bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loop Movement and Catalysis in Creatine Kinase
Authors: Wang Pan‐Fen , Flynn Allen J. , McLeish Michael J. , Kenyon George L. 
Published: September 2005

AbstractRecently the crystal structure of creatine kinase from Torpedocalifornica was determined to 2.1 Å. The dimeric structure revealed two different forms in the unit cell: one monomer was bound to a substrate, MgADP, and the other monomer was bound to a transition‐state analogue complex composed of MgADP, nitrate and creatine. The most striking difference between the structures is the movement of two loops (comprising residues 60 ‐ 70 and residues 323 ‐ 333) into the active site in the transition state structure. This loop movement effectively occludes the active site from solvent, and the loops appear to be locked into place by a salt bridge formed between His66 and Asp326. His66 is of particular interest as it is located within a PGHP motif conserved in all creatine kinases but not found in other guanidino kinases. We have carried out alanine‐scanning mutagenesis of each of the residues in the PGHP motif and determined that only the His66 plays a significant role in the creatine kinase reaction. Although neither residue interacts directly with the substrate, the interaction His66 and Asp326 appears to be important in providing the precise alignment of substrates necessary for phosphoryl group transfer. Finally, it is clear that neither His66 nor Asp326 are responsible for the pKs observed in the pH‐rate profile for HMCK.
IUBMB Life, 57: 355‐362, 2005
Species‐Specific Regulation of the α‐2(I) Procollagen Gene by Proximal Promoter Elements
Authors: Leaner Virna D. , Masemola Agatha , Parker Iqbal M. 
Published: September 2005

AbstractTranscriptional regulation of the human α 2(I) procollagen proximal promoter involves the interaction of trans‐acting factors at the inverted CCAAT box (G/CBE) located at position ‐ 80 and an adjacent GGAGGCCC‐box at ‐ 70. Both these elements have previously been shown to be essential for activity of the human promoter. This study investigated nucleotide differences at three sites (‐74, ‐ 72 and ‐ 71) between the human and mouse promoters that were sufficient to abolish trans‐acting factor binding with the mouse sequence (GGAGACGT). Two distinct DNA‐protein interactions were detected on the human ‐ 107/ + 54 promoter fragment while a single interaction was observed at the equivalent mouse promoter. One of these factors is the CCAAT‐binding factor (CBF) and it's binding was observed on both the human and mouse promoters. Although the GGAGGCCC DNA‐binding element was not detected on the mouse promoter, GGAGGCC‐binding proteins were present in mouse nuclear extracts as observed by their interaction with the human promoter. Functional analysis of the human and mouse ‐ 343/ + 54 and ‐ 107/+ 54 promoter regions revealed significant differences between species; the human constructs having higher activity than the mouse. The differences in promoter activity between species may in part be a result of the nucleotide differences in the GGAGGCCC‐box. Mutations in this region of the human ‐ 107/+ 54 promoter prevented DNA‐protein interaction and lowered promoter activity. These results support the hypothesis that the GGAGGCCC‐box in the human α 2(1) procollagen promoter has a regulatory function and that there exists a species‐specific difference in transcription factor binding and regulation of the gene. IUBMB Life, 57: 363‐370, 2005
How to Clean the Dirtiest Place in the Cell: Cationic Antioxidants as Intramitochondrial ROS Scavengers
Authors: Skulachev Vladimir P. 
Published: September 2005

AbstractMembrane‐penetrating triphenyl alkyl phosphonium cations have been suggested for many years in our group as having the ability to measure mitochondrial potential were recently used by Murphy as vehicles to specifically target CoQ to mitochondria. As was shown in our group, the phosphonium derivative of CoQ (MitoQ) easily penetrates a planar bilayer phospholipid membrane as a cation, generating 60 mV electric potential (ΔΨ) per a 10‐fold MitoQ gradient. This means that MitoQ should be unequally distributed across the inner mitochondrial membrane, the intramitochondrial [MitoQ] = extramitochondrial [MitoQ] × 103 at 180 mV ΔΨ. In line with such a calculation, Murphy and his colleagues reported that antioxidant efficiency of MitoQ added to mitochondria or cells appears to be very much higher than of CoQ. It was found that H2O2‐induced apoptosis (Murphy) and the H2O2‐mediated bystander killing of the cultivated cells (our group) are completely arrested by pretreatement of the cells with 10‐10 ‐ 10‐8 M MitoQ. These effects indicate that MitoQ and similar compounds may be promising in treatment of heart attack, stroke and other diseases accompanied by massive apoptosis in the injured tissue. The very fact that: (i) MitoQ is not only accumulated by mitochondria but also can be regenerated in its reduced form by mitochondrial respiratory chain, (ii) it is the mitochondrial interior that produces a large portion of reactive oxygen species (ROS) in our body, and (iii) the most sensitive ROS targets are localized in the mitochondrial matrix suggest the MitoQ‐like compounds are promising tools of molecular therapy of aerobic cells. In line with this suggestion, we found that addition of MitoQ strongly improves structural and biochemical parameters of cultivated cells. As to cationic tetrapeptides, recently advertised as mitochondrially‐targeted ΔΨ ‐independent antioxidants, their effect is most probably mediated by an opioid activity inherent in some of these substances.
IUBMB Life, 57: 305‐310, 2005
Understanding and Modulating Ageing
Authors: Rattan Suresh IS , Clark Brian FC 
Published: September 2005

AbstractAgeing is characterized by a progressive accumulation of molecular damage in nucleic acids, proteins and lipids. The inefficiency and failure of maintenance, repair and turnover pathways is the main cause of age‐related accumulation of damage. Research in molecular gerontology is aimed at understanding the genetic and epigenetic regulation of survival and maintenance mechanisms at the levels of transcription, post‐transcriptional processing, post‐translational modifications, and interactions among various gene products. Concurrently, several approaches are being tried and tested to modulate ageing in a wide variety of organisms. The ultimate aim of such studies is to improve the quality of human life in old age and prolong the health‐span. Various gerontomodulatory approaches include gene therapy, hormonal supplementation, nutritional modulation and intervention by free radical scavengers and other molecules. A recent approach is that of applying hormesis in ageing research and therapy, which is based on the principle of stimulation of maintenance and repair pathways by repeated exposure to mild stress. A combination of molecular, physiological and psychological modulatory approaches can realize “healthy ageing” as an achievable goal in the not‐so‐distant future.
IUBMB Life, 57: 297‐304, 2005
Are Genetically Modified Plants Useful and Safe?
Authors: Weil Jacques‐Henry 
Published: September 2005

AbstractSo far, plants have been genetically modified essentially to achieve resistance to herbicides, or to pathogens (mainly insects, or viruses), but resistance to abiotic stresses (such as cold, heat, drought, or salt) is also being studied. Genetically modified (GM) plants with improved nutritional qualities have more recently been developed, such as plants containing higher proportions of unsaturated fatty acids (omega‐3 and omega‐6) in their oil (to prevent cardio‐vascular diseases), or containing β‐carotene as in the golden rice (to prevent vitamin A deficiency). Possible risks for human health (such as the production of allergenic proteins), or for the environment (such as the appearance of superweeds as a result from gene flow), should be carefully studied, and a science‐based assessment of benefits vs. risks should be made on a csae by case basis, both for GM plants and for plants obtained by conventional breeding methods.
IUBMB Life, 57: 311‐314, 2005
Control of DNA Replication: Regulation and Activation of Eukaryotic Replicative Helicase, MCM
Authors: Masai Hisao , You Zhiying , Arai Ken‐ichi 
Published: September 2005

AbstractDNA replication is a key event of cell proliferation and the final target of signal transduction induced by growth factor stimulation. It is also strictly regulated during the ongoing cell cycle so that it occurs only once during S phase and that all the genetic materials are faithfully duplicated. DNA replication may be arrested or temporally inihibited due to a varieties of internal and external causes. Cells have developed intricate mechanisms to cope with the arrested replication forks to minimize the adversary effect on the stable maintenance of genetic materials. Helicases play a central role in DNA replication. In eukaryotes, MCM (minichromosome maintenance) protein complex plays essential roles as a replicative helicase. MCM4‐6‐7 complex possesses intrinsic DNA helicase activity which translocates on single‐stranded DNA form 3' to 5'. Mammalian MCM4‐6‐7 helicase and ATPase activities are specifically stimulated by the presence of thymine‐rich single‐stranded DNA sequences onto which it is loaded. The activation appears to depend on the thymine content of this single‐strand, and sequences derived from human replication origins can serve as potent activators of the MCM helicase. MCM is a prime target of Cdc7 kinase, known to be essential for activation of replication origins. We will discuss how the MCM may be activated at the replication origins by template DNA, phosphorylation, and interaction with other replicative proteins, and will present a model of how activation of MCM helicase by specific sequences may contribute to selection of replication initiation sites in higher eukaryotes.
IUBMB Life, 57: 323‐335, 2005
The Thermogenic Activity of Rat Brown Adipose Tissue and Rabbit White Muscle Ca2 + ‐ATPase
Authors: de Meis Leopoldo , Oliveira Gaya M. , Arruda Ana Paula , Santos Reinaldo , Costa Rodrigo Madeiro da , Benchimol Marlene 
Published: September 2005

AbstractThe Ca2 + ‐ATPase (SERCA) found in vesicles derived from the sarco/endoplasmic reticulum vesicles of rats brown adipose tissue and rabbit white muscle were identified by gel electrophoresis, Western blot, electron microscopy and immunolabeling with gold particles. In both tissues, the isoform found was SERCA 1. The Ca2 + affinity of the fat SERCA 1 was different from the muscle isoform. The degree of uncoupling is estimated measuring the ratio between Ca2 + transport and ATP cleaved. In brown fat vesicles the degree of uncoupling varied depending on the Ca2 + concentration of the medium. This was not observed in vesicles derived from muscle. At all Ca2 + concentrations tested, the uncoupling was not related to Ca2 + leakage from the membrane and was far more pronounced in fat than in muscle vesicle. When a Ca2 + gradient was formed across the vesicles membrane the heat released during ATP hydrolysis varied between 22 and 26 Kcal/mol in both fat and muscle vesicles but in the absence of a gradient the heat released was 17 Kcal/mol in fat and 12 Kcal/mol in muscle. The data reported indicate that the SERCA 1 of brown adipocytes is far more thermogenic than the white muscle SERCA 1, and suggest that, in addition to storing Ca2 + inside the endoplasmic reticulum, the SERCA 1 may represent a source of heat production contributing to the thermogenic function of brown adipose tissue.
IUBMB Life, 57: 337‐345, 2005
Dual Nature of the Genome: Genes for the Individual Life and Genes for the Evolutionary Progress of the Population
Authors: Arber Werner 
Published: September 2005

AbstractBiological evolution is here postulated to be driven coordinately by the products of specific evolution genes and by non‐genetic elements such as the intrinsic properties of matter and random encounter with environmental factors. Evolution genes are supposed to have their own evolutionary history in which second‐order selection was exerted at the population level. The products of evolution genes can act as generators of genetic variations and/or as modulators of the frequency of genetic variation. Three major natural strategies, each with a number of specific mechanisms contribute to the overall spontaneous production of genetic variants. Each of these three strategies contributes its own specific quality to genetic variation. The difficulties of experimentally investigating these strategies and a wider discussion of some of the postulates within the scientific community are outlined. Finally, the general relevance of the postulated duality of the genome for our world view is briefly mentioned.
IUBMB Life, 57: 263‐266, 2005
From JNK to Pay Dirt: Jun Kinases, their Biochemistry, Physiology and Clinical Importance
Authors: Karin Michael , Gallagher Ewen 
Published: September 2005

AbstractThe c‐Jun N‐terminal kinases (JNKs) were originally identified by their ability to phosphorylate c‐Jun in response to UV‐irradiation, but now are recognized as critical regulators of various aspects of mammalian physiology, including: cell proliferation, cell survival, cell death, DNA repair and metabolism. JNK‐mediated phosphorylation enhances the ability of c‐Jun, a component of the AP‐1 transcription factor, to activate transcription, in response to a plethora of extracellular stimuli. The JNK activation leads to induction of AP‐1‐dependent target genes involved in cell proliferation, cell death, inflammation, and DNA repair. The JNKs, which are encoded by three different Jnk loci, are now known to be regulated by many other stimuli, from pro‐inflammatory cytokines to obesity, in addition to UV‐irradiation. Targeted disruption of the Jnk loci in mice has proved to be a critical tool in better understanding their physiological functions. Such studies revealed that the JNKs play important roles in numerous cellular processes, including: programmed cell death, T cell differentiation, negative regulation of insulin signaling, control of fat deposition, and epithelial sheet migration. Importantly, the JNKs have become prime targets for drug development in several important clinical areas, including: inflammation, diabetes, and cancer.
IUBMB Life, 57: 283‐295, 2005
Bovine Spongiform Encephalopathy ‐ Some Surprises for Biochemists
Authors: Campbell Peter N. 
Published: September 2005

AbstractBovine 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 surprise that a protein could per se be the active agent but other surprises for our traditional teaching of biochemistry arose. These are explained in a brief summary of our present understanding of the biochemistry of the active agents that cause the diseases.
IUBMB Life, 57: 273‐276, 2005
Jumping Genes and Shrinking Genomes ‐ Probing the Evolution of Eukaryotic Photosynthesis with Genomics
Authors: Archibald John M. 
Published: September 2005

AbstractThe advent of comparative genomics has revolutionized the study of the origin and evolution of eukaryotes and their organelles. Genomic analysis has revealed that the endosymbiosis that gave rise to plastids ‐ the light‐harvesting apparatus of photosynthetic eukaryotes ‐ had a profound impact on the genetic composition of the host, far beyond the contribution of cyanobacterial genes for plastid‐specific functions. Here I discuss recent advances in our appreciation of the mosaic nature of the eukaryotic nuclear genome, and the ongoing role endosymbiosis plays in shaping its content.
IUBMB Life, 57: 539‐547, 2005
Protein Splicing: Its Discovery and Structural Insight into Novel Chemical Mechanisms
Authors: Anraku Yasuhiro , Mizutani Ryuta , Satow Yoshinori 
Published: September 2005

AbstractProtein splicing is a posttranslational cellular process, in which an intervening protein sequence (intein) is self‐catalytically excised out from a nascent protein precursor and the two flanking sequences (N‐ and C‐exteins) are ligated to produce two mature enzymes. This unique reaction was first discovered from studies of the structure and expression of the VMA1 gene in Saccharomyces cerevisiae. VMA1 consists of a single open reading frame and yet comprises two independent genetic information for Vma1p (a catalytic 70‐kDa subunit of the vacuolar H + ‐ATPase) and VDE (a 50‐kDa DNA endonuclease) as an in‐frame spliced insert in the gene. Subsequent studies have demonstrated that protein splicing is not unique for the VMA1 precursor and there are many operons in nature, which implement genetic information editing at protein level. To elucidate its precise reaction mechanisms from a viewpoint of structure‐directed chemistry, a series of crystal structural studies has been carried out with the use of splicing‐inactive and slowly spliceable precursors of VMA1 recombinants. One precursor structure revealed that the N‐terminal junction of the introduced extein polypeptide forms an intermediate containing a five‐membered thiazolidine ring. The other precursor structures showed spliced products with a linkage between the N‐ and C‐extein segments. This article summarizes biochemical and structural studies on a self‐catalytic mechanism for protein splicing that is triggered and terminated solely via thiazolidine intermediates with tetrahedral configurations formed within the splicing sites where proton ingress and egress are driven by balanced protonation and deprotonation.
IUBMB Life, 57: 563‐574, 2005
RNA Silencing of Cks1 Induced G2/M Arrest and Apoptosis in Human Lung Cancer Cells
Authors: Tsai Yi‐Shan , Chang Hui‐Chiu , Chuang Lea‐Yea , Hung Wen‐Chun 
Published: September 2005

AbstractCdc kinase subunit 1 (Cks1) has been shown to involve in the regulation of cell cycle progression and p27Kip1 degradation. To define the role of Cks1 in lung tumorigenesis, we examined the expression of Cks1 in human lung cancer cell lines and tested the effect of Cks1‐specific small interfering RNA (siRNA) on these cells. Reverse transcriptase‐polymerase chain reaction (RT‐PCR) and western blot analysis showed that Cks1 was highly expressed in human lung cancer cells. Transfection of Cks1 siRNA down‐regulated Cdc2 kinase activity and induced G2/M arrest in Cks1‐ overexpressing H358 lung cancer cells. Long‐term treatment of Cks1 siRNA induced caspase activation and apoptosis in H358 cells. On the contrary, Cks1 siRNA did not affect viability of normal human lung fibroblasts under the same experimental condition. Collectively, our results suggest that Cks1 participates in the steps of lung tumorigenesis and this gene may be a target for the treatment of lung cancer.
IUBMB Life, 57: 583‐589, 2005
Structural Studies on the αβ T‐cell Receptor
Authors: Ely Lauren K. , Kjer‐Nielsen Lars , McCluskey James , Rossjohn Jamie 
Published: September 2005

Abstractαβ T‐cell receptor (TcR) recognition of antigenic peptides bound to the major histocompatibility complex (pMHC), is integral to the cellular immune system. Crystallographic studies over the last decade have provided significant insight into this unique trimolecular recognition event. The TcR ‐ pMHC structural information has been paralleled by biophysical studies that have further explored the emerging binding models in an attempt to answer fundamental immunological questions regarding MHC restriction, T‐cell immunodominance and TcR cross‐reactivity. However, despite the important data that has been generated regarding TcR ‐ pMHC interactions, the scope of this information is still incomplete due to the limited range of TcRs that have been studied. These limitations are primarily due to difficulties in obtaining high yields of recombinant αβ TcR for crystallographic and biophysical analysis; here we will discuss some of the protein engineering strategies that have been employed to expand the pool of recombinant TcRs suitable for crystallographic studies and the subsequent studies that have utilized these proteins.
IUBMB Life, 57: 575‐582, 2005
A Drosophila Model of Mitochondrial DNA Replication: Proteins, Genes and Regulation
Authors: Garesse Rafael , Kaguni Laurie S. 
Published: September 2005

AbstractMitochondrial biogenesis is a critical process in animal development, cellular homeostasis and aging. Mitochondrial DNA replication is an essential part of this process, and both nuclear and mitochondrial DNA mutations are found to result in mitochondrial dysfunction that leads to developmental defects and delays, aging and disease. Drosophila provides an amenable model system to study mitochondrial biogenesis in normal and disease states. This review provides an overview of current approaches to study the proteins involved in mitochondrial DNA replication, the genes that encode them and their regulation. It also presents a survey of cell and animal models under development to mimic the pathophysiology of human mitochondrial disorders.
IUBMB Life, 57: 555‐561, 2005
Role of Leptin in Modulation of Porphyromonas gingivalis Lipopolysaccharide‐induced Up‐regulation of Endothelin‐1 in Salivary Gland Acinar Cells
Authors: Slomiany Bronislaw L. , Slomiany Amalia 
Published: September 2005

AbstractLeptin, a pleiotropic cytokine that regulates food intake and metabolic and endocrine responses, has emerged recently as an important regulator of mucosal inflammatory responses to bacterial infection. In this study, we report that in sublingual salivary gland acinar cells leptin plays a role in the suppression of up‐regulation in endothelin‐1 (ET‐1), induced by the LPS of a periodontopathic bacterium P. gingivalis. We show that P. gingivalis LPS detrimental effect on salivary mucin synthesis, associated with up‐regulation (3.9‐fold) in ET‐1 generation and the enhancement (3.2‐fold) in endothelin‐converting enzyme‐1 (ECE‐1) activity, was subject to a dose‐dependent suppression by leptin. The impedance by leptin of the LPS inhibitory effect on mucin synthesis was blocked by wortmannin, an inhibitor of PI3K, as well as by ERK inhibitor, PD98059. However, while the blockade of ERK led also to amplification in the impedance by leptin of the LPS‐induced expression of ECE‐1 and ET‐1, the effect was not observed in the presence of wortmannin. The findings are the first to demonstrate that leptin counters the pathological consequences of P. gingivalis infection on the synthesis of salivary mucin through the involvement in signaling events of PI3K and ERK pathways. We also show that the ERK cascade represents a critical signaling target for leptin in the LPS‐induced up‐regulation in ET‐1.
IUBMB Life, 57: 591‐595, 2005