A new approach to possible substrate binding mechanisms for nitrile hydratase.

Abstract:

:We combined normal mode analysis (NMA) with cavity calculations as a method to get more insight into static crystal structures. We used nitrile hydratase (NHase) as a case study, and the crystal structure of a complex of Pseudonocardia thermophila NHase (1UGP) with n-butyric acid was chosen as a reference structure. The reference structure was compared with the other available NHase crystal structures. Cavity calculations of the static structures showed the entrances to the active site and also a possible function of the N-terminal in the substrate selection of the Co-type NHase. When NMA was combined with cavity calculations, a closing-opening passage was observed. Analysis of low frequency modes combined with cavity calculations led us to propose "breathing" and "flip-flop" mechanisms which might be a key part of the substrate binding mechanism.

authors

Taştan Bishop AO,Sewell T

doi

10.1016/j.bbrc.2006.02.150

subject

Has Abstract

pub_date

2006-04-28 00:00:00

pages

319-25

issue

1

eissn

0006-291X

issn

1090-2104

pii

S0006-291X(06)00420-7

journal_volume

343

pub_type

杂志文章
  • A new form of amyloid protein associated with chronic hemodialysis was identified as beta 2-microglobulin.

    abstract::Amyloid fibrils were isolated from amyloid-laden tissue obtained from a chronic hemodialysis patient with carpal tunnel syndrome. After solubilization in guanidine HCl, a significant amount of the protein was located in a homogeneous low molecular weight fraction. The protein was found to be identical to beta 2-microg...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/0006-291x(85)91948-5

    authors: Gejyo F,Yamada T,Odani S,Nakagawa Y,Arakawa M,Kunitomo T,Kataoka H,Suzuki M,Hirasawa Y,Shirahama T

    更新日期:1985-06-28 00:00:00

  • Loss of MURC/Cavin-4 induces JNK and MMP-9 activity enhancement in vascular smooth muscle cells and exacerbates abdominal aortic aneurysm.

    abstract::Abdominal aortic aneurysm (AAA) is relatively common in elderly patients with atherosclerosis. MURC (muscle-restricted coiled-coil protein)/Cavin-4 modulating the caveolae function of muscle cells is expressed in cardiomyocytes, skeletal muscle cells and smooth muscle cells. Here, we show a novel functional role of MU...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2017.04.096

    authors: Miyagawa K,Ogata T,Ueyama T,Kasahara T,Nakanishi N,Naito D,Taniguchi T,Hamaoka T,Maruyama N,Nishi M,Kimura T,Yamada H,Aoki H,Matoba S

    更新日期:2017-06-03 00:00:00

  • Over expression of the murine myotonic dystrophy protein kinase in the mouse myogenic C2C12 cell line leads to inhibition of terminal differentiation.

    abstract::Myotonic dystrophy (DM) is an autosomal dominant human disorder, caused by the abnormal expansion of a CTG trinucleotide repeat in the 3' untranslated region of a protein kinase gene (DMPK). Muscle symptoms are a common feature of the disorder and in the adult onset cases there are increased patterns of muscle fibre d...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1998.8723

    authors: Okoli G,Carey N,Johnson KJ,Watt DJ

    更新日期:1998-05-29 00:00:00

  • Calmodulin-dependent phosphorylation and dephosphorylation during fertilization in Dictyostelium discoideum.

    abstract::Many calmodulin-dependent biological phenomena are regulated by calmodulin-dependent phosphorylation and dephosphorylation. In Dictyostelium discoideum, cell and pronuclear fusion during fertilization are both calmodulin-dependent biomembrane fusion events. Calmodulin-dependent phosphorylation and dephosphorylation ac...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1993.1526

    authors: Lydan MA,O'Day DH

    更新日期:1993-05-14 00:00:00

  • Lipoprotein lipase: role of intramolecular disulfide bonds in enzyme catalysis.

    abstract::Lipoprotein lipase (LPL) catalyzes the hydrolysis of the triacylglycerol component of triacylglycerol-rich lipoproteins. There are 4 cysteine pairs that are completely conserved among LPLs of all species known. We examined the functional importance of each of the cysteine pairs in enzyme catalysis by examining LPLs pr...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1995.1037

    authors: Lo JY,Smith LC,Chan L

    更新日期:1995-01-05 00:00:00

  • The inhibition of progesterone secretion and the regulation of cyclic nucleotides by atrial natriuretic factor in gonadotropin responsive murine Leydig tumor cells.

    abstract::We have found that atrial natriuretic factor (ANF) has a profound effect on testicular cells in altering intracellular cyclic nucleotide levels as well as progesterone secretion. Using clonal cultured Leydig tumor cells we found that 1 X 10(-8)M ANF caused a two thousand-fold elevation in the accumulation of cellular ...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/0006-291x(85)90975-1

    authors: Pandey KN,Kovacs WJ,Inagami T

    更新日期:1985-12-17 00:00:00

  • Highly expressed lncRNA CCND2-AS1 promotes glioma cell proliferation through Wnt/β-catenin signaling.

    abstract::Glioma is the most common and aggressive primary brain tumor in adults. Long-non coding RNAs (lncRNAs) have been recently shown to play important roles in regulating numerous biological processes both in physiologic and pathologic condition. However, the role of lncRNAs in glioma remains largely unknown. In this study...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2016.12.016

    authors: Zhang H,Wei DL,Wan L,Yan SF,Sun YH

    更新日期:2017-01-22 00:00:00

  • The carbohydrate structures of Trypanosoma brucei brucei MITat 1.6 variant surface glycoprotein. A re-investigation of the C-terminal glycan.

    abstract::We have studied the oligosaccharide chains of the variant surface glycoprotein (VSG) of Trypanosoma brucei brucei MITat 1.6. Glycopeptides were generated by Pronase digestion, purified by gel permeation and ion-exchange chromatography, and structurally characterized by 1H and 31P NMR spectroscopy in combination with c...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1993.2412

    authors: Strang AM,Allen AK,Holder AA,van Halbeek H

    更新日期:1993-11-15 00:00:00

  • DMLR: A toolkit for investigation of deoxyribozyme-mediated ligation based on real time PCR.

    abstract::Deoxyribozymes or DNAzyme are identified as catalytic DNA sequences which catalyze different chemical reactions. Ligating deoxyribozymes catalyze the formation of branched and linear products. Due to the lack of efficient read-out systems, there is no report on in vivo application of ligating deoxyribozymes. To expand...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2020.01.075

    authors: Dehghanian F,Najafi ZB,Hojati Z,Javadi-Zarnaghi F

    更新日期:2020-04-02 00:00:00

  • Recognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies.

    abstract::Immediately from the outset of the COVID-19 pandemic, researchers from diverse biomedical and biological disciplines have united to study the novel pandemic virus, SARS-CoV-2. The antibody response to SARS-CoV-2 has been a major focus of COVID-19 research due to its clinical relevance and importance in vaccine and the...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2020.10.012

    authors: Yuan M,Liu H,Wu NC,Wilson IA

    更新日期:2020-10-10 00:00:00

  • Calmodulin and protein kinase C antagonists also inhibit the Ca2+-dependent protein protease, calpain I.

    abstract::The calmodulin and C-kinase antagonists melittin, calmidazolium, N-(6-aminohexyl)-5-chloro-1-napthalenesulfonamide (W7), and trifluoperazine (TFP) also inhibit the activity of the human erythrocyte Ca2+-dependent protease, calpain I. W-5, the nonchlorinated derivative of W-7, was ineffective as an inhibitor of calpain...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/0006-291x(89)92251-1

    authors: Brumley LM,Wallace RW

    更新日期:1989-03-31 00:00:00

  • A genome-wide screening in Saccharomyces cerevisiae for genes that confer resistance to the anticancer agent cisplatin.

    abstract::Cisplatin is a potent DNA-damaging agent that has demonstrated anticancer activities against several tumors. However, manifestation of cellular resistance is a major obstacle in anticancer therapy that severely limits the curative potential of cisplatin. Therefore, understanding the molecular basis of cisplatin resist...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.2000.2361

    authors: Burger H,Capello A,Schenk PW,Stoter G,Brouwer J,Nooter K

    更新日期:2000-03-24 00:00:00

  • Sensitivity/resistance profile of a simian immunodeficiency virus containing the reverse transcriptase gene of human immunodeficiency virus type 1 (HIV-1) toward the HIV-1-specific non-nucleoside reverse transcriptase inhibitors.

    abstract::To develop an animal model for the therapy of AIDS with human immunodeficiency virus type 1 (HIV-1)-specific reverse transcriptase (RT) inhibitors, we recently constructed a hybrid simian immunodeficiency virus (SIV)/HIV-1 in which the RT gene of SIV was replaced by the RT gene of HIV-1. This chimaeric virus, designat...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1995.1890

    authors: Balzarini J,Weeger M,Camarasa MJ,De Clercq E,Uberla K

    更新日期:1995-06-26 00:00:00

  • PIH1D1, a subunit of R2TP complex, inhibits doxorubicin-induced apoptosis.

    abstract::We have previously reported that the two components of R2TP complex, RNA polymerase II-associated protein 3 (RPAP3), and Reptin, regulate apoptosis. Here we characterize another component of the complex, PIH1 domain containing protein 1 (PIH1D1). PIH1D1 interacts with both RPAP3 and Monad in HEK293 or U2OS cells. PIH1...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2010.11.031

    authors: Inoue M,Saeki M,Egusa H,Niwa H,Kamisaki Y

    更新日期:2010-12-17 00:00:00

  • Mapping of the MRPm5 epitope to the cytosolic region between transmembrane helices 13 and 14 in the drug and organic anion transporter, MRP1 (ABCC1).

    abstract::Multidrug resistance in human tumour cells is often associated with increased expression of the 190kDa multidrug resistance protein, MRP1, that belongs to the ATP-binding cassette superfamily of transport proteins. MRP1 is also an efficient transporter of many organic anions. In the present study, we have mapped the e...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2004.01.111

    authors: Koike K,Deeley RG,Cole SP

    更新日期:2004-03-12 00:00:00

  • The glucocorticoid receptor in the distal nephron is not necessary for the development or maintenance of dexamethasone-induced hypertension.

    abstract::Glucocorticoids are used as a treatment for a variety of conditions and hypertension is a well-recognized side effect of their use. The mechanism of glucocorticoid-induced hypertension is incompletely understood and has traditionally been attributed to promiscuous activation of the mineralocorticoid receptor by cortis...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2010.02.123

    authors: Goodwin JE,Zhang J,Velazquez H,Geller DS

    更新日期:2010-04-02 00:00:00

  • Loss of alpha I type I collagen gene expression in rat clonal bone cell lines is accompanied by DNA methylation.

    abstract::Four clonal cell lines subcloned from a clonal population of fetal rat calvaria cells show a loss of type I collagen synthesis. Northern blot analysis showed that the level of alpha 1(I) collagen mRNA expression in each of the clonal populations parallels the level of collagen protein expression in each of these cell ...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/0006-291x(89)90836-x

    authors: Waye MM,Robinson R,Orfanides AG,Aubin JE

    更新日期:1989-08-15 00:00:00

  • Species dependence of mitochondrial calcium transients during excitation-contraction coupling in isolated cardiomyocytes.

    abstract::Whether mitochondrial Ca(2+) transport is rapid enough to respond to changes in cytosolic [Ca(2+)] ([Ca(2+)](c)) which occur during excitation-contraction coupling in the heart is controversial; different results wereobtained with different techniques and different species. In this study mitochondrial [Ca(2+)] ([Ca(2+...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1999.1311

    authors: Griffiths EJ

    更新日期:1999-09-24 00:00:00

  • Polymorphisms of TNFalpha, IL1beta, and IL1RN genes in chronic obstructive pulmonary disease.

    abstract::It is recognized that genetic factors play a role in the susceptibility to COPD. COPD is characterized by airflow limitation. Chronic inflammation causes small airway disease and parenchymal destruction, leading to the airflow limitation. Polymorphisms in pro-inflammatory cytokine genes may confer a risk for the devel...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2005.02.099

    authors: Hegab AE,Sakamoto T,Saitoh W,Nomura A,Ishii Y,Morishima Y,Iizuka T,Kiwamoto T,Matsuno Y,Massoud HH,Massoud HM,Hassanein KM,Sekizawa K

    更新日期:2005-04-22 00:00:00

  • Activation of glutathione peroxidase via Nrf1 mediates genistein's protection against oxidative endothelial cell injury.

    abstract::Cellular actions of isoflavones may mediate the beneficial health effects associated with high soy consumption. We have investigated protection by genistein and daidzein against oxidative stress-induced endothelial injury. Genistein but not daidzein protected endothelial cells from damage induced by oxidative stress. ...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2006.05.197

    authors: Hernandez-Montes E,Pollard SE,Vauzour D,Jofre-Montseny L,Rota C,Rimbach G,Weinberg PD,Spencer JP

    更新日期:2006-08-04 00:00:00

  • Role of Wnt10b and C/EBPalpha in spontaneous adipogenesis of 243 cells.

    abstract::This report examines the balance of positive and negative adipogenic factors in a line of immortalized 243 embryonic fibroblasts that undergo spontaneous preadipocyte differentiation. Control of adipogenesis reflects the interplay of factors that promote or inhibit expression of C/EBPalpha and PPARgamma. The 243 cells...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/s0006-291x(03)00092-5

    authors: Bennett CN,Hodge CL,MacDougald OA,Schwartz J

    更新日期:2003-02-28 00:00:00

  • The role of EXT1 gene mutation and its high expression of calcitonin gene-related peptide in the development of multiple exostosis.

    abstract:OBJECTIVE:Screening and identifying the gene mutation of EXT1, EXT2 and EXT3 associated with multiple exostosis (ME) and the expression in tumor tissues. METHODS:Nine patients with multiple exostosis were collected and genomic DNA was extracted. Polymerase chain reaction (PCR) amplification and direct sequencing techn...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2018.09.115

    authors: Wu ZY,Wang Y,Wang JW,Chen YZ,Guo Y

    更新日期:2018-11-10 00:00:00

  • A partially folded structure of amyloid-beta(1-40) in an aqueous environment.

    abstract::Aggregation of the Aβ(1-40) peptide is linked to the development of extracellular plaques characteristic of Alzheimer's disease. While previous studies commonly show the Aβ(1-40) is largely unstructured in solution, we show that Aβ(1-40) can adopt a compact, partially folded structure. In this structure (PDB ID: 2LFM)...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2011.06.133

    authors: Vivekanandan S,Brender JR,Lee SY,Ramamoorthy A

    更新日期:2011-07-29 00:00:00

  • Respiratory syncytial virus infection activates STAT signaling in human epithelial cells.

    abstract::Acute respiratory syncytial virus (RSV) infection causes airway inflammation and exacerbates asthma, but the mechanism of inflammation is poorly understood. The role of the STAT-signaling pathway in RSV infection in epithelial cells was examined in this study. DNA microarray analyses of RSV-infected human alveolar typ...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/s0006-291x(03)01008-8

    authors: Kong X,San Juan H,Kumar M,Behera AK,Mohapatra A,Hellermann GR,Mane S,Lockey RF,Mohapatra SS

    更新日期:2003-06-27 00:00:00

  • MicroRNA-21 promotes cell proliferation and down-regulates the expression of programmed cell death 4 (PDCD4) in HeLa cervical carcinoma cells.

    abstract::MicroRNAs are involved in cancer-related processes. The microRNA-21(miR-21) has been identified as the only miRNA over-expressed in a wide variety of cancers, including cervical cancer. However, the function of miR-21 is unknown in cervical carcinomas. In this study, we found that the inhibition of miR-21 in HeLa cerv...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2009.08.044

    authors: Yao Q,Xu H,Zhang QQ,Zhou H,Qu LH

    更新日期:2009-10-23 00:00:00

  • Mouse CD24 as a signaling molecule for integrin-mediated cell binding: functional and physical association with src-kinases.

    abstract::CD24 is a differentiation antigen expressed by murine hematopoietic and neural cells which is linked to the membrane via a glycosylphosphatidylinositol (GPI) anchor. In monocytic ESb-MP cells the molecule serves as a ligand for P-selectin and triggering with CD24 specific antibodies can activate VLA-5/L1-mediated cell...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1997.6639

    authors: Sammar M,Gulbins E,Hilbert K,Lang F,Altevogt P

    更新日期:1997-05-19 00:00:00

  • Trypanosome H2Bv replaces H2B in nucleosomes enriched for H3 K4 and K76 trimethylation.

    abstract::Some inroads have been made into characterizing histone variants and post translational modifications of histones in Trypanosoma brucei. Histone variant H2BV lysine 129 is homologous to Saccharomyces cerevisiae H2B lysine 123, whose ubiquitination is required for methylation of H3 lysines 4 and 79. We show that T. bru...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/j.bbrc.2008.01.144

    authors: Mandava V,Janzen CJ,Cross GA

    更新日期:2008-04-18 00:00:00

  • cDNA cloning of a murine homologue of Drosophila single-minded, its mRNA expression in mouse development, and chromosome localization.

    abstract::A combination of the RT-PCR method and subsequent screening of the cDNA library of mouse skeletal muscle with the cDNA isolated by RT-PCR used as a probe led to isolation of cDNAs encoding a polypeptide (mSim) with bHLH and PAS domains which show high similarity to the corresponding regions of Drosophila Sim, a master...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1006/bbrc.1996.0104

    authors: Ema M,Suzuki M,Morita M,Hirose K,Sogawa K,Matsuda Y,Gotoh O,Saijoh Y,Fujii H,Hamada H,Fujii-Kuriyama Y

    更新日期:1996-01-17 00:00:00

  • Production of recombinant xenotransplantation antigen in Escherichia coli.

    abstract::The synthesis of sufficient amounts of oligosaccharides is the bottleneck for the study of their biological function and their possible use as drug. As an alternative for chemical synthesis, we propose to use Escherichia coli as a "living factory." We have addressed the production of the Galp alpha(1-3)Galp beta(1-4)G...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/s0006-291x(03)00227-4

    authors: Bettler E,Imberty A,Priem B,Chazalet V,Heyraud A,Joziasse DH,Geremia RA

    更新日期:2003-03-14 00:00:00

  • Analysis of the close relationship between human astrocytoma-specific antigens detected by murine monoclonal antibodies and c-kit proto-oncogene product.

    abstract::Tyrosine-specific phosphorylated proteins found exclusively on the cell surface of human astrocytomas were previously identified with murine monoclonal antibodies, designated as GA-17, GB-4 and GC-3. The purpose of this study was to further characterize the antigens and investigate the relationship between them and c-...

    journal_title:Biochemical and biophysical research communications

    pub_type: 杂志文章

    doi:10.1016/0006-291x(92)91756-g

    authors: Kondo S,Miyatake S,Matsumoto M,Nakatsu S,Iwasaki K,Oda Y,Kikuchi H,Namba Y

    更新日期:1992-01-31 00:00:00