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1.
Junlong Ma Heng Chen Jie Yang Zutao Yu Pan Huang Haofeng Yang Bifeng Zheng Rangru Liu Qianbin Li Gaoyun Hu Zhuo Chen 《Bioorganic & medicinal chemistry》2019,27(9):1871-1881
Bromodomain-containing protein 4 (BRD4), consisting of two tandem bromodomains (BD1 and BD2), is key epigenetic regulator in fibrosis and cancer, which has been reported that BD1 and BD2 have distinct roles in post-translational modification. But there are few selective inhibitors toward those two domains. Herein, this study designed and synthesized a series of novel selective BRD4-BD1 inhibitors, using computer-aided drug design (CADD) approach focused on exploring the difference of the binding pockets of BD1 and BD2, and finding the His437 a crucial way to achieve BRD4-BD1 selectivity. Our results revealed that the compound 3u is a potent selective BRD4-BD1 inhibitor with IC50 values of 0.56?μM for BD1 but >100?μM for BD2. The compound exhibited a broad spectrum of anti-proliferative activity against several human cancer and fibroblastic cell lines, which might be related to its capability of reducing the expression of c-Myc and collagen I. Furthermore, it could induce apoptosis in A375 cells. To the contrary, the selective BD2 inhibitor, RVX-208, did not indicate any of these activities. Our findings highlight that the function of BRD4-BD1 might be predominant in fibrosis and cancer. And it is rational to further develop novel selective BRD4-BD1 inhibitors. 相似文献
2.
The structure of root-associated bacterial populations in the legume common bean (Phaseolus vulgaris L.), was studied in plants grown under nitrogen sufficiency and under conditions inducing nitrogen deficiency. Similar cell
numbers were obtained in the rhizosphere of nitrogen-amended plants as compared to nitrogen-deficient plants and between various
root parts—tip, elongation and branching zones—using DAPI staining. In contrast, a higher proportion of DAPI-stained cells
from the nitrogen-amended plants hybridized with a fluorescence-labeled EUB338 probe for theBacteria domain than cells originating from nitrogen-deficient plants. Shifts in the percentages of EUB338-reactive cells—as well
as in absolute cell number—hybridizing to fluorescent rRNA-directed probes specific for the α and γProteobacteria and for high GC content gram-positive bacteria in separated root segments were detected between the treatments. No such differences
were found using β and δProteobacteria or rRNA group I pseudomonad targeted probes. Denaturating gradient gel electrophoresis profiles of PCR products obtained
from the same samples and amplified withBacteria-domain targeted primers supported the results obtained with the whole cell hybridizations. The advantages and drawbacks of
the techniques applied are discussed. 相似文献
3.
Qianqian Wang Ying Li Jiahui Xu Yuwei Wang Danfeng Shi Liang Liu Elaine Lai-Han Leung Xiaojun Yao 《Proteins》2019,87(1):3-11
As a member of the bromodomain and extraterminal domain (BET) family, BRD4 is considered as a potential target for cancer treatment. However, because of the highly conservation of its two homologous bromodomains (BD1/BD2), selective inhibition of each bromodomain remains a challenge. MS402 is a domain-selective inhibitor of BRD4-BD1 over BRD4-BD2 reported recently. Understanding the selectivity mechanism would be very useful for the further design of more potent BD1-selectivity inhibitors. Molecular dynamics simulation, adaptive biasing force and multiple-walker adaptive biasing force were performed to study the inhibition and domain-selective mechanism of MS402 toward BRD4-BD1 over BRD4-BD2 here. Results demonstrate BRD4-BD1 binds to MS402 with lower binding free energy than BRD4-BD2. Residues Gln85, Pro86, Asn140, and Ile146 are crucial for MS402's selectively binding to BRD4-BD1. MS402 needs to overcome more energy barrier to dissociate from BD1 than from BD2 pocket. These findings will be helpful for rational structural modification of existing inhibitors to increase their BD1-selectivity. 相似文献
4.
V. P. Ivanova A. I. Krivchenko 《Journal of Evolutionary Biochemistry and Physiology》2012,48(2):127-139
This review summarizes current data of structure of the most representative group of superfamily of collagens—fibrillar collagens. The attention is focused on structural organization of individual domains and their functional role in the hierarchical stacking of collagen α-chains. There are presented characteristics of the main stages of biosynthesis and the supramolecular processing of fibrillar collagens. Also considered are some aspects of evolution of fibrillar collagens. The role of duplication of genome and genes, intergene combination, and translocation of exons in evolution of collagen genes is discussed. 相似文献
5.
Zhi-Chun Ding Qi Zheng Bin Cai Wen-Hao Yu Xin-Chen Teng Yang Wang Guo-Ming Zhou Hou-Ming Wu Hong-Zhe Sun Ming-Jie Zhang Zhong-Xian Huang 《Journal of biological inorganic chemistry》2007,12(8):1173-1179
Human metallothionein-3 (hMT3), also named human neuronal growth inhibitory factor (hGIF), is attractive due to its distinct
neuronal growth inhibitory activity, which is not shown by other human MT isoforms. It has been reported that the neuronal
growth inhibitory activity arises from the N-terminal β-domain rather than its C-terminal α-domain. However, previous bioassay
results have shown that the single β-domain is less effective at inhibiting the neuron growth than that in intact hMT3 on
a molar basis, which suggests that the α-domain is indispensable to the neuronal growth inhibitory activity of hMT3. In order
to confirm this assumption, we constructed two domain-hybrid mutants, the β(MT3)–β(MT3) mutant and the β(MT3)–α(MT1) mutant,
and investigated their structural and metal binding properties by UV-vis spectroscopy, CD spectroscopy, pH titration, DTNB
reaction, EDTA reaction, etc. The results showed that stability of the Cd3S9 cluster of the β(MT3)–β(MT3) mutant decreased significantly while the Cd3S9 cluster of the β(MT3)–α(MT1) mutant had a similar stability and solvent accessibility to that of hMT3. Interestingly, the
bioassay results showed that the neuronal growth inhibitory activity of the β(MT3)–β(MT3) mutant decreased significantly,
while the β(MT3)–α(MT1) mutant showed similar inhibitory activity to hMT3. Based on these results, we conclude that the α-domain
is indispensable and plays an important role in modulating the stability of the metal cluster in the β-domain by domain–domain
interactions, thus influencing the bioactivity of hMT3.
Z.-C. Ding and Q. Zheng contributed equally to this work. 相似文献
6.
Retinoid X receptors (RXRα, β and γ) are recently known to be cancer chemotherapies targets. The ligand binding domains of
RXRs have been crystallized, but the information of RXRγ ligand binding site is not yet available due to the lack of liganded
complex. A thorough understanding of the ligand binding sites is essential to study RXRs and may result in cancer therapeutic
breakthrough. Thus we aimed to study the RXRγ ligand binding site and find out the differences between the three subtypes.
Alignment and molecular simulation were carried out for identifying the RXRγ ligand binding site, characterizing the RXRγ
ligand binding mode and comparing the three RXRs. The result has indicated that the RXRγ ligand binding site is defined by
helices H5, H10, β-sheet s1 and the end loop. Besides hydrophobic interactions, the ligand 9-cis retinoic acid interacts with
RXRγ through a hydrogen bond with Ala106, a salt bridge with Arg95 and the π-π interactions with Phe217 and Phe218. The binding
modes exhibit some similarities among RXRs, such as the interactions with Arg95 and Ala106. Nonetheless, owing to the absence
of Ile47, Cys48, Ala50, Ala51 and residues 225∼237 in the active site, the binding pocket in RXRγ is two times larger than
those of RXRα and RXRβ. Meanwhile, spatial effects of Trp84, Arg95, Ala106, Phe217 and Phe218 help to create a differently
shaped binding pocket as compared to those of RXRα and RXRβ. Consequently, the ligand in RXRγ undergoes a “standing” posing
which is distinct from the other two RXRs. 相似文献
7.
Giuseppe Digilio Chiara Bracco Laura Vergani Mauro Botta Domenico Osella Aldo Viarengo 《Journal of biological inorganic chemistry》2009,14(2):167-178
The metal–thiolate connectivity of recombinant Cd7-MT10 metallothionein from the sea mussel Mytilus galloprovincialis has been investigated for the first time by means of multinuclear, multidimensional NMR spectroscopy. The internal backbone
dynamics of the protein have been assessed by the analysis of 15N T
1 and T
2 relaxation times and steady state {1H}–15N heteronuclear NOEs. The 113Cd NMR spectrum of mussel MT10 shows unique features, with a remarkably wide dispersion (210 ppm) of 113Cd NMR signals. The complete assignment of cysteine Hα and Hβ proton resonances and the analysis of 2D 113Cd–113Cd COSY and 1H–113Cd HMQC type spectra allowed us to identify a four metal–thiolate cluster (α-domain) and a three metal–thiolate cluster (β-domain),
located at the N-terminal and the C-terminal, respectively. With respect to vertebrate MTs, the mussel MT10 displays an inversion
of the α and β domains inside the chain, similar to what observed in the echinoderm MT-A. Moreover, unlike the MTs characterized
so far, the α-domain of mussel Cd7-MT10 is of the form M4S12 instead of M4S11, and has a novel topology. The β-domain has a metal–thiolate binding pattern similar to other vertebrate MTs, but it is conformationally
more rigid. This feature is quite unusual for MTs, in which the β-domain displays a more disordered conformation than the
α-domain. It is concluded that in mussel Cd7-MT10, the spacing of cysteine residues and the plasticity of the protein backbone (due to the high number of glycine residues)
increase the adaptability of the protein backbone towards enfolding around the metal–thiolate clusters, resulting in minimal
alterations of the ideal tetrahedral geometry around the metal centres. 相似文献
8.
Subunit interactions among the chloroplast ATP synthase subunits were studied using the yeast two-hybrid system. Various pairwise
combinations of genes encoding α, β, γ, δ and ε subunits ofSpinach ATP synthase fused to the binding domain or activation domain of GAL4 DNA were introduced into yeast and then expression
of a reporter gene encoding β-galactosidase was detected. Of all the combinations, that of γ and ε subunit genes showed the
highest level of reporter gene expression, while those of α and β, a and ε, β and ε and β and δ induced stable and significant
reporter gene expression. The combination of δ and ε as well as that of δ and γ induced weak and unstable reporter gene expression.
However, combinations of α and γ, β and γ and α and δ did not induce reporter gene expression. These results suggested that
specific and strong interactions between γ and ε, α and β, α and ε, β and ε and β and δ subunits, and weak and transient interactions
between δ and ε and δ and γ subunits occurred in the yeast cell in the two-hybrid system. These results give a new look into
the structural change of ATP synthase during catalysis. 相似文献
9.
Using yeast two-hybrid system to detect interactions of ATP synthase subunits from Spinacia oleracea
Subunit interactions among the chloroplast ATP synthase subunits were studied using the yeast two-hybrid system. Various pairwise
combinations of genes encoding α, β, γ, δ and ε subunits ofSpinach ATP synthase fused to the binding domain or activation domain of GAL4 DNA were introduced into yeast and then expression
of a reporter gene encoding β-galactosidase was detected. Of all the combinations, that of γ and ε subunit genes showed the
highest level of reporter gene expression, while those of α and β, a and ε, β and ε and β and δ induced stable and significant
reporter gene expression. The combination of δ and ε as well as that of δ and γ induced weak and unstable reporter gene expression.
However, combinations of α and γ, β and γ and α and δ did not induce reporter gene expression. These results suggested that
specific and strong interactions between γ and ε, α and β, α and ε, β and ε and β and δ subunits, and weak and transient interactions
between δ and ε and δ and γ subunits occurred in the yeast cell in the two-hybrid system. These results give a new look into
the structural change of ATP synthase during catalysis. 相似文献
10.
A. P. Kolychev 《Journal of Evolutionary Biochemistry and Physiology》2008,44(6):766-785
The common plan of structure of the main peptides of the vertebrate insulin family—insulin itself, IGF-I, IGF-II, and relaxin—has distinct structural formations. Each of the peptides performs its characteristic function. However, overlapping of insulin and IGF-I actions and its stability in the vertebrate phylogenesis have formed the concept of their regulation of growth and metabolism as a function fixed in phylogenesis for a certain type of structures. At the same time, study of insulin-related peptides in invertebrates has revealed the wider spectrum, than in vertebrates, of biological effects; this indicated that the similarity of the total structure design is not sufficient for judging about their functional role. Functional possibilities of a regulatory peptide depend fundamentally on its capability for binding to the receptor realizing its biological action. However, the binding ability has a wider significance than merely transmission of biological signals. Thus, IGF-II when interacting with receptors realizing its biological effects also binds to the IGF-2 receptor limiting its action and, besides, to the binding proteins (BP) modulating its action. The entire cycle of interactions occurs in the body at different affinity levels. Meanwhile, insulin interacts neither with IGF-2 receptor nor with BP. In this case, specificity and sequence of interaction with each of receptors or with protein are due not to the general design of the peptide structure, but rather to structure of individual submolecular determinants—binding domains. The leading role in disclosure of composition and structure of these domains is played by the “mutant-ligand” approach evaluating affinity of modified analogs. To analyze role of structural elements of the binding domains, the author proposes the system of estimation of affinity of the studied analogs. The present work, alongside with consideration of methodical aspects of the forthcoming analysis, is an introduction to the problem of organization of the binding domains connected directly with functional role of peptides of the insulin type. The proposed analysis is due to necessity of specification of this organization both in one molecule and in different molecules with a similar plan of structure on the basis of not always unanimous literature data and of clarification of principles of structure of these domains. 相似文献
11.
12.
Vuk Micovic Milovan D. Ivanovic Ljiljana Dosen-Micovic 《Journal of molecular modeling》2009,15(3):267-280
An automated docking procedure was used to study binding of a series of δ-selective ligands to three models of the δ-opioid
receptor. These models are thought to represent the three ligand-specific receptor conformations. Docking results are in agreement
with point mutation studies and suggest that different ligands—agonists and antagonists—may bind to the same binding site
under different receptor conformations. Docking to different receptor models (conformations) also suggests that by changing
to a receptor-specific conformation, the receptor may open or close different binding sites to other ligands.
Figure Ligands 5 (green) and 6 (orange) in bindingpocket BP1 of the R1 δ-opioid receptor model 相似文献
13.
Iren Wang Yuan-Chao Lou Yu-Ching Lin Shih-Chi Lo Alan Yueh-Luen Lee Shih-Hsiung Wu Chinpan Chen 《Biomolecular NMR assignments》2007,1(2):201-203
The small α-domain of Lon protease is thought to carry the substrate-recognition, nucleotide-binding, and DNA-binding sites.
Here we report the complete resonance assignment of the α-domain for Bacillus subtilis Lon protease (Bs-Lon α-domain). 相似文献
14.
Enterobacter cloacae NRRL B-23289 was isolated from local decaying wood/corn soil samples while screening for microorganisms for conversion of
l-arabinose to fuel ethanol. The major product of fermentation by the bacterium was meso-2,3-butanediol (2,3-BD). In a typical
fermentation, a BD yield of 0.4 g/g arabinose was obtained with a corresponding productivity of 0.63 g/l per hour at an initial
arabinose concentration of 50 g/l. The effects of initial arabinose concentration, temperature, pH, agitation, various monosaccharides,
and multiple sugar mixtures on 2,3-BD production were investigated. BD productivity, yield, and byproduct formation were influenced
significantly within these parameters. The bacterium utilized sugars from acid plus enzyme saccharified corn fiber and produced
BD (0.35 g/g available sugars). It also produced BD from dilute acid pretreated corn fiber by simultaneous saccharification
and fermentation (0.34 g/g theoretical sugars).
Received: 17 December 1998 / Revision received: 9 March 1999 / Accepted: 20 March 1999 相似文献
15.
Coagulation factor X (FX) zymogen activation by factor IXa (FIXa) enzyme plays a critical role in the middle-phase of coagulation cascade. The activation process is catalytically inert and requires FIXa binding and complex formation with co-factor VIIIa (FVIIIa). In order to understand the structural details of the FVIIIa:FIXa complex, we employed knowledge-driven protein–protein docking and aqueous-phase MD refinement methods to develop a stable structural complex between FVIIIa and FIXa. The model shows that all four domains of FIXa wrap across FVIIIa that spans the co-factor binding surface of A2, A3 and C1 domains. The region surrounding the 558-helix of the A2-domain of FVIIIa is predicted to be the key interaction site with the helical segments of Lys293–Lys301 and Asp332–Arg338 residues of the serine-protease domain of FIXa. The hydrophobic helical stack between the GLA and EGF1 domains of FIXa is predicted to be primary interacting region with the A3–C2 domain interface of FVIIIa. 相似文献
16.
Integrin αXβ2 performs a significant role in leukocyte functions including phagocytosis and migration, and binds to a variety
of ligands, including fibrinogen, iC3b, and ICAM-1. A particular domain of the α subunit of the integrin — the αX I-domain
— is a ligand binding site, and the interaction of the αX I-domain and ICAM-1 on the endothelium is an important step in leukocyte
extravasation. In order to elucidate the structural aspects of this interaction, we defined the moieties of the αX and ICAM-1
relevant to their interaction in this study. It was determined that the ICAM-1 binding sites of the αX I-domain were located
in the α3α4, βDα5, and βFα7 loops at the top surface of the I-domain. The residues Q202, K242, K243, E298 and D299 on these loops were crucial for the recognition of ICAM-1. Among these residues, K242 and K243 on the βDα5 loop were found to be the most salient, thereby suggesting an ionic interaction between these proteins. Domain
3 of ICAM-1 was identified as a primary binding site for the αX I-domain. Two regions of domain 3 (D229QRLNPTV and E254DEGTQRL) perform critical functions in the binding of the αX I-domain. Especially, the residue E254DEG, is most important with regard to the αX I-domain. 相似文献
17.
Pedro J. Silva Baltazar de Castro W. R. Hagen 《Journal of biological inorganic chemistry》1999,4(3):284-291
The sulfhydrogenase complex of Pyrococcus furiosus is an αβγδ heterotetramer with both hydrogenase activity (borne by the αδ subunits) and sulfur reductase activity (carried
by the βγ subunits). The β-subunit contains at least two [4Fe-4S] cubanes and the γ-subunit contains one [2Fe-2S] cluster
and one FAD molecule. The δ-subunit contains three [4Fe-4S] cubanes and the α-subunit carries the NiFe dinuclear center. Only
three Fe/S signals are observed in EPR-monitored reduction by dithionite, NADPH, or internal substrate upon heating. All other
clusters presumably have reduction potentials well below that of the H+/H2 couple. Heat-induced reduction by internal substrate allows, for the first time, EPR monitoring of the NiFe center in a hyperthermophilic
hydrogenase, which passes through a number of states, some of which are similar to states previously defined for mesophilic
hydrogenases. The complexity of the observed transitions reflects a combination of temperature-dependent activation and temperature-dependent
reduction potentials.
Received: 10 December 1998 / Accepted: 16 February 1999 相似文献
18.
Identification of functionally important amino acid residues within the C2-domain of human factor V using alanine-scanning mutagenesis 总被引:9,自引:0,他引:9
Kim SW Quinn-Allen MA Camp JT Macedo-Ribeiro S Fuentes-Prior P Bode W Kane WH 《Biochemistry》2000,39(8):1951-1958
We have previously determined that the C2-domain of human factor V (residues 2037-2196) is required for expression of cofactor activity and binding to phosphatidylserine (PS)-containing membranes. Naturally occurring factor V inhibitors and a monoclonal antibody (HV-1) recognized epitopes in the amino terminus of the C2-domain (residues 2037-2087) and blocked PS binding. We have now investigated the function of individual amino acids within the C2-domain using charge to alanine mutagenesis. Charged residues located within the C2-domain were changed to alanine in clusters of 1-3 mutations per construct. In addition, mutants W2063A, W2064A, (W2063, W2064)A, and L2116A were constructed as well. The resultant 30 mutants were expressed in COS cells using a B-domain deleted factor V construct (rHFV des B). All mutants were expressed efficiently based on the polyclonal antibody ELISA. The charged residues, Arg(2074), Asp(2098), Arg(2171), Arg(2174), and Glu(2189) are required for maintaining the structural integrity of the C2-domain of factor V. Four of these residues (Arg(2074), Asp(2098), Arg(2171), and Arg(2174)) correspond to positions in the factor VIII C-type domains that have been identified as point mutations in patients with hemophilia A. The epitope for the inhibitory monoclonal antibody HV-1 has been localized to Lys(2060) through Glu(2069) in the factor V C2-domain. The epitope for the inhibitory monoclonal antibody 6A5 is composed of amino acids His(2128) through Lys(2137). The PS-binding site in the factor V C2-domain includes amino acid residues Trp(2063) and Trp(2064). This site overlaps with the epitope for monoclonal antibody HV-1. These factor V C2-domain mutants should provide valuable tools for further defining the molecular interactions responsible for factor V binding to phospholipid membranes. 相似文献
19.
Background
Gelsolin, an actin capping protein of osteoclast podosomes, has a unique function in regulating assembly and disassembly of the podosome actin filament. Previously, we have reported that osteopontin (OPN) binding to integrin αvβ3 increased the levels of gelsolin-associated polyphosphoinositides, podosome assembly/disassembly, and actin filament formation. The present study was undertaken to identify the possible role of polyphosphoinositides and phosphoinositides binding domains (PBDs) of gelsolin in the osteoclast cytoskeletal structural organization and osteoclast function. 相似文献20.
Mauro Angeletti Giulio Lupidi Anna Maria Eleuteri Rosalia Tacconi Evandro Fioretti M. Coletta 《Journal of biological inorganic chemistry》1997,2(3):320-326
The effect of aluminum ions on the binding properties of α-chymotrypsin has been studied. The results show that aluminum
does not affect the catalytic rate constant k
cat, but it acts as an enzyme activator favoring the binding of the substrate to the catalytic site (i.e. decreasing K
m). Furthermore, aluminum binding to α-chymotrypsin displays about a threefold decrease in its affinity for the macromolecular
inhibitor bovine pancreatic trypsin inhibitor (BPTI). Altogether, the different effect of aluminum on the binding of synthetic
substrates (e.g. N-α-benzoyl-l-tyrosine ethyl ester, BTEE) and macromolecular inhibitors (e.g. BPTI) to α-chymotrypsin suggests the occurrence of an aluminum-linked
conformational change in the enzyme molecule which brings about a marked structural change at the primary and secondary recognition
sites for substrates and inhibitors. The modulative effect exerted by aluminum on the enzyme hydrolytic activity has been
investigated also as a function of pH. The ion-linked effect appears to be dependent on the pH in a complex fashion, which
suggests that aluminum binding is controlled by the protonation of at least two classes of residues on the enzyme molecule.
Received: 5 December 1996 / Accepted: 11 March 1997 相似文献