Structural and functional characterization of gene products encoded in the human genome by homology detection.

Abstract:

:Availability of the human genome data has enabled the exploration of a huge amount of biological information encoded in it. There are extensive ongoing experimental efforts to understand the biological functions of the gene products encoded in the human genome. However, computational analysis can aid immensely in the interpretation of biological function by associating known functional/structural domains to the human proteins. In this article we have discussed the implications of such associations. The association of structural domains to human proteins could help in prioritizing the targets for structure determination in the structural genomics initiatives. The protein kinase family is one of the most frequently occurring protein domain families in the human proteome while P-loop hydrolase, which comprises many GTPases and ATPases, is a highly represented superfamily. Using the superfamily relationships between families of unknown and known structures we could increase structural information content of the human genome by about 5%. We could also make new associations of domain families to 33 human proteins that are potentially linked to genetically inherited diseases.

journal_name

IUBMB Life

journal_title

IUBMB life

authors

Pandit SB,Balaji S,Srinivasan N

doi

10.1080/15216540400006105

keywords:

subject

Has Abstract

pub_date

2004-06-01 00:00:00

pages

317-31

issue

6

eissn

1521-6543

issn

1521-6551

pii

VY3PBQPC3MLYRD3J

journal_volume

56

pub_type

杂志文章,评审
  • Bovine spongiform encephalopathy--some surprises for biochemists.

    abstract::Bovine Spongiform Encephalopathy (BSE) is typical of the dementias that affect both animals and man; Scrapie in sheep, Creutzfeldt-Jakob disease in man. Global efforts have been made to determine the nature of the active agents in these diseases. At present the 'protein only hypothesis' of Prusiner holds. It was a sur...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1080/15216540500097152

    authors: Campbell PN

    更新日期:2005-04-01 00:00:00

  • Mass spectrometry-based proteomic analysis of FSCN1-interacting proteins in laryngeal squamous cell carcinoma cells.

    abstract::Fascin actin-bundling protein 1 (FSCN1) is an evolutionarily conserved actin-bundling protein that plays a critical role in cell migration, motility, adhesion, and cellular interactions. Although multiple clinical studies have implicated the expression of FSCN1 in laryngeal squamous cell carcinoma (LSCC) progression, ...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.2121

    authors: Liu H,Cui J,Zhang Y,Niu M,Xue X,Yin H,Tang Y,Dai L,Dai F,Guo Y,Wu Y,Gao W

    更新日期:2019-11-01 00:00:00

  • A genetic variant in a homocysteine metabolic gene that increases the risk of congenital cardiac septal defects in Han Chinese populations.

    abstract::Elevated homocysteine levels are known to be a risk factor for congenital cardiac septal defects (CCSDs), but the mechanism underlying this effect is unknown. The genetic variants that were significantly associated with circulating homocysteine concentrations have been systematically identified through the genome-wide...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.1651

    authors: Xie HH,Li J,Li PQ,Zhang AA,Li Y,Wang YZ,Xie DX,Xie XD

    更新日期:2017-09-01 00:00:00

  • Biochemical characterization of argininosuccinate lyase from M. tuberculosis: significance of a c-terminal cysteine in catalysis and thermal stability.

    abstract::Arginine biosynthesis pathway is crucial to the survival and pathogenesis of Mycobacterium tuberculosis (Mtb). Arginine is a critical amino acid that contributes to the inflection of cellular immune responses during pathogenesis. Argininosuccinate lyase from Mtb (MtArgH), the last enzyme in the pathway, catalyzes the ...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.1683

    authors: Mishra A,Surolia A

    更新日期:2017-11-01 00:00:00

  • Genetic basis of antibiotic resistance in pathogenic Acinetobacter species.

    abstract::Antibiotic resistance in Acinetobacter spp., particularly Acinetobacter baumannii, is increasing rapidly. A. baumannii possesses two intrinsic β-lactamase genes, in addition to weak permeability and efflux systems, that together confer a natural reduced susceptibility to antibiotics. In addition, numerous acquired mec...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1002/iub.532

    authors: Poirel L,Bonnin RA,Nordmann P

    更新日期:2011-12-01 00:00:00

  • GABA increases Ca2+ in cerebellar granule cell precursors via depolarization: implications for proliferation.

    abstract::The amino acids glutamate and gamma-aminobutyric acid (GABA) have primarily been characterized as the most prevalent excitatory and inhibitory, respectively, neurotransmitters in the vertebrate central nervous system. However, the role of these signaling molecules extends far beyond the synapse. GABA, glutamate, and t...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1002/iub.185

    authors: Dave KA,Bordey A

    更新日期:2009-05-01 00:00:00

  • A role for human neuroglobin in apoptosis.

    abstract::Over the past decade, following the discovery of the human heme protein neuroglobin, many studies have searched for evidence for this protein's mechanism of action. Much data has accrued showing that high levels of neuroglobin will protect cells from apoptotic cell death, following a wide range of challenges. Various ...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1002/iub.405

    authors: Brittain T,Skommer J,Henty K,Birch N,Raychaudhuri S

    更新日期:2010-12-01 00:00:00

  • Potential role of potassium and chloride channels in regulation of silymarin-induced apoptosis in Candida albicans.

    abstract::Silymarin, which is derived from the seeds of Silybum marianum, has been widely used to prevent and treat liver diseases. In our previous study, we reported that at concentrations above the minimal inhibitory concentration (MIC), silymarin exhibited antifungal activity against Candida albicans by targeting its plasma ...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.1716

    authors: Lee W,Lee DG

    更新日期:2018-03-01 00:00:00

  • Uncoupling proteins--how do they work and how are they regulated.

    abstract::Uncoupling proteins (UCPs) are regulated H+ transporters and a subfamily of the mitochondrial carrier family. Whereas UCP1 in brown adipose tissue has a well-defined role in thermogenesis, the roles of other UCPs are still tentative, such as in control of immune response, oxygen radical formation, and insulin secretio...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1080/15216540152845975

    authors: Klingenberg M

    更新日期:2001-09-01 00:00:00

  • The HCV ARFP/F/core+1 protein: production and functional analysis of an unconventional viral product.

    abstract::Hepatitis C virus (HCV) is an enveloped positive-strand RNA virus of the Flaviviridae family. It has a genome of about 9,600 nucleotides encoding a large polyprotein (about 3,000 amino acids) that is processed by cellular and viral proteases into at least 10 structural and nonstructural viral proteins. A novel HCV pro...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1002/iub.201

    authors: Vassilaki N,Mavromara P

    更新日期:2009-07-01 00:00:00

  • Emerging roles of the αC-β4 loop in protein kinase structure, function, evolution, and disease.

    abstract::The faithful propagation of cellular signals in most organisms relies on the coordinated functions of a large family of protein kinases that share a conserved catalytic domain. The catalytic domain is a dynamic scaffold that undergoes large conformational changes upon activation. Most of these conformational changes, ...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.2253

    authors: Yeung W,Ruan Z,Kannan N

    更新日期:2020-06-01 00:00:00

  • Ambient pH sensing in filamentous fungi: pitfalls in elucidating regulatory hierarchical signaling networks.

    abstract::In this article, the experiments used to construct the ambient pH-signaling network involved in the secretion of enzymes by filamentous fungi have been reviewed, focusing on the phosphate-repressible phosphatases in Aspergillus nidulans. Classic and molecular genetics have been used to demonstrate that proteolysis of ...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.1217

    authors: Rossi A,Cruz AH,Santos RS,Silva PM,Silva EM,Mendes NS,Martinez-Rossi NM

    更新日期:2013-11-01 00:00:00

  • Cholesterol and Alzheimer's disease: a still poorly understood correlation.

    abstract::A large amount of evidence suggests a pathogenic link between cholesterol homeostasis dysregulation and Alzheimer's disease (AD). In cell culture systems, the production of amyloid-β (Aβ) is modulated by cholesterol, and studies on animal models have consistently demonstrated that hypercholesterolemia is associated wi...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1002/iub.1091

    authors: Ricciarelli R,Canepa E,Marengo B,Marinari UM,Poli G,Pronzato MA,Domenicotti C

    更新日期:2012-12-01 00:00:00

  • Evolutionary conservation of the membrane fusion machine.

    abstract::Recent structural studies of proteins mediating membrane fusion reveal intriguing similarities between diverse viral and mammalian systems. Particularly striking is the close similarity between the transmembrane envelope glycoproteins from the retrovirus HTLV-1 and the filovirus Ebola. These similarities suggest simil...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1080/713803503

    authors: Poumbourios P,Center RJ,Wilson KA,Kemp BE,Kobe B

    更新日期:1999-08-01 00:00:00

  • Adenylyl cyclase expression and regulation during the differentiation of Dictyostelium discoideum.

    abstract::Cyclic AMP metabolism is essential for the survival of the social amoebae Dictyostelium discoideum. Three distinct adenylyl cyclases are expressed and required for the normal development of this simple eukaryote. The adenylyl cyclase expressed during aggregation, ACA, is related to the mammalian and Drosophila G prote...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1080/15216540400013887

    authors: Kriebel PW,Parent CA

    更新日期:2004-09-01 00:00:00

  • Antizyme suppression leads to an increment of the cellular redox potential and an induction of HIF-1alpha: its involvement in resistance to gamma-radiation.

    abstract::The mammalian antizyme (AZ) promotes ubiqutin-independent degradation of ornithine decarboxylase, a key enzyme in polyamine biosynthesis. This study shows that AZ suppression in human lung carcinoma A549 cells caused growth defects and death, but made the cells resistant to DNA damaging agents such as gamma-radiation ...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.49

    authors: Kim JS,Kim TL,Cho EW,Paik SG,Chung HW,Kim IG

    更新日期:2008-06-01 00:00:00

  • Hypoxia inducible factor 1 alpha down-regulates type i collagen through Sp3 transcription factor in human chondrocytes.

    abstract::Cartilage engineering is one challenging issue in regenerative medicine. Low oxygen tension or hypoxia inducible factor-1 (HIF-1α) gene therapy are promising strategies in the field of cartilage repair. Previously, we showed that hypoxia and its mediator HIF-1 regulate matrix genes expression (collagens and aggrecan)....

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.1539

    authors: Duval E,Bouyoucef M,Leclercq S,Baugé C,Boumédiene K

    更新日期:2016-09-01 00:00:00

  • Association of the glucocorticoid receptor with STAT3, C/EBPbeta, and the hormone-responsive element within the rat haptoglobin gene promoter during the acute phase response.

    abstract::Upregulation of haptoglobin (Hp) expression in the rat during the acute phase (AP) response is the result of synergistic effects of IL-6-, IL-1beta-, and corticosterone-activated signaling pathways. IL-6 signaling terminates in cis-trans interactions of the Hp gene hormone-responsive element (HRE) with transcription f...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.313

    authors: Arambasić J,Poznanović G,Ivanović-Matić S,Bogojević D,Mihailović M,Uskoković A,Grigorov I

    更新日期:2010-03-01 00:00:00

  • LncRNA MEG3 suppresses migration and promotes apoptosis by sponging miR-548d-3p to modulate JAK-STAT pathway in oral squamous cell carcinoma.

    abstract::Oral squamous cell carcinoma (OSCC) is a lethal malignancy and its prognosis remains dismal. Thus, a deeper understanding of the mechanisms is needed to provide a new insight for new therapies. It has been reported that long noncoding RNA (lncRNA) maternally expressed gene 3 (MEG3) was downregulated in OSCC tissues, h...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.2012

    authors: Tan J,Xiang L,Xu G

    更新日期:2019-07-01 00:00:00

  • Mechanism of DNA depurination by carcinogens in relation to cancer initiation.

    abstract::Depurinating DNA adducts formed by aromatic hydrocarbons and catechol estrogen quinones play a major role in cancer initiation. Most of these adducts depurinate instantaneously, but some guanine adducts depurinate from DNA with half-lives of hours. We report here, that after 10 h at 37 °C, reaction of estradiol-3,4-qu...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.586

    authors: Cavalieri E,Saeed M,Zahid M,Cassada D,Snow D,Miljkovic M,Rogan E

    更新日期:2012-02-01 00:00:00

  • Cell-penetrating peptides: A tool for effective delivery in gene-targeted therapies.

    abstract::The current landscapes of novel therapeutic approaches rely mostly on gene-targeted technologies, enabling to fight rare genomic diseases, from infections to cancer and hereditary diseases. Although, reaching the action-site for this novel treatments requires to deliver nucleic acids, or other macromolecules into cell...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1002/iub.1257

    authors: de Figueiredo IR,Freire JM,Flores L,Veiga AS,Castanho MARB

    更新日期:2014-03-01 00:00:00

  • Nuclear factor of activated T cells (NFAT1-C) represses the enhancer II and pregenomic promoter (EnII/Cp) of hepatitis B virus (HBV) through its responsive site GGAGA and nullifies the HBx-driven transcriptional activation.

    abstract::The immunosuppressant cyclosporin A (CsA)-sensitive nuclear factor of activated T cells 1 (NFAT1) has been known to be a transcriptional regulator of cytokine and viral genes during the immune response. By analyses of serial deletion, mutation, and heterologous promoter assay, we report here that the CsA-sensitive NFA...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1080/152165401753311807

    authors: Lee JH,Rho HM

    更新日期:2001-04-01 00:00:00

  • Artemisinin and curcumin inhibit Drosophila brain tumor, prolong life span, and restore locomotor activity.

    abstract::Deletion of tumor suppressor gene, lethal(2)giant larvae [l(2)gl], leads to brain tumor in Drosophila melanogaster at larval stage of development and severe brain dysplasia in mice. We have studied the effect of two potential antitumor drugs artemisinin and curcumin in the perspective of inhibiting l(2)gl brain tumor....

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.1284

    authors: Das SS,Nanda GG,Alone DP

    更新日期:2014-07-01 00:00:00

  • p38 kinase and c-Jun N-terminal kinase oppositely regulates tumor necrosis factor alpha-induced vascular cell adhesion molecule-1 expression and cell adhesion in chondrosarcoma cells.

    abstract::We investigated signaling pathways leading to tumor necrosis factor (TNF) alpha-induced intercellular adhesion molecule (ICAM)-1 and vascular cell adhesion molecule (VCAM)-1 expression in chondrosarcoma cells, and determined the functional significance of their expression by examining Jurkat T cell adhesion. TNFalpha ...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1080/15216540215674

    authors: Ju JW,Kim SJ,Jun CD,Chun JS

    更新日期:2002-11-01 00:00:00

  • Involvement of PIN-like domain nucleases in tRNA processing and translation regulation.

    abstract::Transfer RNAs require essential maturation steps to become functional. Among them, RNase P removes 5' leader sequences of pre-tRNAs. Although RNase P was long thought to occur universally as ribonucleoproteins, different types of protein-only RNase P enzymes were discovered in both eukaryotes and prokaryotes. Interest...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1002/iub.2062

    authors: Gobert A,Bruggeman M,Giegé P

    更新日期:2019-08-01 00:00:00

  • 1,25-Dihydroxyvitamin D3 Deficiency is Involved in the Pathogenesis of Diabetic Retinopathy in the Uygur Population of China.

    abstract::1,25-Dihydroxyvitamin D3 [1,25(OH)2 D3 ] has recently been shown to have immunomodulatory property. This study aimed to investigate the expression and potential role of 1,25(OH)2 D3 in the pathogenesis of diabetic retinopathy (DR) in the Uygur population. Blood samples were obtained from 22 patients with proliferative...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1002/iub.1501

    authors: Yi X,Sun J,Li L,Wei Q,Qian Y,Chen X,Ma L

    更新日期:2016-06-01 00:00:00

  • The ubiquitin ligase ability of IAPs regulates apoptosis.

    abstract::Accumulating evidence indicates that there is a critical role of the ubiquitin/proteasome pathway in the regulation of apoptosis. Among the important molecules that couple these two fundamental cellular activities are members of the inhibitor of apoptosis (IAP) protein family. In addition to their well-studied ability...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1080/15216540500389013

    authors: Ni T,Li W,Zou F

    更新日期:2005-12-01 00:00:00

  • Carbon monoxide: A new player in the redox regulation of connexin hemichannels.

    abstract::Carbon monoxide (CO) is a gaseous transmitter that is known to be involved in several physiological processes, but surprisingly it is also becoming a promising molecule to treat several pathologies including stroke and cancer. CO can cross the plasma membrane and activate guanylate cyclase, increasing the cGMP concent...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1002/iub.1388

    authors: Retamal MA,León-Paravic CG,Ezquer M,Ezquer F,Del Rio R,Pupo A,Martínez AD,González C

    更新日期:2015-06-01 00:00:00

  • The NADPH oxidase of endothelial cells.

    abstract::The best known NADPH oxidase is that of phagocytes-neutrophils and monocytes. In these cells, the enzyme manufactures large quantities of O2- and other reactive oxidants that are used for the purpose of killing invading microorganisms. Recent studies, however, have suggested that a number of other tissues contain NADP...

    journal_title:IUBMB life

    pub_type: 杂志文章,评审

    doi:10.1080/713803730

    authors: Babior BM

    更新日期:2000-10-01 00:00:00

  • Effect of ribozyme against transforming growth factorbeta1 on biological character of activated HSCs.

    abstract::Transforming growth factorbeta1 (TGFbeta1) is considered to be the principal contributor to liver fibrosis. So in this study the ribozymes against TGFbeta1 were designed. The in vitro cleavage activities of the ribozymes were assayed through incubation of (32)p-labeled target RNAs and (32)p-labeled ribozymes in differ...

    journal_title:IUBMB life

    pub_type: 杂志文章

    doi:10.1080/15216540400024470

    authors: Song YH,Zhou XM,Xue XN,Liu NZ,Tian DA,Kong XJ,Wu XL,Lin JS,Jin YX

    更新日期:2005-01-01 00:00:00