coincide with the recognition sites for antibodies, as the epitopes of four monoclonal antibodies and two polyclonal antibodies were shown to overlap with the UPMs. Most of the UPMs were found to correlate well with the potential antigenic regions predicted by PROTEAN. Furthermore, an accuracy of 70% can be achieved in terms of mapping a UPM to an epitope.

Our study provides a bioinformatic approach for searching and predicting potential epitopes and interacting motifs that distinguish different members of a protein family.

• Algorithms
• Amino Acid Motifs
• Amino Acid Sequence
• Conserved Sequence
• Models, Chemical
• Models, Molecular
• Molecular Sequence Data
• Protein Conformation
• Proteins/chemistry
• Proteins/classification
• Sequence Alignment/methods
• Sequence Analysis, Protein/methods
• Sequence Homology, Amino Acid
• Structure-Activity Relationship

• Acetylation
• Animals
• Butyrates/pharmacology
• Cell Differentiation/drug effects
• Cell Division
• Enzyme Inhibitors/pharmacology
• Eosinophil Cationic Protein/physiology
• Eosinophil Granule Proteins/physiology
• Eosinophils/cytology
• Eosinophils/physiology
• HL-60 Cells/cytology
• Histone Deacetylase Inhibitors
• Histones
• Humans
• Hydroxamic Acids/pharmacology
• Hypersensitivity/etiology
• Inflammation/etiology
• Interleukin-5/physiology
• Peptides, Cyclic/pharmacology
• Rats
• Recombinant Proteins

• Amino Acid Sequence
• Animals
• Birds/genetics
• Chickens/genetics
• Eosinophil Cationic Protein/genetics
• Evolution, Molecular
• Gene Duplication
• Humans
• Mammals/genetics
• Mice
• Molecular Sequence Data
• Multigene Family
• Phylogeny
• Rats
• Ribonuclease, Pancreatic/genetics
• Sequence Homology, Amino Acid

• GM67030 NIGMS NIH HHS